From 2785caf1882324ffaeced04f6ec2aede2b57cda6 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 27 May 2022 09:25:13 -0600 Subject: [PATCH 001/408] Seperate out nrepr loops into ones for matrixcn off and on --- src/biogeochem/CNCStateUpdate1Mod.F90 | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 717b524383..8c6fc11602 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -430,18 +430,18 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end if cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_livestemc_patch(p)*dt cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_livestemc_storage_patch(p)*dt - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_patch(p,1)*dt - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_storage_patch(p,1)*dt + do k = 1, nrepr + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_patch(p,k)*dt + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt + end do if(.not. use_matrixcn)then cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) + cf_veg%cpool_to_livestemc_patch(p)*dt cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) + cf_veg%cpool_to_livestemc_storage_patch(p)*dt do k = 1, nrepr - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_patch(p,k)*dt - cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) & - + cf_veg%cpool_to_reproductivec_patch(p,k)*dt - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt + cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) & + + cf_veg%cpool_to_reproductivec_patch(p,k)*dt cs_veg%reproductivec_storage_patch(p,k) = cs_veg%reproductivec_storage_patch(p,k) & - + cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt + + cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt end do else ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) From 9a4ec5702f84db07d18b9dbbba7366ca684fa95c Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Mon, 3 Oct 2022 17:51:53 -0500 Subject: [PATCH 002/408] Modify Urban Time Varying data 1. `src\cpl\share_esmf\UrbanTimeVarType.F90`: Modify `stream_varnames` dimensions so that it becomes independent of urban density type indices (7-9), to prepare for future time varying data input for `p_ac` (and `p_h`, possibly); 2. `src\biogeophys\UrbBuildTempOleson2015Mod.F90`: Add `p_ac` to the equation of `eflx_urban_ac`; not being implemented yet. --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 4 + src/cpl/share_esmf/UrbanTimeVarType.F90 | 82 +++++++++++++++----- 2 files changed, 66 insertions(+), 20 deletions(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index bf8b68c7eb..e13f7e1b47 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -924,8 +924,12 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, if (t_building_bef_hac(l) > t_building_max(l)) then t_building(l) = t_building_max(l) + ! [Cathy] orig: eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) + ! [Cathy] dev: + ! eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & + ! - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) else if (t_building_bef_hac(l) < t_building_min(l)) then t_building(l) = t_building_min(l) eflx_urban_heat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index cc48bf4833..a76c176f1c 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -12,7 +12,7 @@ module UrbanTimeVarType use abortutils , only : endrun use decompMod , only : bounds_type, subgrid_level_landunit use clm_varctl , only : iulog - use landunit_varcon , only : isturb_MIN, isturb_MAX + use landunit_varcon , only : isturb_MIN, isturb_MAX ! Cathy: min and max types urban; equals 7 and 9, resp. use clm_varcon , only : spval use LandunitType , only : lun use GridcellType , only : grc @@ -24,6 +24,8 @@ module UrbanTimeVarType type, public :: urbantv_type ! real(r8), public, pointer :: t_building_max(:) ! lun maximum internal building air temperature (K) + ! ! Cathy [dev] + ! real(r8), public, pointer :: p_ac(:) ! lun air-conditioning ownership rate (unitless, between 0 and 1) type(shr_strdata_type) :: sdat_urbantv ! urban time varying input data stream contains ! !PUBLIC MEMBER FUNCTIONS: @@ -31,8 +33,11 @@ module UrbanTimeVarType procedure, public :: urbantv_init ! Initialize urban time varying stream procedure, public :: urbantv_interp ! Interpolate urban time varying stream end type urbantv_type - - character(15), private :: stream_varnames(isturb_MIN:isturb_MAX) + + ! Cathy [orig] + ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX) + ! Cathy [dev] + character(15), private :: stream_varnames(1:3) character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -63,6 +68,8 @@ subroutine Init(this, bounds, NLFilename) ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan + ! ! Cathy [dev] + ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan call this%urbantv_init(bounds, NLFilename) call this%urbantv_interp(bounds) @@ -72,6 +79,11 @@ subroutine Init(this, bounds, NLFilename) avgflag='A', long_name='prescribed maximum interior building temperature', & ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & l2g_scale_type='unity') + ! ! Cathy [dev] + ! call hist_addfld1d (fname='P_AC', units='unitless', & + avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)', & + ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & + l2g_scale_type='unity') end subroutine Init @@ -85,7 +97,7 @@ subroutine urbantv_init(this, bounds, NLFilename) use clm_nlUtilsMod , only : find_nlgroup_name use spmdMod , only : masterproc, mpicom, iam use shr_mpi_mod , only : shr_mpi_bcast - use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md + use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md ! Cathy: equals 7, 8 and 9 use dshr_strdata_mod , only : shr_strdata_init_from_inline use lnd_comp_shr , only : mesh, model_clock ! @@ -93,22 +105,23 @@ subroutine urbantv_init(this, bounds, NLFilename) implicit none class(urbantv_type) :: this type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename + character(len=*), intent(in) :: NLFilename ! Namelist filename ???is this the netCDF file name? ! ! !LOCAL VARIABLES: integer :: n integer :: stream_year_first_urbantv ! first year in urban tv stream to use integer :: stream_year_last_urbantv ! last year in urban tv stream to use integer :: model_year_align_urbantv ! align stream_year_first_urbantv with this model year - integer :: nu_nml ! unit for namelist file + integer :: nu_nml ! unit for namelist file ??? integer :: nml_error ! namelist i/o error flag - character(len=CL) :: stream_fldFileName_urbantv ! urban tv streams filename - character(len=CL) :: stream_meshfile_urbantv ! urban tv streams filename - character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac + character(len=CL) :: stream_fldFileName_urbantv ! urban tv streams filename ??? + character(len=CL) :: stream_meshfile_urbantv ! urban tv streams filename ??? + character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac ??? character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm integer :: rc ! error code - character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string - character(*), parameter :: subName = "('urbantv_init')" + ! Cathy [orig] + ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string ??? + character(*), parameter :: subName = "('urbantv_init')" ! ??? !----------------------------------------------------------------------- namelist /urbantv_streams/ & @@ -126,9 +139,14 @@ subroutine urbantv_init(this, bounds, NLFilename) model_year_align_urbantv = 1 ! align stream_year_first_urbantv with this model year stream_fldFileName_urbantv = ' ' stream_meshfile_urbantv = ' ' - stream_varnames(isturb_tbd) = urbantvString//"TBD" - stream_varnames(isturb_hd) = urbantvString//"HD" - stream_varnames(isturb_md) = urbantvString//"MD" + ! Cathy [orig] + ! stream_varnames(isturb_tbd) = urbantvString//"TBD" + ! stream_varnames(isturb_hd) = urbantvString//"HD" + ! stream_varnames(isturb_md) = urbantvString//"MD" + ! Cathy [dev] + stream_varnames(1) = "tbuildmax_TBD" + stream_varnames(2) = "tbuildmax_HD" + stream_varnames(3) = "tbuildmax_MD" ! Read urbantv_streams namelist if (masterproc) then @@ -159,7 +177,10 @@ subroutine urbantv_init(this, bounds, NLFilename) write(iulog,'(a,a)' ) ' stream_fldFileName_urbantv = ',stream_fldFileName_urbantv write(iulog,'(a,a)' ) ' stream_meshfile_urbantv = ',stream_meshfile_urbantv write(iulog,'(a,a)' ) ' urbantv_tintalgo = ',urbantv_tintalgo - do n = isturb_tbd,isturb_md + ! Cathy [orig] + ! do n = isturb_tbd,isturb_md + ! Cathy [dev] + do n = 1,3 write(iulog,'(a,a)' ) ' stream_varname = ',trim(stream_varnames(n)) end do write(iulog,*) ' ' @@ -176,8 +197,12 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_lev_dimname = 'null', & stream_mapalgo = trim(urbantvmapalgo), & stream_filenames = (/trim(stream_fldfilename_urbantv)/), & - stream_fldlistFile = stream_varnames(isturb_tbd:isturb_md),& - stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),& + ! Cathy [orig] + ! stream_fldlistFile = stream_varnames(isturb_tbd:isturb_md),& + ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),& + ! Cathy [dev] + stream_fldlistFile = stream_varnames(1:3), & + stream_fldListModel = stream_varnames(1:3), & stream_yearFirst = stream_year_first_urbantv, & stream_yearLast = stream_year_last_urbantv, & stream_yearAlign = model_year_align_urbantv, & @@ -235,8 +260,12 @@ subroutine urbantv_interp(this, bounds) ! Create 2d array for all stream variable data lsize = bounds%endg - bounds%begg + 1 - allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX)) - do n = isturb_MIN,isturb_MAX + ! Cathy [orig] + ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX)) + ! do n = isturb_MIN,isturb_MAX + ! Cathy [dev] + allocate(dataptr2d(lsize, 1:3)) + do n = 1,3 call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), & fldptr1=dataptr1d, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -257,13 +286,20 @@ subroutine urbantv_interp(this, bounds) ig = ig+1 if (g == lun%gridcell(l)) exit end do - do n = isturb_MIN,isturb_MAX + ! Cathy [orig] + ! do n = isturb_MIN,isturb_MAX + ! Cathy [dev] + do n = 1,3 if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then this%t_building_max(l) = dataptr2d(ig,n) + ! ! Cathy [dev] + ! this%p_ac(l) = dataptr2d(ig,n) ! ??? end if end do else this%t_building_max(l) = spval + ! ! Cathy [dev] + ! this%p_ac(l) = spval end if end do deallocate(dataptr2d) @@ -277,7 +313,11 @@ subroutine urbantv_interp(this, bounds) ig = ig+1 if (g == lun%gridcell(l)) exit end do + ! Cathy [orig] if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then + ! Cathy [dev] + ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) + ! & .or. (this%p_ac(l) <= 0._r8) .or. (this%p_ac(l) >= 1._r8)) then found = .true. gindx = g lindx = l @@ -290,6 +330,8 @@ subroutine urbantv_interp(this, bounds) write(iulog,*)'landunit type: ',lun%itype(lindx) write(iulog,*)'urban_valid: ',urban_valid(gindx) write(iulog,*)'t_building_max: ',this%t_building_max(lindx) + ! ! Cathy [dev] + ! write(iulog,*)'p_ac: ',this%p_ac(lindx) call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, & msg=errmsg(sourcefile, __LINE__)) end if From eb160f2827f14666e06e38ac390802138620cb04 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 5 Oct 2022 17:07:24 -0500 Subject: [PATCH 003/408] Update UrbanTimeVarType.F90 Add missing comment signs --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index a76c176f1c..cf379801ce 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -81,9 +81,9 @@ subroutine Init(this, bounds, NLFilename) l2g_scale_type='unity') ! ! Cathy [dev] ! call hist_addfld1d (fname='P_AC', units='unitless', & - avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)', & - ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & - l2g_scale_type='unity') + ! avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)', & + ! ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & + ! l2g_scale_type='unity') end subroutine Init From 8cec89cefeec0f5ac5a523ec260430be7258b489 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 6 Oct 2022 16:44:51 -0500 Subject: [PATCH 004/408] Update UrbanTimeVarType.F90 [dev.01] Debugging after first test run. Problem: First test run (job 6762983) returned all URBAN_AC results as 0. Suspect a mismatch between the indices of `stream_varnames` and `t_building_max`, which may have resulted in all `t_building_max` being set to nan/very large number. Solution: Modify subroutine `urbantv_interp` by hard-coding *land unit type - 6* to ensure the if statement criterion returns true. --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index cf379801ce..1bed4e2967 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -60,7 +60,7 @@ subroutine Init(this, bounds, NLFilename) character(len=*) , intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: - integer :: begl, endl + integer :: begl, endl ! Cathy: beginning and ending landunit index, from src/main/decompMod !--------------------------------------------------------------------- begl = bounds%begl; endl = bounds%endl @@ -75,6 +75,7 @@ subroutine Init(this, bounds, NLFilename) call this%urbantv_interp(bounds) ! Add history fields + ! Cathy: the subroutine is in scr/main/histFileMod.F90 call hist_addfld1d (fname='TBUILD_MAX', units='K', & avgflag='A', long_name='prescribed maximum interior building temperature', & ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & @@ -290,14 +291,17 @@ subroutine urbantv_interp(this, bounds) ! do n = isturb_MIN,isturb_MAX ! Cathy [dev] do n = 1,3 - if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then + ! Cathy [orig] + ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then + ! Cathy [dev.01] + if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then this%t_building_max(l) = dataptr2d(ig,n) ! ! Cathy [dev] ! this%p_ac(l) = dataptr2d(ig,n) ! ??? end if end do else - this%t_building_max(l) = spval + this%t_building_max(l) = spval ! Cathy: special value for real data, set to 1.e36 in src/main/clm_varcon ! ! Cathy [dev] ! this%p_ac(l) = spval end if From 07b787382cf4fcce7a445a1c196373aa816eb081 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Tue, 24 Jan 2023 18:22:03 -0600 Subject: [PATCH 005/408] Add p_ac to urban time varying data 1. `src\cpl\share_esmf\UrbanTimeVarType.F90`: Add 3 more dimensions to `stream_varnames` (4,5,6) for `p_ac`; 2. `src\biogeophys\UrbBuildTempOleson2015Mod.F90`: Use `p_ac` in the equation of `eflx_urban_ac`. --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 6 +- src/cpl/share_esmf/UrbanTimeVarType.F90 | 64 ++++++++++---------- 2 files changed, 36 insertions(+), 34 deletions(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index e13f7e1b47..260c6658af 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -925,11 +925,11 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, if (t_building_bef_hac(l) > t_building_max(l)) then t_building(l) = t_building_max(l) ! [Cathy] orig: - eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & + ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) ! [Cathy] dev: - ! eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - ! - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) + eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & + - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) else if (t_building_bef_hac(l) < t_building_min(l)) then t_building(l) = t_building_min(l) eflx_urban_heat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 01f924935e..d96cc11157 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -24,8 +24,8 @@ module UrbanTimeVarType type, public :: urbantv_type ! real(r8), public, pointer :: t_building_max(:) ! lun maximum internal building air temperature (K) - ! ! Cathy [dev] - ! real(r8), public, pointer :: p_ac(:) ! lun air-conditioning ownership rate (unitless, between 0 and 1) + ! Cathy [dev] + real(r8), public, pointer :: p_ac(:) ! lun air-conditioning ownership rate (unitless, between 0 and 1) type(shr_strdata_type) :: sdat_urbantv ! urban time varying input data stream contains ! !PUBLIC MEMBER FUNCTIONS: @@ -36,8 +36,8 @@ module UrbanTimeVarType ! Cathy [orig] ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX) - ! Cathy [dev] - character(15), private :: stream_varnames(1:3) + ! Cathy [dev]: + character(15), private :: stream_varnames(1:6) ! 1-3 for t_building_max, 4-6 for p_ac character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -68,23 +68,22 @@ subroutine Init(this, bounds, NLFilename) ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan - ! ! Cathy [dev] - ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan + ! Cathy [dev] + allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan call this%urbantv_init(bounds, NLFilename) call this%urbantv_interp(bounds) - ! Add history fields - ! Cathy: the subroutine is in scr/main/histFileMod.F90 + ! Add history fields ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90 call hist_addfld1d (fname='TBUILD_MAX', units='K', & avgflag='A', long_name='prescribed maximum interior building temperature', & ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & l2g_scale_type='unity') - ! ! Cathy [dev] - ! call hist_addfld1d (fname='P_AC', units='unitless', & - ! avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)', & - ! ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & - ! l2g_scale_type='unity') + ! Cathy [dev] + call hist_addfld1d (fname='P_AC', units='unitless', & + avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)', & + ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & + l2g_scale_type='unity') end subroutine Init @@ -120,8 +119,8 @@ subroutine urbantv_init(this, bounds, NLFilename) character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac ??? character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm integer :: rc ! error code - ! Cathy [orig] - ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string ??? + ! Cathy [orig]: this is taken out because field strings are now hard coded in + ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string character(*), parameter :: subName = "('urbantv_init')" ! ??? !----------------------------------------------------------------------- @@ -148,6 +147,9 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_varnames(1) = "tbuildmax_TBD" stream_varnames(2) = "tbuildmax_HD" stream_varnames(3) = "tbuildmax_MD" + stream_varnames(4) = "p_ac_TBD" + stream_varnames(5) = "p_ac_HD" + stream_varnames(6) = "p_ac_MD" ! Read urbantv_streams namelist if (masterproc) then @@ -181,7 +183,7 @@ subroutine urbantv_init(this, bounds, NLFilename) ! Cathy [orig] ! do n = isturb_tbd,isturb_md ! Cathy [dev] - do n = 1,3 + do n = 1,6 write(iulog,'(a,a)' ) ' stream_varname = ',trim(stream_varnames(n)) end do write(iulog,*) ' ' @@ -202,8 +204,8 @@ subroutine urbantv_init(this, bounds, NLFilename) ! stream_fldlistFile = stream_varnames(isturb_tbd:isturb_md),& ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),& ! Cathy [dev] - stream_fldlistFile = stream_varnames(1:3), & - stream_fldListModel = stream_varnames(1:3), & + stream_fldlistFile = stream_varnames(1:6), & + stream_fldListModel = stream_varnames(1:6), & stream_yearFirst = stream_year_first_urbantv, & stream_yearLast = stream_year_last_urbantv, & stream_yearAlign = model_year_align_urbantv, & @@ -265,8 +267,8 @@ subroutine urbantv_interp(this, bounds) ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX)) ! do n = isturb_MIN,isturb_MAX ! Cathy [dev] - allocate(dataptr2d(lsize, 1:3)) - do n = 1,3 + allocate(dataptr2d(lsize, 1:6)) + do n = 1,6 call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), & fldptr1=dataptr1d, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -290,20 +292,20 @@ subroutine urbantv_interp(this, bounds) ! Cathy [orig] ! do n = isturb_MIN,isturb_MAX ! Cathy [dev] - do n = 1,3 + do n = 1,6 ! Cathy [orig] ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then - ! Cathy [dev.01] + ! Cathy [dev.02] if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then this%t_building_max(l) = dataptr2d(ig,n) - ! ! Cathy [dev] - ! this%p_ac(l) = dataptr2d(ig,n) ! ??? + if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then + this%p_ac(l) = dataptr2d(ig,n) end if end do else this%t_building_max(l) = spval ! Cathy: special value for real data, set to 1.e36 in src/main/clm_varcon - ! ! Cathy [dev] - ! this%p_ac(l) = spval + ! Cathy [dev] + this%p_ac(l) = 0._r8 ! Cathy: set to 0 for non-urban landunit end if end do deallocate(dataptr2d) @@ -318,10 +320,10 @@ subroutine urbantv_interp(this, bounds) if (g == lun%gridcell(l)) exit end do ! Cathy [orig] - if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then + ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then ! Cathy [dev] - ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) - ! & .or. (this%p_ac(l) <= 0._r8) .or. (this%p_ac(l) >= 1._r8)) then + if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) & + .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then found = .true. gindx = g lindx = l @@ -334,8 +336,8 @@ subroutine urbantv_interp(this, bounds) write(iulog,*)'landunit type: ',lun%itype(lindx) write(iulog,*)'urban_valid: ',urban_valid(gindx) write(iulog,*)'t_building_max: ',this%t_building_max(lindx) - ! ! Cathy [dev] - ! write(iulog,*)'p_ac: ',this%p_ac(lindx) + ! Cathy [dev] + write(iulog,*)'p_ac: ',this%p_ac(lindx) call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, & msg=errmsg(sourcefile, __LINE__)) end if From e621628352f457bfadb118ca67b7b4c4634d668a Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 25 Jan 2023 00:13:28 -0600 Subject: [PATCH 006/408] Update UrbanTimeVarType.F90 Bug fix: added missing "end if" --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index d96cc11157..bc0c82af6a 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -298,6 +298,7 @@ subroutine urbantv_interp(this, bounds) ! Cathy [dev.02] if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then this%t_building_max(l) = dataptr2d(ig,n) + end if if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then this%p_ac(l) = dataptr2d(ig,n) end if From eabe116800f8cf40c1a17755205e2d72b80df033 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 25 Jan 2023 10:58:24 -0600 Subject: [PATCH 007/408] Update UrbBuildTempOleson2015Mod.F90 Bug fix: declare p_ac type; comment out original code --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index 260c6658af..d54d3ff86d 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -324,6 +324,8 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, t_floor => temperature_inst%t_floor_lun , & ! InOut: [real(r8) (:)] floor temperature (K) t_building => temperature_inst%t_building_lun , & ! InOut: [real(r8) (:)] internal building air temperature (K) + ! Cathy [dev] + p_ac => urbantv_inst%p_ac , & ! Input: [real(r8) (:)] air-conditioning penetration rate (-) t_building_max => urbantv_inst%t_building_max , & ! Input: [real(r8) (:)] maximum internal building air temperature (K) t_building_min => urbanparams_inst%t_building_min , & ! Input: [real(r8) (:)] minimum internal building air temperature (K) @@ -926,7 +928,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, t_building(l) = t_building_max(l) ! [Cathy] orig: ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) + ! - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) ! [Cathy] dev: eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) From ed26fd3a2b66429204b47a043a43ca5051786659 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 26 Jan 2023 12:22:47 -0600 Subject: [PATCH 008/408] Debug dev.02 --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 27 +++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index bc0c82af6a..d542d2440e 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -72,6 +72,10 @@ subroutine Init(this, bounds, NLFilename) allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan call this%urbantv_init(bounds, NLFilename) + + ! Cathy [dev.02] + write(*,*) 'Cathy: urbantv_init done.' + call this%urbantv_interp(bounds) ! Add history fields ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90 @@ -188,6 +192,9 @@ subroutine urbantv_init(this, bounds, NLFilename) end do write(iulog,*) ' ' endif + + ! Cathy [dev.02] + write(*,*) 'Cathy: before shr_strdata_init_from_inline' ! Initialize the cdeps data type this%sdat_urbantv call shr_strdata_init_from_inline(this%sdat_urbantv, & @@ -215,6 +222,10 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_tintalgo = urbantv_tintalgo, & stream_name = 'Urban time varying data', & rc = rc) + + ! Cathy [dev.02] + write(*,*) 'Cathy: before shr_strdata_init_from_inline' + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -253,14 +264,24 @@ subroutine urbantv_interp(this, bounds) real(r8), pointer :: dataptr2d(:,:) !----------------------------------------------------------------------- + ! Cathy [dev.02] + write(*,*) 'Cathy: before get_curr_date' + ! Advance sdat stream call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day + + ! Cathy [dev.02] + write(*,*) 'Cathy: after get_curr_date, before shr_strdata_advance' + call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + ! Cathy [dev.02] + write(*,*) 'Cathy: before creating 2d array' + ! Create 2d array for all stream variable data lsize = bounds%endg - bounds%begg + 1 ! Cathy [orig] @@ -281,6 +302,9 @@ subroutine urbantv_interp(this, bounds) end do end do + ! Cathy [dev.02] + write(*,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits' + ! Determine this%tbuilding_max for all landunits do l = bounds%begl,bounds%endl if (lun%urbpoi(l)) then @@ -311,6 +335,9 @@ subroutine urbantv_interp(this, bounds) end do deallocate(dataptr2d) + ! Cathy [dev.02] + write(*,*) 'Cathy: after determining t_building_max and p_ac for all landunits' + ! Error check found = .false. do l = bounds%begl,bounds%endl From e10e338f2b165a2c8dbe122598e5caf5efd620c4 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 26 Jan 2023 13:41:40 -0600 Subject: [PATCH 009/408] Update UrbanTimeVarType.F90 --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index d542d2440e..1f679b88a3 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -74,7 +74,7 @@ subroutine Init(this, bounds, NLFilename) call this%urbantv_init(bounds, NLFilename) ! Cathy [dev.02] - write(*,*) 'Cathy: urbantv_init done.' + write(iulog,*) 'Cathy: urbantv_init done.' call this%urbantv_interp(bounds) @@ -190,11 +190,14 @@ subroutine urbantv_init(this, bounds, NLFilename) do n = 1,6 write(iulog,'(a,a)' ) ' stream_varname = ',trim(stream_varnames(n)) end do - write(iulog,*) ' ' + ! Cathy [orig] + ! write(iulog,*) ' ' + ! Cathy [dev.02] + write(iulog,*) 'Cathy: does write statements have to be inside if?' endif ! Cathy [dev.02] - write(*,*) 'Cathy: before shr_strdata_init_from_inline' + write(iulog,*) 'Cathy: before shr_strdata_init_from_inline' ! Initialize the cdeps data type this%sdat_urbantv call shr_strdata_init_from_inline(this%sdat_urbantv, & @@ -224,7 +227,7 @@ subroutine urbantv_init(this, bounds, NLFilename) rc = rc) ! Cathy [dev.02] - write(*,*) 'Cathy: before shr_strdata_init_from_inline' + write(iulog,*) 'Cathy: before shr_strdata_init_from_inline' if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) @@ -265,14 +268,14 @@ subroutine urbantv_interp(this, bounds) !----------------------------------------------------------------------- ! Cathy [dev.02] - write(*,*) 'Cathy: before get_curr_date' + write(iulog,*) 'Cathy: before get_curr_date' ! Advance sdat stream call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day ! Cathy [dev.02] - write(*,*) 'Cathy: after get_curr_date, before shr_strdata_advance' + write(iulog,*) 'Cathy: after get_curr_date, before shr_strdata_advance' call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -280,7 +283,7 @@ subroutine urbantv_interp(this, bounds) end if ! Cathy [dev.02] - write(*,*) 'Cathy: before creating 2d array' + write(iulog,*) 'Cathy: before creating 2d array' ! Create 2d array for all stream variable data lsize = bounds%endg - bounds%begg + 1 @@ -303,7 +306,7 @@ subroutine urbantv_interp(this, bounds) end do ! Cathy [dev.02] - write(*,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits' + write(iulog,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits' ! Determine this%tbuilding_max for all landunits do l = bounds%begl,bounds%endl @@ -336,7 +339,7 @@ subroutine urbantv_interp(this, bounds) deallocate(dataptr2d) ! Cathy [dev.02] - write(*,*) 'Cathy: after determining t_building_max and p_ac for all landunits' + write(iulog,*) 'Cathy: after determining t_building_max and p_ac for all landunits' ! Error check found = .false. From 436329500392af185d640b1200e4a72c46200141 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 8 Feb 2023 12:43:44 -0600 Subject: [PATCH 010/408] [dev.03] Fix interior building temperature update 1. changed how interior building temperature is updated based on proposed scheme, by adding back the heat not removed by AC; 2. added an intermediate local variable `efllx_urban_ac_sat`; 3. `t_building_max` now indicates the saturation setpoints. --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index d54d3ff86d..024922348a 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -236,6 +236,8 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, real(r8) :: t_floor_bef(bounds%begl:bounds%endl) ! floor temperature at previous time step (K) real(r8) :: t_building_bef(bounds%begl:bounds%endl) ! internal building air temperature at previous time step [K] real(r8) :: t_building_bef_hac(bounds%begl:bounds%endl)! internal building air temperature before applying HAC [K] + ! Cathy [dev.03] + real(r8) :: eflx_urban_ac_sat(bounds%begl:bounds%endl) ! urban air conditioning flux under AC adoption saturation (W/m**2) real(r8) :: hcv_roofi(bounds%begl:bounds%endl) ! roof convective heat transfer coefficient (W m-2 K-1) real(r8) :: hcv_sunwi(bounds%begl:bounds%endl) ! sunwall convective heat transfer coefficient (W m-2 K-1) real(r8) :: hcv_shdwi(bounds%begl:bounds%endl) ! shadewall convective heat transfer coefficient (W m-2 K-1) @@ -925,13 +927,17 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, ! rho_dair(l) = pstd / (rair*t_building(l)) if (t_building_bef_hac(l) > t_building_max(l)) then - t_building(l) = t_building_max(l) - ! [Cathy] orig: + ! Cathy [orig] + ! t_building(l) = t_building_max(l) ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & ! - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) - ! [Cathy] dev: - eflx_urban_ac(l) = wtlunit_roof(l) * p_ac(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) + ! Cathy [dev.03] ! after the change, t_building_max is saturation setpoint + eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) & + - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) + t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urbann_ac_sat(l) & + * dtime / (ht_roof(l) * rho_dair(l) * cpair) + eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l) + else if (t_building_bef_hac(l) < t_building_min(l)) then t_building(l) = t_building_min(l) eflx_urban_heat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & From ab0f8e15a64b8391a49b02d9a1f789a3cbbeaa4b Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 8 Feb 2023 16:47:07 -0600 Subject: [PATCH 011/408] [dev03] Fix typo --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index 024922348a..e5626cb65c 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -934,7 +934,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, ! Cathy [dev.03] ! after the change, t_building_max is saturation setpoint eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) - t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urbann_ac_sat(l) & + t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) & * dtime / (ht_roof(l) * rho_dair(l) * cpair) eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l) From aa68753b6a7339808350ba8c23b83e6d494131ac Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 22 Feb 2023 23:56:54 -0600 Subject: [PATCH 012/408] [dev.03] Remove write statements Remove 8 write to log statements (added in as part of dev.02 for debugging) to fix the timing issues --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 32 ++----------------------- 1 file changed, 2 insertions(+), 30 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 1f679b88a3..ae34449c1e 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -72,10 +72,6 @@ subroutine Init(this, bounds, NLFilename) allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan call this%urbantv_init(bounds, NLFilename) - - ! Cathy [dev.02] - write(iulog,*) 'Cathy: urbantv_init done.' - call this%urbantv_interp(bounds) ! Add history fields ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90 @@ -190,14 +186,8 @@ subroutine urbantv_init(this, bounds, NLFilename) do n = 1,6 write(iulog,'(a,a)' ) ' stream_varname = ',trim(stream_varnames(n)) end do - ! Cathy [orig] - ! write(iulog,*) ' ' - ! Cathy [dev.02] - write(iulog,*) 'Cathy: does write statements have to be inside if?' + write(iulog,*) ' ' endif - - ! Cathy [dev.02] - write(iulog,*) 'Cathy: before shr_strdata_init_from_inline' ! Initialize the cdeps data type this%sdat_urbantv call shr_strdata_init_from_inline(this%sdat_urbantv, & @@ -226,9 +216,6 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_name = 'Urban time varying data', & rc = rc) - ! Cathy [dev.02] - write(iulog,*) 'Cathy: before shr_strdata_init_from_inline' - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -267,23 +254,14 @@ subroutine urbantv_interp(this, bounds) real(r8), pointer :: dataptr2d(:,:) !----------------------------------------------------------------------- - ! Cathy [dev.02] - write(iulog,*) 'Cathy: before get_curr_date' - ! Advance sdat stream call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day - ! Cathy [dev.02] - write(iulog,*) 'Cathy: after get_curr_date, before shr_strdata_advance' - call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - - ! Cathy [dev.02] - write(iulog,*) 'Cathy: before creating 2d array' + end if ! Create 2d array for all stream variable data lsize = bounds%endg - bounds%begg + 1 @@ -305,9 +283,6 @@ subroutine urbantv_interp(this, bounds) end do end do - ! Cathy [dev.02] - write(iulog,*) 'Cathy: after creating 2d array, before determining t_building_max and p_ac for all landunits' - ! Determine this%tbuilding_max for all landunits do l = bounds%begl,bounds%endl if (lun%urbpoi(l)) then @@ -338,9 +313,6 @@ subroutine urbantv_interp(this, bounds) end do deallocate(dataptr2d) - ! Cathy [dev.02] - write(iulog,*) 'Cathy: after determining t_building_max and p_ac for all landunits' - ! Error check found = .false. do l = bounds%begl,bounds%endl From e6b80df3c8d37f7d262123e2ac5f82227bd04a45 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 1 Mar 2023 17:41:22 -0600 Subject: [PATCH 013/408] [dev.04] Add toggle `urban_explicit_ac` 1. Add a new logical variable `urban_explicit_ac` (default true) in __UrbanParamsType.F90__; 2. Add if-else block to building interior building temperature and AC flux calculation in __UrbBuildTempOleson2015Mod.F90__: use p_ac if `urban_explicit_ac` is set to true, otherwise use the original way of calculation; 3. Add `urban_explicit_ac` to __namelist_definition_ctsm.xml__; and 4. Add `urban_explicit_ac` default value (.true.) to __namelist_defaults_ctsm.xml__. --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++++ .../namelist_definition_ctsm.xml | 8 +++++++ src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 24 ++++++++++++------- src/biogeophys/UrbanParamsType.F90 | 11 ++++++++- 4 files changed, 39 insertions(+), 10 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 69643041a4..5be2604c36 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -166,6 +166,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case). FAST NONE + + + +.true. +.true. + .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index bc1dd034aa..aae38a5cec 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -947,6 +947,14 @@ Turn urban air conditioning/heating ON or OFF and add wasteheat: ON_WASTEHEAT = Air conditioning/heating is ON and waste-heat sent to urban canyon + + + + +If TRUE, use explicit, time-varying AC adoption rate for air-conditioning flux and interior building temperature calculations. + + If TRUE, urban traffic flux will be activated (Currently NOT implemented). diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index e5626cb65c..0ab72ac0a6 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -210,7 +210,10 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, use clm_varctl , only : iulog use abortutils , only : endrun use clm_varpar , only : nlevurb, nlevsno, nlevmaxurbgrnd - use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on + ! Cathy [orig]: + ! use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on + ! Cathy [dev.04]: + use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on, urban_explicit_ac ! ! !ARGUMENTS: implicit none @@ -927,16 +930,19 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, ! rho_dair(l) = pstd / (rair*t_building(l)) if (t_building_bef_hac(l) > t_building_max(l)) then - ! Cathy [orig] - ! t_building(l) = t_building_max(l) - ! eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - ! - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) - ! Cathy [dev.03] ! after the change, t_building_max is saturation setpoint - eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) & + ! Cathy [dev.04] + if (urban_explicit_ac) then ! use explicit ac adoption rate: + ! Cathy [dev.03] ! after the change, t_building_max is saturation setpoint + eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) - t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) & + t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) & * dtime / (ht_roof(l) * rho_dair(l) * cpair) - eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l) + eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l) + else + ! Cathy [orig] + t_building(l) = t_building_max(l) + eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & + - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) else if (t_building_bef_hac(l) < t_building_min(l)) then t_building(l) = t_building_min(l) diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90 index c490ad27cc..c674aac2db 100644 --- a/src/biogeophys/UrbanParamsType.F90 +++ b/src/biogeophys/UrbanParamsType.F90 @@ -101,6 +101,8 @@ module UrbanParamsType character(len= *), parameter, public :: urban_hac_on = 'ON' character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT' character(len= 16), public :: urban_hac = urban_hac_off + ! Cathy [dev.04] + logical, public :: urban_explicit_ac = .true. ! whether to use explicit, time-varying AC adoption rate logical, public :: urban_traffic = .false. ! urban traffic fluxes ! !PRIVATE MEMBER DATA: @@ -847,7 +849,10 @@ subroutine UrbanReadNML ( NLFilename ) integer :: unitn ! unit for namelist file character(len=32) :: subname = 'UrbanReadNML' ! subroutine name - namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method + ! Cathy [orig]: + ! namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method + ! Cathy [dev.04]: + namelist / clmu_inparm / urban_hac, urban_explicit_ac, urban_traffic, building_temp_method !EOP !----------------------------------------------------------------------- @@ -875,6 +880,8 @@ subroutine UrbanReadNML ( NLFilename ) ! Broadcast namelist variables read in call shr_mpi_bcast(urban_hac, mpicom) + ! Cathy [dev.04]: + call shr_mpi_bcast(urban_explicit_ac, mpicom) call shr_mpi_bcast(urban_traffic, mpicom) call shr_mpi_bcast(building_temp_method, mpicom) @@ -886,6 +893,8 @@ subroutine UrbanReadNML ( NLFilename ) ! if ( masterproc )then write(iulog,*) ' urban air conditioning/heating and wasteheat = ', urban_hac + ! Cathy [dev.04]: + write(iulog,*) ' urban explicit air-conditioning adoption rate = ', urban_explicit_ac write(iulog,*) ' urban traffic flux = ', urban_traffic end if From 30af382df1b3bb0b00ba7c9cfb3b115fa751eee4 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 1 Mar 2023 17:51:09 -0600 Subject: [PATCH 014/408] [dev. 04] Add toggle `urban_explicit_ac` (cont'd) 5. Add `urban_explicit_ac` to __CLMBuildNamelist.pm__. --- bld/CLMBuildNamelist.pm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c2a32da4ac..a56e5b12b7 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2111,6 +2111,8 @@ sub setup_logic_urban { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac'); + # Cathy [dev.04] + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac') add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic'); } From 4726cede9bb015acdcf8090440eda62d252314b8 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 1 Mar 2023 18:01:23 -0600 Subject: [PATCH 015/408] [dev.04] debug Add missing ";" --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index a56e5b12b7..7c185ff6a0 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2112,7 +2112,7 @@ sub setup_logic_urban { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac'); # Cathy [dev.04] - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac') + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic'); } From ab2e87aa8fd6e591c7721011ecc14788fb9d87b9 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 1 Mar 2023 18:13:04 -0600 Subject: [PATCH 016/408] [dev.04] debug Add "`end if`" --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index 0ab72ac0a6..2a5440e324 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -943,6 +943,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, t_building(l) = t_building_max(l) eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) + end if else if (t_building_bef_hac(l) < t_building_min(l)) then t_building(l) = t_building_min(l) From 70125066da34fb3aa6a90cea491b3b99e9429db3 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Mon, 24 Apr 2023 16:30:53 -0500 Subject: [PATCH 017/408] Update clm_varpar.F90 Changed nlevurb to 10 (line 207) to conform to the new surfdata file. --- src/main/clm_varpar.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90 index f54b750181..7c7c1681b7 100644 --- a/src/main/clm_varpar.F90 +++ b/src/main/clm_varpar.F90 @@ -203,7 +203,8 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft) max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb) nlevsoifl = 10 - nlevurb = 5 + [Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10] + nlevurb = 10 ! originally 5 if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined if ( masterproc ) write(iulog, *) 'soil_layerstruct_userdefined varpar ', soil_layerstruct_userdefined From 23876810d4f7eefd81dbe9d442edaf01b83b58de Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Mon, 24 Apr 2023 16:38:52 -0500 Subject: [PATCH 018/408] Update clm_varpar.F90 Fix syntax error --- src/main/clm_varpar.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90 index 7c7c1681b7..e1179e43b3 100644 --- a/src/main/clm_varpar.F90 +++ b/src/main/clm_varpar.F90 @@ -203,7 +203,7 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft) max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb) nlevsoifl = 10 - [Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10] + ![Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10] nlevurb = 10 ! originally 5 if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined From 302556635395e7d30c58ef097219a1b242ff4dbf Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 13 Jul 2023 12:49:08 +0800 Subject: [PATCH 019/408] Update UrbBuildTempOleson2015Mod.F90 Bug fix: t_building calculation --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index 2a5440e324..e8f7555e0e 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -936,7 +936,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) & - * dtime / (ht_roof(l) * rho_dair(l) * cpair) + * dtime / (ht_roof(l) * rho_dair(l) * cpair * wtlunit_roof(l)) eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l) else ! Cathy [orig] From af82c41c4ec51f471552295475e63d5d2b31bde5 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 11 Oct 2023 15:51:57 -0500 Subject: [PATCH 020/408] Bug fix Bug fix on view factor and radiative energy balance check --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index e8f7555e0e..f6330ec10b 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -432,7 +432,10 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, vf_wf(l) = 0.5_r8*(1._r8 - vf_rf(l)) ! This view factor implicitly converts from per unit floor area to per unit wall area - vf_fw(l) = vf_wf(l) / building_hwr(l) + ! Cathy [orig] + ! vf_fw(l) = vf_wf(l) / building_hwr(l) + ! Cathy [bugfix] + vf_fw(l) = vf_wf(l) ! This view factor implicitly converts from per unit roof area to per unit wall area vf_rw(l) = vf_fw(l) @@ -838,7 +841,10 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, + em_floori(l)*sb*t_floor_bef(l)**4._r8 & + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l)) - qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l) + ! Cathy [orig] + ! qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l) + ! Cathy [bugfix] + qrd_building(l) = qrd_roof(l) + qrd_sunw(l) + qrd_shdw(l) + qrd_floor(l) if (abs(qrd_building(l)) > .10_r8 ) then write (iulog,*) 'urban inside building net longwave radiation balance error ',qrd_building(l) From effacf2b1db196c7bf4c4fa87d45628fd25e9e00 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 28 Nov 2023 14:27:07 -0700 Subject: [PATCH 021/408] Corrections for cheyenne test-suite to pass --- src/biogeochem/CNCStateUpdate1Mod.F90 | 6 ------ src/biogeochem/CNNStateUpdate1Mod.F90 | 14 ++++++++------ 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 8c6fc11602..76b14585b4 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -325,15 +325,9 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & - cf_veg%crop_seedc_to_leaf_patch(p) * dt do k = repr_grain_min, repr_grain_max - cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) & - - (cf_veg%repr_grainc_to_food_patch(p,k) + cf_veg%repr_grainc_to_seed_patch(p,k))*dt cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & + cf_veg%repr_grainc_to_seed_patch(p,k) * dt end do - do k = repr_structure_min, repr_structure_max - cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) & - - (cf_veg%repr_structurec_to_cropprod_patch(p,k) + cf_veg%repr_structurec_to_litter_patch(p,k))*dt - end do end if end if !not use_matrixcn diff --git a/src/biogeochem/CNNStateUpdate1Mod.F90 b/src/biogeochem/CNNStateUpdate1Mod.F90 index 8aa24e3aa3..4a9e081583 100644 --- a/src/biogeochem/CNNStateUpdate1Mod.F90 +++ b/src/biogeochem/CNNStateUpdate1Mod.F90 @@ -226,21 +226,23 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p) - nf_veg%leafn_to_biofueln_patch(p)*dt ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - nf_veg%livestemn_to_retransn_patch(p)*dt ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) + nf_veg%livestemn_to_retransn_patch(p)*dt + do k = repr_grain_min, repr_grain_max + ns_veg%reproductiven_patch(p,k) = ns_veg%reproductiven_patch(p,k) & + - (nf_veg%repr_grainn_to_food_patch(p,k) + nf_veg%repr_grainn_to_seed_patch(p,k))*dt + end do + do k = repr_structure_min, repr_structure_max + ns_veg%reproductiven_patch(p,k) = ns_veg%reproductiven_patch(p,k) & + - (nf_veg%repr_structuren_to_cropprod_patch(p,k) + nf_veg%repr_structuren_to_litter_patch(p,k))*dt + end do else ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) end if !not use_matrixcn ns_veg%cropseedn_deficit_patch(p) = ns_veg%cropseedn_deficit_patch(p) & - nf_veg%crop_seedn_to_leaf_patch(p) * dt do k = repr_grain_min, repr_grain_max - ns_veg%reproductiven_patch(p,k) = ns_veg%reproductiven_patch(p,k) & - - (nf_veg%repr_grainn_to_food_patch(p,k) + nf_veg%repr_grainn_to_seed_patch(p,k))*dt ns_veg%cropseedn_deficit_patch(p) = ns_veg%cropseedn_deficit_patch(p) & + nf_veg%repr_grainn_to_seed_patch(p,k) * dt end do - do k = repr_structure_min, repr_structure_max - ns_veg%reproductiven_patch(p,k) = ns_veg%reproductiven_patch(p,k) & - - (nf_veg%repr_structuren_to_cropprod_patch(p,k) + nf_veg%repr_structuren_to_litter_patch(p,k))*dt - end do end if ! uptake from soil mineral N pool From ffc6acc0184df317314d5d2cdd36076627d854a1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 29 Nov 2023 17:47:40 -0700 Subject: [PATCH 022/408] Upd. expected fails, test list, and relevant error checks --- bld/CLMBuildNamelist.pm | 7 ++++ cime_config/testdefs/ExpectedTestFails.xml | 28 +++++++++++++++ cime_config/testdefs/testlist_clm.xml | 40 ++++++++++++++++++++++ src/biogeochem/CropReprPoolsMod.F90 | 11 ++++++ 4 files changed, 86 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index b0d533ebde..b92acc34c7 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4222,6 +4222,13 @@ sub setup_logic_cnmatrix { } # Otherwise for CN or BGC mode } else { + # If matrixcn is on, for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool must be off + if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_second_grain_pool"}) ) { + $log->fatal_error("for_testing_use_second_grain_pool can NOT be on when use_matrixcn is on" ); + } + if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_repr_structure_pool"}) ) { + $log->fatal_error("for_testing_use_repr_structure_pool can NOT be on when use_matrixcn is on" ); + } # If both matrixcn and soil_matrix are off outmatrix can't be on if ( ! &value_is_true($nl->get_value("use_matrixcn")) && ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) { my $var = "is_outmatrix"; diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 2656079bf7..a55ce73634 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,6 +44,34 @@ + + + FAIL + #640, same test with clm-ciso_soil_matrixcn_only works + + + + + + FAIL + #640, same test with clm-ciso_soil_matrixcn_only works + + + + + + FAIL + #640, same test with clm-ciso_soil_matrixcn_only works + + + + + + FAIL + #640, same test with clm-ciso_soil_matrixcn_only works + + + diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index e570603ff7..100067f90d 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2599,6 +2599,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/biogeochem/CropReprPoolsMod.F90 b/src/biogeochem/CropReprPoolsMod.F90 index 780b9f2d52..82469b074f 100644 --- a/src/biogeochem/CropReprPoolsMod.F90 +++ b/src/biogeochem/CropReprPoolsMod.F90 @@ -57,6 +57,11 @@ subroutine crop_repr_pools_init() ! !DESCRIPTION: ! Initialize module-level data ! + ! !USES: + use clm_varctl, only: use_matrixcn + use abortutils, only: endrun + use shr_log_mod, only: errmsg => shr_log_errMsg + ! ! !ARGUMENTS: ! ! !LOCAL VARIABLES: @@ -77,11 +82,17 @@ subroutine crop_repr_pools_init() ! repr_hist_fnames(1) = 'GRAIN_MEAL', grain_hist_fnames(2) = 'GRAIN_OIL', etc. if (for_testing_use_second_grain_pool) then nrepr_grain = 2 + if (use_matrixcn) then + call endrun(msg="ERROR: for_testing_use_second_grain_pool should be .false. when use_matrixcn = .true."//errmsg(sourcefile, __LINE__)) + end if else nrepr_grain = 1 end if if (for_testing_use_repr_structure_pool) then nrepr_structure = 2 + if (use_matrixcn) then + call endrun(msg="ERROR: for_testing_use_repr_structure_pool should be .false. when use_matrixcn = .true."//errMsg(sourcefile, __LINE__)) + end if else nrepr_structure = 0 end if From 040111314eb439f6815b4519174d179882650c42 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 1 Dec 2023 15:50:14 -0700 Subject: [PATCH 023/408] Update expected fails and testlist files --- bld/CLMBuildNamelist.pm | 5 +++++ cime_config/testdefs/ExpectedTestFails.xml | 13 +++---------- cime_config/testdefs/testlist_clm.xml | 12 ------------ 3 files changed, 8 insertions(+), 22 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index b92acc34c7..f02be0c91a 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4222,6 +4222,11 @@ sub setup_logic_cnmatrix { } # Otherwise for CN or BGC mode } else { + # TODO (slevis 2023/12/1) The next two if statements do nothing. Erik K and Sam L found that + # for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool + # are empty rather than .true. or .false., but we did not get to the bottom + # of why, yet. The same error-check in the code does get triggered at run-time, + # so we will not pursue fixing this right now. # If matrixcn is on, for_testing_use_second_grain_pool and for_testing_use_repr_structure_pool must be off if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_second_grain_pool"}) ) { $log->fatal_error("for_testing_use_second_grain_pool can NOT be on when use_matrixcn is on" ); diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index a55ce73634..18619818fa 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -30,17 +30,10 @@ - - + + FAIL - PGI problems with the nuopc driver - - - - - - FAIL - PGI problems with the nuopc driver + Accessing incorrect url for neon data; will resolve itself when we update cnmatrix to some newer tag diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 100067f90d..ede4f6d278 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1177,7 +1177,6 @@ - @@ -1431,7 +1430,6 @@ - @@ -1446,15 +1444,6 @@ - - - - - - - - - @@ -1548,7 +1537,6 @@ - From 529bd1593064060ef5234089ccaa43fba379775b Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Fri, 1 Dec 2023 17:26:58 -0600 Subject: [PATCH 024/408] preparing for PR Formalized comments in the code --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- .../namelist_definition_ctsm.xml | 2 +- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 22 ++++---- src/biogeophys/UrbanParamsType.F90 | 10 ++-- src/cpl/share_esmf/UrbanTimeVarType.F90 | 56 +++++++++---------- src/main/clm_varpar.F90 | 2 +- 7 files changed, 48 insertions(+), 48 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 7c185ff6a0..0895a89ebb 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2111,7 +2111,7 @@ sub setup_logic_urban { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac'); - # Cathy [dev.04] + # X. Li [dev.04] add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic'); } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 5be2604c36..a3f488b8f9 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -167,7 +167,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). NONE - + .true. .true. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index aae38a5cec..5f89da9d29 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -948,7 +948,7 @@ Turn urban air conditioning/heating ON or OFF and add wasteheat: - + diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index f6330ec10b..c07b1ad0e3 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -210,9 +210,9 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, use clm_varctl , only : iulog use abortutils , only : endrun use clm_varpar , only : nlevurb, nlevsno, nlevmaxurbgrnd - ! Cathy [orig]: + ! X. Li [orig]: ! use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on - ! Cathy [dev.04]: + ! X. Li [dev.04]: use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on, urban_explicit_ac ! ! !ARGUMENTS: @@ -239,7 +239,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, real(r8) :: t_floor_bef(bounds%begl:bounds%endl) ! floor temperature at previous time step (K) real(r8) :: t_building_bef(bounds%begl:bounds%endl) ! internal building air temperature at previous time step [K] real(r8) :: t_building_bef_hac(bounds%begl:bounds%endl)! internal building air temperature before applying HAC [K] - ! Cathy [dev.03] + ! X. Li [dev.03] real(r8) :: eflx_urban_ac_sat(bounds%begl:bounds%endl) ! urban air conditioning flux under AC adoption saturation (W/m**2) real(r8) :: hcv_roofi(bounds%begl:bounds%endl) ! roof convective heat transfer coefficient (W m-2 K-1) real(r8) :: hcv_sunwi(bounds%begl:bounds%endl) ! sunwall convective heat transfer coefficient (W m-2 K-1) @@ -329,7 +329,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, t_floor => temperature_inst%t_floor_lun , & ! InOut: [real(r8) (:)] floor temperature (K) t_building => temperature_inst%t_building_lun , & ! InOut: [real(r8) (:)] internal building air temperature (K) - ! Cathy [dev] + ! X. Li [dev] p_ac => urbantv_inst%p_ac , & ! Input: [real(r8) (:)] air-conditioning penetration rate (-) t_building_max => urbantv_inst%t_building_max , & ! Input: [real(r8) (:)] maximum internal building air temperature (K) t_building_min => urbanparams_inst%t_building_min , & ! Input: [real(r8) (:)] minimum internal building air temperature (K) @@ -432,9 +432,9 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, vf_wf(l) = 0.5_r8*(1._r8 - vf_rf(l)) ! This view factor implicitly converts from per unit floor area to per unit wall area - ! Cathy [orig] + ! X. Li [orig] ! vf_fw(l) = vf_wf(l) / building_hwr(l) - ! Cathy [bugfix] + ! X. Li [bugfix] vf_fw(l) = vf_wf(l) ! This view factor implicitly converts from per unit roof area to per unit wall area @@ -841,9 +841,9 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, + em_floori(l)*sb*t_floor_bef(l)**4._r8 & + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l)) - ! Cathy [orig] + ! X. Li [orig] ! qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l) - ! Cathy [bugfix] + ! X. Li [bugfix] qrd_building(l) = qrd_roof(l) + qrd_sunw(l) + qrd_shdw(l) + qrd_floor(l) if (abs(qrd_building(l)) > .10_r8 ) then @@ -936,16 +936,16 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, ! rho_dair(l) = pstd / (rair*t_building(l)) if (t_building_bef_hac(l) > t_building_max(l)) then - ! Cathy [dev.04] + ! X. Li [dev.04] if (urban_explicit_ac) then ! use explicit ac adoption rate: - ! Cathy [dev.03] ! after the change, t_building_max is saturation setpoint + ! X. Li [dev.03] ! after the change, t_building_max is saturation setpoint eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) & * dtime / (ht_roof(l) * rho_dair(l) * cpair * wtlunit_roof(l)) eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l) else - ! Cathy [orig] + ! X. Li [orig] t_building(l) = t_building_max(l) eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90 index c674aac2db..16da4b3ad0 100644 --- a/src/biogeophys/UrbanParamsType.F90 +++ b/src/biogeophys/UrbanParamsType.F90 @@ -101,7 +101,7 @@ module UrbanParamsType character(len= *), parameter, public :: urban_hac_on = 'ON' character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT' character(len= 16), public :: urban_hac = urban_hac_off - ! Cathy [dev.04] + ! X. Li [dev.04] logical, public :: urban_explicit_ac = .true. ! whether to use explicit, time-varying AC adoption rate logical, public :: urban_traffic = .false. ! urban traffic fluxes @@ -849,9 +849,9 @@ subroutine UrbanReadNML ( NLFilename ) integer :: unitn ! unit for namelist file character(len=32) :: subname = 'UrbanReadNML' ! subroutine name - ! Cathy [orig]: + ! X. Li [orig]: ! namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method - ! Cathy [dev.04]: + ! X. Li [dev.04]: namelist / clmu_inparm / urban_hac, urban_explicit_ac, urban_traffic, building_temp_method !EOP !----------------------------------------------------------------------- @@ -880,7 +880,7 @@ subroutine UrbanReadNML ( NLFilename ) ! Broadcast namelist variables read in call shr_mpi_bcast(urban_hac, mpicom) - ! Cathy [dev.04]: + ! X. Li [dev.04]: call shr_mpi_bcast(urban_explicit_ac, mpicom) call shr_mpi_bcast(urban_traffic, mpicom) call shr_mpi_bcast(building_temp_method, mpicom) @@ -893,7 +893,7 @@ subroutine UrbanReadNML ( NLFilename ) ! if ( masterproc )then write(iulog,*) ' urban air conditioning/heating and wasteheat = ', urban_hac - ! Cathy [dev.04]: + ! X. Li [dev.04]: write(iulog,*) ' urban explicit air-conditioning adoption rate = ', urban_explicit_ac write(iulog,*) ' urban traffic flux = ', urban_traffic end if diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index ae34449c1e..23dbf54086 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -12,7 +12,7 @@ module UrbanTimeVarType use abortutils , only : endrun use decompMod , only : bounds_type, subgrid_level_landunit use clm_varctl , only : iulog - use landunit_varcon , only : isturb_MIN, isturb_MAX ! Cathy: min and max types urban; equals 7 and 9, resp. + use landunit_varcon , only : isturb_MIN, isturb_MAX ! X. Li: min and max types urban; equals 7 and 9, resp. use clm_varcon , only : spval use LandunitType , only : lun use GridcellType , only : grc @@ -24,7 +24,7 @@ module UrbanTimeVarType type, public :: urbantv_type ! real(r8), public, pointer :: t_building_max(:) ! lun maximum internal building air temperature (K) - ! Cathy [dev] + ! X. Li [dev] real(r8), public, pointer :: p_ac(:) ! lun air-conditioning ownership rate (unitless, between 0 and 1) type(shr_strdata_type) :: sdat_urbantv ! urban time varying input data stream contains @@ -34,9 +34,9 @@ module UrbanTimeVarType procedure, public :: urbantv_interp ! Interpolate urban time varying stream end type urbantv_type - ! Cathy [orig] + ! X. Li [orig] ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX) - ! Cathy [dev]: + ! X. Li [dev]: character(15), private :: stream_varnames(1:6) ! 1-3 for t_building_max, 4-6 for p_ac character(len=*), parameter, private :: sourcefile = & @@ -60,7 +60,7 @@ subroutine Init(this, bounds, NLFilename) character(len=*) , intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: - integer :: begl, endl ! Cathy: beginning and ending landunit index, from src/main/decompMod + integer :: begl, endl ! X. Li: beginning and ending landunit index, from src/main/decompMod !--------------------------------------------------------------------- begl = bounds%begl; endl = bounds%endl @@ -68,18 +68,18 @@ subroutine Init(this, bounds, NLFilename) ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan - ! Cathy [dev] + ! X. Li [dev] allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan call this%urbantv_init(bounds, NLFilename) call this%urbantv_interp(bounds) - ! Add history fields ! Cathy: this adds an output field. the subroutine is in scr/main/histFileMod.F90 + ! Add history fields ! X. Li: this adds an output field. the subroutine is in scr/main/histFileMod.F90 call hist_addfld1d (fname='TBUILD_MAX', units='K', & avgflag='A', long_name='prescribed maximum interior building temperature', & ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & l2g_scale_type='unity') - ! Cathy [dev] + ! X. Li [dev] call hist_addfld1d (fname='P_AC', units='unitless', & avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)', & ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & @@ -97,7 +97,7 @@ subroutine urbantv_init(this, bounds, NLFilename) use clm_nlUtilsMod , only : find_nlgroup_name use spmdMod , only : masterproc, mpicom, iam use shr_mpi_mod , only : shr_mpi_bcast - use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md ! Cathy: equals 7, 8 and 9 + use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md ! X. Li: equals 7, 8 and 9 use dshr_strdata_mod , only : shr_strdata_init_from_inline use lnd_comp_shr , only : mesh, model_clock ! @@ -119,7 +119,7 @@ subroutine urbantv_init(this, bounds, NLFilename) character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac ??? character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm integer :: rc ! error code - ! Cathy [orig]: this is taken out because field strings are now hard coded in + ! X. Li [orig]: this is taken out because field strings are now hard coded in ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string character(*), parameter :: subName = "('urbantv_init')" ! ??? !----------------------------------------------------------------------- @@ -139,11 +139,11 @@ subroutine urbantv_init(this, bounds, NLFilename) model_year_align_urbantv = 1 ! align stream_year_first_urbantv with this model year stream_fldFileName_urbantv = ' ' stream_meshfile_urbantv = ' ' - ! Cathy [orig] + ! X. Li [orig] ! stream_varnames(isturb_tbd) = urbantvString//"TBD" ! stream_varnames(isturb_hd) = urbantvString//"HD" ! stream_varnames(isturb_md) = urbantvString//"MD" - ! Cathy [dev] + ! X. Li [dev] stream_varnames(1) = "tbuildmax_TBD" stream_varnames(2) = "tbuildmax_HD" stream_varnames(3) = "tbuildmax_MD" @@ -180,9 +180,9 @@ subroutine urbantv_init(this, bounds, NLFilename) write(iulog,'(a,a)' ) ' stream_fldFileName_urbantv = ',stream_fldFileName_urbantv write(iulog,'(a,a)' ) ' stream_meshfile_urbantv = ',stream_meshfile_urbantv write(iulog,'(a,a)' ) ' urbantv_tintalgo = ',urbantv_tintalgo - ! Cathy [orig] + ! X. Li [orig] ! do n = isturb_tbd,isturb_md - ! Cathy [dev] + ! X. Li [dev] do n = 1,6 write(iulog,'(a,a)' ) ' stream_varname = ',trim(stream_varnames(n)) end do @@ -200,10 +200,10 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_lev_dimname = 'null', & stream_mapalgo = trim(urbantvmapalgo), & stream_filenames = (/trim(stream_fldfilename_urbantv)/), & - ! Cathy [orig] + ! X. Li [orig] ! stream_fldlistFile = stream_varnames(isturb_tbd:isturb_md),& ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),& - ! Cathy [dev] + ! X. Li [dev] stream_fldlistFile = stream_varnames(1:6), & stream_fldListModel = stream_varnames(1:6), & stream_yearFirst = stream_year_first_urbantv, & @@ -265,10 +265,10 @@ subroutine urbantv_interp(this, bounds) ! Create 2d array for all stream variable data lsize = bounds%endg - bounds%begg + 1 - ! Cathy [orig] + ! X. Li [orig] ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX)) ! do n = isturb_MIN,isturb_MAX - ! Cathy [dev] + ! X. Li [dev] allocate(dataptr2d(lsize, 1:6)) do n = 1,6 call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), & @@ -291,13 +291,13 @@ subroutine urbantv_interp(this, bounds) ig = ig+1 if (g == lun%gridcell(l)) exit end do - ! Cathy [orig] + ! X. Li [orig] ! do n = isturb_MIN,isturb_MAX - ! Cathy [dev] + ! X. Li [dev] do n = 1,6 - ! Cathy [orig] + ! X. Li [orig] ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then - ! Cathy [dev.02] + ! X. Li [dev.02] if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then this%t_building_max(l) = dataptr2d(ig,n) end if @@ -306,9 +306,9 @@ subroutine urbantv_interp(this, bounds) end if end do else - this%t_building_max(l) = spval ! Cathy: special value for real data, set to 1.e36 in src/main/clm_varcon - ! Cathy [dev] - this%p_ac(l) = 0._r8 ! Cathy: set to 0 for non-urban landunit + this%t_building_max(l) = spval ! X. Li: special value for real data, set to 1.e36 in src/main/clm_varcon + ! X. Li [dev] + this%p_ac(l) = 0._r8 ! X. Li: set to 0 for non-urban landunit end if end do deallocate(dataptr2d) @@ -322,9 +322,9 @@ subroutine urbantv_interp(this, bounds) ig = ig+1 if (g == lun%gridcell(l)) exit end do - ! Cathy [orig] + ! X. Li [orig] ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then - ! Cathy [dev] + ! X. Li [dev] if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) & .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then found = .true. @@ -339,7 +339,7 @@ subroutine urbantv_interp(this, bounds) write(iulog,*)'landunit type: ',lun%itype(lindx) write(iulog,*)'urban_valid: ',urban_valid(gindx) write(iulog,*)'t_building_max: ',this%t_building_max(lindx) - ! Cathy [dev] + ! X. Li [dev] write(iulog,*)'p_ac: ',this%p_ac(lindx) call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, & msg=errmsg(sourcefile, __LINE__)) diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90 index e1179e43b3..3ef9cf48a2 100644 --- a/src/main/clm_varpar.F90 +++ b/src/main/clm_varpar.F90 @@ -203,7 +203,7 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft) max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb) nlevsoifl = 10 - ![Cathy: to run prod.02 using new surf data from Keer, changed below from 5 to 10] + ! X. Li: changed below from 5 to 10 to match new surface data nlevurb = 10 ! originally 5 if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined From def2f7506284508182898bc0d1edeb2c12812572 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 12 Dec 2023 12:16:39 -0700 Subject: [PATCH 025/408] Change failing SMS_Ln9_P72x2 test to passing SMS_Ln9_P360x2 --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 81ad8bced4..52ccfbf2db 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -322,7 +322,7 @@ - + From 08768f9b877caed6efd3c8fbb38f1ac3bbf29991 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 18 Dec 2023 15:25:38 -0700 Subject: [PATCH 026/408] To pass test, add use_matrixcn=.false. to luna testmod --- cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm index cbfbb9f525..fb796ebfaf 100644 --- a/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/luna/user_nl_clm @@ -1,3 +1,3 @@ use_luna = .true. use_flexibleCN = .false. - + use_matrixcn = .false. From 8b2cb728ac99a2e6c8a7be5738f8b709b5e336b5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 19 Dec 2023 12:46:43 -0700 Subject: [PATCH 027/408] Remove two clm45 tests from ExpectedTestFails --- cime_config/testdefs/ExpectedTestFails.xml | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 18619818fa..8a43eb0acc 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,13 +44,6 @@ - - - FAIL - #640, same test with clm-ciso_soil_matrixcn_only works - - - FAIL @@ -58,13 +51,6 @@ - - - FAIL - #640, same test with clm-ciso_soil_matrixcn_only works - - - From ddfac7b299d8143fdf2c2d7438cf2729fe1a047d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 22 Dec 2023 15:35:13 -0700 Subject: [PATCH 028/408] Backed dev100 mods out of 3 more files for 1x1_brazil test to pass --- src/biogeochem/CNCStateUpdate1Mod.F90 | 232 ++---- src/biogeochem/CNPhenologyMod.F90 | 680 +++++++++--------- .../SoilBiogeochemNStateUpdate1Mod.F90 | 70 +- 3 files changed, 429 insertions(+), 553 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 8cac85824e..f73453476e 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -2,9 +2,6 @@ module CNCStateUpdate1Mod !----------------------------------------------------------------------- ! Module for carbon state variable update, non-mortality fluxes. - ! When the matrix solution is being used (use_matrixcn and use_soil_matrixcn) - ! only some state updates are done here, the other state updates happen - ! after the matrix is solved in VegMatrix and SoilMatrix. ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 @@ -19,7 +16,8 @@ module CNCStateUpdate1Mod use CNVegCarbonFluxType , only : cnveg_carbonflux_type use CropType , only : crop_type use CropReprPoolsMod , only : nrepr, repr_grain_min, repr_grain_max, repr_structure_min, repr_structure_max - use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn + use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con + use SoilBiogeochemDecompCascadeConType , only : use_soil_matrixcn use SoilBiogeochemCarbonFluxType , only : soilbiogeochem_carbonflux_type use SoilBiogeochemCarbonStateType , only : soilbiogeochem_carbonstate_type use PatchType , only : patch @@ -193,9 +191,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) - ! - ! State update without the matrix solution - ! if (.not. use_soil_matrixcn) then ! phenology and dynamic land cover fluxes do i = i_litr_min, i_litr_max @@ -207,12 +202,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! terms have been moved to CStateUpdateDynPatch. I think this is zeroed every ! time step, but to be safe, I'm explicitly setting it to zero here. cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8 - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in SoilMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! else ! phenology and dynamic land cover fluxes do i = i_litr_min, i_litr_max @@ -243,15 +232,11 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) - ! - ! State update without the matrix solution - ! if (.not. use_soil_matrixcn) then cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & - - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt - ! else ! not needed here? - end if !not use_soil_matrixcn + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & + - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt + end if !not use_soil_matrixcn end do end do end do @@ -260,14 +245,10 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) - ! - ! State update without the matrix solution - ! if (.not. use_soil_matrixcn) then cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) & - + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt - ! else ! not needed here? + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) & + + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt end if !not use_soil_matrixcn end do end do @@ -275,17 +256,13 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end do end if - if (.not. use_fates) then + if (.not. use_fates) then ptch: do fp = 1,num_soilp p = filter_soilp(fp) c = patch%column(p) ! phenology: transfer growth fluxes - - ! - ! State update without the matrix solution - ! - if(.not. use_matrixcn)then + if(.not. use_matrixcn)then ! NOTE: Any changes that go here MUST be applied to the matrix ! version as well cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) + cf_veg%leafc_xfer_to_leafc_patch(p)*dt @@ -314,11 +291,11 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end do end if - ! phenology: litterfall fluxes + ! phenology: litterfall fluxes cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) - cf_veg%leafc_to_litter_patch(p)*dt cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p) - cf_veg%frootc_to_litter_patch(p)*dt - - ! livewood turnover fluxes + + ! livewood turnover fluxes if (woody(ivt(p)) == 1._r8) then cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) - cf_veg%livestemc_to_deadstemc_patch(p)*dt cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p) + cf_veg%livestemc_to_deadstemc_patch(p)*dt @@ -342,81 +319,57 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & - (cf_veg%repr_structurec_to_cropprod_patch(p,k) + cf_veg%repr_structurec_to_litter_patch(p,k))*dt end do end if - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in VegMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! - else - ! NOTE: Changes for above that apply for matrix code are in CNPhenology EBK (11/26/2019) - - ! This part below MUST match exactly the code for the non-matrix part - ! above! - if (ivt(p) >= npcropmin) then - cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & - - cf_veg%crop_seedc_to_leaf_patch(p) * dt - do k = repr_grain_min, repr_grain_max - cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & - + cf_veg%repr_grainc_to_seed_patch(p,k) * dt - end do -! else ! slevis: I think I rejected this alternative due to a balance error -! ! NOTE: Changes for above that apply for matrix code are in CNPhenology EBK (11/26/2019) - -! ! This part below MUST match exactly the code for the non-matrix part -! ! above! -! if (ivt(p) >= npcropmin) then -! cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & -! - cf_veg%crop_seedc_to_leaf_patch(p) * dt -! do k = repr_grain_min, repr_grain_max -! cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) & -! - (cf_veg%repr_grainc_to_food_patch(p,k) + cf_veg%repr_grainc_to_seed_patch(p,k))*dt -! cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & -! + cf_veg%repr_grainc_to_seed_patch(p,k) * dt -! end do -! do k = repr_structure_min, repr_structure_max -! cs_veg%reproductivec_patch(p,k) = cs_veg%reproductivec_patch(p,k) & -! - (cf_veg%repr_structurec_to_cropprod_patch(p,k) + cf_veg%repr_structurec_to_litter_patch(p,k))*dt -! end do - end if - end if !not use_matrixcn + else + ! NOTE: Changes for above that apply for matrix code are in CNPhenology EBK (11/26/2019) + + ! This part below MUST match exactly the code for the non-matrix part + ! above! + if (ivt(p) >= npcropmin) then + cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & + - cf_veg%crop_seedc_to_leaf_patch(p) * dt + do k = repr_grain_min, repr_grain_max + cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & + + cf_veg%repr_grainc_to_seed_patch(p,k) * dt + end do + end if + end if !not use_matrixcn - check_cpool = cs_veg%cpool_patch(p)- cf_veg%psnsun_to_cpool_patch(p)*dt-cf_veg%psnshade_to_cpool_patch(p)*dt - cpool_delta = cs_veg%cpool_patch(p) + check_cpool = cs_veg%cpool_patch(p)- cf_veg%psnsun_to_cpool_patch(p)*dt-cf_veg%psnshade_to_cpool_patch(p)*dt + cpool_delta = cs_veg%cpool_patch(p) - ! maintenance respiration fluxes from cpool + ! maintenance respiration fluxes from cpool - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_xsmrpool_patch(p)*dt - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%leaf_curmr_patch(p)*dt - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%froot_curmr_patch(p)*dt - If (woody(ivt(p)) == 1._r8) then + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_xsmrpool_patch(p)*dt + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%leaf_curmr_patch(p)*dt + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%froot_curmr_patch(p)*dt + If (woody(ivt(p)) == 1._r8) then cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%livestem_curmr_patch(p)*dt cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%livecroot_curmr_patch(p)*dt - end if - if (ivt(p) >= npcropmin) then ! skip 2 generic crops + end if + if (ivt(p) >= npcropmin) then ! skip 2 generic crops cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%livestem_curmr_patch(p)*dt do k = 1, nrepr cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%reproductive_curmr_patch(p,k)*dt end do - end if + end if - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_resp_patch(p)*dt + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_resp_patch(p)*dt - !RF Add in the carbon spent on uptake respiration - cs_veg%cpool_patch(p)= cs_veg%cpool_patch(p) - cf_veg%soilc_change_patch(p)*dt + !RF Add in the carbon spent on uptake respiration. + cs_veg%cpool_patch(p)= cs_veg%cpool_patch(p) - cf_veg%soilc_change_patch(p)*dt - ! maintenance respiration fluxes from xsmrpool - cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) + cf_veg%cpool_to_xsmrpool_patch(p)*dt - cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%leaf_xsmr_patch(p)*dt - cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%froot_xsmr_patch(p)*dt - if (woody(ivt(p)) == 1._r8) then + ! maintenance respiration fluxes from xsmrpool + cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) + cf_veg%cpool_to_xsmrpool_patch(p)*dt + cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%leaf_xsmr_patch(p)*dt + cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%froot_xsmr_patch(p)*dt + if (woody(ivt(p)) == 1._r8) then cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%livestem_xsmr_patch(p)*dt cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) - cf_veg%livecroot_xsmr_patch(p)*dt - end if + end if - ! allocation fluxes - if (carbon_resp_opt == 1) then + ! allocation fluxes + if (carbon_resp_opt == 1) then cf_veg%cpool_to_leafc_patch(p) = cf_veg%cpool_to_leafc_patch(p) - cf_veg%cpool_to_leafc_resp_patch(p) cf_veg%cpool_to_leafc_storage_patch(p) = cf_veg%cpool_to_leafc_storage_patch(p) - & cf_veg%cpool_to_leafc_storage_resp_patch(p) @@ -427,21 +380,12 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_leafc_patch(p)*dt cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_leafc_storage_patch(p)*dt cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_frootc_patch(p)*dt - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_frootc_storage_patch(p)*dt - ! - ! State update without the matrix solution - ! - if(.not. use_matrixcn) then + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_frootc_storage_patch(p)*dt + if(.not. use_matrixcn) then cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) + cf_veg%cpool_to_leafc_patch(p)*dt cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p) + cf_veg%cpool_to_leafc_storage_patch(p)*dt cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p) + cf_veg%cpool_to_frootc_patch(p)*dt cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) + cf_veg%cpool_to_frootc_storage_patch(p)*dt - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in VegMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! else ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) end if !not use_matrixcn @@ -461,10 +405,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_livecrootc_patch(p)*dt cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_livecrootc_storage_patch(p)*dt cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_deadcrootc_patch(p)*dt - cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_deadcrootc_storage_patch(p)*dt - ! - ! State update without the matrix solution - ! + cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_deadcrootc_storage_patch(p)*dt if(.not. use_matrixcn)then cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) + cf_veg%cpool_to_livestemc_patch(p)*dt cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) + cf_veg%cpool_to_livestemc_storage_patch(p)*dt @@ -474,12 +415,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%livecrootc_storage_patch(p) = cs_veg%livecrootc_storage_patch(p) + cf_veg%cpool_to_livecrootc_storage_patch(p)*dt cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p) + cf_veg%cpool_to_deadcrootc_patch(p)*dt cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) + cf_veg%cpool_to_deadcrootc_storage_patch(p)*dt - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in VegMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! else ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) end if !not use_matrixcn @@ -496,9 +431,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_patch(p,k)*dt cs_veg%cpool_patch(p) = cs_veg%cpool_patch(p) - cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt end do - ! - ! State update without the matrix solution - ! if(.not. use_matrixcn)then cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) + cf_veg%cpool_to_livestemc_patch(p)*dt cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) + cf_veg%cpool_to_livestemc_storage_patch(p)*dt @@ -508,12 +440,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%reproductivec_storage_patch(p,k) = cs_veg%reproductivec_storage_patch(p,k) & + cf_veg%cpool_to_reproductivec_storage_patch(p,k)*dt end do - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in VegMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! else ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) end if !not use_matrixcn @@ -576,30 +502,17 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) + cf_veg%cpool_to_gresp_storage_patch(p)*dt ! move storage pools into transfer pools - - ! - ! State update without the matrix solution - ! - if(.not. use_matrixcn)then - cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p) - cf_veg%leafc_storage_to_xfer_patch(p)*dt - cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p) + cf_veg%leafc_storage_to_xfer_patch(p)*dt - cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) - cf_veg%frootc_storage_to_xfer_patch(p)*dt - cs_veg%frootc_xfer_patch(p) = cs_veg%frootc_xfer_patch(p) + cf_veg%frootc_storage_to_xfer_patch(p)*dt - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in VegMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! + if(.not. use_matrixcn)then + cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p) - cf_veg%leafc_storage_to_xfer_patch(p)*dt + cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p) + cf_veg%leafc_storage_to_xfer_patch(p)*dt + cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) - cf_veg%frootc_storage_to_xfer_patch(p)*dt + cs_veg%frootc_xfer_patch(p) = cs_veg%frootc_xfer_patch(p) + cf_veg%frootc_storage_to_xfer_patch(p)*dt else - ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) + ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) end if !not use_matrixcn if (woody(ivt(p)) == 1._r8) then cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) - cf_veg%gresp_storage_to_xfer_patch(p)*dt cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p) + cf_veg%gresp_storage_to_xfer_patch(p)*dt - ! - ! State update without the matrix solution - ! if(.not. use_matrixcn)then cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) - cf_veg%livestemc_storage_to_xfer_patch(p)*dt cs_veg%livestemc_xfer_patch(p) = cs_veg%livestemc_xfer_patch(p) + cf_veg%livestemc_storage_to_xfer_patch(p)*dt @@ -609,21 +522,12 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%livecrootc_xfer_patch(p) = cs_veg%livecrootc_xfer_patch(p) + cf_veg%livecrootc_storage_to_xfer_patch(p)*dt cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p)- cf_veg%deadcrootc_storage_to_xfer_patch(p)*dt cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p) + cf_veg%deadcrootc_storage_to_xfer_patch(p)*dt - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in VegMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! else ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) end if !not use_matrixcn end if if (ivt(p) >= npcropmin) then ! skip 2 generic crops ! lines here for consistency; the transfer terms are zero - ! - ! State update without the matrix solution - ! if(.not. use_matrixcn)then ! lines here for consistency; the transfer terms are zero cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) - cf_veg%livestemc_storage_to_xfer_patch(p)*dt @@ -634,12 +538,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%reproductivec_xfer_patch(p,k) = cs_veg%reproductivec_xfer_patch(p,k) & + cf_veg%reproductivec_storage_to_xfer_patch(p,k)*dt end do - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in VegMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! else ! NOTE: The equivalent changes for matrix code are in CNPhenology EBK (11/26/2019) end if !not use_matrixcn @@ -655,20 +553,16 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! an intent(inout) ! fluxes should not be updated in this module - not sure where ! this belongs - ! DML (06-20-2017) While debugging crop isotope code, found that cpool_patch and frootc_patch - ! could occasionally be very small but nonzero numbers after crop harvest, which persists + ! DML (06-20-2017) While debugging crop isotope code, found that cpool_patch and frootc_patch + ! could occasionally be very small but nonzero numbers after crop harvest, which persists ! through to next planting and for reasons that could not 100% ! isolate, caused C12/C13 ratios to occasionally go out of ! bounds. Zeroing out these small pools and putting them into the flux to the ! atmosphere solved many of the crop isotope problems - ! Instantly release XSMRPOOL to atmosphere if ( .not. dribble_crophrv_xsmrpool_2atm ) then cf_veg%xsmrpool_to_atm_patch(p) = cf_veg%xsmrpool_to_atm_patch(p) + cs_veg%xsmrpool_patch(p)/dt cf_veg%xsmrpool_to_atm_patch(p) = cf_veg%xsmrpool_to_atm_patch(p) + cs_veg%cpool_patch(p)/dt - ! - ! State update without the matrix solution - ! if(.not. use_matrixcn)then cf_veg%xsmrpool_to_atm_patch(p) = cf_veg%xsmrpool_to_atm_patch(p) + cs_veg%frootc_patch(p)/dt else @@ -684,9 +578,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%xsmrpool_loss_patch(p) = cs_veg%xsmrpool_loss_patch(p) + & cs_veg%xsmrpool_patch(p) + & cs_veg%cpool_patch(p) - ! - ! State update without the matrix solution - ! if(.not. use_matrixcn)then cs_veg%xsmrpool_loss_patch(p) = cs_veg%xsmrpool_loss_patch(p) + cs_veg%frootc_patch(p) else @@ -694,9 +585,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & + cs_veg%frootc_patch(p) * matrix_update_phc(p,cf_veg%ifroot_to_iout_ph,1._r8/dt,dt,cnveg_carbonflux_inst,.true.,.true.) end if end if - ! - ! State update without the matrix solution - ! if (.not. use_matrixcn) then cs_veg%frootc_patch(p) = 0._r8 end if @@ -713,8 +601,8 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end if end if - end do ptch ! end of patch loop - end if ! end of NOT fates + end do ptch ! end of patch loop + end if ! end of NOT fates end associate diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 5d666c0ffb..e804c0658b 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -136,10 +136,8 @@ module CNPhenologyMod integer, allocatable :: maxplantjday(:,:) ! maximum planting julian day integer :: jdayyrstart(inSH) ! julian day of start of year - ! Two matrix check parameters that will be invoked when the matrix solution - ! comes in (use_matrixcn) - logical,parameter :: matrixcheck_ph = .True. ! Matrix solution check - logical,parameter :: acc_ph = .False. ! Another matrix solution check + logical,parameter :: matrixcheck_ph = .True. ! Matrix check + logical,parameter :: acc_ph = .False. ! Another matrix check real(r8), private :: initial_seed_at_planting = 3._r8 ! Initial seed at planting @@ -641,114 +639,115 @@ subroutine CNEvergreenPhenology (num_soilp, filter_soilp , & integer :: p ! indices integer :: fp ! lake filter patch index - real(r8):: tranr + real(r8):: tranr real(r8):: t1 ! temporary variable !----------------------------------------------------------------------- associate( & - ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type - evergreen => pftcon%evergreen , & ! Input: binary flag for evergreen leaf habit (0 or 1) - leaf_long => pftcon%leaf_long , & ! Input: leaf longevity (yrs) + evergreen => pftcon%evergreen , & ! Input: binary flag for evergreen leaf habit (0 or 1) + leaf_long => pftcon%leaf_long , & ! Input: leaf longevity (yrs) - woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) + woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) - leafc_storage => cnveg_carbonstate_inst%leafc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) leaf C storage - frootc_storage => cnveg_carbonstate_inst%frootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C storage - livestemc_storage => cnveg_carbonstate_inst%livestemc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) live stem C storage - deadstemc_storage => cnveg_carbonstate_inst%deadstemc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) dead stem C storage - livecrootc_storage => cnveg_carbonstate_inst%livecrootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) live coarse root C storage - deadcrootc_storage => cnveg_carbonstate_inst%deadcrootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) dead coarse root C storage - gresp_storage => cnveg_carbonstate_inst%gresp_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) growth respiration storage - leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) leaf C transfer - frootc_xfer => cnveg_carbonstate_inst%frootc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) fine root C transfer - livestemc_xfer => cnveg_carbonstate_inst%livestemc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) live stem C transfer - deadstemc_xfer => cnveg_carbonstate_inst%deadstemc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) dead stem C transfer - livecrootc_xfer => cnveg_carbonstate_inst%livecrootc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) live coarse root C transfer - deadcrootc_xfer => cnveg_carbonstate_inst%deadcrootc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) dead coarse root C transfer - - leafn_storage => cnveg_nitrogenstate_inst%leafn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) leaf N storage - frootn_storage => cnveg_nitrogenstate_inst%frootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) fine root N storage - livestemn_storage => cnveg_nitrogenstate_inst%livestemn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) live stem N storage - deadstemn_storage => cnveg_nitrogenstate_inst%deadstemn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) dead stem N storage - livecrootn_storage => cnveg_nitrogenstate_inst%livecrootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) live coarse root N storage - deadcrootn_storage => cnveg_nitrogenstate_inst%deadcrootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) dead coarse root N storage - leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) leaf N transfer - frootn_xfer => cnveg_nitrogenstate_inst%frootn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) fine root N transfer - livestemn_xfer => cnveg_nitrogenstate_inst%livestemn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) live stem N transfer - deadstemn_xfer => cnveg_nitrogenstate_inst%deadstemn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) dead stem N transfer - livecrootn_xfer => cnveg_nitrogenstate_inst%livecrootn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) live coarse root N transfer - deadcrootn_xfer => cnveg_nitrogenstate_inst%deadcrootn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) dead coarse root N transfer - - leafc_storage_to_xfer => cnveg_carbonflux_inst%leafc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - frootc_storage_to_xfer => cnveg_carbonflux_inst%frootc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - livestemc_storage_to_xfer => cnveg_carbonflux_inst%livestemc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - deadstemc_storage_to_xfer => cnveg_carbonflux_inst%deadstemc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - livecrootc_storage_to_xfer => cnveg_carbonflux_inst%livecrootc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - deadcrootc_storage_to_xfer => cnveg_carbonflux_inst%deadcrootc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - gresp_storage_to_xfer => cnveg_carbonflux_inst%gresp_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - leafc_xfer_to_leafc => cnveg_carbonflux_inst%leafc_xfer_to_leafc_patch , & ! InOut: [real(r8) (:)] - frootc_xfer_to_frootc => cnveg_carbonflux_inst%frootc_xfer_to_frootc_patch , & ! InOut: [real(r8) (:)] - livestemc_xfer_to_livestemc => cnveg_carbonflux_inst%livestemc_xfer_to_livestemc_patch , & ! InOut: [real(r8) (:)] - deadstemc_xfer_to_deadstemc => cnveg_carbonflux_inst%deadstemc_xfer_to_deadstemc_patch , & ! InOut: [real(r8) (:)] - livecrootc_xfer_to_livecrootc => cnveg_carbonflux_inst%livecrootc_xfer_to_livecrootc_patch , & ! InOut: [real(r8) (:)] - deadcrootc_xfer_to_deadcrootc => cnveg_carbonflux_inst%deadcrootc_xfer_to_deadcrootc_patch , & ! InOut: [real(r8) (:)] - - leafn_storage_to_xfer => cnveg_nitrogenflux_inst%leafn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - frootn_storage_to_xfer => cnveg_nitrogenflux_inst%frootn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - livestemn_storage_to_xfer => cnveg_nitrogenflux_inst%livestemn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - deadstemn_storage_to_xfer => cnveg_nitrogenflux_inst%deadstemn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - livecrootn_storage_to_xfer => cnveg_nitrogenflux_inst%livecrootn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - deadcrootn_storage_to_xfer => cnveg_nitrogenflux_inst%deadcrootn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] - leafn_xfer_to_leafn => cnveg_nitrogenflux_inst%leafn_xfer_to_leafn_patch , & ! InOut: [real(r8) (:)] - frootn_xfer_to_frootn => cnveg_nitrogenflux_inst%frootn_xfer_to_frootn_patch , & ! InOut: [real(r8) (:)] - livestemn_xfer_to_livestemn => cnveg_nitrogenflux_inst%livestemn_xfer_to_livestemn_patch , & ! InOut: [real(r8) (:)] - deadstemn_xfer_to_deadstemn => cnveg_nitrogenflux_inst%deadstemn_xfer_to_deadstemn_patch , & ! InOut: [real(r8) (:)] - livecrootn_xfer_to_livecrootn => cnveg_nitrogenflux_inst%livecrootn_xfer_to_livecrootn_patch , & ! InOut: [real(r8) (:)] - deadcrootn_xfer_to_deadcrootn => cnveg_nitrogenflux_inst%deadcrootn_xfer_to_deadcrootn_patch , & ! InOut: [real(r8) (:)] - - bglfr => cnveg_state_inst%bglfr_patch , & ! Output: [real(r8) (:) ] background litterfall rate (1/s) - bgtr => cnveg_state_inst%bgtr_patch , & ! Output: [real(r8) (:) ] background transfer growth rate (1/s) - lgsf => cnveg_state_inst%lgsf_patch , & ! Output: [real(r8) (:) ] long growing season factor [0-1] - ileafst_to_ileafxf_phc => cnveg_carbonflux_inst%ileafst_to_ileafxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool - ileafxf_to_ileaf_phc => cnveg_carbonflux_inst%ileafxf_to_ileaf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool - ifrootst_to_ifrootxf_phc => cnveg_carbonflux_inst%ifrootst_to_ifrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool - ifrootxf_to_ifroot_phc => cnveg_carbonflux_inst%ifrootxf_to_ifroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool - ilivestemst_to_ilivestemxf_phc => cnveg_carbonflux_inst%ilivestemst_to_ilivestemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool - ilivestemxf_to_ilivestem_phc => cnveg_carbonflux_inst%ilivestemxf_to_ilivestem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool - ideadstemst_to_ideadstemxf_phc => cnveg_carbonflux_inst%ideadstemst_to_ideadstemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool - ideadstemxf_to_ideadstem_phc => cnveg_carbonflux_inst%ideadstemxf_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool - ilivecrootst_to_ilivecrootxf_phc => cnveg_carbonflux_inst%ilivecrootst_to_ilivecrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool - ilivecrootxf_to_ilivecroot_phc => cnveg_carbonflux_inst%ilivecrootxf_to_ilivecroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool - ideadcrootst_to_ideadcrootxf_phc => cnveg_carbonflux_inst%ideadcrootst_to_ideadcrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool - ideadcrootxf_to_ideadcroot_phc => cnveg_carbonflux_inst%ideadcrootxf_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool - ilivestem_to_ideadstem_phc => cnveg_carbonflux_inst%ilivestem_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool - ilivecroot_to_ideadcroot_phc => cnveg_carbonflux_inst%ilivecroot_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool - ileaf_to_iout_phc => cnveg_carbonflux_inst%ileaf_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools - ifroot_to_iout_phc => cnveg_carbonflux_inst%ifroot_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools - ilivestem_to_iout_phc => cnveg_carbonflux_inst%ilivestem_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools - igrain_to_iout_phc => cnveg_carbonflux_inst%igrain_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools - ileafst_to_ileafxf_phn => cnveg_nitrogenflux_inst%ileafst_to_ileafxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool - ileafxf_to_ileaf_phn => cnveg_nitrogenflux_inst%ileafxf_to_ileaf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool - ifrootst_to_ifrootxf_phn => cnveg_nitrogenflux_inst%ifrootst_to_ifrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool - ifrootxf_to_ifroot_phn => cnveg_nitrogenflux_inst%ifrootxf_to_ifroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool - ilivestemst_to_ilivestemxf_phn => cnveg_nitrogenflux_inst%ilivestemst_to_ilivestemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool - ilivestemxf_to_ilivestem_phn => cnveg_nitrogenflux_inst%ilivestemxf_to_ilivestem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool - ideadstemst_to_ideadstemxf_phn => cnveg_nitrogenflux_inst%ideadstemst_to_ideadstemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool - ideadstemxf_to_ideadstem_phn => cnveg_nitrogenflux_inst%ideadstemxf_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool - ilivecrootst_to_ilivecrootxf_phn => cnveg_nitrogenflux_inst%ilivecrootst_to_ilivecrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool - ilivecrootxf_to_ilivecroot_phn => cnveg_nitrogenflux_inst%ilivecrootxf_to_ilivecroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool - ideadcrootst_to_ideadcrootxf_phn => cnveg_nitrogenflux_inst%ideadcrootst_to_ideadcrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool - ideadcrootxf_to_ideadcroot_phn => cnveg_nitrogenflux_inst%ideadcrootxf_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool - ilivestem_to_ideadstem_phn => cnveg_nitrogenflux_inst%ilivestem_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool - ilivecroot_to_ideadcroot_phn => cnveg_nitrogenflux_inst%ilivecroot_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool - ileaf_to_iout_phn => cnveg_nitrogenflux_inst%ileaf_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools - ifroot_to_iout_phn => cnveg_nitrogenflux_inst%ifroot_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools - ilivestem_to_iout_phn => cnveg_nitrogenflux_inst%ilivestem_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools - ileaf_to_iretransn_phn => cnveg_nitrogenflux_inst%ileaf_to_iretransn_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to retranslocation pool - ilivestem_to_iretransn_phn => cnveg_nitrogenflux_inst%ilivestem_to_iretransn_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to retranslocation pool - ilivecroot_to_iretransn_phn => cnveg_nitrogenflux_inst%ilivecroot_to_iretransn_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root pool to retranslocation pool - igrain_to_iout_phn => cnveg_nitrogenflux_inst%igrain_to_iout_ph & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools + leafc_storage => cnveg_carbonstate_inst%leafc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) leaf C storage + frootc_storage => cnveg_carbonstate_inst%frootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C storage + livestemc_storage => cnveg_carbonstate_inst%livestemc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) live stem C storage + deadstemc_storage => cnveg_carbonstate_inst%deadstemc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) dead stem C storage + livecrootc_storage => cnveg_carbonstate_inst%livecrootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) live coarse root C storage + deadcrootc_storage => cnveg_carbonstate_inst%deadcrootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) dead coarse root C storage + gresp_storage => cnveg_carbonstate_inst%gresp_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) growth respiration storage + leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) leaf C transfer + frootc_xfer => cnveg_carbonstate_inst%frootc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) fine root C transfer + livestemc_xfer => cnveg_carbonstate_inst%livestemc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) live stem C transfer + deadstemc_xfer => cnveg_carbonstate_inst%deadstemc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) dead stem C transfer + livecrootc_xfer => cnveg_carbonstate_inst%livecrootc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) live coarse root C transfer + deadcrootc_xfer => cnveg_carbonstate_inst%deadcrootc_xfer_patch , & ! InOut: [real(r8) (:)] (gC/m2) dead coarse root C transfer + + leafn_storage => cnveg_nitrogenstate_inst%leafn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) leaf N storage + frootn_storage => cnveg_nitrogenstate_inst%frootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) fine root N storage + livestemn_storage => cnveg_nitrogenstate_inst%livestemn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) live stem N storage + deadstemn_storage => cnveg_nitrogenstate_inst%deadstemn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) dead stem N storage + livecrootn_storage => cnveg_nitrogenstate_inst%livecrootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) live coarse root N storage + deadcrootn_storage => cnveg_nitrogenstate_inst%deadcrootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) dead coarse root N storage + leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) leaf N transfer + frootn_xfer => cnveg_nitrogenstate_inst%frootn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) fine root N transfer + livestemn_xfer => cnveg_nitrogenstate_inst%livestemn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) live stem N transfer + deadstemn_xfer => cnveg_nitrogenstate_inst%deadstemn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) dead stem N transfer + livecrootn_xfer => cnveg_nitrogenstate_inst%livecrootn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) live coarse root N transfer + deadcrootn_xfer => cnveg_nitrogenstate_inst%deadcrootn_xfer_patch , & ! InOut: [real(r8) (:)] (gN/m2) dead coarse root N transfer + + leafc_storage_to_xfer => cnveg_carbonflux_inst%leafc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + frootc_storage_to_xfer => cnveg_carbonflux_inst%frootc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + livestemc_storage_to_xfer => cnveg_carbonflux_inst%livestemc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + deadstemc_storage_to_xfer => cnveg_carbonflux_inst%deadstemc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + livecrootc_storage_to_xfer => cnveg_carbonflux_inst%livecrootc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + deadcrootc_storage_to_xfer => cnveg_carbonflux_inst%deadcrootc_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + gresp_storage_to_xfer => cnveg_carbonflux_inst%gresp_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + leafc_xfer_to_leafc => cnveg_carbonflux_inst%leafc_xfer_to_leafc_patch , & ! InOut: [real(r8) (:)] + frootc_xfer_to_frootc => cnveg_carbonflux_inst%frootc_xfer_to_frootc_patch , & ! InOut: [real(r8) (:)] + livestemc_xfer_to_livestemc => cnveg_carbonflux_inst%livestemc_xfer_to_livestemc_patch , & ! InOut: [real(r8) (:)] + deadstemc_xfer_to_deadstemc => cnveg_carbonflux_inst%deadstemc_xfer_to_deadstemc_patch , & ! InOut: [real(r8) (:)] + livecrootc_xfer_to_livecrootc => cnveg_carbonflux_inst%livecrootc_xfer_to_livecrootc_patch , & ! InOut: [real(r8) (:)] + deadcrootc_xfer_to_deadcrootc => cnveg_carbonflux_inst%deadcrootc_xfer_to_deadcrootc_patch , & ! InOut: [real(r8) (:)] + + leafn_storage_to_xfer => cnveg_nitrogenflux_inst%leafn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + frootn_storage_to_xfer => cnveg_nitrogenflux_inst%frootn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + livestemn_storage_to_xfer => cnveg_nitrogenflux_inst%livestemn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + deadstemn_storage_to_xfer => cnveg_nitrogenflux_inst%deadstemn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + livecrootn_storage_to_xfer => cnveg_nitrogenflux_inst%livecrootn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + deadcrootn_storage_to_xfer => cnveg_nitrogenflux_inst%deadcrootn_storage_to_xfer_patch , & ! InOut: [real(r8) (:)] + leafn_xfer_to_leafn => cnveg_nitrogenflux_inst%leafn_xfer_to_leafn_patch , & ! InOut: [real(r8) (:)] + frootn_xfer_to_frootn => cnveg_nitrogenflux_inst%frootn_xfer_to_frootn_patch , & ! InOut: [real(r8) (:)] + livestemn_xfer_to_livestemn => cnveg_nitrogenflux_inst%livestemn_xfer_to_livestemn_patch , & ! InOut: [real(r8) (:)] + deadstemn_xfer_to_deadstemn => cnveg_nitrogenflux_inst%deadstemn_xfer_to_deadstemn_patch , & ! InOut: [real(r8) (:)] + livecrootn_xfer_to_livecrootn => cnveg_nitrogenflux_inst%livecrootn_xfer_to_livecrootn_patch , & ! InOut: [real(r8) (:)] + deadcrootn_xfer_to_deadcrootn => cnveg_nitrogenflux_inst%deadcrootn_xfer_to_deadcrootn_patch , & ! InOut: [real(r8) (:)] + + bglfr => cnveg_state_inst%bglfr_patch , & ! Output: [real(r8) (:) ] background litterfall rate (1/s) + bgtr => cnveg_state_inst%bgtr_patch , & ! Output: [real(r8) (:) ] background transfer growth rate (1/s) + lgsf => cnveg_state_inst%lgsf_patch , & ! Output: [real(r8) (:) ] long growing season factor [0-1] + + ileafst_to_ileafxf_phc => cnveg_carbonflux_inst%ileafst_to_ileafxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool + ileafxf_to_ileaf_phc => cnveg_carbonflux_inst%ileafxf_to_ileaf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool + ifrootst_to_ifrootxf_phc => cnveg_carbonflux_inst%ifrootst_to_ifrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool + ifrootxf_to_ifroot_phc => cnveg_carbonflux_inst%ifrootxf_to_ifroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool + ilivestemst_to_ilivestemxf_phc => cnveg_carbonflux_inst%ilivestemst_to_ilivestemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool + ilivestemxf_to_ilivestem_phc => cnveg_carbonflux_inst%ilivestemxf_to_ilivestem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool + ideadstemst_to_ideadstemxf_phc => cnveg_carbonflux_inst%ideadstemst_to_ideadstemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool + ideadstemxf_to_ideadstem_phc => cnveg_carbonflux_inst%ideadstemxf_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool + ilivecrootst_to_ilivecrootxf_phc => cnveg_carbonflux_inst%ilivecrootst_to_ilivecrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool + ilivecrootxf_to_ilivecroot_phc => cnveg_carbonflux_inst%ilivecrootxf_to_ilivecroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool + ideadcrootst_to_ideadcrootxf_phc => cnveg_carbonflux_inst%ideadcrootst_to_ideadcrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool + ideadcrootxf_to_ideadcroot_phc => cnveg_carbonflux_inst%ideadcrootxf_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool + ilivestem_to_ideadstem_phc => cnveg_carbonflux_inst%ilivestem_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool + ilivecroot_to_ideadcroot_phc => cnveg_carbonflux_inst%ilivecroot_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool + ileaf_to_iout_phc => cnveg_carbonflux_inst%ileaf_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools + ifroot_to_iout_phc => cnveg_carbonflux_inst%ifroot_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools + ilivestem_to_iout_phc => cnveg_carbonflux_inst%ilivestem_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools + igrain_to_iout_phc => cnveg_carbonflux_inst%igrain_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools + ileafst_to_ileafxf_phn => cnveg_nitrogenflux_inst%ileafst_to_ileafxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool + ileafxf_to_ileaf_phn => cnveg_nitrogenflux_inst%ileafxf_to_ileaf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool + ifrootst_to_ifrootxf_phn => cnveg_nitrogenflux_inst%ifrootst_to_ifrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool + ifrootxf_to_ifroot_phn => cnveg_nitrogenflux_inst%ifrootxf_to_ifroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root transfer pool to fine root pool + ilivestemst_to_ilivestemxf_phn => cnveg_nitrogenflux_inst%ilivestemst_to_ilivestemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem storage pool to live stem transfer pool + ilivestemxf_to_ilivestem_phn => cnveg_nitrogenflux_inst%ilivestemxf_to_ilivestem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem transfer pool to live stem pool + ideadstemst_to_ideadstemxf_phn => cnveg_nitrogenflux_inst%ideadstemst_to_ideadstemxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem storage pool to dead stem transfer pool + ideadstemxf_to_ideadstem_phn => cnveg_nitrogenflux_inst%ideadstemxf_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead stem transfer pool to dead stem pool + ilivecrootst_to_ilivecrootxf_phn => cnveg_nitrogenflux_inst%ilivecrootst_to_ilivecrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root storage pool to live coarse root transfer pool + ilivecrootxf_to_ilivecroot_phn => cnveg_nitrogenflux_inst%ilivecrootxf_to_ilivecroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root transfer pool to live coarse root pool + ideadcrootst_to_ideadcrootxf_phn => cnveg_nitrogenflux_inst%ideadcrootst_to_ideadcrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root storage pool to dead coarse root transfer pool + ideadcrootxf_to_ideadcroot_phn => cnveg_nitrogenflux_inst%ideadcrootxf_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from dead coarse root transfer pool to dead coarse root pool + ilivestem_to_ideadstem_phn => cnveg_nitrogenflux_inst%ilivestem_to_ideadstem_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to dead stem pool + ilivecroot_to_ideadcroot_phn => cnveg_nitrogenflux_inst%ilivecroot_to_ideadcroot_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root to dead coarse root pool + ileaf_to_iout_phn => cnveg_nitrogenflux_inst%ileaf_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to outside of vegetation pools + ifroot_to_iout_phn => cnveg_nitrogenflux_inst%ifroot_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root pool to outside of vegetation pools + ilivestem_to_iout_phn => cnveg_nitrogenflux_inst%ilivestem_to_iout_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to outside of vegetation pools + ileaf_to_iretransn_phn => cnveg_nitrogenflux_inst%ileaf_to_iretransn_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf pool to retranslocation pool + ilivestem_to_iretransn_phn => cnveg_nitrogenflux_inst%ilivestem_to_iretransn_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live stem pool to retranslocation pool + ilivecroot_to_iretransn_phn => cnveg_nitrogenflux_inst%ilivecroot_to_iretransn_ph , & ! Input: [integer (:)] Index of phenology related C transfer from live coarse root pool to retranslocation pool + igrain_to_iout_phn => cnveg_nitrogenflux_inst%igrain_to_iout_ph & ! Input: [integer (:)] Index of phenology related C transfer from grain pool to outside of vegetation pools ) avg_dayspyr = get_average_days_per_year() @@ -770,17 +769,7 @@ subroutine CNEvergreenPhenology (num_soilp, filter_soilp , & tranr=0.0002_r8 ! set carbon fluxes for shifting storage pools to transfer pools - if (.not. use_matrixcn) then - leafc_storage_to_xfer(p) = tranr * leafc_storage(p)/dt - frootc_storage_to_xfer(p) = tranr * frootc_storage(p)/dt - if (woody(ivt(p)) == 1.0_r8) then - livestemc_storage_to_xfer(p) = tranr * livestemc_storage(p)/dt - deadstemc_storage_to_xfer(p) = tranr * deadstemc_storage(p)/dt - livecrootc_storage_to_xfer(p) = tranr * livecrootc_storage(p)/dt - deadcrootc_storage_to_xfer(p) = tranr * deadcrootc_storage(p)/dt - gresp_storage_to_xfer(p) = tranr * gresp_storage(p)/dt - end if - else + if (use_matrixcn) then leafc_storage_to_xfer(p) = leafc_storage(p) * matrix_update_phc(p,ileafst_to_ileafxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) frootc_storage_to_xfer(p) = frootc_storage(p) * matrix_update_phc(p,ifrootst_to_ifrootxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) if (woody(ivt(p)) == 1.0_r8) then @@ -789,7 +778,18 @@ subroutine CNEvergreenPhenology (num_soilp, filter_soilp , & livecrootc_storage_to_xfer(p) = livecrootc_storage(p) * matrix_update_phc(p,ilivecrootst_to_ilivecrootxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) deadcrootc_storage_to_xfer(p) = deadcrootc_storage(p) * matrix_update_phc(p,ideadcrootst_to_ideadcrootxf_phc,tranr/dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) end if - end if !not use_matrixcn + else + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) + leafc_storage_to_xfer(p) = tranr * leafc_storage(p)/dt + frootc_storage_to_xfer(p) = tranr * frootc_storage(p)/dt + if (woody(ivt(p)) == 1.0_r8) then + livestemc_storage_to_xfer(p) = tranr * livestemc_storage(p)/dt + deadstemc_storage_to_xfer(p) = tranr * deadstemc_storage(p)/dt + livecrootc_storage_to_xfer(p) = tranr * livecrootc_storage(p)/dt + deadcrootc_storage_to_xfer(p) = tranr * deadcrootc_storage(p)/dt + gresp_storage_to_xfer(p) = tranr * gresp_storage(p)/dt + end if + end if !use_matrixcn ! set nitrogen fluxes for shifting storage pools to transfer pools if (use_matrixcn) then @@ -1849,37 +1849,36 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , & ! between leafc and leafc_store in the flux. RosieF, Nov5 2015. leafc_storage_to_xfer(p) = max(0.0_r8,(leafc_storage(p)-leafc(p))) * bgtr(p) frootc_storage_to_xfer(p) = max(0.0_r8,(frootc_storage(p)-frootc(p))) * bgtr(p) - if (use_matrixcn) then - if(leafc_storage(p) > 0._r8)then + if(leafc_storage(p) .gt. 0)then leafc_storage_to_xfer(p) = leafc_storage(p) * matrix_update_phc(p,ileafst_to_ileafxf_phc,& leafc_storage_to_xfer(p) / leafc_storage(p), dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - leafc_storage_to_xfer(p) = 0._r8 + leafc_storage_to_xfer(p) = 0 end if - if(frootc_storage(p) > 0._r8)then + if(frootc_storage(p) .gt. 0)then frootc_storage_to_xfer(p) = frootc_storage(p) * matrix_update_phc(p,ifrootst_to_ifrootxf_phc,& frootc_storage_to_xfer(p) / frootc_storage(p), dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - frootc_storage_to_xfer(p) = 0._r8 + frootc_storage_to_xfer(p) = 0 end if - if (woody(ivt(p)) == 1.0_r8) then + if (woody(ivt(p)) == 1.0_r8) then livestemc_storage_to_xfer(p) = livestemc_storage(p) * matrix_update_phc(p,ilivestemst_to_ilivestemxf_phc ,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) deadstemc_storage_to_xfer(p) = deadstemc_storage(p) * matrix_update_phc(p,ideadstemst_to_ideadstemxf_phc ,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) livecrootc_storage_to_xfer(p) = livecrootc_storage(p) * matrix_update_phc(p,ilivecrootst_to_ilivecrootxf_phc,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) deadcrootc_storage_to_xfer(p) = deadcrootc_storage(p) * matrix_update_phc(p,ideadcrootst_to_ideadcrootxf_phc,bgtr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) - end if - else - ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) - ! and CNNStateUpdate1::NStateUpdate1 - if (woody(ivt(p)) == 1.0_r8) then - livestemc_storage_to_xfer(p) = livestemc_storage(p) * bgtr(p) - deadstemc_storage_to_xfer(p) = deadstemc_storage(p) * bgtr(p) - livecrootc_storage_to_xfer(p) = livecrootc_storage(p) * bgtr(p) - deadcrootc_storage_to_xfer(p) = deadcrootc_storage(p) * bgtr(p) - gresp_storage_to_xfer(p) = gresp_storage(p) * bgtr(p) - end if - end if !use_matrixcn + end if + else + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) + ! and CNNStateUpdate1::NStateUpdate1 + if (woody(ivt(p)) == 1.0_r8) then + livestemc_storage_to_xfer(p) = livestemc_storage(p) * bgtr(p) + deadstemc_storage_to_xfer(p) = deadstemc_storage(p) * bgtr(p) + livecrootc_storage_to_xfer(p) = livecrootc_storage(p) * bgtr(p) + deadcrootc_storage_to_xfer(p) = deadcrootc_storage(p) * bgtr(p) + gresp_storage_to_xfer(p) = gresp_storage(p) * bgtr(p) + end if + end if !use_matrixcn ! set nitrogen fluxes for shifting storage pools to transfer pools if (use_matrixcn) then @@ -2920,22 +2919,7 @@ subroutine CNOnsetGrowth (num_soilp, filter_soilp, & ! pools should be moved to displayed growth in each timestep. if (bgtr(p) > 0._r8) then - if(.not. use_matrixcn)then - leafc_xfer_to_leafc(p) = leafc_xfer(p) / dt - frootc_xfer_to_frootc(p) = frootc_xfer(p) / dt - leafn_xfer_to_leafn(p) = leafn_xfer(p) / dt - frootn_xfer_to_frootn(p) = frootn_xfer(p) / dt - if (woody(ivt(p)) == 1.0_r8) then - livestemc_xfer_to_livestemc(p) = livestemc_xfer(p) / dt - deadstemc_xfer_to_deadstemc(p) = deadstemc_xfer(p) / dt - livecrootc_xfer_to_livecrootc(p) = livecrootc_xfer(p) / dt - deadcrootc_xfer_to_deadcrootc(p) = deadcrootc_xfer(p) / dt - livestemn_xfer_to_livestemn(p) = livestemn_xfer(p) / dt - deadstemn_xfer_to_deadstemn(p) = deadstemn_xfer(p) / dt - livecrootn_xfer_to_livecrootn(p) = livecrootn_xfer(p) / dt - deadcrootn_xfer_to_deadcrootn(p) = deadcrootn_xfer(p) / dt - end if - else + if(use_matrixcn)then leafc_xfer_to_leafc(p) = leafc_xfer(p) * matrix_update_phc(p,ileafxf_to_ileaf_phc,1._r8 / dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) frootc_xfer_to_frootc(p) = frootc_xfer(p) * matrix_update_phc(p,ifrootxf_to_ifroot_phc,1._r8 / dt,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) leafn_xfer_to_leafn(p) = leafn_xfer(p) * matrix_update_phn(p,ileafxf_to_ileaf_phn,1._r8 / dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) @@ -2952,7 +2936,24 @@ subroutine CNOnsetGrowth (num_soilp, filter_soilp, & livecrootn_xfer_to_livecrootn(p) = livecrootn_xfer(p) * matrix_update_phn(p,ilivecrootxf_to_ilivecroot_phn,1._r8 / dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) deadcrootn_xfer_to_deadcrootn(p) = deadcrootn_xfer(p) * matrix_update_phn(p,ideadcrootxf_to_ideadcroot_phn,1._r8 / dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) end if - end if !not use_matrixcn + else + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) + ! and CNNStateUpdate1::NStateUpdate1 + leafc_xfer_to_leafc(p) = leafc_xfer(p) / dt + frootc_xfer_to_frootc(p) = frootc_xfer(p) / dt + leafn_xfer_to_leafn(p) = leafn_xfer(p) / dt + frootn_xfer_to_frootn(p) = frootn_xfer(p) / dt + if (woody(ivt(p)) == 1.0_r8) then + livestemc_xfer_to_livestemc(p) = livestemc_xfer(p) / dt + deadstemc_xfer_to_deadstemc(p) = deadstemc_xfer(p) / dt + livecrootc_xfer_to_livecrootc(p) = livecrootc_xfer(p) / dt + deadcrootc_xfer_to_deadcrootc(p) = deadcrootc_xfer(p) / dt + livestemn_xfer_to_livestemn(p) = livestemn_xfer(p) / dt + deadstemn_xfer_to_deadstemn(p) = deadstemn_xfer(p) / dt + livecrootn_xfer_to_livecrootn(p) = livecrootn_xfer(p) / dt + deadcrootn_xfer_to_deadcrootn(p) = deadcrootn_xfer(p) / dt + end if + end if !use_matrixcn end if ! end if bgtr end do ! end patch loop @@ -3113,26 +3114,26 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & if (abs(offset_counter(p) - dt) <= dt/2._r8) then t1 = 1.0_r8 / dt + frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p) + + ! biofuel_harvfrac is only non-zero for prognostic crops. + leafc_to_litter(p) = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_leafc(p) - ! leafc_litter and frootc_to_litter for matrix if (use_matrixcn) then - if(leafc(p) > 0._r8)then + if(leafc(p) .gt. 0)then leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - leafc_to_litter(p) = 0._r8 + leafc_to_litter(p) = 0 end if - if(frootc(p) > 0._r8)then + if(frootc(p) .gt. 0)then frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - frootc_to_litter(p) = 0._r8 + frootc_to_litter(p) = 0 end if else - frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p) - - ! biofuel_harvfrac is only non-zero for prognostic crops. - leafc_to_litter(p) = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_leafc(p) + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) + ! and CNNStateUpdate1::NStateUpdate1 end if ! use_matrixcn - ! this assumes that offset_counter == dt for crops ! if this were ever changed, we'd need to add code to the "else" if (ivt(p) >= npcropmin) then @@ -3176,101 +3177,105 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & * (1._r8 - repr_structure_harvfrac(ivt(p), k)) end do - ! Matrix for grain, livestem to litter and biofuel + ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of leaf C + ! and move this fration of leaf C to biofuel C, rather than move it to litter + leafc_to_biofuelc(p) = t1 * leafc(p) * biofuel_harvfrac(ivt(p)) + leafn_to_biofueln(p) = t1 * leafn(p) * biofuel_harvfrac(ivt(p)) + + ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of livestem C + ! and move this fration of leaf C to biofuel C, rather than move it to litter + livestemc_to_litter(p) = t1 * livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_livestemc(p) + livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p)) + livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p)) + if(use_matrixcn)then - if(reproductivec(p,1) > 0._r8)then + if(reproductivec(p,1) .gt. 0)then grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - repr_grainc_to_seed(p,1) = 0._r8 - repr_grainc_to_food(p,1) = 0._r8 + repr_grainc_to_seed(p,1) = 0 + repr_grainc_to_food(p,1) = 0 end if - if(reproductiven(p,1) > 0._r8)then + if(reproductiven(p,1) .gt. 0)then grainn_to_out = reproductiven(p,1) * matrix_update_phn(p,igrain_to_iout_phn,(repr_grainn_to_seed(p,1) + repr_grainn_to_food(p,1)) / reproductiven(p,1),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - repr_grainn_to_seed(p,1) = 0._r8 - repr_grainn_to_food(p,1) = 0._r8 + repr_grainn_to_seed(p,1) = 0 + repr_grainn_to_food(p,1) = 0 end if - if(livestemc(p) > 0._r8)then + if(livestemc(p) .gt. 0)then livestemc_to_litter(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_iout_phc,livestemc_to_litter(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - livestemc_to_litter(p) = 0._r8 + livestemc_to_litter(p) = 0 end if - if(livestemn(p) > 0._r8)then + if(livestemn(p) .gt. 0)then livestemn_to_biofueln(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_biofueln(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) else - livestemn_to_biofueln(p) = 0._r8 + livestemn_to_biofueln(p) = 0 end if - if(leafn(p) > 0._r8)then + if(leafn(p) > 0)then leafn_to_biofueln(p) = leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_biofueln(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) else - leafn_to_biofueln(p) = 0._r8 + leafn_to_biofueln(p) = 0 end if - if (leafc(p) > 0._r8)then + if (leafc(p) > 0)then leafc_to_biofuelc(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) else - leafc_to_biofuelc(p) = 0._r8 + leafc_to_biofuelc(p) = 0 end if - if(livestemc(p) > 0._r8)then + if(livestemc(p) .gt. 0)then livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) else - livestemc_to_biofuelc(p) = 0._r8 + livestemc_to_biofuelc(p) = 0 end if else - ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of leaf C - ! and move this fration of leaf C to biofuel C, rather than move it to litter - leafc_to_biofuelc(p) = t1 * leafc(p) * biofuel_harvfrac(ivt(p)) - leafn_to_biofueln(p) = t1 * leafn(p) * biofuel_harvfrac(ivt(p)) - - ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of livestem C - ! and move this fration of leaf C to biofuel C, rather than move it to litter - livestemc_to_litter(p) = t1 * livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_livestemc(p) - livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p)) - livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p)) + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) + ! and CNNStateUpdate1::NStateUpdate1 end if ! use_matrixcn end if else - ! Matrix for leafc and frootc to litter + t1 = dt * 2.0_r8 / (offset_counter(p) * offset_counter(p)) + leafc_to_litter(p) = prev_leafc_to_litter(p) + t1*(leafc(p) - prev_leafc_to_litter(p)*offset_counter(p)) + frootc_to_litter(p) = prev_frootc_to_litter(p) + t1*(frootc(p) - prev_frootc_to_litter(p)*offset_counter(p)) + if (use_matrixcn) then - if(leafc(p) > 0._r8)then + if(leafc(p) .gt. 0)then leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - leafc_to_litter(p) = 0._r8 + leafc_to_litter(p) = 0 end if - if(frootc(p) > 0._r8)then + if(frootc(p) .gt. 0)then frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - frootc_to_litter(p) = 0._r8 + frootc_to_litter(p) = 0 end if else - t1 = dt * 2.0_r8 / (offset_counter(p) * offset_counter(p)) - leafc_to_litter(p) = prev_leafc_to_litter(p) + t1*(leafc(p) - prev_leafc_to_litter(p)*offset_counter(p)) - frootc_to_litter(p) = prev_frootc_to_litter(p) + t1*(frootc(p) - prev_frootc_to_litter(p)*offset_counter(p)) + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) + ! and CNNStateUpdate1::NStateUpdate1 end if !use_matrixcn end if if ( use_fun ) then if(leafc_to_litter(p)*dt.gt.leafc(p))then - ! Matrix for leafc to litter - if (use_matrixcn) then - if(leafc(p) > 0._r8)then + leafc_to_litter(p) = leafc(p)/dt + cpool_to_leafc(p) + if (use_matrixcn) then + if(leafc(p) .gt. 0)then leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - leafc_to_litter(p) = 0._r8 + leafc_to_litter(p) = 0 end if - else - leafc_to_litter(p) = leafc(p)/dt + cpool_to_leafc(p) - end if !use_matrixcn + else + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) + end if !use_matrixcn endif if(frootc_to_litter(p)*dt.gt.frootc(p))then - ! Matrix update for frootc to litter + frootc_to_litter(p) = frootc(p)/dt + cpool_to_frootc(p) if (use_matrixcn) then - if(frootc(p) > 0._r8)then + if(frootc(p) .gt. 0)then frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - frootc_to_litter(p) = 0._r8 + frootc_to_litter(p) = 0 end if else - frootc_to_litter(p) = frootc(p)/dt + cpool_to_frootc(p) + ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) end if !use_matrixcn endif end if @@ -3279,8 +3284,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & if ( use_fun ) then leafc_to_litter_fun(p) = leafc_to_litter(p) leafn_to_retransn(p) = paid_retransn_to_npool(p) + free_retransn_to_npool(p) - if (leafn(p) > 0._r8) then - if (leafn(p)-leafn_to_retransn(p)*dt > 0._r8) then + if (leafn(p).gt.0._r8) then + if (leafn(p)-leafn_to_retransn(p)*dt.gt.0._r8) then leafcn_offset(p) = leafc(p)/(leafn(p)-leafn_to_retransn(p)*dt) else leafcn_offset(p) = leafc(p)/leafn(p) @@ -3290,15 +3295,13 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & end if leafn_to_litter(p) = leafc_to_litter(p)/leafcn_offset(p) - leafn_to_retransn(p) leafn_to_litter(p) = max(leafn_to_litter(p),0._r8) - - ! Matrix update for leafn to litter and retrans if (use_matrixcn) then - if(leafn(p) > 0._r8)then + if(leafn(p) .gt. 0)then leafn_to_litter(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - leafn_to_litter(p) = 0._r8 - leafn_to_retransn(p) = 0._r8 + leafn_to_litter(p) = 0 + leafn_to_retransn(p) = 0 end if else ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) @@ -3315,21 +3318,20 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & end if else - if (CNratio_floating) then + if (CNratio_floating .eqv. .true.) then fr_leafn_to_litter = 0.5_r8 ! assuming 50% of nitrogen turnover goes to litter end if ! calculate the leaf N litterfall and retranslocation leafn_to_litter(p) = leafc_to_litter(p) / lflitcn(ivt(p)) leafn_to_retransn(p) = (leafc_to_litter(p) / leafcn(ivt(p))) - leafn_to_litter(p) - ! Matrix update for leafn to litter and retrans if (use_matrixcn) then - if(leafn(p) > 0._r8)then + if(leafn(p) .gt. 0)then leafn_to_litter(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - leafn_to_litter(p) = 0._r8 - leafn_to_retransn(p) = 0._r8 + leafn_to_litter(p) = 0 + leafn_to_retransn(p) = 0 end if else ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) @@ -3338,49 +3340,44 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! calculate fine root N litterfall (no retranslocation of fine root N) frootn_to_litter(p) = frootc_to_litter(p) / frootcn(ivt(p)) - - ! Matrix update for frootn to litter if (use_matrixcn) then - if(frootn(p) > 0._r8)then + if(frootn(p) .gt. 0)then frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,frootn_to_litter(p) / frootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - frootn_to_litter(p) = 0._r8 + frootn_to_litter(p) = 0 end if else ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) end if !use_matrixcn - if (CNratio_floating) then - if (.not. use_matrixcn) then - if (leafc(p) == 0.0_r8) then - ntovr_leaf = 0.0_r8 - else - ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p)) - end if + if (CNratio_floating .eqv. .true.) then + if (leafc(p) == 0.0_r8) then + ntovr_leaf = 0.0_r8 + else + ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p)) + end if - leafn_to_litter(p) = fr_leafn_to_litter * ntovr_leaf - leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p) - else ! Matrix update for leafn to litter and retrans - if(leafn(p) > 0._r8)then + leafn_to_litter(p) = fr_leafn_to_litter * ntovr_leaf + leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p) + if (use_matrixcn) then + if(leafn(p) .gt. 0)then leafn_to_litter(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - leafn_to_litter(p) = 0._r8 - leafn_to_retransn(p) = 0._r8 + leafn_to_litter(p) = 0 + leafn_to_retransn(p) = 0 end if - end if ! .not. use_matrixcn + end if !use_matrixcn if (frootc(p) == 0.0_r8) then frootn_to_litter(p) = 0.0_r8 - else + else frootn_to_litter(p) = frootc_to_litter(p) * (frootn(p) / frootc(p)) - end if - - ! Matrix update for frootn to litter + end if if (use_matrixcn) then - if(frootn(p) > 0._r8)then + if(frootn(p) .gt. 0)then frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,frootn_to_litter(p) / frootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - frootn_to_litter(p) = 0._r8 + frootn_to_litter(p) = 0 end if else ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) @@ -3389,26 +3386,21 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & if ( use_fun ) then if(frootn_to_litter(p)*dt.gt.frootn(p))then - - ! Send all frootn to litter if (.not. use_matrixcn) then frootn_to_litter(p) = frootn(p)/dt else - ! Matrix update for frootn to litter frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,1._r8/dt,dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) end if endif end if if (ivt(p) >= npcropmin) then - ! Matrix update for livestemn to litter + ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn + !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p)) + ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead + livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p))) if(use_matrixcn)then livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) - else - ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn - !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p)) - ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead - livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p))) end if end if @@ -3477,7 +3469,7 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, & leafc_to_litter_fun => cnveg_carbonflux_inst%leafc_to_litter_fun_patch, & ! Output: [real(r8) (:) ] leaf C litterfall used by FUN (gC/m2/s) leafcn_offset => cnveg_state_inst%leafcn_offset_patch , & ! Output: [real(r8) (:) ] Leaf C:N used by FUN free_retransn_to_npool=> cnveg_nitrogenflux_inst%free_retransn_to_npool_patch , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s) - paid_retransn_to_npool=> cnveg_nitrogenflux_inst%retransn_to_npool_patch , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s) + paid_retransn_to_npool=> cnveg_nitrogenflux_inst%retransn_to_npool_patch , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s) ileafst_to_ileafxf_phc => cnveg_carbonflux_inst%ileafst_to_ileafxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool ileafxf_to_ileaf_phc => cnveg_carbonflux_inst%ileafxf_to_ileaf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool @@ -3526,36 +3518,35 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, & ! only calculate these fluxes if the background litterfall rate is non-zero if (bglfr(p) > 0._r8) then - ! Matrix update for leafc and frootc to litter + ! units for bglfr are already 1/s + leafc_to_litter(p) = bglfr(p) * leafc(p) + frootc_to_litter(p) = bglfr(p) * frootc(p) if (use_matrixcn) then leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,bglfr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,bglfr(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) - else - ! units for bglfr are already 1/s - leafc_to_litter(p) = bglfr(p) * leafc(p) - frootc_to_litter(p) = bglfr(p) * frootc(p) end if if ( use_fun ) then - if(.not. use_matrixcn)then - leafc_to_litter_fun(p) = leafc_to_litter(p) - leafn_to_retransn(p) = paid_retransn_to_npool(p) + free_retransn_to_npool(p) - if (leafn(p).gt.0._r8) then - if (leafn(p)-leafn_to_retransn(p)*dt.gt.0._r8) then - leafcn_offset(p) = leafc(p)/(leafn(p)-leafn_to_retransn(p)*dt) - else - leafcn_offset(p) = leafc(p)/leafn(p) - end if + leafc_to_litter_fun(p) = leafc_to_litter(p) + leafn_to_retransn(p) = paid_retransn_to_npool(p) + free_retransn_to_npool(p) + if (leafn(p).gt.0._r8) then + if (leafn(p)-leafn_to_retransn(p)*dt.gt.0._r8) then + leafcn_offset(p) = leafc(p)/(leafn(p)-leafn_to_retransn(p)*dt) else - leafcn_offset(p) = leafcn(ivt(p)) + leafcn_offset(p) = leafc(p)/leafn(p) end if - leafn_to_litter(p) = leafc_to_litter(p)/leafcn_offset(p) - leafn_to_retransn(p) - leafn_to_litter(p) = max(leafn_to_litter(p),0._r8) - else ! Matrix update for leafn to litter and retrans + else + leafcn_offset(p) = leafcn(ivt(p)) + end if + leafn_to_litter(p) = leafc_to_litter(p)/leafcn_offset(p) - leafn_to_retransn(p) + leafn_to_litter(p) = max(leafn_to_litter(p),0._r8) + if(use_matrixcn)then if(leafn(p) .ne. 0._r8)then leafn_to_litter(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) end if - end if ! .not. use_matrixcn + else + ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) + end if !use_matrixcn denom = ( leafn_to_retransn(p) + leafn_to_litter(p) ) if ( denom /= 0.0_r8 ) then @@ -3568,45 +3559,46 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, & else - if (CNratio_floating) then + if (CNratio_floating .eqv. .true.) then fr_leafn_to_litter = 0.5_r8 ! assuming 50% of nitrogen turnover goes to litter end if - ! Matrix update for leafn to litter and retrans + ! calculate the leaf N litterfall and retranslocation + leafn_to_litter(p) = leafc_to_litter(p) / lflitcn(ivt(p)) + leafn_to_retransn(p) = (leafc_to_litter(p) / leafcn(ivt(p))) - leafn_to_litter(p) + if (use_matrixcn) then - if(leafn(p) .ne. 0._r8)then + if(leafn(p) .ne. 0)then leafn_to_litter(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) end if else ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) - ! calculate the leaf N litterfall and retranslocation - leafn_to_litter(p) = leafc_to_litter(p) / lflitcn(ivt(p)) - leafn_to_retransn(p) = (leafc_to_litter(p) / leafcn(ivt(p))) - leafn_to_litter(p) end if !use_matrixcn end if ! calculate fine root N litterfall (no retranslocation of fine root N) frootn_to_litter(p) = frootc_to_litter(p) / frootcn(ivt(p)) - if (CNratio_floating) then - if (.not. use_matrixcn) then - if (leafc(p) == 0.0_r8) then - ntovr_leaf = 0.0_r8 - else - ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p)) - end if + if (CNratio_floating .eqv. .true.) then + if (leafc(p) == 0.0_r8) then + ntovr_leaf = 0.0_r8 + else + ntovr_leaf = leafc_to_litter(p) * (leafn(p) / leafc(p)) + end if - leafn_to_litter(p) = fr_leafn_to_litter * ntovr_leaf - leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p) - else ! Matrix update for leafn to litter and retrans - if(leafn(p) > 0._r8)then + leafn_to_litter(p) = fr_leafn_to_litter * ntovr_leaf + leafn_to_retransn(p) = ntovr_leaf - leafn_to_litter(p) + if (use_matrixcn) then + if(leafn(p) .gt. 0)then leafn_to_litter(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iout_phn,leafn_to_litter(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) leafn_to_retransn(p) = leafn(p) * matrix_update_phn(p,ileaf_to_iretransn_phn,leafn_to_retransn(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - leafn_to_litter(p) = 0._r8 - leafn_to_retransn(p) = 0._r8 + leafn_to_litter(p) = 0 + leafn_to_retransn(p) = 0 end if - end if ! .not. use_matrixcn + else + ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) + end if !use_matrixcn if (frootc(p) == 0.0_r8) then frootn_to_litter(p) = 0.0_r8 else @@ -3620,9 +3612,8 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, & endif end if - ! Matrix update for frootn to litter if (use_matrixcn) then - if(frootn(p) /= 0._r8)then + if(frootn(p) .ne. 0)then frootn_to_litter(p) = frootn(p) * matrix_update_phn(p,ifroot_to_iout_phn,frootn_to_litter(p) / frootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) end if else @@ -3682,7 +3673,7 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, & livestemn_to_retransn => cnveg_nitrogenflux_inst%livestemn_to_retransn_patch , & ! Output: [real(r8) (:) ] livecrootn_to_deadcrootn => cnveg_nitrogenflux_inst%livecrootn_to_deadcrootn_patch , & ! Output: [real(r8) (:) ] livecrootn_to_retransn => cnveg_nitrogenflux_inst%livecrootn_to_retransn_patch , & ! Output: [real(r8) (:) ] - free_retransn_to_npool => cnveg_nitrogenflux_inst%free_retransn_to_npool_patch , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s) + free_retransn_to_npool => cnveg_nitrogenflux_inst%free_retransn_to_npool_patch , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s) ileafst_to_ileafxf_phc => cnveg_carbonflux_inst%ileafst_to_ileafxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf storage pool to leaf transfer pool ileafxf_to_ileaf_phc => cnveg_carbonflux_inst%ileafxf_to_ileaf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from leaf transfer pool to leaf pool ifrootst_to_ifrootxf_phc => cnveg_carbonflux_inst%ifrootst_to_ifrootxf_ph , & ! Input: [integer (:)] Index of phenology related C transfer from fine root storage pool to fine root transfer pool @@ -3736,38 +3727,40 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, & ! live stem to dead stem turnover - ! Matrix update for livestemc to deadstem + ctovr = livestemc(p) * lwtop + ntovr = ctovr / livewdcn(ivt(p)) + livestemc_to_deadstemc(p) = ctovr + livestemn_to_deadstemn(p) = ctovr / deadwdcn(ivt(p)) if( use_matrixcn)then livestemc_to_deadstemc(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_ideadstem_phc,lwtop,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) if (livestemn(p) .gt. 0.0_r8) then livestemn_to_deadstemn(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_ideadstem_phn,livestemn_to_deadstemn(p)/livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - livestemn_to_deadstemn(p) = 0._r8 + livestemn_to_deadstemn(p) = 0 end if else ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) ! and CNNStateUpdate1::NStateUpdate1 - ctovr = livestemc(p) * lwtop - ntovr = ctovr / livewdcn(ivt(p)) - livestemc_to_deadstemc(p) = ctovr - livestemn_to_deadstemn(p) = ctovr / deadwdcn(ivt(p)) end if - if (CNratio_floating) then + if (CNratio_floating .eqv. .true.) then if (livestemc(p) == 0.0_r8) then ntovr = 0.0_r8 livestemn_to_deadstemn(p) = 0.0_r8 - else + else ntovr = ctovr * (livestemn(p) / livestemc(p)) livestemn_to_deadstemn(p) = ctovr / deadwdcn(ivt(p)) - end if - if (use_matrixcn)then ! Matrix update for livestemn to deadstem + end if + + if (use_matrixcn)then if (livestemn(p) .gt. 0.0_r8) then livestemn_to_deadstemn(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_ideadstem_phn,& livestemn_to_deadstemn(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else livestemn_to_deadstemn(p) = 0 end if - end if ! use_matrixcn + else + ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) + end if end if livestemn_to_retransn(p) = ntovr - livestemn_to_deadstemn(p) @@ -3777,19 +3770,17 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, & ctovr = livecrootc(p) * lwtop ntovr = ctovr / livewdcn(ivt(p)) - if(.not. use_matrixcn)then ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) ! and CNNStateUpdate1::NStateUpdate1 livecrootc_to_deadcrootc(p) = ctovr livecrootn_to_deadcrootn(p) = ctovr / deadwdcn(ivt(p)) else - ! Matrix update for livecroot to deadcroot livecrootc_to_deadcrootc(p) = livecrootc(p) * matrix_update_phc(p,ilivecroot_to_ideadcroot_phc,lwtop,dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) livecrootn_to_deadcrootn(p) = livecrootn(p) * matrix_update_phn(p,ilivecroot_to_ideadcroot_phn,lwtop/deadwdcn(ivt(p)),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) end if !use_matrixcn - if (CNratio_floating) then + if (CNratio_floating .eqv. .true.) then if (livecrootc(p) == 0.0_r8) then ntovr = 0.0_r8 livecrootn_to_deadcrootn(p) = 0.0_r8 @@ -3797,50 +3788,49 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, & ntovr = ctovr * (livecrootn(p) / livecrootc(p)) livecrootn_to_deadcrootn(p) = ctovr / deadwdcn(ivt(p)) end if - if (use_matrixcn)then ! Matrix update for livecroot to deadcroot + + if (use_matrixcn)then if (livecrootn(p) .ne.0.0_r8 )then livecrootn_to_deadcrootn(p) = matrix_update_phn(p,ilivecroot_to_ideadcroot_phn,& livecrootn_to_deadcrootn(p) / livecrootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livecrootn(p) end if - end if ! use_matrixcn + else + ! NOTE: The non matrix version of this is in CNNStateUpdate1::NStateUpdate1 EBK (11/26/2019) + end if !use_matrixcn end if livecrootn_to_retransn(p) = ntovr - livecrootn_to_deadcrootn(p) - - ! Matrix update for livecrootn and livestemn to retrans as well as free retransn to npool with FUN - if(use_matrixcn)then - if(livecrootn(p) .gt. 0.0_r8) then - livecrootn_to_retransn(p) = matrix_update_phn(p,ilivecroot_to_iretransn_phn,& - livecrootn_to_retransn(p) / livecrootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livecrootn(p) - else - livecrootn_to_retransn(p) = 0 - end if - if(livestemn(p) .gt. 0.0_r8) then - livestemn_to_retransn(p) = matrix_update_phn(p,ilivestem_to_iretransn_phn,& - livestemn_to_retransn(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livestemn(p) - else - livestemn_to_retransn(p) = 0 - end if - ! WW change logic so livestem_retrans goes to npool (via - ! free_retrans flux) - ! this should likely be done more cleanly if it works, i.e. not - ! update fluxes w/ states - ! additional considerations for crop? - ! The non-matrix version of this is in NStateUpdate1 - if (use_fun) then - if (retransn(p) .gt. 0._r8) then - ! The acc matrix check MUST be turned on, or this will - ! fail with Nitrogen balance error EBK 03/11/2021 - free_retransn_to_npool(p) = free_retransn_to_npool(p) + retransn(p) * matrix_update_phn(p,iretransn_to_iout, & - (livestemn_to_retransn(p) + livecrootn_to_retransn(p)) / retransn(p),dt, & - cnveg_nitrogenflux_inst, matrixcheck_ph, acc=.true.) + if(use_matrixcn)then + if(livecrootn(p) .gt. 0.0_r8) then + livecrootn_to_retransn(p) = matrix_update_phn(p,ilivecroot_to_iretransn_phn,& + livecrootn_to_retransn(p) / livecrootn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livecrootn(p) else - free_retransn_to_npool(p) = 0._r8 + livecrootn_to_retransn(p) = 0 end if - end if - else - ! The non-matrix version of this is in NStateUpdate1 - end if !use_matrixcn + if(livestemn(p) .gt. 0.0_r8) then + livestemn_to_retransn(p) = matrix_update_phn(p,ilivestem_to_iretransn_phn,& + livestemn_to_retransn(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) * livestemn(p) + else + livestemn_to_retransn(p) = 0 + end if + ! WW change logic so livestem_retrans goes to npool (via + ! free_retrans flux) + ! this should likely be done more cleanly if it works, i.e. not + ! update fluxes w/ states + ! additional considerations for crop? + ! The non-matrix version of this is in NStateUpdate1 + if (use_fun) then + if (retransn(p) .gt. 0._r8) then + ! The acc matrix check MUST be turned on, or this will + ! fail with Nitrogen balance error EBK 03/11/2021 + free_retransn_to_npool(p) = free_retransn_to_npool(p) + retransn(p) * matrix_update_phn(p,iretransn_to_iout, & + (livestemn_to_retransn(p) + livecrootn_to_retransn(p)) / retransn(p),dt, & + cnveg_nitrogenflux_inst, matrixcheck_ph, acc=.true.) + else + free_retransn_to_npool(p) = 0._r8 + end if + end if + end if !use_matrixcn end if diff --git a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 index d7b3c01fc1..4f221c6910 100644 --- a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 @@ -9,11 +9,12 @@ module SoilBiogeochemNStateUpdate1Mod use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevdecomp, ndecomp_cascade_transitions use clm_varctl , only : iulog, use_nitrif_denitrif, use_crop + use SoilBiogeochemDecompCascadeConType , only : use_soil_matrixcn use clm_varcon , only : nitrif_n2o_loss_frac use SoilBiogeochemStateType , only : soilbiogeochem_state_type use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use SoilBiogeochemNitrogenfluxType , only : soilbiogeochem_nitrogenflux_type - use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn + use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con use CNSharedParamsMod , only : use_fun use ColumnType , only : col ! @@ -118,50 +119,47 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & end if ! decomposition fluxes - if (.not. use_soil_matrixcn) then - do k = 1, ndecomp_cascade_transitions + if (.not. use_soil_matrixcn) then + do k = 1, ndecomp_cascade_transitions + do j = 1, nlevdecomp + ! column loop + do fc = 1,num_soilc + c = filter_soilc(fc) + + nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = & + nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - & + nf%decomp_cascade_ntransfer_vr_col(c,j,k) * dt + end do + end do + end do + + + do k = 1, ndecomp_cascade_transitions + if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions do j = 1, nlevdecomp ! column loop do fc = 1,num_soilc c = filter_soilc(fc) + nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & + nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) + & + (nf%decomp_cascade_ntransfer_vr_col(c,j,k) + & + nf%decomp_cascade_sminn_flux_vr_col(c,j,k)) * dt + end do + end do + else ! terminal transitions + do j = 1, nlevdecomp + ! column loop + do fc = 1,num_soilc + c = filter_soilc(fc) nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = & nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - & - nf%decomp_cascade_ntransfer_vr_col(c,j,k) * dt + nf%decomp_cascade_sminn_flux_vr_col(c,j,k) * dt end do end do - end do - - - do k = 1, ndecomp_cascade_transitions - if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions - do j = 1, nlevdecomp - ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) - - nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & - nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) + & - (nf%decomp_cascade_ntransfer_vr_col(c,j,k) + & - nf%decomp_cascade_sminn_flux_vr_col(c,j,k)) * dt - end do - end do - else ! terminal transitions - do j = 1, nlevdecomp - ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) - nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = & - nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - & - nf%decomp_cascade_sminn_flux_vr_col(c,j,k) * dt - end do - end do - end if - end do - else - ! Matrix solution equvalent to above is in CNSoilMatrixMod.F90? - ! TODO check on this - end if ! + end if + end do + end if ! if (.not. use_nitrif_denitrif) then From 42af57b7f6584610e5127874f55044fe16da2ccb Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 28 Dec 2023 13:18:15 -0700 Subject: [PATCH 029/408] Matrixcn updates pertaining to GULU (gross unrep. landuse chg) --- src/biogeochem/CNBalanceCheckMod.F90 | 1 - src/biogeochem/CNCStateUpdate2Mod.F90 | 132 ++++++++++------- src/biogeochem/CNNStateUpdate2Mod.F90 | 129 +++++++++------- src/biogeochem/dynGrossUnrepMod.F90 | 205 +++++++++++++++++++------- src/dyn_subgrid/dynHarvestMod.F90 | 19 +-- 5 files changed, 313 insertions(+), 173 deletions(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index fbf30e9549..5b253fdd00 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -60,7 +60,6 @@ module CNBalanceCheckMod !----------------------------------------------------------------------- subroutine Init(this, bounds) - use CNSharedParamsMod, only : use_matrixcn class(cn_balance_type) :: this type(bounds_type) , intent(in) :: bounds diff --git a/src/biogeochem/CNCStateUpdate2Mod.F90 b/src/biogeochem/CNCStateUpdate2Mod.F90 index 76fcc340b6..2890c7d1fd 100644 --- a/src/biogeochem/CNCStateUpdate2Mod.F90 +++ b/src/biogeochem/CNCStateUpdate2Mod.F90 @@ -370,15 +370,27 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & do fc = 1,num_soilc c = filter_soilc(fc) - ! column gross unrepresented landcover change fluxes - do i = i_litr_min, i_litr_max - cs_soil%decomp_cpools_vr_col(c,j,i) = & - cs_soil%decomp_cpools_vr_col(c,j,i) + cf_veg%gru_c_to_litr_c_col(c,j,i) * dt - end do - cs_soil%decomp_cpools_vr_col(c,j,i_cwd) = & - cs_soil%decomp_cpools_vr_col(c,j,i_cwd) + cf_veg%gru_c_to_cwdc_col(c,j) * dt + if (.not. use_soil_matrixcn)then + ! column gross unrepresented landcover change fluxes + do i = i_litr_min, i_litr_max + cs_soil%decomp_cpools_vr_col(c,j,i) = & + cs_soil%decomp_cpools_vr_col(c,j,i) + cf_veg%gru_c_to_litr_c_col(c,j,i) * dt + end do + cs_soil%decomp_cpools_vr_col(c,j,i_cwd) = & + cs_soil%decomp_cpools_vr_col(c,j,i_cwd) + cf_veg%gru_c_to_cwdc_col(c,j) * dt - ! wood to product pools - states updated in CNProducts + ! wood to product pools - states updated in CNProducts + else + ! Match above for soil-matrix + do i = i_litr_min, i_litr_max + cf_soil%matrix_Cinput%V(c,j+(i-1)*nlevdecomp) = & + cf_soil%matrix_Cinput%V(c,j+(i-1)*nlevdecomp) + cf_veg%gru_c_to_litr_c_col(c,j,i) * dt + end do + ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and + ! i_cwd = 0 if fates, so not including in the i-loop + cf_soil%matrix_Cinput%V(c,j+(i_cwd-1)*nlevdecomp) = & + cf_soil%matrix_Cinput%V(c,j+(i_cwd-1)*nlevdecomp) + cf_veg%gru_c_to_cwdc_col(c,j) * dt + end if !soil_matrix end do end do @@ -387,58 +399,66 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & p = filter_soilp(fp) ! patch-level carbon fluxes from gross unrepresented landcover change mortality - ! displayed pools - cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) & - - cf_veg%gru_leafc_to_litter_patch(p) * dt - cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p) & - - cf_veg%gru_frootc_to_litter_patch(p) * dt - cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) & - - cf_veg%gru_livestemc_to_atm_patch(p) * dt - cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p) & - - cf_veg%gru_deadstemc_to_atm_patch(p) * dt - cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p) & - - cf_veg%gru_wood_productc_gain_patch(p) * dt - cs_veg%livecrootc_patch(p) = cs_veg%livecrootc_patch(p) & - - cf_veg%gru_livecrootc_to_litter_patch(p) * dt - cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p) & - - cf_veg%gru_deadcrootc_to_litter_patch(p) * dt + ! + ! State update without the matrix solution + ! + if(.not. use_matrixcn)then + ! displayed pools + cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) & + - cf_veg%gru_leafc_to_litter_patch(p) * dt + cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p) & + - cf_veg%gru_frootc_to_litter_patch(p) * dt + cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) & + - cf_veg%gru_livestemc_to_atm_patch(p) * dt + cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p) & + - cf_veg%gru_deadstemc_to_atm_patch(p) * dt + cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p) & + - cf_veg%gru_wood_productc_gain_patch(p) * dt + cs_veg%livecrootc_patch(p) = cs_veg%livecrootc_patch(p) & + - cf_veg%gru_livecrootc_to_litter_patch(p) * dt + cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p) & + - cf_veg%gru_deadcrootc_to_litter_patch(p) * dt - ! xsmrpool - cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) & - - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt + ! xsmrpool + cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) & + - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt - ! storage pools - cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p) & - - cf_veg%gru_leafc_storage_to_atm_patch(p) * dt - cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) & - - cf_veg%gru_frootc_storage_to_atm_patch(p) * dt - cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) & - - cf_veg%gru_livestemc_storage_to_atm_patch(p) * dt - cs_veg%deadstemc_storage_patch(p) = cs_veg%deadstemc_storage_patch(p) & - - cf_veg%gru_deadstemc_storage_to_atm_patch(p) * dt - cs_veg%livecrootc_storage_patch(p) = cs_veg%livecrootc_storage_patch(p) & - - cf_veg%gru_livecrootc_storage_to_atm_patch(p) * dt - cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) & - - cf_veg%gru_deadcrootc_storage_to_atm_patch(p) * dt - cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) & - - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt + ! storage pools + cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p) & + - cf_veg%gru_leafc_storage_to_atm_patch(p) * dt + cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) & + - cf_veg%gru_frootc_storage_to_atm_patch(p) * dt + cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) & + - cf_veg%gru_livestemc_storage_to_atm_patch(p) * dt + cs_veg%deadstemc_storage_patch(p) = cs_veg%deadstemc_storage_patch(p) & + - cf_veg%gru_deadstemc_storage_to_atm_patch(p) * dt + cs_veg%livecrootc_storage_patch(p) = cs_veg%livecrootc_storage_patch(p) & + - cf_veg%gru_livecrootc_storage_to_atm_patch(p) * dt + cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) & + - cf_veg%gru_deadcrootc_storage_to_atm_patch(p) * dt + cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) & + - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt - ! transfer pools - cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p) & - - cf_veg%gru_leafc_xfer_to_atm_patch(p) * dt - cs_veg%frootc_xfer_patch(p) = cs_veg%frootc_xfer_patch(p) & - - cf_veg%gru_frootc_xfer_to_atm_patch(p) * dt - cs_veg%livestemc_xfer_patch(p) = cs_veg%livestemc_xfer_patch(p) & - - cf_veg%gru_livestemc_xfer_to_atm_patch(p) * dt - cs_veg%deadstemc_xfer_patch(p) = cs_veg%deadstemc_xfer_patch(p) & - - cf_veg%gru_deadstemc_xfer_to_atm_patch(p) * dt - cs_veg%livecrootc_xfer_patch(p) = cs_veg%livecrootc_xfer_patch(p) & - - cf_veg%gru_livecrootc_xfer_to_atm_patch(p) * dt - cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p) & - - cf_veg%gru_deadcrootc_xfer_to_atm_patch(p) * dt - cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p) & - - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt + ! transfer pools + cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p) & + - cf_veg%gru_leafc_xfer_to_atm_patch(p) * dt + cs_veg%frootc_xfer_patch(p) = cs_veg%frootc_xfer_patch(p) & + - cf_veg%gru_frootc_xfer_to_atm_patch(p) * dt + cs_veg%livestemc_xfer_patch(p) = cs_veg%livestemc_xfer_patch(p) & + - cf_veg%gru_livestemc_xfer_to_atm_patch(p) * dt + cs_veg%deadstemc_xfer_patch(p) = cs_veg%deadstemc_xfer_patch(p) & + - cf_veg%gru_deadstemc_xfer_to_atm_patch(p) * dt + cs_veg%livecrootc_xfer_patch(p) = cs_veg%livecrootc_xfer_patch(p) & + - cf_veg%gru_livecrootc_xfer_to_atm_patch(p) * dt + cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p) & + - cf_veg%gru_deadcrootc_xfer_to_atm_patch(p) * dt + cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p) & + - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt + else + ! NB (slevis) The matrix equivalent of the above is in + ! dynGrossUnrepMod::CNGrossUnrep* + end if end do ! end of patch loop end associate diff --git a/src/biogeochem/CNNStateUpdate2Mod.F90 b/src/biogeochem/CNNStateUpdate2Mod.F90 index 2702b80de5..2dbba68b82 100644 --- a/src/biogeochem/CNNStateUpdate2Mod.F90 +++ b/src/biogeochem/CNNStateUpdate2Mod.F90 @@ -358,14 +358,29 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) - do i = i_litr_min, i_litr_max - ns_soil%decomp_npools_vr_col(c,j,i) = & - ns_soil%decomp_npools_vr_col(c,j,i) + nf_veg%gru_n_to_litr_n_col(c,j,i) * dt - end do - ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and - ! i_cwd = 0 if fates, so not including in the i-loop - ns_soil%decomp_npools_vr_col(c,j,i_cwd) = & - ns_soil%decomp_npools_vr_col(c,j,i_cwd) + nf_veg%gru_n_to_cwdn_col(c,j) * dt + ! + ! State update without the matrix solution + ! + if (.not. use_soil_matrixcn)then + do i = i_litr_min, i_litr_max + ns_soil%decomp_npools_vr_col(c,j,i) = & + ns_soil%decomp_npools_vr_col(c,j,i) + nf_veg%gru_n_to_litr_n_col(c,j,i) * dt + end do + ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and + ! i_cwd = 0 if fates, so not including in the i-loop + ns_soil%decomp_npools_vr_col(c,j,i_cwd) = & + ns_soil%decomp_npools_vr_col(c,j,i_cwd) + nf_veg%gru_n_to_cwdn_col(c,j) * dt + else + ! Do above for the matrix solution + do i = i_litr_min, i_litr_max + nf_soil%matrix_Ninput%V(c,j+(i-1)*nlevdecomp) = & + nf_soil%matrix_Ninput%V(c,j+(i-1)*nlevdecomp) + nf_veg%gru_n_to_litr_n_col(c,j,i) * dt + end do + ! Currently i_cwd .ne. i_litr_max + 1 if .not. fates and + ! i_cwd = 0 if fates, so not including in the i-loop + nf_soil%matrix_Ninput%V(c,j+(i_cwd-1)*nlevdecomp) = & + nf_soil%matrix_Ninput%V(c,j+(i_cwd-1)*nlevdecomp) + nf_veg%gru_n_to_cwdn_col(c,j) * dt + end if !not use_soil_matrixcn end do end do @@ -374,51 +389,59 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & do fp = 1,num_soilp p = filter_soilp(fp) - ! displayed pools - ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p) & - - nf_veg%gru_leafn_to_litter_patch(p) * dt - ns_veg%frootn_patch(p) = ns_veg%frootn_patch(p) & - - nf_veg%gru_frootn_to_litter_patch(p) * dt - ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) & - - nf_veg%gru_livestemn_to_atm_patch(p) * dt - ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p) & - - nf_veg%gru_deadstemn_to_atm_patch(p) * dt - ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p) & - - nf_veg%gru_wood_productn_gain_patch(p) * dt - ns_veg%livecrootn_patch(p) = ns_veg%livecrootn_patch(p) & - - nf_veg%gru_livecrootn_to_litter_patch(p) * dt - ns_veg%deadcrootn_patch(p) = ns_veg%deadcrootn_patch(p) & - - nf_veg%gru_deadcrootn_to_litter_patch(p) * dt - ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) & - - nf_veg%gru_retransn_to_litter_patch(p) * dt - - ! storage pools - ns_veg%leafn_storage_patch(p) = ns_veg%leafn_storage_patch(p) & - - nf_veg%gru_leafn_storage_to_atm_patch(p) * dt - ns_veg%frootn_storage_patch(p) = ns_veg%frootn_storage_patch(p) & - - nf_veg%gru_frootn_storage_to_atm_patch(p) * dt - ns_veg%livestemn_storage_patch(p) = ns_veg%livestemn_storage_patch(p) & - - nf_veg%gru_livestemn_storage_to_atm_patch(p) * dt - ns_veg%deadstemn_storage_patch(p) = ns_veg%deadstemn_storage_patch(p) & - - nf_veg%gru_deadstemn_storage_to_atm_patch(p) * dt - ns_veg%livecrootn_storage_patch(p) = ns_veg%livecrootn_storage_patch(p) & - - nf_veg%gru_livecrootn_storage_to_atm_patch(p) * dt - ns_veg%deadcrootn_storage_patch(p) = ns_veg%deadcrootn_storage_patch(p) & - - nf_veg%gru_deadcrootn_storage_to_atm_patch(p) * dt - - ! transfer pools - ns_veg%leafn_xfer_patch(p) = ns_veg%leafn_xfer_patch(p) & - - nf_veg%gru_leafn_xfer_to_atm_patch(p) *dt - ns_veg%frootn_xfer_patch(p) = ns_veg%frootn_xfer_patch(p) & - - nf_veg%gru_frootn_xfer_to_atm_patch(p) *dt - ns_veg%livestemn_xfer_patch(p) = ns_veg%livestemn_xfer_patch(p) & - - nf_veg%gru_livestemn_xfer_to_atm_patch(p) *dt - ns_veg%deadstemn_xfer_patch(p) = ns_veg%deadstemn_xfer_patch(p) & - - nf_veg%gru_deadstemn_xfer_to_atm_patch(p) *dt - ns_veg%livecrootn_xfer_patch(p) = ns_veg%livecrootn_xfer_patch(p) & - - nf_veg%gru_livecrootn_xfer_to_atm_patch(p) *dt - ns_veg%deadcrootn_xfer_patch(p) = ns_veg%deadcrootn_xfer_patch(p) & - - nf_veg%gru_deadcrootn_xfer_to_atm_patch(p) *dt + ! + ! State update without the matrix solution + ! + if(.not. use_matrixcn)then + ! displayed pools + ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p) & + - nf_veg%gru_leafn_to_litter_patch(p) * dt + ns_veg%frootn_patch(p) = ns_veg%frootn_patch(p) & + - nf_veg%gru_frootn_to_litter_patch(p) * dt + ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) & + - nf_veg%gru_livestemn_to_atm_patch(p) * dt + ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p) & + - nf_veg%gru_deadstemn_to_atm_patch(p) * dt + ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p) & + - nf_veg%gru_wood_productn_gain_patch(p) * dt + ns_veg%livecrootn_patch(p) = ns_veg%livecrootn_patch(p) & + - nf_veg%gru_livecrootn_to_litter_patch(p) * dt + ns_veg%deadcrootn_patch(p) = ns_veg%deadcrootn_patch(p) & + - nf_veg%gru_deadcrootn_to_litter_patch(p) * dt + ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) & + - nf_veg%gru_retransn_to_litter_patch(p) * dt + + ! storage pools + ns_veg%leafn_storage_patch(p) = ns_veg%leafn_storage_patch(p) & + - nf_veg%gru_leafn_storage_to_atm_patch(p) * dt + ns_veg%frootn_storage_patch(p) = ns_veg%frootn_storage_patch(p) & + - nf_veg%gru_frootn_storage_to_atm_patch(p) * dt + ns_veg%livestemn_storage_patch(p) = ns_veg%livestemn_storage_patch(p) & + - nf_veg%gru_livestemn_storage_to_atm_patch(p) * dt + ns_veg%deadstemn_storage_patch(p) = ns_veg%deadstemn_storage_patch(p) & + - nf_veg%gru_deadstemn_storage_to_atm_patch(p) * dt + ns_veg%livecrootn_storage_patch(p) = ns_veg%livecrootn_storage_patch(p) & + - nf_veg%gru_livecrootn_storage_to_atm_patch(p) * dt + ns_veg%deadcrootn_storage_patch(p) = ns_veg%deadcrootn_storage_patch(p) & + - nf_veg%gru_deadcrootn_storage_to_atm_patch(p) * dt + + ! transfer pools + ns_veg%leafn_xfer_patch(p) = ns_veg%leafn_xfer_patch(p) & + - nf_veg%gru_leafn_xfer_to_atm_patch(p) *dt + ns_veg%frootn_xfer_patch(p) = ns_veg%frootn_xfer_patch(p) & + - nf_veg%gru_frootn_xfer_to_atm_patch(p) *dt + ns_veg%livestemn_xfer_patch(p) = ns_veg%livestemn_xfer_patch(p) & + - nf_veg%gru_livestemn_xfer_to_atm_patch(p) *dt + ns_veg%deadstemn_xfer_patch(p) = ns_veg%deadstemn_xfer_patch(p) & + - nf_veg%gru_deadstemn_xfer_to_atm_patch(p) *dt + ns_veg%livecrootn_xfer_patch(p) = ns_veg%livecrootn_xfer_patch(p) & + - nf_veg%gru_livecrootn_xfer_to_atm_patch(p) *dt + ns_veg%deadcrootn_xfer_patch(p) = ns_veg%deadcrootn_xfer_patch(p) & + - nf_veg%gru_deadcrootn_xfer_to_atm_patch(p) *dt + else + ! NB (slevis) The equivalent changes for matrix code are in + ! dynGrossUnrepMod::CNGrossUnrep* + end if !not use_matrixcn end do diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90 index bc49e72f4c..b354744b61 100644 --- a/src/biogeochem/dynGrossUnrepMod.F90 +++ b/src/biogeochem/dynGrossUnrepMod.F90 @@ -24,6 +24,7 @@ module dynGrossUnrepMod use clm_varpar , only : natpft_size, i_litr_min, i_litr_max, i_met_lit use ColumnType , only : col use PatchType , only : patch + use CNSharedParamsMod , only : use_matrixcn ! ! !PUBLIC MEMBER FUNCTIONS: implicit none @@ -296,61 +297,157 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & m = 0._r8 end if - ! patch-level gross unrepresented landcover change carbon fluxes - ! displayed pools - gru_leafc_to_litter(p) = leafc(p) * m - gru_frootc_to_litter(p) = frootc(p) * m - gru_livestemc_to_atm(p) = livestemc(p) * m - gru_deadstemc_to_atm(p) = deadstemc(p) * m * convfrac(ivt(p)) - gru_wood_productc_gain(p) = deadstemc(p) * m * (1._r8 - convfrac(ivt(p))) - gru_livecrootc_to_litter(p) = livecrootc(p) * m - gru_deadcrootc_to_litter(p) = deadcrootc(p) * m - gru_xsmrpool_to_atm(p) = xsmrpool(p) * m - - ! storage pools - gru_leafc_storage_to_atm(p) = leafc_storage(p) * m - gru_frootc_storage_to_atm(p) = frootc_storage(p) * m - gru_livestemc_storage_to_atm(p) = livestemc_storage(p) * m - gru_deadstemc_storage_to_atm(p) = deadstemc_storage(p) * m - gru_livecrootc_storage_to_atm(p) = livecrootc_storage(p) * m - gru_deadcrootc_storage_to_atm(p) = deadcrootc_storage(p) * m - gru_gresp_storage_to_atm(p) = gresp_storage(p) * m - - ! transfer pools - gru_leafc_xfer_to_atm(p) = leafc_xfer(p) * m - gru_frootc_xfer_to_atm(p) = frootc_xfer(p) * m - gru_livestemc_xfer_to_atm(p) = livestemc_xfer(p) * m - gru_deadstemc_xfer_to_atm(p) = deadstemc_xfer(p) * m - gru_livecrootc_xfer_to_atm(p) = livecrootc_xfer(p) * m - gru_deadcrootc_xfer_to_atm(p) = deadcrootc_xfer(p) * m - gru_gresp_xfer_to_atm(p) = gresp_xfer(p) * m + if(.not. use_matrixcn)then + ! patch-level gross unrepresented landcover change carbon fluxes + ! displayed pools + gru_leafc_to_litter(p) = leafc(p) * m + gru_frootc_to_litter(p) = frootc(p) * m + gru_livestemc_to_atm(p) = livestemc(p) * m + gru_deadstemc_to_atm(p) = deadstemc(p) * m * convfrac(ivt(p)) + gru_wood_productc_gain(p) = deadstemc(p) * m * (1._r8 - convfrac(ivt(p))) + gru_livecrootc_to_litter(p) = livecrootc(p) * m + gru_deadcrootc_to_litter(p) = deadcrootc(p) * m + gru_xsmrpool_to_atm(p) = xsmrpool(p) * m + + ! storage pools + gru_leafc_storage_to_atm(p) = leafc_storage(p) * m + gru_frootc_storage_to_atm(p) = frootc_storage(p) * m + gru_livestemc_storage_to_atm(p) = livestemc_storage(p) * m + gru_deadstemc_storage_to_atm(p) = deadstemc_storage(p) * m + gru_livecrootc_storage_to_atm(p) = livecrootc_storage(p) * m + gru_deadcrootc_storage_to_atm(p) = deadcrootc_storage(p) * m + gru_gresp_storage_to_atm(p) = gresp_storage(p) * m + + ! transfer pools + gru_leafc_xfer_to_atm(p) = leafc_xfer(p) * m + gru_frootc_xfer_to_atm(p) = frootc_xfer(p) * m + gru_livestemc_xfer_to_atm(p) = livestemc_xfer(p) * m + gru_deadstemc_xfer_to_atm(p) = deadstemc_xfer(p) * m + gru_livecrootc_xfer_to_atm(p) = livecrootc_xfer(p) * m + gru_deadcrootc_xfer_to_atm(p) = deadcrootc_xfer(p) * m + gru_gresp_xfer_to_atm(p) = gresp_xfer(p) * m - ! patch-level gross unrepresented landcover change mortality nitrogen fluxes - ! displayed pools - gru_leafn_to_litter(p) = leafn(p) * m - gru_frootn_to_litter(p) = frootn(p) * m - gru_livestemn_to_atm(p) = livestemn(p) * m - gru_deadstemn_to_atm(p) = deadstemn(p) * m * convfrac(ivt(p)) - gru_wood_productn_gain(p) = deadstemn(p) * m * (1._r8 - convfrac(ivt(p))) - gru_livecrootn_to_litter(p) = livecrootn(p) * m - gru_deadcrootn_to_litter(p) = deadcrootn(p) * m - gru_retransn_to_litter(p) = retransn(p) * m - - ! storage pools - gru_leafn_storage_to_atm(p) = leafn_storage(p) * m - gru_frootn_storage_to_atm(p) = frootn_storage(p) * m - gru_livestemn_storage_to_atm(p) = livestemn_storage(p) * m - gru_deadstemn_storage_to_atm(p) = deadstemn_storage(p) * m - gru_livecrootn_storage_to_atm(p) = livecrootn_storage(p) * m - gru_deadcrootn_storage_to_atm(p) = deadcrootn_storage(p) * m - - ! transfer pools - gru_leafn_xfer_to_atm(p) = leafn_xfer(p) * m - gru_frootn_xfer_to_atm(p) = frootn_xfer(p) * m - gru_livestemn_xfer_to_atm(p) = livestemn_xfer(p) * m - gru_deadstemn_xfer_to_atm(p) = deadstemn_xfer(p) * m - gru_livecrootn_xfer_to_atm(p) = livecrootn_xfer(p) * m - gru_deadcrootn_xfer_to_atm(p) = deadcrootn_xfer(p) * m + ! patch-level gross unrepresented landcover change mortality nitrogen fluxes + ! displayed pools + gru_leafn_to_litter(p) = leafn(p) * m + gru_frootn_to_litter(p) = frootn(p) * m + gru_livestemn_to_atm(p) = livestemn(p) * m + gru_deadstemn_to_atm(p) = deadstemn(p) * m * convfrac(ivt(p)) + gru_wood_productn_gain(p) = deadstemn(p) * m * (1._r8 - convfrac(ivt(p))) + gru_livecrootn_to_litter(p) = livecrootn(p) * m + gru_deadcrootn_to_litter(p) = deadcrootn(p) * m + gru_retransn_to_litter(p) = retransn(p) * m + + ! storage pools + gru_leafn_storage_to_atm(p) = leafn_storage(p) * m + gru_frootn_storage_to_atm(p) = frootn_storage(p) * m + gru_livestemn_storage_to_atm(p) = livestemn_storage(p) * m + gru_deadstemn_storage_to_atm(p) = deadstemn_storage(p) * m + gru_livecrootn_storage_to_atm(p) = livecrootn_storage(p) * m + gru_deadcrootn_storage_to_atm(p) = deadcrootn_storage(p) * m + + ! transfer pools + gru_leafn_xfer_to_atm(p) = leafn_xfer(p) * m + gru_frootn_xfer_to_atm(p) = frootn_xfer(p) * m + gru_livestemn_xfer_to_atm(p) = livestemn_xfer(p) * m + gru_deadstemn_xfer_to_atm(p) = deadstemn_xfer(p) * m + gru_livecrootn_xfer_to_atm(p) = livecrootn_xfer(p) * m + gru_deadcrootn_xfer_to_atm(p) = deadcrootn_xfer(p) * m + else ! matrixcn solution + ! patch-level gross unrepresented landcover change carbon fluxes + ! displayed pools + gru_leafc_to_litter(p) = matrix_update_gmc(p,ileaf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + leafc(p) + gru_frootc_to_litter(p) = matrix_update_gmc(p,ifroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + frootc(p) + gru_livestemc_to_atm(p) = matrix_update_gmc(p,ilivestem_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + livestemc(p) + gru_deadstemc_to_atm(p) = matrix_update_gmc(p,ideadstem_to_iout_gmc,m * convfrac(ivt(p)),dtime,cnveg_carbonflux_inst,.True.,.True.) * & + deadstemc(p) + gru_wood_productc_gain(p) = matrix_update_gmc(p,ideadstem_to_iout_gmc,m * (1._r8 - convfrac(ivt(p))),dtime,cnveg_carbonflux_inst,.True.,.True.) * & + deadstemc(p) + gru_livecrootc_to_litter(p) = matrix_update_gmc(p,ilivecroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + livecrootc(p) + gru_deadcrootc_to_litter(p) = matrix_update_gmc(p,ideadcroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + deadcrootc(p) + gru_xsmrpool_to_atm(p) = xsmrpool(p) * m + + ! storage pools + gru_leafc_storage_to_atm(p) = matrix_update_gmc(p,ileafst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + leafc_storage(p) + gru_frootc_storage_to_atm(p) = matrix_update_gmc(p,ifrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + frootc_storage(p) + gru_livestemc_storage_to_atm(p) = matrix_update_gmc(p,ilivestemst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + livestemc_storage(p) + gru_deadstemc_storage_to_atm(p) = matrix_update_gmc(p,ideadstemst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + deadstemc_storage(p) + gru_livecrootc_storage_to_atm(p) = matrix_update_gmc(p,ilivecrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + livecrootc_storage(p) + gru_deadcrootc_storage_to_atm(p) = matrix_update_gmc(p,ideadcrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + deadcrootc_storage(p) + gru_gresp_storage_to_atm(p) = gresp_storage(p) * m + + ! transfer pools + gru_leafc_xfer_to_atm(p) = matrix_update_gmc(p,ileafxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + leafc_xfer(p) + gru_frootc_xfer_to_atm(p) = matrix_update_gmc(p,ifrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + frootc_xfer(p) + gru_livestemc_xfer_to_atm(p) = matrix_update_gmc(p,ilivestemxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + livestemc_xfer(p) + gru_deadstemc_xfer_to_atm(p) = matrix_update_gmc(p,ideadstemxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + deadstemc_xfer(p) + gru_livecrootc_xfer_to_atm(p) = matrix_update_gmc(p,ilivecrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + livecrootc_xfer(p) + gru_deadcrootc_xfer_to_atm(p) = matrix_update_gmc(p,ideadcrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & + deadcrootc_xfer(p) + gru_gresp_xfer_to_atm(p) = gresp_xfer(p) * m + + ! patch-level gross unrepresented landcover change mortality nitrogen fluxes + ! displayed pools + gru_leafn_to_litter(p) = matrix_update_gmn(p,ileaf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + leafn(p) + gru_frootn_to_litter(p) = matrix_update_gmn(p,ifroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + frootn(p) + gru_livestemn_to_atm(p) = matrix_update_gmn(p,ilivestem_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + livestemn(p) + gru_deadstemn_to_atm(p) = matrix_update_gmn(p,ideadstem_to_iout_gmn,m * convfrac(ivt(p)),dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + deadstemn(p) + gru_wood_productn_gain(p) = matrix_update_gmn(p,ideadstem_to_iout_gmn,m * (1._r8 - convfrac(ivt(p))),dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + deadstemn(p) + gru_livecrootn_to_litter(p) = matrix_update_gmn(p,ilivecroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + livecrootn(p) + gru_deadcrootn_to_litter(p) = matrix_update_gmn(p,ideadcroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + deadcrootn(p) + gru_retransn_to_litter(p) = matrix_update_gmn(p,iretransn_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + retransn(p) + + ! storage pools + gru_leafn_storage_to_atm(p) = matrix_update_gmn(p,ileafst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + leafn_storage(p) + gru_frootn_storage_to_atm(p) = matrix_update_gmn(p,ifrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + frootn_storage(p) + gru_livestemn_storage_to_atm(p) = matrix_update_gmn(p,ilivestemst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + livestemn_storage(p) + gru_deadstemn_storage_to_atm(p) = matrix_update_gmn(p,ideadstemst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + deadstemn_storage(p) + gru_livecrootn_storage_to_atm(p) = matrix_update_gmn(p,ilivecrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)* & + livecrootn_storage(p) + gru_deadcrootn_storage_to_atm(p) = matrix_update_gmn(p,ideadcrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)* & + deadcrootn_storage(p) + ! transfer pools + gru_leafn_xfer_to_atm(p) = matrix_update_gmn(p,ileafxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + leafn_xfer(p) + gru_frootn_xfer_to_atm(p) = matrix_update_gmn(p,ifrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + frootn_xfer(p) + gru_livestemn_xfer_to_atm(p) = matrix_update_gmn(p,ilivestemxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + livestemn_xfer(p) + gru_deadstemn_xfer_to_atm(p) = matrix_update_gmn(p,ideadstemxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + deadstemn_xfer(p) + gru_livecrootn_xfer_to_atm(p) = matrix_update_gmn(p,ilivecrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + livecrootn_xfer(p) + gru_deadcrootn_xfer_to_atm(p) = matrix_update_gmn(p,ideadcrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & + deadcrootn_xfer(p) + end if end if ! end tree block diff --git a/src/dyn_subgrid/dynHarvestMod.F90 b/src/dyn_subgrid/dynHarvestMod.F90 index b662d67d73..609ba6679b 100644 --- a/src/dyn_subgrid/dynHarvestMod.F90 +++ b/src/dyn_subgrid/dynHarvestMod.F90 @@ -434,9 +434,9 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & m = 0._r8 end if - ! patch-level harvest carbon fluxes - ! displayed pools if(.not. use_matrixcn)then + ! patch-level harvest carbon fluxes + ! displayed pools hrv_leafc_to_litter(p) = leafc(p) * m hrv_frootc_to_litter(p) = frootc(p) * m hrv_livestemc_to_litter(p) = livestemc(p) * m @@ -492,6 +492,8 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & ! NOTE: The non-matrix part of this update is in CNCStatUpdate2 CStateUpdate2h (EBK 11/25/2019) ! and for Nitrogen The non-matrix part of this update is in CNNStatUpdate2 NStateUpdate2h (EBK 11/25/2019) else + ! patch-level harvest carbon fluxes + ! displayed pools hrv_leafc_to_litter(p) = matrix_update_gmc(p,ileaf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & leafc(p) hrv_frootc_to_litter(p) = matrix_update_gmc(p,ifroot_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & @@ -506,7 +508,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & deadcrootc(p) hrv_xsmrpool_to_atm(p) = xsmrpool(p) * m - ! storage pools + ! storage pools hrv_leafc_storage_to_litter(p) = matrix_update_gmc(p,ileafst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & leafc_storage(p) hrv_frootc_storage_to_litter(p) = matrix_update_gmc(p,ifrootst_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & @@ -521,8 +523,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & deadcrootc_storage(p) hrv_gresp_storage_to_litter(p) = gresp_storage(p) * m - - ! transfer pools + ! transfer pools hrv_leafc_xfer_to_litter(p) = matrix_update_gmc(p,ileafxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & leafc_xfer(p) hrv_frootc_xfer_to_litter(p) = matrix_update_gmc(p,ifrootxf_to_iout_gmc,m,dtime,cnveg_carbonflux_inst,.True.,.True.) * & @@ -537,6 +538,8 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & deadcrootc_xfer(p) hrv_gresp_xfer_to_litter(p) = gresp_xfer(p) * m + ! patch-level harvest mortality nitrogen fluxes + ! displayed pools hrv_leafn_to_litter(p) = matrix_update_gmn(p,ileaf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & leafn(p) hrv_frootn_to_litter(p) = matrix_update_gmn(p,ifroot_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & @@ -552,7 +555,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & hrv_retransn_to_litter(p) = matrix_update_gmn(p,iretransn_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & retransn(p) - ! storage pools + ! storage pools hrv_leafn_storage_to_litter(p) = matrix_update_gmn(p,ileafst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) *& leafn_storage(p) hrv_frootn_storage_to_litter(p) = matrix_update_gmn(p,ifrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) *& @@ -565,7 +568,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & livecrootn_storage(p) hrv_deadcrootn_storage_to_litter(p) = matrix_update_gmn(p,ideadcrootst_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.)*& deadcrootn_storage(p) - ! transfer pools + ! transfer pools hrv_leafn_xfer_to_litter(p) = matrix_update_gmn(p,ileafxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & leafn_xfer(p) hrv_frootn_xfer_to_litter(p) = matrix_update_gmn(p,ifrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & @@ -578,9 +581,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & livecrootn_xfer(p) hrv_deadcrootn_xfer_to_litter(p) = matrix_update_gmn(p,ideadcrootxf_to_iout_gmn,m,dtime,cnveg_nitrogenflux_inst,.True.,.True.) * & deadcrootn_xfer(p) - end if - end if ! end tree block end do ! end of pft loop From 57aa176ae3f28dbea9a9a20c3953fe4c6c1bae12 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 28 Dec 2023 15:55:12 -0700 Subject: [PATCH 030/408] Additional updates for matrixcn to work with GULU --- src/biogeochem/CNCStateUpdate2Mod.F90 | 5 +++- src/biogeochem/CNDriverMod.F90 | 12 +++++--- src/biogeochem/CNNStateUpdate2Mod.F90 | 5 +++- src/biogeochem/dynGrossUnrepMod.F90 | 40 ++++++++++++++++++++++++++- 4 files changed, 55 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate2Mod.F90 b/src/biogeochem/CNCStateUpdate2Mod.F90 index 2890c7d1fd..c59d7d47f1 100644 --- a/src/biogeochem/CNCStateUpdate2Mod.F90 +++ b/src/biogeochem/CNCStateUpdate2Mod.F90 @@ -335,7 +335,8 @@ end subroutine CStateUpdate2h !----------------------------------------------------------------------- subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst) + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst) ! ! !DESCRIPTION: ! Update all the prognostic carbon state @@ -348,6 +349,7 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst + type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst ! ! !LOCAL VARIABLES: @@ -359,6 +361,7 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & associate( & cf_veg => cnveg_carbonflux_inst , & cs_veg => cnveg_carbonstate_inst , & + cf_soil => soilbiogeochem_carbonflux_inst, & cs_soil => soilbiogeochem_carbonstate_inst & ) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 3d75ee51f0..d7eb964f1d 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -799,18 +799,22 @@ subroutine CNDriverNoLeaching(bounds, end if call CStateUpdate2g( num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst) + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst) if ( use_c13 ) then call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & - c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst) + c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & + c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst) end if if ( use_c14 ) then call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & - c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst) + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & + c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst) end if call NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst) + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, & + soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) call t_stopf('CNUpdate2') diff --git a/src/biogeochem/CNNStateUpdate2Mod.F90 b/src/biogeochem/CNNStateUpdate2Mod.F90 index 2dbba68b82..4b6174195e 100644 --- a/src/biogeochem/CNNStateUpdate2Mod.F90 +++ b/src/biogeochem/CNNStateUpdate2Mod.F90 @@ -321,7 +321,8 @@ end subroutine NStateUpdate2h !----------------------------------------------------------------------- subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst) + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, & + soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) ! ! !DESCRIPTION: ! Update all the prognostic nitrogen state @@ -337,6 +338,7 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & type(cnveg_nitrogenflux_type) , intent(in) :: cnveg_nitrogenflux_inst type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst + type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst ! ! !LOCAL VARIABLES: integer :: c,p,j,l,i ! indices @@ -347,6 +349,7 @@ subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & associate( & nf_veg => cnveg_nitrogenflux_inst , & ns_veg => cnveg_nitrogenstate_inst , & + nf_soil => soilbiogeochem_nitrogenflux_inst, & ns_soil => soilbiogeochem_nitrogenstate_inst & ) diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90 index b354744b61..0c9b1e2c53 100644 --- a/src/biogeochem/dynGrossUnrepMod.F90 +++ b/src/biogeochem/dynGrossUnrepMod.F90 @@ -158,6 +158,7 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & use pftconMod , only : noveg, nbrdlf_evr_shrub, nc4_grass use clm_varcon , only : secspday use clm_time_manager, only : get_step_size_real, is_beg_curr_year + use CNVegMatrixMod , only : matrix_update_gmc, matrix_update_gmn ! ! !ARGUMENTS: integer , intent(in) :: num_soilc ! number of soil columns in filter @@ -269,7 +270,44 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & gru_livestemn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_livestemn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] gru_deadstemn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_deadstemn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] gru_livecrootn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_livecrootn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] - gru_deadcrootn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_deadcrootn_xfer_to_atm_patch & ! Output: [real(r8) (:)] + gru_deadcrootn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_deadcrootn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + ileaf_to_iout_gmc => cnveg_carbonflux_inst%ileaf_to_iout_gm , & + ileafst_to_iout_gmc => cnveg_carbonflux_inst%ileafst_to_iout_gm , & + ileafxf_to_iout_gmc => cnveg_carbonflux_inst%ileafxf_to_iout_gm , & + ifroot_to_iout_gmc => cnveg_carbonflux_inst%ifroot_to_iout_gm , & + ifrootst_to_iout_gmc => cnveg_carbonflux_inst%ifrootst_to_iout_gm , & + ifrootxf_to_iout_gmc => cnveg_carbonflux_inst%ifrootxf_to_iout_gm , & + ilivestem_to_iout_gmc => cnveg_carbonflux_inst%ilivestem_to_iout_gm , & + ilivestemst_to_iout_gmc => cnveg_carbonflux_inst%ilivestemst_to_iout_gm , & + ilivestemxf_to_iout_gmc => cnveg_carbonflux_inst%ilivestemxf_to_iout_gm , & + ideadstem_to_iout_gmc => cnveg_carbonflux_inst%ideadstem_to_iout_gm , & + ideadstemst_to_iout_gmc => cnveg_carbonflux_inst%ideadstemst_to_iout_gm , & + ideadstemxf_to_iout_gmc => cnveg_carbonflux_inst%ideadstemxf_to_iout_gm , & + ilivecroot_to_iout_gmc => cnveg_carbonflux_inst%ilivecroot_to_iout_gm , & + ilivecrootst_to_iout_gmc => cnveg_carbonflux_inst%ilivecrootst_to_iout_gm , & + ilivecrootxf_to_iout_gmc => cnveg_carbonflux_inst%ilivecrootxf_to_iout_gm , & + ideadcroot_to_iout_gmc => cnveg_carbonflux_inst%ideadcroot_to_iout_gm , & + ideadcrootst_to_iout_gmc => cnveg_carbonflux_inst%ideadcrootst_to_iout_gm , & + ideadcrootxf_to_iout_gmc => cnveg_carbonflux_inst%ideadcrootxf_to_iout_gm , & + ileaf_to_iout_gmn => cnveg_nitrogenflux_inst%ileaf_to_iout_gm , & + ileafst_to_iout_gmn => cnveg_nitrogenflux_inst%ileafst_to_iout_gm , & + ileafxf_to_iout_gmn => cnveg_nitrogenflux_inst%ileafxf_to_iout_gm , & + ifroot_to_iout_gmn => cnveg_nitrogenflux_inst%ifroot_to_iout_gm , & + ifrootst_to_iout_gmn => cnveg_nitrogenflux_inst%ifrootst_to_iout_gm , & + ifrootxf_to_iout_gmn => cnveg_nitrogenflux_inst%ifrootxf_to_iout_gm , & + ilivestem_to_iout_gmn => cnveg_nitrogenflux_inst%ilivestem_to_iout_gm , & + ilivestemst_to_iout_gmn => cnveg_nitrogenflux_inst%ilivestemst_to_iout_gm , & + ilivestemxf_to_iout_gmn => cnveg_nitrogenflux_inst%ilivestemxf_to_iout_gm , & + ideadstem_to_iout_gmn => cnveg_nitrogenflux_inst%ideadstem_to_iout_gm , & + ideadstemst_to_iout_gmn => cnveg_nitrogenflux_inst%ideadstemst_to_iout_gm , & + ideadstemxf_to_iout_gmn => cnveg_nitrogenflux_inst%ideadstemxf_to_iout_gm , & + ilivecroot_to_iout_gmn => cnveg_nitrogenflux_inst%ilivecroot_to_iout_gm , & + ilivecrootst_to_iout_gmn => cnveg_nitrogenflux_inst%ilivecrootst_to_iout_gm , & + ilivecrootxf_to_iout_gmn => cnveg_nitrogenflux_inst%ilivecrootxf_to_iout_gm , & + ideadcroot_to_iout_gmn => cnveg_nitrogenflux_inst%ideadcroot_to_iout_gm , & + ideadcrootst_to_iout_gmn => cnveg_nitrogenflux_inst%ideadcrootst_to_iout_gm , & + ideadcrootxf_to_iout_gmn => cnveg_nitrogenflux_inst%ideadcrootxf_to_iout_gm , & + iretransn_to_iout_gmn => cnveg_nitrogenflux_inst%iretransn_to_iout_gm & ) dtime = get_step_size_real() From 1242be2f5b74d65729682322c4c8228a0b6e07aa Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 28 Dec 2023 20:44:17 -0700 Subject: [PATCH 031/408] Cheyenne GULU test now passes with these additional updates --- src/biogeochem/CNCStateUpdate2Mod.F90 | 18 ++++++++++-------- src/biogeochem/CNGapMortalityMod.F90 | 5 ----- src/biogeochem/dynGrossUnrepMod.F90 | 2 +- src/dyn_subgrid/dynHarvestMod.F90 | 5 ----- 4 files changed, 11 insertions(+), 19 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate2Mod.F90 b/src/biogeochem/CNCStateUpdate2Mod.F90 index c59d7d47f1..5fb7a283e9 100644 --- a/src/biogeochem/CNCStateUpdate2Mod.F90 +++ b/src/biogeochem/CNCStateUpdate2Mod.F90 @@ -401,6 +401,16 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & do fp = 1,num_soilp p = filter_soilp(fp) + ! xsmrpool + cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) & + - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt + ! gresp storage pool + cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) & + - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt + ! gresp transfer pool + cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p) & + - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt + ! patch-level carbon fluxes from gross unrepresented landcover change mortality ! ! State update without the matrix solution @@ -422,10 +432,6 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p) & - cf_veg%gru_deadcrootc_to_litter_patch(p) * dt - ! xsmrpool - cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) & - - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt - ! storage pools cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p) & - cf_veg%gru_leafc_storage_to_atm_patch(p) * dt @@ -439,8 +445,6 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cf_veg%gru_livecrootc_storage_to_atm_patch(p) * dt cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) & - cf_veg%gru_deadcrootc_storage_to_atm_patch(p) * dt - cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) & - - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt ! transfer pools cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p) & @@ -455,8 +459,6 @@ subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cf_veg%gru_livecrootc_xfer_to_atm_patch(p) * dt cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p) & - cf_veg%gru_deadcrootc_xfer_to_atm_patch(p) * dt - cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p) & - - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt else ! NB (slevis) The matrix equivalent of the above is in diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90 index e9013e03b1..c99660e3c6 100644 --- a/src/biogeochem/CNGapMortalityMod.F90 +++ b/src/biogeochem/CNGapMortalityMod.F90 @@ -24,11 +24,6 @@ module CNGapMortalityMod use PatchType , only : patch use GridcellType , only : grc use CNSharedParamsMod , only : use_matrixcn - use clm_varpar , only : ileaf,ileaf_st,ileaf_xf,ifroot,ifroot_st,ifroot_xf,& - ilivestem,ilivestem_st,ilivestem_xf,& - ideadstem,ideadstem_st,ideadstem_xf,& - ilivecroot,ilivecroot_st,ilivecroot_xf,& - ideadcroot,ideadcroot_st,ideadcroot_xf,iretransn,ioutc,ioutn use CNVegMatrixMod , only : matrix_update_gmc, matrix_update_gmn ! implicit none diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90 index 0c9b1e2c53..1da39a0b64 100644 --- a/src/biogeochem/dynGrossUnrepMod.F90 +++ b/src/biogeochem/dynGrossUnrepMod.F90 @@ -364,7 +364,7 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & gru_livecrootc_xfer_to_atm(p) = livecrootc_xfer(p) * m gru_deadcrootc_xfer_to_atm(p) = deadcrootc_xfer(p) * m gru_gresp_xfer_to_atm(p) = gresp_xfer(p) * m - + ! patch-level gross unrepresented landcover change mortality nitrogen fluxes ! displayed pools gru_leafn_to_litter(p) = leafn(p) * m diff --git a/src/dyn_subgrid/dynHarvestMod.F90 b/src/dyn_subgrid/dynHarvestMod.F90 index 609ba6679b..2936a41545 100644 --- a/src/dyn_subgrid/dynHarvestMod.F90 +++ b/src/dyn_subgrid/dynHarvestMod.F90 @@ -25,11 +25,6 @@ module dynHarvestMod use PatchType , only : patch use CNSharedParamsMod , only : use_matrixcn use clm_varctl , only : use_fates - use clm_varpar , only : ileaf,ileaf_st,ileaf_xf,ifroot,ifroot_st,ifroot_xf,& - ilivestem,ilivestem_st,ilivestem_xf,& - ideadstem,ideadstem_st,ideadstem_xf,& - ilivecroot,ilivecroot_st,ilivecroot_xf,& - ideadcroot,ideadcroot_st,ideadcroot_xf,ioutc,ioutn ! ! !PUBLIC MEMBER FUNCTIONS: implicit none From 46cbf4b3e67b1b55260b6b5b6d57778c1cc54db7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 Dec 2023 16:04:20 -0700 Subject: [PATCH 032/408] Remove PS from SMS_Ld3_PS test for it to work with matrixcn --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index e1f26f0703..3551d34b1a 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -536,7 +536,7 @@ - + From 2287bb6b7b4fdb66a97dc462d37173b72a46ec73 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 Dec 2023 19:04:24 -0700 Subject: [PATCH 033/408] Corrections for model to build and a test to pass Used this one for testing: SMS_D.1x1_brazil.I1850Clm51BgcCrop.cheyenne_gnu.clm-mimics_matrixcn --- src/biogeochem/CNCStateUpdate1Mod.F90 | 61 ++++--------------- src/biogeochem/CNDriverMod.F90 | 8 +-- .../SoilBiogeochemNitrogenStateType.F90 | 1 + 3 files changed, 17 insertions(+), 53 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index c342e36a22..e839136e11 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -215,6 +215,18 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! terms have been moved to CStateUpdateDynPatch. I think this is zeroed every ! time step, but to be safe, I'm explicitly setting it to zero here. cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8 + + ! litter and SOM HR fluxes + do k = 1, ndecomp_cascade_transitions + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & + - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) * dt + if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) & + + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k) * dt + end if + end do else ! ! For the matrix solution the actual state update comes after the matrix @@ -233,55 +245,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end if fates_if end do fc_loop - - - ! litter and SOM HR fluxes - do k = 1, ndecomp_cascade_transitions - do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) - ! - ! State update without the matrix solution - ! - if (.not. use_soil_matrixcn) then - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & - - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt - end if !not use_soil_matrixcn - end do - end do - end do - do k = 1, ndecomp_cascade_transitions - if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions - do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) - if (.not. use_soil_matrixcn) then - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & - - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt - end if !not use_soil_matrixcn - end do - end do - end do - do k = 1, ndecomp_cascade_transitions - if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions - do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) - ! - ! State update without the matrix solution - ! - if (.not. use_soil_matrixcn) then - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) & - + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt - end if !not use_soil_matrixcn - end do - end do - end do - end if - end do soilpatch_loop: do fp = 1,num_soilp p = filter_soilp(fp) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index be341477a5..67eaba1013 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -1097,10 +1097,10 @@ subroutine CNDriverLeaching(bounds, & if ( use_matrixcn ) then call t_startf('CNVMatrix') - call CNVegMatrix(bounds,num_bgc_soilp,filter_bgc_soilp(1:num_bgc_soilp),num_actfirep,filter_actfirep,cnveg_carbonstate_inst,cnveg_nitrogenstate_inst,& - cnveg_carbonflux_inst, cnveg_nitrogenflux_inst,cnveg_state_inst,soilbiogeochem_nitrogenflux_inst,& - c13_cnveg_carbonstate_inst,c14_cnveg_carbonstate_inst,c13_cnveg_carbonflux_inst,& - c14_cnveg_carbonflux_inst) + call CNVegMatrix(bounds, num_bgc_vegp, filter_bgc_vegp(1:num_bgc_vegp), & + num_actfirep, filter_actfirep, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & + cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, cnveg_state_inst,soilbiogeochem_nitrogenflux_inst, & + c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst) call t_stopf('CNVMatrix') end if diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index e97ed3e6eb..a0cbc81a9e 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -15,6 +15,7 @@ module SoilBiogeochemNitrogenStateType use clm_varctl , only : iulog, override_bgc_restart_mismatch_dump, spinup_state use landunit_varcon , only : istcrop, istsoil use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn + use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, century_decomp, decomp_method use LandunitType , only : lun use ColumnType , only : col use GridcellType , only : grc From 107f854c89a237b2d1d99ad36b78ce2ef2ad2544 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Sat, 30 Dec 2023 21:42:36 -0700 Subject: [PATCH 034/408] Fix for FatesCold simulations to pass --- src/biogeochem/CNCStateUpdate1Mod.F90 | 30 +++++++++++++++++---------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index e839136e11..4eb52d9c10 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -216,17 +216,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! time step, but to be safe, I'm explicitly setting it to zero here. cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8 - ! litter and SOM HR fluxes - do k = 1, ndecomp_cascade_transitions - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & - - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) * dt - if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) & - + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k) * dt - end if - end do else ! ! For the matrix solution the actual state update comes after the matrix @@ -243,6 +232,25 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end do end if fates_if + + do j = 1,nlevdecomp + ! + ! State update without the matrix solution + ! + if (.not. use_soil_matrixcn) then + ! litter and SOM HR fluxes + do k = 1, ndecomp_cascade_transitions + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & + - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) * dt + if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) & + + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k) * dt + end if + end do + end if + end do end do fc_loop From 3af4aedfbb8bc7a8b0076184197141c463e6c8fd Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 2 Jan 2024 18:39:00 -0700 Subject: [PATCH 035/408] Corrections from comparing model versions --- src/biogeochem/CNPhenologyMod.F90 | 40 +++++++++---------------------- 1 file changed, 11 insertions(+), 29 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e1b7b2edb6..2d9ab51473 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3506,17 +3506,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & t1 = 1.0_r8 / dt frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p) - ! TODO slevis: This line didn't appear in dev159. Remove? - ! biofuel_harvfrac is only non-zero for prognostic crops. - leafc_to_litter(p) = t1 * leafc(p) * (1._r8 - biofuel_harvfrac(ivt(p))) + cpool_to_leafc(p) - - ! leafc_litter and frootc_to_litter for matrix + ! frootc_to_litter for matrix if (use_matrixcn) then - if(leafc(p) .gt. 0)then - leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) - else - leafc_to_litter(p) = 0 - end if if(frootc(p) .gt. 0)then frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else @@ -3618,6 +3609,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! as well as leaf C:N ratio (unaffected by biofuel harvest). It thus does not ! need to be updated here. + ! Matrix for grain, livestem to litter, leaf to litter, and biofuel if(use_matrixcn)then if(reproductivec(p,1) .gt. 0)then grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) @@ -3633,13 +3625,17 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & end if if(livestemc(p) .gt. 0)then livestemc_to_litter(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_iout_phc,livestemc_to_litter(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) + livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) else livestemc_to_litter(p) = 0 + livestemc_to_biofuelc(p) = 0 end if if(livestemn(p) .gt. 0)then livestemn_to_biofueln(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_biofueln(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) + livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else livestemn_to_biofueln(p) = 0 + livestemn_to_litter(p) = 0 end if if(leafn(p) > 0)then leafn_to_biofueln(p) = leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_biofueln(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) @@ -3647,14 +3643,11 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & leafn_to_biofueln(p) = 0 end if if (leafc(p) > 0)then - leafc_to_biofuelc(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) - else - leafc_to_biofuelc(p) = 0 - end if - if(livestemc(p) .gt. 0)then - livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) + leafc_to_biofuelc(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) + leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - livestemc_to_biofuelc(p) = 0 + leafc_to_biofuelc(p) = 0 + leafc_to_litter(p) = 0 end if else ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) @@ -3675,7 +3668,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & if(frootc(p) .gt. 0)then frootc_to_litter(p) = frootc(p) * matrix_update_phc(p,ifroot_to_iout_phc,frootc_to_litter(p) / frootc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - frootc_to_litter(p) = 0 + frootc_to_litter(p) = 0 ! TODO slevis here and elsewhere end if else ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) @@ -3824,17 +3817,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & endif end if - ! TODO slevis: This paragraph didn't appear in dev159. Remove? - if (ivt(p) >= npcropmin) then - ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn - !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p)) - ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead - livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p))) - if(use_matrixcn)then - livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) - end if - end if - ! save the current litterfall fluxes prev_leafc_to_litter(p) = leafc_to_litter(p) prev_frootc_to_litter(p) = frootc_to_litter(p) From 2ea1cecedd3a00cd98d962f9de1eaac2159ace05 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 2 Jan 2024 18:46:58 -0700 Subject: [PATCH 036/408] Corrections to lists of tests and expected failures --- cime_config/testdefs/ExpectedTestFails.xml | 4 ++-- cime_config/testdefs/testlist_clm.xml | 18 +++++++++--------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 6be036c485..b0f7fa860b 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -50,13 +50,13 @@ #1733 - + FAIL #640, same test with clm-ciso_soil_matrixcn_only works - + FAIL #640, same test with clm-ciso_soil_matrixcn_only works diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 114e3781a0..5ec791b7d4 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -373,7 +373,7 @@ - + @@ -632,7 +632,7 @@ - + @@ -641,7 +641,7 @@ - + @@ -729,7 +729,7 @@ - + @@ -808,7 +808,7 @@ - + @@ -1005,7 +1005,7 @@ - + @@ -1014,7 +1014,7 @@ - + @@ -2383,7 +2383,7 @@ - + @@ -2603,7 +2603,7 @@ - + From 2d8a0cf52ff3918280e28672033415aaefc81c2a Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:17:23 -0600 Subject: [PATCH 037/408] Resolve comments on pull request 2275 to CTSM main Changes done: 1. Removed and modified comments as suggested 2. Changed `urban_explicit_ac` default under clm5_0 to .false. 3. Removed changes that are already/going to be on main (bugfix for view factor and number of urban layers) --- bld/CLMBuildNamelist.pm | 1 - bld/namelist_files/namelist_defaults_ctsm.xml | 6 +-- .../namelist_definition_ctsm.xml | 3 -- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 21 ++-------- src/biogeophys/UrbanParamsType.F90 | 6 --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 42 +++++++------------ src/main/clm_varpar.F90 | 3 +- 7 files changed, 23 insertions(+), 59 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 0895a89ebb..0b9b161c20 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2111,7 +2111,6 @@ sub setup_logic_urban { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'building_temp_method'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_hac'); - # X. Li [dev.04] add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_explicit_ac'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'urban_traffic'); } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index a3f488b8f9..0d8e45a779 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -166,11 +166,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). FAST NONE - - - + .true. -.true. +.false. .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 5f89da9d29..8334b46d2a 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -947,9 +947,6 @@ Turn urban air conditioning/heating ON or OFF and add wasteheat: ON_WASTEHEAT = Air conditioning/heating is ON and waste-heat sent to urban canyon - - - If TRUE, use explicit, time-varying AC adoption rate for air-conditioning flux and interior building temperature calculations. diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index c07b1ad0e3..2e588e2e88 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -210,9 +210,6 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, use clm_varctl , only : iulog use abortutils , only : endrun use clm_varpar , only : nlevurb, nlevsno, nlevmaxurbgrnd - ! X. Li [orig]: - ! use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on - ! X. Li [dev.04]: use UrbanParamsType , only : urban_hac, urban_hac_off, urban_hac_on, urban_wasteheat_on, urban_explicit_ac ! ! !ARGUMENTS: @@ -239,7 +236,6 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, real(r8) :: t_floor_bef(bounds%begl:bounds%endl) ! floor temperature at previous time step (K) real(r8) :: t_building_bef(bounds%begl:bounds%endl) ! internal building air temperature at previous time step [K] real(r8) :: t_building_bef_hac(bounds%begl:bounds%endl)! internal building air temperature before applying HAC [K] - ! X. Li [dev.03] real(r8) :: eflx_urban_ac_sat(bounds%begl:bounds%endl) ! urban air conditioning flux under AC adoption saturation (W/m**2) real(r8) :: hcv_roofi(bounds%begl:bounds%endl) ! roof convective heat transfer coefficient (W m-2 K-1) real(r8) :: hcv_sunwi(bounds%begl:bounds%endl) ! sunwall convective heat transfer coefficient (W m-2 K-1) @@ -329,7 +325,6 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, t_floor => temperature_inst%t_floor_lun , & ! InOut: [real(r8) (:)] floor temperature (K) t_building => temperature_inst%t_building_lun , & ! InOut: [real(r8) (:)] internal building air temperature (K) - ! X. Li [dev] p_ac => urbantv_inst%p_ac , & ! Input: [real(r8) (:)] air-conditioning penetration rate (-) t_building_max => urbantv_inst%t_building_max , & ! Input: [real(r8) (:)] maximum internal building air temperature (K) t_building_min => urbanparams_inst%t_building_min , & ! Input: [real(r8) (:)] minimum internal building air temperature (K) @@ -432,10 +427,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, vf_wf(l) = 0.5_r8*(1._r8 - vf_rf(l)) ! This view factor implicitly converts from per unit floor area to per unit wall area - ! X. Li [orig] - ! vf_fw(l) = vf_wf(l) / building_hwr(l) - ! X. Li [bugfix] - vf_fw(l) = vf_wf(l) + vf_fw(l) = vf_wf(l) / building_hwr(l) ! This view factor implicitly converts from per unit roof area to per unit wall area vf_rw(l) = vf_fw(l) @@ -841,10 +833,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, + em_floori(l)*sb*t_floor_bef(l)**4._r8 & + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l)) - ! X. Li [orig] - ! qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l) - ! X. Li [bugfix] - qrd_building(l) = qrd_roof(l) + qrd_sunw(l) + qrd_shdw(l) + qrd_floor(l) + qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l) if (abs(qrd_building(l)) > .10_r8 ) then write (iulog,*) 'urban inside building net longwave radiation balance error ',qrd_building(l) @@ -936,16 +925,14 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, ! rho_dair(l) = pstd / (rair*t_building(l)) if (t_building_bef_hac(l) > t_building_max(l)) then - ! X. Li [dev.04] - if (urban_explicit_ac) then ! use explicit ac adoption rate: - ! X. Li [dev.03] ! after the change, t_building_max is saturation setpoint + if (urban_explicit_ac) then ! use explicit ac adoption rate parameterization scheme: + ! Here, t_building_max is the AC saturation setpoint eflx_urban_ac_sat(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_max(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) t_building(l) = t_building_max(l) + ( 1._r8 - p_ac(l) ) * eflx_urban_ac_sat(l) & * dtime / (ht_roof(l) * rho_dair(l) * cpair * wtlunit_roof(l)) eflx_urban_ac(l) = p_ac(l) * eflx_urban_ac_sat(l) else - ! X. Li [orig] t_building(l) = t_building_max(l) eflx_urban_ac(l) = wtlunit_roof(l) * abs( (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building(l) & - (ht_roof(l) * rho_dair(l) * cpair / dtime) * t_building_bef_hac(l) ) diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90 index 16da4b3ad0..4b7b80e4fe 100644 --- a/src/biogeophys/UrbanParamsType.F90 +++ b/src/biogeophys/UrbanParamsType.F90 @@ -101,7 +101,6 @@ module UrbanParamsType character(len= *), parameter, public :: urban_hac_on = 'ON' character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT' character(len= 16), public :: urban_hac = urban_hac_off - ! X. Li [dev.04] logical, public :: urban_explicit_ac = .true. ! whether to use explicit, time-varying AC adoption rate logical, public :: urban_traffic = .false. ! urban traffic fluxes @@ -849,9 +848,6 @@ subroutine UrbanReadNML ( NLFilename ) integer :: unitn ! unit for namelist file character(len=32) :: subname = 'UrbanReadNML' ! subroutine name - ! X. Li [orig]: - ! namelist / clmu_inparm / urban_hac, urban_traffic, building_temp_method - ! X. Li [dev.04]: namelist / clmu_inparm / urban_hac, urban_explicit_ac, urban_traffic, building_temp_method !EOP !----------------------------------------------------------------------- @@ -880,7 +876,6 @@ subroutine UrbanReadNML ( NLFilename ) ! Broadcast namelist variables read in call shr_mpi_bcast(urban_hac, mpicom) - ! X. Li [dev.04]: call shr_mpi_bcast(urban_explicit_ac, mpicom) call shr_mpi_bcast(urban_traffic, mpicom) call shr_mpi_bcast(building_temp_method, mpicom) @@ -893,7 +888,6 @@ subroutine UrbanReadNML ( NLFilename ) ! if ( masterproc )then write(iulog,*) ' urban air conditioning/heating and wasteheat = ', urban_hac - ! X. Li [dev.04]: write(iulog,*) ' urban explicit air-conditioning adoption rate = ', urban_explicit_ac write(iulog,*) ' urban traffic flux = ', urban_traffic end if diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 23dbf54086..54d5c61d19 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -12,7 +12,7 @@ module UrbanTimeVarType use abortutils , only : endrun use decompMod , only : bounds_type, subgrid_level_landunit use clm_varctl , only : iulog - use landunit_varcon , only : isturb_MIN, isturb_MAX ! X. Li: min and max types urban; equals 7 and 9, resp. + use landunit_varcon , only : isturb_MIN, isturb_MAX use clm_varcon , only : spval use LandunitType , only : lun use GridcellType , only : grc @@ -24,8 +24,7 @@ module UrbanTimeVarType type, public :: urbantv_type ! real(r8), public, pointer :: t_building_max(:) ! lun maximum internal building air temperature (K) - ! X. Li [dev] - real(r8), public, pointer :: p_ac(:) ! lun air-conditioning ownership rate (unitless, between 0 and 1) + real(r8), public, pointer :: p_ac(:) ! lun air-conditioning adoption rate (unitless, between 0 and 1) type(shr_strdata_type) :: sdat_urbantv ! urban time varying input data stream contains ! !PUBLIC MEMBER FUNCTIONS: @@ -60,7 +59,7 @@ subroutine Init(this, bounds, NLFilename) character(len=*) , intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: - integer :: begl, endl ! X. Li: beginning and ending landunit index, from src/main/decompMod + integer :: begl, endl !--------------------------------------------------------------------- begl = bounds%begl; endl = bounds%endl @@ -68,20 +67,18 @@ subroutine Init(this, bounds, NLFilename) ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan - ! X. Li [dev] allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan call this%urbantv_init(bounds, NLFilename) call this%urbantv_interp(bounds) - ! Add history fields ! X. Li: this adds an output field. the subroutine is in scr/main/histFileMod.F90 + ! Add history fields call hist_addfld1d (fname='TBUILD_MAX', units='K', & avgflag='A', long_name='prescribed maximum interior building temperature', & ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & l2g_scale_type='unity') - ! X. Li [dev] call hist_addfld1d (fname='P_AC', units='unitless', & - avgflag='A', long_name='prescribed air-conditioning ownership rate (decimal)', & + avgflag='A', long_name='prescribed air-conditioning ownership rate (unitless, between 0 and 1)', & ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & l2g_scale_type='unity') @@ -97,7 +94,7 @@ subroutine urbantv_init(this, bounds, NLFilename) use clm_nlUtilsMod , only : find_nlgroup_name use spmdMod , only : masterproc, mpicom, iam use shr_mpi_mod , only : shr_mpi_bcast - use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md ! X. Li: equals 7, 8 and 9 + use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md use dshr_strdata_mod , only : shr_strdata_init_from_inline use lnd_comp_shr , only : mesh, model_clock ! @@ -105,23 +102,23 @@ subroutine urbantv_init(this, bounds, NLFilename) implicit none class(urbantv_type) :: this type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename ???is this the netCDF file name? + character(len=*), intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: integer :: n integer :: stream_year_first_urbantv ! first year in urban tv stream to use integer :: stream_year_last_urbantv ! last year in urban tv stream to use integer :: model_year_align_urbantv ! align stream_year_first_urbantv with this model year - integer :: nu_nml ! unit for namelist file ??? + integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag - character(len=CL) :: stream_fldFileName_urbantv ! urban tv streams filename ??? - character(len=CL) :: stream_meshfile_urbantv ! urban tv streams filename ??? - character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac ??? + character(len=CL) :: stream_fldFileName_urbantv ! urban tv streams filename + character(len=CL) :: stream_meshfile_urbantv ! urban tv streams filename + character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm integer :: rc ! error code ! X. Li [orig]: this is taken out because field strings are now hard coded in ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string - character(*), parameter :: subName = "('urbantv_init')" ! ??? + character(*), parameter :: subName = "('urbantv_init')" !----------------------------------------------------------------------- namelist /urbantv_streams/ & @@ -215,7 +212,6 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_tintalgo = urbantv_tintalgo, & stream_name = 'Urban time varying data', & rc = rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -257,11 +253,10 @@ subroutine urbantv_interp(this, bounds) ! Advance sdat stream call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day - call shr_strdata_advance(this%sdat_urbantv, ymd=mcdate, tod=sec, logunit=iulog, istr='hdmdyn', rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if + end if ! Create 2d array for all stream variable data lsize = bounds%endg - bounds%begg + 1 @@ -306,9 +301,8 @@ subroutine urbantv_interp(this, bounds) end if end do else - this%t_building_max(l) = spval ! X. Li: special value for real data, set to 1.e36 in src/main/clm_varcon - ! X. Li [dev] - this%p_ac(l) = 0._r8 ! X. Li: set to 0 for non-urban landunit + this%t_building_max(l) = spval + this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit end if end do deallocate(dataptr2d) @@ -322,11 +316,8 @@ subroutine urbantv_interp(this, bounds) ig = ig+1 if (g == lun%gridcell(l)) exit end do - ! X. Li [orig] - ! if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then - ! X. Li [dev] if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) & - .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then + .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then ! check if AC adoption rate is outside of range 0 to 1 found = .true. gindx = g lindx = l @@ -339,7 +330,6 @@ subroutine urbantv_interp(this, bounds) write(iulog,*)'landunit type: ',lun%itype(lindx) write(iulog,*)'urban_valid: ',urban_valid(gindx) write(iulog,*)'t_building_max: ',this%t_building_max(lindx) - ! X. Li [dev] write(iulog,*)'p_ac: ',this%p_ac(lindx) call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, & msg=errmsg(sourcefile, __LINE__)) diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90 index 3ef9cf48a2..f54b750181 100644 --- a/src/main/clm_varpar.F90 +++ b/src/main/clm_varpar.F90 @@ -203,8 +203,7 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft) max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb) nlevsoifl = 10 - ! X. Li: changed below from 5 to 10 to match new surface data - nlevurb = 10 ! originally 5 + nlevurb = 5 if ( masterproc ) write(iulog, *) 'soil_layerstruct_predefined varpar ', soil_layerstruct_predefined if ( masterproc ) write(iulog, *) 'soil_layerstruct_userdefined varpar ', soil_layerstruct_userdefined From 3b4d882878204b3dcda3a651375d12a9a074940f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 12 Mar 2024 15:51:13 -0600 Subject: [PATCH 038/408] Add matrixcn code for residue removal variables --- src/biogeochem/CNPhenologyMod.F90 | 42 ++++++++++++++++++------------- 1 file changed, 25 insertions(+), 17 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 619b28801b..b53c195418 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3605,43 +3605,51 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! Matrix for grain, livestem to litter, leaf to litter, and biofuel if(use_matrixcn)then - if(reproductivec(p,1) .gt. 0)then + if(reproductivec(p,1) > 0._r8)then grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - repr_grainc_to_seed(p,1) = 0 - repr_grainc_to_food(p,1) = 0 + repr_grainc_to_seed(p,1) = 0._r8 + repr_grainc_to_food(p,1) = 0._r8 end if - if(reproductiven(p,1) .gt. 0)then + if(reproductiven(p,1) > 0._r8)then grainn_to_out = reproductiven(p,1) * matrix_update_phn(p,igrain_to_iout_phn,(repr_grainn_to_seed(p,1) + repr_grainn_to_food(p,1)) / reproductiven(p,1),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - repr_grainn_to_seed(p,1) = 0 - repr_grainn_to_food(p,1) = 0 + repr_grainn_to_seed(p,1) = 0._r8 + repr_grainn_to_food(p,1) = 0._r8 end if - if(livestemc(p) .gt. 0)then + if(livestemc(p) > 0._r8)then livestemc_to_litter(p) = livestemc(p) * matrix_update_phc(p,ilivestem_to_iout_phc,livestemc_to_litter(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) + livestemc_to_removedresiduec(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_removedresiduec(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) livestemc_to_biofuelc(p) = livestemc(p) * matrix_update_gmc(p,ilivestem_to_iout_gmc,livestemc_to_biofuelc(p) / livestemc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) else - livestemc_to_litter(p) = 0 - livestemc_to_biofuelc(p) = 0 + livestemc_to_litter(p) = 0._r8 + livestemc_to_removedresiduec(p) = 0._r8 + livestemc_to_biofuelc(p) = 0._r8 end if - if(livestemn(p) .gt. 0)then + if(livestemn(p) > 0._r8)then livestemn_to_biofueln(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_biofueln(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) + livestemn_to_removedresiduen(p) = livestemn(p) * matrix_update_gmn(p,ilivestem_to_iout_gmn,livestemn_to_removedresiduen(p) / livestemn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) livestemn_to_litter(p) = livestemn(p) * matrix_update_phn(p,ilivestem_to_iout_phn, (1._r8- biofuel_harvfrac(ivt(p)))/dt, dt,cnveg_nitrogenflux_inst,matrixcheck_ph,acc_ph) else - livestemn_to_biofueln(p) = 0 - livestemn_to_litter(p) = 0 + livestemn_to_biofueln(p) = 0._r8 + livestemn_to_removedresiduen(p) = 0._r8 + livestemn_to_litter(p) = 0._r8 end if - if(leafn(p) > 0)then + if(leafn(p) > 0._r8)then leafn_to_biofueln(p) = leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_biofueln(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) + leafn_to_removedresiduen(p) = leafn(p) * matrix_update_gmn(p,ileaf_to_iout_gmn,leafn_to_removedresiduen(p) / leafn(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) else - leafn_to_biofueln(p) = 0 + leafn_to_biofueln(p) = 0._r8 + leafn_to_removedresiduen(p) = 0._r8 end if - if (leafc(p) > 0)then + if (leafc(p) > 0._r8)then leafc_to_biofuelc(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) + leafc_to_removedresiduec(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_removedresiduec(p) / leafc(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else - leafc_to_biofuelc(p) = 0 - leafc_to_litter(p) = 0 + leafc_to_biofuelc(p) = 0._r8 + leafc_to_removedresiduec(p) = 0._r8 + leafc_to_litter(p) = 0._r8 end if else ! NOTE: The non matrix version of this is in CNCStateUpdate1::CStateUpdate1 EBK (11/26/2019) From fe50ce16c03446c86b7018d1c655ca9a71b61982 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 12 Mar 2024 16:08:18 -0600 Subject: [PATCH 039/408] Update comment based on most recent code changes --- src/biogeochem/CNPhenologyMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b53c195418..c6e6cf3635 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3603,7 +3603,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! as well as leaf C:N ratio (unaffected by biofuel harvest). It thus does not ! need to be updated here. - ! Matrix for grain, livestem to litter, leaf to litter, and biofuel + ! Matrix for grain + ! Matrix for livestem/leaf to litter, biofuel, and removed residue if(use_matrixcn)then if(reproductivec(p,1) > 0._r8)then grainc_to_out = reproductivec(p,1) * matrix_update_phc(p,igrain_to_iout_phc,(repr_grainc_to_seed(p,1) + repr_grainc_to_food(p,1)) / reproductivec(p,1),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) From acd1413ef75868c873e72c17810704049495c00f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 12 Mar 2024 16:25:36 -0600 Subject: [PATCH 040/408] Correction to latest code mods --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c6e6cf3635..c81dd4215d 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3645,7 +3645,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & end if if (leafc(p) > 0._r8)then leafc_to_biofuelc(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_biofuelc(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) - leafc_to_removedresiduec(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_removedresiduec(p) / leafc(p),dt,cnveg_nitrogenflux_inst,matrixcheck_ph,.True.) + leafc_to_removedresiduec(p) = leafc(p) * matrix_update_gmc(p,ileaf_to_iout_gmc,leafc_to_removedresiduec(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,.True.) leafc_to_litter(p) = leafc(p) * matrix_update_phc(p,ileaf_to_iout_phc,leafc_to_litter(p) / leafc(p),dt,cnveg_carbonflux_inst,matrixcheck_ph,acc_ph) else leafc_to_biofuelc(p) = 0._r8 From 82c1903287d254dc5b8ed5084c38118029eab90c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 19 Mar 2024 11:23:05 -0600 Subject: [PATCH 041/408] Corrections for PEM...till test to PASS --- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 21 +++++---------- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 26 +++++++++++++++++-- 2 files changed, 31 insertions(+), 16 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 139cdbba32..49fc95d6f5 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -911,23 +911,16 @@ subroutine decomp_rate_constants_bgc(bounds, num_bgc_soilc, filter_bgc_soilc, & ! Above into soil matrix if(use_soil_matrixcn)then - Ksoil%DM(c,j+nlevdecomp*(i_met_lit-1)) = k_l1 * t_scalar(c,j) * w_scalar(c,j) * & - depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_l1(c) * dt - Ksoil%DM(c,j+nlevdecomp*(i_cel_lit-1)) = k_l2_l3 * t_scalar(c,j) * w_scalar(c,j) * & - depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_l23(c) * dt - Ksoil%DM(c,j+nlevdecomp*(i_lig_lit-1)) = k_l2_l3 * t_scalar(c,j) * w_scalar(c,j) * & - depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_l23(c) * dt - Ksoil%DM(c,j+nlevdecomp*(i_act_som-1)) = k_s1 * t_scalar(c,j) * w_scalar(c,j) * & - depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_s1(c) * dt - Ksoil%DM(c,j+nlevdecomp*(i_slo_som-1)) = k_s2 * t_scalar(c,j) * w_scalar(c,j) * & - depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_s2(c) * dt - Ksoil%DM(c,j+nlevdecomp*(i_pas_som-1)) = k_s3 * t_scalar(c,j) * w_scalar(c,j) * & - depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_s3(c) * dt + Ksoil%DM(c,j+nlevdecomp*(i_met_lit-1)) = decomp_k(c,j,i_met_lit) * dt + Ksoil%DM(c,j+nlevdecomp*(i_cel_lit-1)) = decomp_k(c,j,i_cel_lit) * dt + Ksoil%DM(c,j+nlevdecomp*(i_lig_lit-1)) = decomp_k(c,j,i_lig_lit) * dt + Ksoil%DM(c,j+nlevdecomp*(i_act_som-1)) = decomp_k(c,j,i_act_som) * dt + Ksoil%DM(c,j+nlevdecomp*(i_slo_som-1)) = decomp_k(c,j,i_slo_som) * dt + Ksoil%DM(c,j+nlevdecomp*(i_pas_som-1)) = decomp_k(c,j,i_pas_som) * dt ! same for cwd but only if fates is not enabled; fates handles CWD ! on its own structure if (.not. use_fates) then - Ksoil%DM(c,j+nlevdecomp*(i_cwd-1)) = k_frag * t_scalar(c,j) * w_scalar(c,j) * depth_scalar(c,j) * & - o_scalar(c,j) * spinup_geogterm_cwd(c) * dt + Ksoil%DM(c,j+nlevdecomp*(i_cwd-1)) = decomp_k(c,j,i_cwd) * dt end if end if !use_soil_matrixcn end do diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index 65091755f5..e9bb60bcec 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -18,7 +18,7 @@ module SoilBiogeochemDecompCascadeMIMICSMod use spmdMod , only : masterproc use abortutils , only : endrun use CNSharedParamsMod , only : CNParamsShareInst, nlev_soildecomp_standard - use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con + use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, InitSoilTransfer, use_soil_matrixcn use SoilBiogeochemStateType , only : soilbiogeochem_state_type use SoilBiogeochemCarbonFluxType , only : soilbiogeochem_carbonflux_type use SoilBiogeochemCarbonStateType , only : soilbiogeochem_carbonstate_type @@ -734,6 +734,8 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat nue_decomp_cascade(i_cwdl2) = 1.0_r8 end if + if (use_soil_matrixcn) call InitSoilTransfer() + deallocate(params_inst%mimics_mge) deallocate(params_inst%mimics_vmod) deallocate(params_inst%mimics_vint) @@ -763,7 +765,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & ! decomposition cascade model ! ! !USES: - use clm_time_manager , only : get_average_days_per_year + use clm_time_manager , only : get_average_days_per_year, get_step_size use clm_varcon , only : secspday, secsphr, tfrz use clm_varcon , only : g_to_mg, cm3_to_m3 use subgridAveMod , only : p2c @@ -822,6 +824,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & integer :: p, fp, c, fc, j, k, l, s ! indices integer :: pf ! fates patch index integer :: nc ! clump index + real(r8):: dt ! decomposition time step real(r8):: days_per_year ! days per year real(r8):: depth_scalar(bounds%begc:bounds%endc,1:nlevdecomp) real(r8):: w_d_o_scalars ! product of w_scalar * depth_scalar * o_scalar @@ -882,6 +885,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & cn_col => soilbiogeochem_carbonflux_inst%cn_col , & ! Output: [real(r8) (:,:) ] C:N ratio ligninNratioAvg => soilbiogeochem_carbonflux_inst%litr_lig_c_to_n_col, & ! Input: [real(r8) (:) ] C:N ratio of litter lignin decomp_k => soilbiogeochem_carbonflux_inst%decomp_k_col , & ! Output: [real(r8) (:,:,:) ] rate for decomposition (1./sec) + Ksoil => soilbiogeochem_carbonflux_inst%Ksoil , & ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) spinup_factor => decomp_cascade_con%spinup_factor & ! Input: [real(r8) (:) ] factor for AD spinup associated with each pool ) @@ -892,6 +896,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & mino2lim = CNParamsShareInst%mino2lim days_per_year = get_average_days_per_year() + dt = real( get_step_size(), r8 ) ! ! Set "decomp_depth_efolding" parameter ! decomp_depth_efolding = CNParamsShareInst%decomp_depth_efolding @@ -1311,6 +1316,23 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & if (get_do_tillage()) then call get_apply_tillage_multipliers(idop, c, j, decomp_k(c,j,:)) end if + +! Above into soil matrix + if(use_soil_matrixcn)then + Ksoil%DM(c,j+nlevdecomp*(i_met_lit-1)) = decomp_k(c,j,i_met_lit) * dt + Ksoil%DM(c,j+nlevdecomp*(i_str_lit-1)) = decomp_k(c,j,i_str_lit) * dt + Ksoil%DM(c,j+nlevdecomp*(i_avl_som-1)) = decomp_k(c,j,i_avl_som) * dt + Ksoil%DM(c,j+nlevdecomp*(i_phys_som-1)) = decomp_k(c,j,i_phys_som) * dt + Ksoil%DM(c,j+nlevdecomp*(i_chem_som-1)) = decomp_k(c,j,i_chem_som) * dt + Ksoil%DM(c,j+nlevdecomp*(i_cop_mic-1)) = decomp_k(c,j,i_cop_mic) * dt + Ksoil%DM(c,j+nlevdecomp*(i_oli_mic-1)) = decomp_k(c,j,i_oli_mic) * dt + ! same for cwd but only if fates is not enabled; fates handles + ! CWD + ! on its own structure + if (.not. use_fates) then + Ksoil%DM(c,j+nlevdecomp*(i_cwd-1)) = decomp_k(c,j,i_cwd) * dt + end if + end if !use_soil_matrixcn end do end do From d1d21137041ea091b8743ce3801eb7ff99960a34 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Wed, 20 Mar 2024 15:17:23 -0500 Subject: [PATCH 042/408] Fix backward compatibility & p_ac dynamic read-in 1. set different paths for default stream_fldfilename_urbantv based on urban_explicit_ac (currently points to the file in my work directory when urban_explicit_ac=.true.) 2. only read in p_ac when urban_explicit_ac is true --- bld/namelist_files/namelist_defaults_ctsm.xml | 15 +++++ src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 2 +- src/cpl/share_esmf/UrbanTimeVarType.F90 | 57 ++++++++++++++----- 3 files changed, 60 insertions(+), 14 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0d8e45a779..0f7d9b948a 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1744,6 +1744,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 2106 + +lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc +/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc +lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1_ESMFmesh_cdf5_100621.nc + +lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc +/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc +lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1_ESMFmesh_cdf5_100621.nc lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index 2e588e2e88..ee824931cd 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -325,7 +325,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, t_floor => temperature_inst%t_floor_lun , & ! InOut: [real(r8) (:)] floor temperature (K) t_building => temperature_inst%t_building_lun , & ! InOut: [real(r8) (:)] internal building air temperature (K) - p_ac => urbantv_inst%p_ac , & ! Input: [real(r8) (:)] air-conditioning penetration rate (-) + p_ac => urbantv_inst%p_ac , & ! Input: [real(r8) (:)] air-conditioning penetration rate (a fraction between 0 and 1) t_building_max => urbantv_inst%t_building_max , & ! Input: [real(r8) (:)] maximum internal building air temperature (K) t_building_min => urbanparams_inst%t_building_min , & ! Input: [real(r8) (:)] minimum internal building air temperature (K) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 54d5c61d19..5f507a1e9c 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -36,7 +36,11 @@ module UrbanTimeVarType ! X. Li [orig] ! character(15), private :: stream_varnames(isturb_MIN:isturb_MAX) ! X. Li [dev]: - character(15), private :: stream_varnames(1:6) ! 1-3 for t_building_max, 4-6 for p_ac + ! character(15), private :: stream_varnames(1:6) ! 1-3 for t_building_max, 4-6 for p_ac + ! X. Li [03.19] + integer , private :: stream_varname_MIN ! minimum index for stream_varnames + integer , private :: stream_varname_MAX ! maximum index for stream_varnames + character(15), private :: stream_varnames(:) ! urban time varying variable names character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -67,7 +71,9 @@ subroutine Init(this, bounds, NLFilename) ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan - allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan + ! X. Li [03.19] + ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan + allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8 call this%urbantv_init(bounds, NLFilename) call this%urbantv_interp(bounds) @@ -77,8 +83,8 @@ subroutine Init(this, bounds, NLFilename) avgflag='A', long_name='prescribed maximum interior building temperature', & ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & l2g_scale_type='unity') - call hist_addfld1d (fname='P_AC', units='unitless', & - avgflag='A', long_name='prescribed air-conditioning ownership rate (unitless, between 0 and 1)', & + call hist_addfld1d (fname='P_AC', units='a fraction between 0 and 1', & + avgflag='A', long_name='prescribed air-conditioning ownership rate', & ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & l2g_scale_type='unity') @@ -97,6 +103,8 @@ subroutine urbantv_init(this, bounds, NLFilename) use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md use dshr_strdata_mod , only : shr_strdata_init_from_inline use lnd_comp_shr , only : mesh, model_clock + ! X. Li [03.19] + use UrbanParamsType , only : urban_explicit_ac ! ! !ARGUMENTS: implicit none @@ -136,6 +144,15 @@ subroutine urbantv_init(this, bounds, NLFilename) model_year_align_urbantv = 1 ! align stream_year_first_urbantv with this model year stream_fldFileName_urbantv = ' ' stream_meshfile_urbantv = ' ' + ! X. Li [03.19] + stream_varname_MIN = 1 + ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, + ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes; + ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. + if (urban_explicit_ac) then + stream_varname_MAX = 6 + else + stream_varname_MAX = 3 ! X. Li [orig] ! stream_varnames(isturb_tbd) = urbantvString//"TBD" ! stream_varnames(isturb_hd) = urbantvString//"HD" @@ -144,9 +161,11 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_varnames(1) = "tbuildmax_TBD" stream_varnames(2) = "tbuildmax_HD" stream_varnames(3) = "tbuildmax_MD" - stream_varnames(4) = "p_ac_TBD" - stream_varnames(5) = "p_ac_HD" - stream_varnames(6) = "p_ac_MD" + ! X. Li [03.19] + if (urban_explicit_ac) then + stream_varnames(4) = "p_ac_TBD" + stream_varnames(5) = "p_ac_HD" + stream_varnames(6) = "p_ac_MD" ! Read urbantv_streams namelist if (masterproc) then @@ -180,7 +199,9 @@ subroutine urbantv_init(this, bounds, NLFilename) ! X. Li [orig] ! do n = isturb_tbd,isturb_md ! X. Li [dev] - do n = 1,6 + ! do n = 1,6 + ! X. Li [03.19] + do n = stream_varname_MIN,stream_varname_MAX write(iulog,'(a,a)' ) ' stream_varname = ',trim(stream_varnames(n)) end do write(iulog,*) ' ' @@ -201,8 +222,11 @@ subroutine urbantv_init(this, bounds, NLFilename) ! stream_fldlistFile = stream_varnames(isturb_tbd:isturb_md),& ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),& ! X. Li [dev] - stream_fldlistFile = stream_varnames(1:6), & - stream_fldListModel = stream_varnames(1:6), & + ! stream_fldlistFile = stream_varnames(1:6), & + ! stream_fldListModel = stream_varnames(1:6), & + ! X. Li [03.19] + stream_fldlistFile = stream_varnames(stream_varname_MIN:stream_varname_MAX), & + stream_fldListModel = stream_varnames(stream_varname_MIN:stream_varname_MAX), & stream_yearFirst = stream_year_first_urbantv, & stream_yearLast = stream_year_last_urbantv, & stream_yearAlign = model_year_align_urbantv, & @@ -266,6 +290,9 @@ subroutine urbantv_interp(this, bounds) ! X. Li [dev] allocate(dataptr2d(lsize, 1:6)) do n = 1,6 + ! X. Li [03.19] + allocate(dataptr2d(lsize, stream_varname_MIN:stream_varname_MAX)) + do n = stream_varname_MIN,stream_varname_MAX call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), & fldptr1=dataptr1d, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -278,7 +305,7 @@ subroutine urbantv_interp(this, bounds) end do end do - ! Determine this%tbuilding_max for all landunits + ! Determine this%tbuilding_max (and this%p_ac, if applicable) for all landunits do l = bounds%begl,bounds%endl if (lun%urbpoi(l)) then ig = 0 @@ -289,7 +316,9 @@ subroutine urbantv_interp(this, bounds) ! X. Li [orig] ! do n = isturb_MIN,isturb_MAX ! X. Li [dev] - do n = 1,6 + ! do n = 1,6 + ! X. Li [03.19] + do n = stream_varname_MIN,stream_varname_MAX ! X. Li [orig] ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then ! X. Li [dev.02] @@ -302,7 +331,9 @@ subroutine urbantv_interp(this, bounds) end do else this%t_building_max(l) = spval - this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit + ! this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit + ! X. Li [03.19] + this%p_ac(l) = nan ! set to nan for non-urban landunit end if end do deallocate(dataptr2d) From 79790a0d392178ca95b4a0bcf2b7e3a02618896c Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 21 Mar 2024 16:08:23 -0500 Subject: [PATCH 043/408] Bug fix Closed if blocks, commented out extra lines, defined nan --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 5f507a1e9c..fc670ca830 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -38,9 +38,9 @@ module UrbanTimeVarType ! X. Li [dev]: ! character(15), private :: stream_varnames(1:6) ! 1-3 for t_building_max, 4-6 for p_ac ! X. Li [03.19] - integer , private :: stream_varname_MIN ! minimum index for stream_varnames - integer , private :: stream_varname_MAX ! maximum index for stream_varnames - character(15), private :: stream_varnames(:) ! urban time varying variable names + integer , private :: stream_varname_MIN ! minimum index for stream_varnames + integer , private :: stream_varname_MAX ! maximum index for stream_varnames + character(15), private, allocatable :: stream_varnames(:) ! urban time varying variable names character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -153,6 +153,7 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_varname_MAX = 6 else stream_varname_MAX = 3 + end if ! X. Li [orig] ! stream_varnames(isturb_tbd) = urbantvString//"TBD" ! stream_varnames(isturb_hd) = urbantvString//"HD" @@ -166,6 +167,7 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_varnames(4) = "p_ac_TBD" stream_varnames(5) = "p_ac_HD" stream_varnames(6) = "p_ac_MD" + end if ! Read urbantv_streams namelist if (masterproc) then @@ -253,6 +255,7 @@ subroutine urbantv_interp(this, bounds) use clm_instur , only : urban_valid use dshr_methods_mod , only : dshr_fldbun_getfldptr use dshr_strdata_mod , only : shr_strdata_advance + use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) ! ! !ARGUMENTS: class(urbantv_type) :: this @@ -288,8 +291,8 @@ subroutine urbantv_interp(this, bounds) ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX)) ! do n = isturb_MIN,isturb_MAX ! X. Li [dev] - allocate(dataptr2d(lsize, 1:6)) - do n = 1,6 + ! allocate(dataptr2d(lsize, 1:6)) + ! do n = 1,6 ! X. Li [03.19] allocate(dataptr2d(lsize, stream_varname_MIN:stream_varname_MAX)) do n = stream_varname_MIN,stream_varname_MAX From c383dee0be598f52766c330ff59965fd6b4eaa0c Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Fri, 22 Mar 2024 16:55:12 -0500 Subject: [PATCH 044/408] Fixing error SIGSEGV, segmentation fault occurred Trying to fix this error by changing "allocatable" to "pointer" for the variable `stream_varnames`, since the error message points to the line where this variable was first assigned values. --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index fc670ca830..5cd3f607ca 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -40,7 +40,7 @@ module UrbanTimeVarType ! X. Li [03.19] integer , private :: stream_varname_MIN ! minimum index for stream_varnames integer , private :: stream_varname_MAX ! maximum index for stream_varnames - character(15), private, allocatable :: stream_varnames(:) ! urban time varying variable names + character(15), private, pointer :: stream_varnames(:) ! urban time varying variable names character(len=*), parameter, private :: sourcefile = & __FILE__ From 0081443d8662dacce74da1790b922c98a7edfd64 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Fri, 22 Mar 2024 18:12:21 -0500 Subject: [PATCH 045/408] Fixing the error SIGSEGV cont'd Adding parameter" attribute to `stream_varname_MIN/MAX` to see if it helps --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 5cd3f607ca..ffecf07c2d 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -38,9 +38,9 @@ module UrbanTimeVarType ! X. Li [dev]: ! character(15), private :: stream_varnames(1:6) ! 1-3 for t_building_max, 4-6 for p_ac ! X. Li [03.19] - integer , private :: stream_varname_MIN ! minimum index for stream_varnames - integer , private :: stream_varname_MAX ! maximum index for stream_varnames - character(15), private, pointer :: stream_varnames(:) ! urban time varying variable names + integer , private, parameter :: stream_varname_MIN ! minimum index for stream_varnames + integer , private, parameter :: stream_varname_MAX ! maximum index for stream_varnames + character(15), private, pointer :: stream_varnames(stream_varname_MIN:stream_varname_MAX) ! urban time varying variable names character(len=*), parameter, private :: sourcefile = & __FILE__ From e4a42c8fec448dacd53bcb37c18fd05bc05161cb Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Fri, 22 Mar 2024 18:55:02 -0500 Subject: [PATCH 046/408] Fixing the error SIGSEGV cont'd Trying out determining `stream_varname_MIN/MAX` and allocating `stream_varnames` in a different subroutine, before stream_varnames are assigned values --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 39 +++++++++++++++++-------- 1 file changed, 27 insertions(+), 12 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index ffecf07c2d..f9aab74b09 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -38,9 +38,9 @@ module UrbanTimeVarType ! X. Li [dev]: ! character(15), private :: stream_varnames(1:6) ! 1-3 for t_building_max, 4-6 for p_ac ! X. Li [03.19] - integer , private, parameter :: stream_varname_MIN ! minimum index for stream_varnames - integer , private, parameter :: stream_varname_MAX ! maximum index for stream_varnames - character(15), private, pointer :: stream_varnames(stream_varname_MIN:stream_varname_MAX) ! urban time varying variable names + integer , private :: stream_varname_MIN ! minimum index for stream_varnames + integer , private :: stream_varname_MAX ! maximum index for stream_varnames + character(15), private, pointer :: stream_varnames(:) ! urban time varying variable names character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -56,6 +56,8 @@ subroutine Init(this, bounds, NLFilename) ! !USES: use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) use histFileMod , only : hist_addfld1d + ! X. Li [03.22] + use UrbanParamsType , only : urban_explicit_ac ! ! !ARGUMENTS: class(urbantv_type) :: this @@ -68,12 +70,25 @@ subroutine Init(this, bounds, NLFilename) begl = bounds%begl; endl = bounds%endl + ! X. Li [03.22] + ! Determine the minimum and maximum indices for stream_varnames + stream_varname_MIN = 1 + ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, + ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes; + ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. + if (urban_explicit_ac) then + stream_varname_MAX = 6 + else + stream_varname_MAX = 3 + end if + ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan ! X. Li [03.19] ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8 + allocate(this%stream_varnames(stream_varname_MIN:stream_varname_MAX)) call this%urbantv_init(bounds, NLFilename) call this%urbantv_interp(bounds) @@ -145,15 +160,15 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_fldFileName_urbantv = ' ' stream_meshfile_urbantv = ' ' ! X. Li [03.19] - stream_varname_MIN = 1 - ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, - ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes; - ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. - if (urban_explicit_ac) then - stream_varname_MAX = 6 - else - stream_varname_MAX = 3 - end if + ! stream_varname_MIN = 1 + ! ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, + ! ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes; + ! ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. + ! if (urban_explicit_ac) then + ! stream_varname_MAX = 6 + ! else + ! stream_varname_MAX = 3 + ! end if ! X. Li [orig] ! stream_varnames(isturb_tbd) = urbantvString//"TBD" ! stream_varnames(isturb_hd) = urbantvString//"HD" From f69173523060c05c06a665fd9c500fae43f5dab2 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Fri, 22 Mar 2024 19:05:49 -0500 Subject: [PATCH 047/408] Fixing the error SIGSEGV cont'd Previous build had error "This is not a component name that is defined in the encompassing structure" for `stream_varnames` allocation, so removed "this%" --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index f9aab74b09..1a29abb9af 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -88,7 +88,7 @@ subroutine Init(this, bounds, NLFilename) ! X. Li [03.19] ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8 - allocate(this%stream_varnames(stream_varname_MIN:stream_varname_MAX)) + allocate(stream_varnames(stream_varname_MIN:stream_varname_MAX)) call this%urbantv_init(bounds, NLFilename) call this%urbantv_interp(bounds) From 64870fa5b51fef1f93a4d05488c0a18e2d65d7d4 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 25 Mar 2024 09:53:37 -0600 Subject: [PATCH 048/408] Getting around "file not found" error for /run directory --- cime_config/SystemTests/sspmatrixcn.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py index bd41d84651..5f2d3e065e 100644 --- a/cime_config/SystemTests/sspmatrixcn.py +++ b/cime_config/SystemTests/sspmatrixcn.py @@ -207,7 +207,9 @@ def run_phase(self): linkfile = os.path.join(rundir, os.path.basename(item)) if os.path.exists(linkfile): os.remove( linkfile ) - os.symlink(item, linkfile ) + self._case.flush() + if os.path.exists(rundir): + os.symlink(item, linkfile ) for item in glob.glob("{}/*rpointer*".format(rest_path)): shutil.copy(item, rundir) @@ -215,7 +217,8 @@ def run_phase(self): # # Run the case (Archiving on) # - self._case.flush() + if not os.path.exists(rundir): + self._case.flush() self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True) # From ccb91e21abd4f8bb6437f551b025444126787c94 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Mon, 25 Mar 2024 20:03:01 -0500 Subject: [PATCH 049/408] Prepare for PR review Remove comments no longer needed to prepare for PR review --- bld/namelist_files/namelist_defaults_ctsm.xml | 11 ---- src/cpl/share_esmf/UrbanTimeVarType.F90 | 57 ------------------- 2 files changed, 68 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0f7d9b948a..be3d776c2f 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1744,17 +1744,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 2106 - lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc shr_infnan_nan, assignment(=) use histFileMod , only : hist_addfld1d - ! X. Li [03.22] use UrbanParamsType , only : urban_explicit_ac ! ! !ARGUMENTS: @@ -70,7 +64,6 @@ subroutine Init(this, bounds, NLFilename) begl = bounds%begl; endl = bounds%endl - ! X. Li [03.22] ! Determine the minimum and maximum indices for stream_varnames stream_varname_MIN = 1 ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, @@ -85,8 +78,6 @@ subroutine Init(this, bounds, NLFilename) ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan - ! X. Li [03.19] - ! allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8 allocate(stream_varnames(stream_varname_MIN:stream_varname_MAX)) @@ -118,7 +109,6 @@ subroutine urbantv_init(this, bounds, NLFilename) use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md use dshr_strdata_mod , only : shr_strdata_init_from_inline use lnd_comp_shr , only : mesh, model_clock - ! X. Li [03.19] use UrbanParamsType , only : urban_explicit_ac ! ! !ARGUMENTS: @@ -139,8 +129,6 @@ subroutine urbantv_init(this, bounds, NLFilename) character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm integer :: rc ! error code - ! X. Li [orig]: this is taken out because field strings are now hard coded in - ! character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string character(*), parameter :: subName = "('urbantv_init')" !----------------------------------------------------------------------- @@ -159,25 +147,9 @@ subroutine urbantv_init(this, bounds, NLFilename) model_year_align_urbantv = 1 ! align stream_year_first_urbantv with this model year stream_fldFileName_urbantv = ' ' stream_meshfile_urbantv = ' ' - ! X. Li [03.19] - ! stream_varname_MIN = 1 - ! ! Get value for the maximum index for stream_varnames: if using explicit AC adoption scheme, - ! ! then set maximum index to 6 for reading in tbuildmax and p_ac for three urban density classes; - ! ! otherwise, set to 3 to only read in tbuildmax for three urban density classes. - ! if (urban_explicit_ac) then - ! stream_varname_MAX = 6 - ! else - ! stream_varname_MAX = 3 - ! end if - ! X. Li [orig] - ! stream_varnames(isturb_tbd) = urbantvString//"TBD" - ! stream_varnames(isturb_hd) = urbantvString//"HD" - ! stream_varnames(isturb_md) = urbantvString//"MD" - ! X. Li [dev] stream_varnames(1) = "tbuildmax_TBD" stream_varnames(2) = "tbuildmax_HD" stream_varnames(3) = "tbuildmax_MD" - ! X. Li [03.19] if (urban_explicit_ac) then stream_varnames(4) = "p_ac_TBD" stream_varnames(5) = "p_ac_HD" @@ -213,11 +185,6 @@ subroutine urbantv_init(this, bounds, NLFilename) write(iulog,'(a,a)' ) ' stream_fldFileName_urbantv = ',stream_fldFileName_urbantv write(iulog,'(a,a)' ) ' stream_meshfile_urbantv = ',stream_meshfile_urbantv write(iulog,'(a,a)' ) ' urbantv_tintalgo = ',urbantv_tintalgo - ! X. Li [orig] - ! do n = isturb_tbd,isturb_md - ! X. Li [dev] - ! do n = 1,6 - ! X. Li [03.19] do n = stream_varname_MIN,stream_varname_MAX write(iulog,'(a,a)' ) ' stream_varname = ',trim(stream_varnames(n)) end do @@ -235,13 +202,6 @@ subroutine urbantv_init(this, bounds, NLFilename) stream_lev_dimname = 'null', & stream_mapalgo = trim(urbantvmapalgo), & stream_filenames = (/trim(stream_fldfilename_urbantv)/), & - ! X. Li [orig] - ! stream_fldlistFile = stream_varnames(isturb_tbd:isturb_md),& - ! stream_fldListModel = stream_varnames(isturb_tbd:isturb_md),& - ! X. Li [dev] - ! stream_fldlistFile = stream_varnames(1:6), & - ! stream_fldListModel = stream_varnames(1:6), & - ! X. Li [03.19] stream_fldlistFile = stream_varnames(stream_varname_MIN:stream_varname_MAX), & stream_fldListModel = stream_varnames(stream_varname_MIN:stream_varname_MAX), & stream_yearFirst = stream_year_first_urbantv, & @@ -302,13 +262,6 @@ subroutine urbantv_interp(this, bounds) ! Create 2d array for all stream variable data lsize = bounds%endg - bounds%begg + 1 - ! X. Li [orig] - ! allocate(dataptr2d(lsize, isturb_MIN:isturb_MAX)) - ! do n = isturb_MIN,isturb_MAX - ! X. Li [dev] - ! allocate(dataptr2d(lsize, 1:6)) - ! do n = 1,6 - ! X. Li [03.19] allocate(dataptr2d(lsize, stream_varname_MIN:stream_varname_MAX)) do n = stream_varname_MIN,stream_varname_MAX call dshr_fldbun_getFldPtr(this%sdat_urbantv%pstrm(1)%fldbun_model, trim(stream_varnames(n)), & @@ -331,15 +284,7 @@ subroutine urbantv_interp(this, bounds) ig = ig+1 if (g == lun%gridcell(l)) exit end do - ! X. Li [orig] - ! do n = isturb_MIN,isturb_MAX - ! X. Li [dev] - ! do n = 1,6 - ! X. Li [03.19] do n = stream_varname_MIN,stream_varname_MAX - ! X. Li [orig] - ! if (stream_varnames(lun%itype(l)) == stream_varnames(n)) then - ! X. Li [dev.02] if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then this%t_building_max(l) = dataptr2d(ig,n) end if @@ -349,8 +294,6 @@ subroutine urbantv_interp(this, bounds) end do else this%t_building_max(l) = spval - ! this%p_ac(l) = 0._r8 ! set to 0 for non-urban landunit - ! X. Li [03.19] this%p_ac(l) = nan ! set to nan for non-urban landunit end if end do From 25f0236576b01044df8509e865dbce35587983ca Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 26 Mar 2024 09:49:24 -0600 Subject: [PATCH 050/408] Getting around "file not found" error for rundir (this time test passes) --- cime_config/SystemTests/sspmatrixcn.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py index 5f2d3e065e..eec462e72c 100644 --- a/cime_config/SystemTests/sspmatrixcn.py +++ b/cime_config/SystemTests/sspmatrixcn.py @@ -207,9 +207,9 @@ def run_phase(self): linkfile = os.path.join(rundir, os.path.basename(item)) if os.path.exists(linkfile): os.remove( linkfile ) - self._case.flush() - if os.path.exists(rundir): - os.symlink(item, linkfile ) + if not os.path.isdir(rundir): + os.makedirs(rundir) + os.symlink(item, linkfile ) for item in glob.glob("{}/*rpointer*".format(rest_path)): shutil.copy(item, rundir) @@ -217,8 +217,7 @@ def run_phase(self): # # Run the case (Archiving on) # - if not os.path.exists(rundir): - self._case.flush() + self._case.flush() self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True) # From d4cbc8c58570b027adbc155b7f39d0c2faaf3f38 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 26 Mar 2024 13:03:46 -0600 Subject: [PATCH 051/408] Bug-fix discovered by izumi_nag test --- src/main/surfrdUtilsMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/surfrdUtilsMod.F90 b/src/main/surfrdUtilsMod.F90 index 97f5b7d80f..ac7c1304b8 100644 --- a/src/main/surfrdUtilsMod.F90 +++ b/src/main/surfrdUtilsMod.F90 @@ -282,8 +282,8 @@ subroutine collapse_to_dominant(weight, lower_bound, upper_bound, begg, endg, n_ ! original sum of all the weights wt_sum(g) = sum(weight(g,:)) - if (present(do_not_collapse) .and. do_not_collapse(g)) then - cycle + if (present(do_not_collapse)) then + if (do_not_collapse(g)) cycle end if max_indices = 0 ! initialize From f06ceb8c8e3b47d96f363a7d2c681c7a68c1432e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 26 Mar 2024 13:15:26 -0600 Subject: [PATCH 052/408] Update derecho test from failing P64x2 to passing P24x2 --- cime_config/testdefs/testlist_clm.xml | 14 +------------- 1 file changed, 1 insertion(+), 13 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 3d713e98ec..04200b7271 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2835,19 +2835,7 @@ - - - - - - - - - - - - - + From 0ebb7e0415809c49250ecbc1bbd355227068ae35 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Mar 2024 13:22:13 -0600 Subject: [PATCH 053/408] Rename isspinup -> spinup_matrixcn, is_outmatrix -> hist_wrt_matrixcn_diag Ran aux_clm on derecho and got expected results --- bld/CLMBuildNamelist.pm | 28 +++++++++---------- bld/namelist_files/namelist_defaults_ctsm.xml | 16 +++++------ .../namelist_definition_ctsm.xml | 6 ++-- bld/unit_testers/build-namelist_test.pl | 18 ++++++------ cime_config/SystemTests/sspmatrixcn.py | 2 +- .../clm/ciso_monthly_matrixcn/user_nl_clm | 2 +- src/biogeochem/CNVegMatrixMod.F90 | 14 +++++----- src/main/clm_varctl.F90 | 4 +-- src/main/controlMod.F90 | 10 +++---- src/soilbiogeochem/CNSoilMatrixMod.F90 | 16 +++++------ 10 files changed, 58 insertions(+), 58 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 67b8bd3b5c..ca0221277f 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -114,7 +114,7 @@ OPTIONS off : run in normal mode (spinup_state = 0) To spinup using the CN soil matrix method use "sasu" SemiAnalytic Spin-Up (SASU) - sasu: Turn on matrix spinup (isspinup=T) + sasu: Turn on matrix spinup (spinup_matrixcn=T) Normal spinup sequence is: on, sasu, off Default is set by clm_accelerated_spinup mode. @@ -1234,21 +1234,21 @@ sub setup_cmdl_spinup { } $nl_flags->{$var} = $val; if ( &value_is_true($nl_flags->{'use_soil_matrixcn'}) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "isspinup", + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "spinup_matrixcn", , 'use_fates'=>$nl_flags->{'use_fates'}, 'bgc_mode'=>$nl_flags->{'bgc_mode'} , 'phys'=>$nl_flags->{'phys'}, 'use_soil_matrixcn'=>$nl_flags->{'use_soil_matrixcn'}, , clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} ); my $spinup; - if ( &value_is_true($nl->get_value("isspinup") ) ) { + if ( &value_is_true($nl->get_value("spinup_matrixcn") ) ) { $spinup = ".true."; } else { $spinup = ".false."; } - $nl_flags->{'isspinup'} = $spinup; - if ( &value_is_true($nl_flags->{'isspinup'}) ) { + $nl_flags->{'spinup_matrixcn'} = $spinup; + if ( &value_is_true($nl_flags->{'spinup_matrixcn'}) ) { $nl_flags->{'bgc_spinup'} = "on"; if ( $nl_flags->{'clm_accelerated_spinup'} eq "off" ) { - $log->fatal_error("matrix spinup (isspinup) is True, but clm_accelerated_spinup is off, change one or the other"); + $log->fatal_error("matrix spinup (spinup_matrixcn) is True, but clm_accelerated_spinup is off, change one or the other"); } } else { $nl_flags->{'bgc_spinup'} = "off"; @@ -4569,14 +4569,14 @@ sub setup_logic_cnmatrix { # my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - my @matrixlist = ( "use_matrixcn", "is_outmatrix" ); + my @matrixlist = ( "use_matrixcn", "hist_wrt_matrixcn_diag" ); foreach my $var ( @matrixlist ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var , 'use_fates'=>$nl_flags->{'use_fates'}, 'bgc_mode'=>$nl_flags->{'bgc_mode'} , 'phys'=>$nl_flags->{'phys'}, 'use_soil_matrixcn'=>$nl_flags->{'use_soil_matrixcn'}, - , 'isspinup'=>$nl_flags->{'isspinup'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); + , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); } - @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "is_outmatrix", "isspinup" ); + @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" ); # Matrix items can't be on for SP mode if ( $nl_flags->{'bgc_mode'} eq "sp" ) { foreach my $var ( @matrixlist ) { @@ -4607,14 +4607,14 @@ sub setup_logic_cnmatrix { } # If both matrixcn and soil_matrix are off outmatrix can't be on if ( ! &value_is_true($nl->get_value("use_matrixcn")) && ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) { - my $var = "is_outmatrix"; + my $var = "hist_wrt_matrixcn_diag"; if ( &value_is_true($nl->get_value($var)) ) { $log->fatal_error("$var can NOT be on when both use_matrixcn and use_soil_matrixcn are off" ); } } # If soil_matrix is off ispspinup can't be on if ( ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) { - my $var = "isspinup"; + my $var = "spinup_matrixcn"; if ( &value_is_true($nl->get_value($var)) ) { $log->fatal_error("$var can NOT be on when use_soil_matrixcn is off" ); } @@ -4623,10 +4623,10 @@ sub setup_logic_cnmatrix { # if soil matrix is on and spinup is on, set spinup specific variables my @spinup_vars = ( "nyr_forcing", "nyr_sasu", "iloop_avg" ); foreach my $var ( @spinup_vars ) { - if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'isspinup'}) ) { + if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'spinup_matrixcn'}) ) { if ( $var ne "nyr_sasu" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - , 'phys'=>$nl_flags->{'phys'}, 'isspinup'=>$nl_flags->{'isspinup'} ); + , 'phys'=>$nl_flags->{'phys'}, 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'} ); } else { # Set SASU spinup period to nyr_forcing (slow mode) by default add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, @@ -4644,7 +4644,7 @@ sub setup_logic_cnmatrix { } } } - if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'isspinup'}) ) { + if ( &value_is_true($nl_flags->{"use_soil_matrixcn"}) && &value_is_true($nl_flags->{'spinup_matrixcn'}) ) { my $nyr_forcing = $nl->get_value('nyr_forcing'); my $nyr_sasu = $nl->get_value('nyr_sasu'); if ( $nyr_sasu > $nyr_forcing ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index f2e42dd6e0..1455bbf873 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -661,18 +661,18 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .false. -.false. -.false. -.false. -.true. -.true. -.false. +.false. +.false. +.false. +.true. +.true. +.false. 1 -20 +20 1 -999 --999 +-999 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 5214c20942..4cf8b8ad7d 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1149,12 +1149,12 @@ Turn on the Matrix solution for above ground biogeochemistry, requires CN to be Turn on the Matrix solution for soil biogeochemistry - Turn on extra output for the matrix solution - Turn on semi-analytic spinup solution for the CN/Soil matrix, requires soil matrix to be on This will drive the solution to equilibrium @@ -1162,7 +1162,7 @@ This will drive the solution to equilibrium -Number of years to average the storage capacitance over for the soil Matrix solution during semi-analytic spinup (isspinup=T) +Number of years to average the storage capacitance over for the soil Matrix solution during semi-analytic spinup (spinup_matrixcn=T) Normally should be the same as the number of years the atmospheric forcing is run over diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 3c3a42abc9..83429d2f18 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -326,8 +326,8 @@ sub cat_and_create_namelistinfile { "-res 0.9x1.25 -use_case 1850_control", "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'", "-res 1x1_brazil", - "-namelist '&a use_matrixcn=F,use_soil_matrixcn=F,is_outmatrix=F,isspinup=F/' -bgc sp", - "-namelist '&a use_matrixcn=T,use_soil_matrixcn=T,is_outmatrix=T,isspinup=T/' -bgc bgc -crop -clm_accelerated_spinup on", + "-namelist '&a use_matrixcn=F,use_soil_matrixcn=F,hist_wrt_matrixcn_diag=F,spinup_matrixcn=F/' -bgc sp", + "-namelist '&a use_matrixcn=T,use_soil_matrixcn=T,hist_wrt_matrixcn_diag=T,spinup_matrixcn=T/' -bgc bgc -crop -clm_accelerated_spinup on", "-namelist \"&a soil_decomp_method='MIMICSWieder2015',use_matrixcn=F/\" -bgc bgc -crop", "-namelist \"&a soil_decomp_method='MIMICSWieder2015',use_matrixcn=T/\" -bgc bgc -crop", "-bgc bgc -crop -clm_accelerated_spinup sasu", @@ -970,12 +970,12 @@ sub cat_and_create_namelistinfile { phys=>"clm5_0", }, "outmatrixWOmatrix" =>{ options=>"-envxml_dir . -bgc bgc", - namelst=>"use_soil_matrixcn=.false.,use_matrixcn=F,is_outmatrix=T", + namelst=>"use_soil_matrixcn=.false.,use_matrixcn=F,hist_wrt_matrixcn_diag=T", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, "spinupWOsoilmatrix" =>{ options=>"-envxml_dir . -bgc bgc", - namelst=>"use_soil_matrixcn=F,use_matrixcn=T,isspinup=T", + namelst=>"use_soil_matrixcn=F,use_matrixcn=T,spinup_matrixcn=T", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, @@ -990,27 +990,27 @@ sub cat_and_create_namelistinfile { phys=>"clm5_1", }, "nyrforceWOspinup" =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu", - namelst=>"use_matrixcn=.false.,isspinup=F,nyr_forcing=20", + namelst=>"use_matrixcn=.false.,spinup_matrixcn=F,nyr_forcing=20", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, "nyrsasuGTnyrforce" =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu", - namelst=>"use_matrixcn=.false.,isspinup=T,nyr_forcing=20,nyr_sasu=21", + namelst=>"use_matrixcn=.false.,spinup_matrixcn=T,nyr_forcing=20,nyr_sasu=21", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, "iloopZero" =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu", - namelst=>"use_matrixcn=.false.,isspinup=T,iloop_avg=0", + namelst=>"use_matrixcn=.false.,spinup_matrixcn=T,iloop_avg=0", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, "matrixspinupWADmode" =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup sasu", - namelst=>"isspinup=T,spinup_state=2", + namelst=>"spinup_matrixcn=T,spinup_state=2", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, "matrixspinupWclmaccell" =>{ options=>"-envxml_dir . -bgc bgc -clm_accelerated_spinup off", - namelst=>"use_soil_matrixcn=T,isspinup=T", + namelst=>"use_soil_matrixcn=T,spinup_matrixcn=T", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py index eec462e72c..0e0d57e6c2 100644 --- a/cime_config/SystemTests/sspmatrixcn.py +++ b/cime_config/SystemTests/sspmatrixcn.py @@ -130,7 +130,7 @@ def append_user_nl(self, caseroot, n=0): # For all but last step turn extra matrix output to off b4last = self.n_steps() - 1 if ( n < b4last ): - contents_to_append = contents_to_append + ", is_outmatrix = .False." + contents_to_append = contents_to_append + ", hist_wrt_matrixcn_diag = .False." # For matrix spinup steps, set the matrix spinup and other variables associated with it if ( self.spin[n] == "sasu" ): contents_to_append = contents_to_append + ", nyr_forcing = "+str(self.nyr_forcing) diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm index 56d4261a45..6b7eb4347d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn/user_nl_clm @@ -1,3 +1,3 @@ use_matrixcn = .true. use_soil_matrixcn = .true. - is_outmatrix = .true. + hist_wrt_matrixcn_diag = .true. diff --git a/src/biogeochem/CNVegMatrixMod.F90 b/src/biogeochem/CNVegMatrixMod.F90 index c171490bf0..bf7527bc71 100644 --- a/src/biogeochem/CNVegMatrixMod.F90 +++ b/src/biogeochem/CNVegMatrixMod.F90 @@ -41,7 +41,7 @@ module CNVegMatrixMod use CNVegNitrogenFluxType , only : cnveg_nitrogenflux_type use CNVegStateType , only : cnveg_state_type use SoilBiogeochemNitrogenFluxType , only : soilbiogeochem_nitrogenflux_type - use clm_varctl , only : isspinup, is_outmatrix, nyr_forcing, nyr_SASU, iloop_avg + use clm_varctl , only : spinup_matrixcn, hist_wrt_matrixcn_diag, nyr_forcing, nyr_SASU, iloop_avg use clm_varctl , only : use_c13, use_c14 use SparseMatrixMultiplyMod , only : sparse_matrix_type,diag_matrix_type,vector_type use MatrixMod , only : inverse @@ -1253,7 +1253,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire if(mod(iyr-1,nyr_forcing) .eq. 0)then iloop = iloop + 1 end if - if(.not. isspinup .or. isspinup .and. mod(iyr-1,nyr_SASU) .eq. 0)then + if(.not. spinup_matrixcn .or. spinup_matrixcn .and. mod(iyr-1,nyr_SASU) .eq. 0)then do fp = 1,num_soilp p = filter_soilp(fp) leafc0(p) = max(leafc(p), epsi) @@ -1683,7 +1683,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire ! Accumulate transfers during the whole calendar year call t_startf('CN veg matrix-accum. trans.') - if(isspinup .or. is_outmatrix)then + if(spinup_matrixcn .or. hist_wrt_matrixcn_diag)then do fp = 1,num_soilp p = filter_soilp(fp) matrix_calloc_leaf_acc(p) = matrix_calloc_leaf_acc(p) + vegmatrixc_input%V(p,ileaf) @@ -2439,8 +2439,8 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire call t_stopf('CN veg matrix-assign new value') ! Calculate C storage capacity. 2D matrix instead of sparse matrix is still used when calculating the inverse - if(isspinup .or. is_outmatrix)then - if((.not. isspinup .and. is_end_curr_year()) .or. (isspinup .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then + if(spinup_matrixcn .or. hist_wrt_matrixcn_diag)then + if((.not. spinup_matrixcn .and. is_end_curr_year()) .or. (spinup_matrixcn .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then do fp = 1,num_soilp call t_startf('CN veg matrix-prepare AK^-1') p = filter_soilp(fp) @@ -2881,7 +2881,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire call t_startf('CN veg matrix-finalize spinup') - if(isspinup .and. .not. is_first_step_of_this_run_segment())then + if(spinup_matrixcn .and. .not. is_first_step_of_this_run_segment())then deadstemc(p) = vegmatrixc_rt(ideadstem) deadstemc_storage(p) = vegmatrixc_rt(ideadstem_st) deadcrootc(p) = vegmatrixc_rt(ideadcroot) @@ -3184,7 +3184,7 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire end if ! Save C storage capacity from temporary variables to module variables - if(is_outmatrix)then + if(hist_wrt_matrixcn_diag)then matrix_cap_leafc(p) = vegmatrixc_rt(ileaf) matrix_cap_leafc_storage(p) = vegmatrixc_rt(ileaf_st) matrix_cap_leafc_xfer(p) = vegmatrixc_rt(ileaf_xf) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index ffc43b4200..faead44399 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -280,8 +280,8 @@ module clm_varctl !---------------------------------------------------------- ! CN matrix !---------------------------------------------------------- - logical, public :: isspinup = .false. !.false. ! true => use acc spinup - logical, public :: is_outmatrix = .false.!.false. ! true => use acc spinup + logical, public :: spinup_matrixcn = .false. !.false. ! true => use acc spinup + logical, public :: hist_wrt_matrixcn_diag = .false.!.false. ! true => use acc spinup ! SASU integer, public :: nyr_forcing = 10 ! length of forcing years for the spin up. eg. if DATM_CLMNCEP_YR_START=1901;DATM_CLMNCEP_YR_END=1920, then nyr_forcing = 20 integer, public :: nyr_SASU = 1 ! length of each semi-analytic solution. eg. nyr_SASU=5, analytic solutions will be calculated every five years. diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index ef006bcc42..acb4d6491b 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -189,7 +189,7 @@ subroutine control_init(dtime) ! CN Matrix solution namelist /clm_inparm / & - use_matrixcn, use_soil_matrixcn, is_outmatrix, isspinup, nyr_forcing, nyr_sasu, iloop_avg + use_matrixcn, use_soil_matrixcn, hist_wrt_matrixcn_diag, spinup_matrixcn, nyr_forcing, nyr_sasu, iloop_avg ! lake_melt_icealb is of dimension numrad @@ -325,8 +325,8 @@ subroutine control_init(dtime) if(use_fates)then use_matrixcn = .false. use_soil_matrixcn = .false. - is_outmatrix = .false. - isspinup = .false. + hist_wrt_matrixcn_diag = .false. + spinup_matrixcn = .false. end if nyr_forcing = 10 @@ -850,8 +850,8 @@ subroutine control_spmd() call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_matrixcn, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_soil_matrixcn, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (is_outmatrix, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (isspinup, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (hist_wrt_matrixcn_diag, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (spinup_matrixcn, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (nyr_forcing, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (nyr_sasu, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (iloop_avg, 1, MPI_INTEGER, 0, mpicom, ier) diff --git a/src/soilbiogeochem/CNSoilMatrixMod.F90 b/src/soilbiogeochem/CNSoilMatrixMod.F90 index 1248c5e1d6..56c1f11b5c 100644 --- a/src/soilbiogeochem/CNSoilMatrixMod.F90 +++ b/src/soilbiogeochem/CNSoilMatrixMod.F90 @@ -34,7 +34,7 @@ module CNSoilMatrixMod use SoilBiogeochemNitrogenFluxType , only : soilbiogeochem_nitrogenflux_type use CNSharedParamsMod , only : CNParamsShareInst use SoilStateType , only : soilstate_type - use clm_varctl , only : isspinup, is_outmatrix, nyr_forcing, nyr_SASU, iloop_avg + use clm_varctl , only : spinup_matrixcn, hist_wrt_matrixcn_diag, nyr_forcing, nyr_SASU, iloop_avg use ColumnType , only : col use GridcellType , only : grc use clm_varctl , only : use_c13, use_c14, iulog @@ -67,14 +67,14 @@ subroutine CNSoilMatrixInit( ) if ( use_soil_matrixcn ) then write(iulog,*) 'CN Soil matrix solution is on' write(iulog,*) '*****************************' - if ( isspinup ) then + if ( spinup_matrixcn ) then write(iulog,*) ' Matrix spinup is on' write(iulog,*) ' *******************' write(iulog,*) ' nyr_forcing = ', nyr_forcing write(iulog,*) ' nyr_SASU = ', nyr_SASU write(iulog,*) ' iloop_avg = ', iloop_avg end if - if ( is_outmatrix )then + if ( hist_wrt_matrixcn_diag )then write(iulog,*) ' Extra matrix solution tracability output is turned on' else write(iulog,*) ' no extra matrix solution tracability output' @@ -343,7 +343,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act if(mod(iyr-1,nyr_forcing) .eq. 0)then iloop = iloop + 1 end if - if(.not. isspinup .or. isspinup .and. mod(iyr-1,nyr_SASU) .eq. 0)then + if(.not. spinup_matrixcn .or. spinup_matrixcn .and. mod(iyr-1,nyr_SASU) .eq. 0)then do i = 1,ndecomp_pools do j = 1, nlevdecomp do fc = 1,num_soilc @@ -550,7 +550,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act call t_stopf('CN Soil matrix-assign back') - if(use_soil_matrixcn .and. (is_outmatrix .or. isspinup))then + if(use_soil_matrixcn .and. (hist_wrt_matrixcn_diag .or. spinup_matrixcn))then ! Accumulate C transfers during a whole calendar year to calculate the C and N capacity do j=1,ndecomp_pools*nlevdecomp @@ -665,7 +665,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end if call t_startf('CN Soil matrix-calc. C capacity') - if((.not. isspinup .and. is_end_curr_year()) .or. (isspinup .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then + if((.not. spinup_matrixcn .and. is_end_curr_year()) .or. (spinup_matrixcn .and. is_end_curr_year() .and. mod(iyr,nyr_SASU) .eq. 0))then ! Copy C transfers from sparse matrix to 2D temporary variables tran_acc and tran_nacc ! Calculate the C and N transfer rate by dividing CN transfer by base value saved at begin of each year. do fc = 1,num_soilc @@ -816,7 +816,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) - if(isspinup .and. .not. is_first_step_of_this_run_segment())then + if(spinup_matrixcn .and. .not. is_first_step_of_this_run_segment())then cs_soil%decomp_cpools_vr_col(c,j,i) = soilmatrixc_cap(c,j+(i-1)*nlevdecomp,1) if(use_c13)then cs13_soil%decomp_cpools_vr_col(c,j,i) = soilmatrixc13_cap(c,j+(i-1)*nlevdecomp,1) @@ -871,7 +871,7 @@ subroutine CNSoilMatrix(bounds,num_soilc, filter_soilc, num_actfirec, filter_act end do end do - if(isspinup)call update_DA_nstep() + if(spinup_matrixcn)call update_DA_nstep() if(iloop .eq. iloop_avg .and. iyr .eq. nyr_forcing)iloop = 0 if(iyr .eq. nyr_forcing)iyr = 0 From 1a2ddffdffbae8b3140b0e751b530f21db9c5afb Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Mar 2024 13:24:58 -0600 Subject: [PATCH 054/408] Replace 1.e+36 with spval in cnmatrix code --- src/biogeochem/CNVegMatrixMod.F90 | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNVegMatrixMod.F90 b/src/biogeochem/CNVegMatrixMod.F90 index bf7527bc71..5582afeffe 100644 --- a/src/biogeochem/CNVegMatrixMod.F90 +++ b/src/biogeochem/CNVegMatrixMod.F90 @@ -23,6 +23,7 @@ module CNVegMatrixMod use clm_time_manager , only : get_step_size,is_end_curr_year,is_first_step_of_this_run_segment,& is_beg_curr_year,update_DA_nstep use decompMod , only : bounds_type + use clm_varcon , only : spval use clm_varpar , only : nlevdecomp, nvegcpool, nvegnpool use clm_varpar , only : ileaf,ileaf_st,ileaf_xf,ifroot,ifroot_st,ifroot_xf,& ilivestem,ilivestem_st,ilivestem_xf,& @@ -2711,27 +2712,27 @@ subroutine CNVegMatrix(bounds,num_soilp,filter_soilp,num_actfirep,filter_actfire matrix_ntransfer_acc(iretransn,iretransn) = -matrix_nturnover_retransn_acc(p) do i=1,nvegcpool - if(matrix_ctransfer_acc(i,i) .eq. 0)then - matrix_ctransfer_acc(i,i) = 1.e+36 + if(matrix_ctransfer_acc(i,i) == 0)then + matrix_ctransfer_acc(i,i) = spval end if end do if(use_c13)then do i=1,nvegcpool - if(matrix_c13transfer_acc(i,i) .eq. 0)then - matrix_c13transfer_acc(i,i) = 1.e+36 + if(matrix_c13transfer_acc(i,i) == 0)then + matrix_c13transfer_acc(i,i) = spval end if end do end if if(use_c14)then do i=1,nvegcpool - if(matrix_c14transfer_acc(i,i) .eq. 0)then - matrix_c14transfer_acc(i,i) = 1.e+36 + if(matrix_c14transfer_acc(i,i) == 0)then + matrix_c14transfer_acc(i,i) = spval end if end do end if do i=1,nvegnpool - if(matrix_ntransfer_acc(i,i) .eq. 0)then - matrix_ntransfer_acc(i,i) = 1.e+36 + if(matrix_ntransfer_acc(i,i) == 0)then + matrix_ntransfer_acc(i,i) = spval end if end do From 47839a77229c61555e3b8932927bb54cdc511b27 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Mar 2024 14:39:43 -0600 Subject: [PATCH 055/408] Black reformatting of two files --- cime_config/SystemTests/sspmatrixcn.py | 455 ++++++++++++++----------- cime_config/buildnml | 72 ++-- 2 files changed, 295 insertions(+), 232 deletions(-) diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py index 0e0d57e6c2..37d4154121 100644 --- a/cime_config/SystemTests/sspmatrixcn.py +++ b/cime_config/SystemTests/sspmatrixcn.py @@ -14,15 +14,15 @@ """ import shutil, glob, os, sys -if __name__ == '__main__': - CIMEROOT = os.environ.get("CIMEROOT") - if CIMEROOT is None: - CIMEROOT = "../../cime"; +if __name__ == "__main__": + CIMEROOT = os.environ.get("CIMEROOT") + if CIMEROOT is None: + CIMEROOT = "../../cime" - sys.path.append(os.path.join( CIMEROOT, "scripts", "lib")) - sys.path.append(os.path.join( CIMEROOT, "scripts" ) ) + sys.path.append(os.path.join(CIMEROOT, "scripts", "lib")) + sys.path.append(os.path.join(CIMEROOT, "scripts")) else: - from CIME.utils import append_testlog + from CIME.utils import append_testlog from CIME.XML.standard_module_setup import * from CIME.SystemTests.system_tests_common import SystemTestsCommon @@ -31,123 +31,170 @@ logger = logging.getLogger(__name__) + class SSPMATRIXCN(SystemTestsCommon): # Class data nyr_forcing = 2 # Get different integer multiples of the number of forcing years - full = nyr_forcing - twice = 2 * nyr_forcing + full = nyr_forcing + twice = 2 * nyr_forcing thrice = 3 * nyr_forcing # Define the settings that will be used for each step - steps = ["0-AD", "1-SASU", "2-norm" ] - desc = ["Accell-Decomp(AD)-coldstart", "slow-mode Semi-Analytic SpinUp(SASU)", "normal" ] - runtyp = ["startup", "hybrid", "branch" ] - spin = ["on", "sasu", "off" ] - stop_n = [5, thrice, thrice ] - cold = [True, False, False ] - iloop = [-999, -999, -999 ] - sasu = [-999, -999, -999 ] + steps = ["0-AD", "1-SASU", "2-norm"] + desc = [ + "Accell-Decomp(AD)-coldstart", + "slow-mode Semi-Analytic SpinUp(SASU)", + "normal", + ] + runtyp = ["startup", "hybrid", "branch"] + spin = ["on", "sasu", "off"] + stop_n = [5, thrice, thrice] + cold = [True, False, False] + iloop = [-999, -999, -999] + sasu = [-999, -999, -999] def __init__(self, case=None): """ initialize an object interface to the SSPMATRIXCN system test """ - expect ( len(self.steps) == len(self.sasu), "length of steps must be the same as sasu" ) - expect ( len(self.steps) == len(self.spin), "length of steps must be the same as spin" ) - expect ( len(self.steps) == len(self.desc), "length of steps must be the same as desc" ) - expect ( len(self.steps) == len(self.cold), "length of steps must be the same as cold" ) - expect ( len(self.steps) == len(self.runtyp), "length of steps must be the same as runtyp" ) - expect ( len(self.steps) == len(self.iloop), "length of steps must be the same as iloop" ) - expect ( len(self.steps) == len(self.stop_n), "length of steps must be the same as stop_n" ) - - if __name__ != '__main__': - SystemTestsCommon.__init__(self, case) - ystart = int(self._case.get_value("DATM_YR_START")) - yend = int(self._case.get_value("DATM_YR_END")) - self.comp = self._case.get_value("COMP_LND") + expect( + len(self.steps) == len(self.sasu), + "length of steps must be the same as sasu", + ) + expect( + len(self.steps) == len(self.spin), + "length of steps must be the same as spin", + ) + expect( + len(self.steps) == len(self.desc), + "length of steps must be the same as desc", + ) + expect( + len(self.steps) == len(self.cold), + "length of steps must be the same as cold", + ) + expect( + len(self.steps) == len(self.runtyp), + "length of steps must be the same as runtyp", + ) + expect( + len(self.steps) == len(self.iloop), + "length of steps must be the same as iloop", + ) + expect( + len(self.steps) == len(self.stop_n), + "length of steps must be the same as stop_n", + ) + + if __name__ != "__main__": + SystemTestsCommon.__init__(self, case) + ystart = int(self._case.get_value("DATM_YR_START")) + yend = int(self._case.get_value("DATM_YR_END")) + self.comp = self._case.get_value("COMP_LND") else: - self._case = None - self.comp = "clm" - ystart = 2000 - yend = 2001 + self._case = None + self.comp = "clm" + ystart = 2000 + yend = 2001 for n in range(len(self.steps)): - if ( n == 0 ): - expect( self.cold[n] == True, "First step MUST be a cold-start" ) - expect( self.runtyp[n] == "startup", "First step MUST be a startup" ) - else: - expect( self.cold[n] == False, "Other steps must NOT be a cold-start" ) - expect( self.runtyp[n] != "startup", "Other steps MUST NOT be a startup" ) - - if ( self.spin[n] == "sasu" ): - expect( self.cold[n] == False, "SASU step should NOT be a cold-start" ) - if ( self.sasu[n] != -999 ): - expect( self.sasu[n] > 0, "SASU steps must set SASU cycle" ) - expect( self.sasu[n] <= self.nyr_forcing, "SASU cycles can't be greater than a full forcing cycle" ) - - expect( yend-ystart+1 == self.nyr_forcing, "Number of years run over MUST correspond to nyr_forcing" ) + if n == 0: + expect(self.cold[n] == True, "First step MUST be a cold-start") + expect(self.runtyp[n] == "startup", "First step MUST be a startup") + else: + expect(self.cold[n] == False, "Other steps must NOT be a cold-start") + expect(self.runtyp[n] != "startup", "Other steps MUST NOT be a startup") + + if self.spin[n] == "sasu": + expect(self.cold[n] == False, "SASU step should NOT be a cold-start") + if self.sasu[n] != -999: + expect(self.sasu[n] > 0, "SASU steps must set SASU cycle") + expect( + self.sasu[n] <= self.nyr_forcing, + "SASU cycles can't be greater than a full forcing cycle", + ) + + expect( + yend - ystart + 1 == self.nyr_forcing, + "Number of years run over MUST correspond to nyr_forcing", + ) self._testname = "SSPMATRIX" - def check_n( self, n): + def check_n(self, n): "Check if n is within range" - expect( ( (n >= 0) and (n < self.n_steps()) ), "Step number is out of range = " + str(n) ) + expect( + ((n >= 0) and (n < self.n_steps())), + "Step number is out of range = " + str(n), + ) def __logger__(self, n=0): "Log info on this step" - self.check_n( n ) - msg = "Step {}: {}: doing a {} run for {} years".format( self.steps[n], self.runtyp[n], self.desc[n], self.stop_n[n] ) + self.check_n(n) + msg = "Step {}: {}: doing a {} run for {} years".format( + self.steps[n], self.runtyp[n], self.desc[n], self.stop_n[n] + ) logger.info(msg) - logger.info(" spinup type: {}".format( self.spin[n] ) ) - if __name__ != '__main__': - append_testlog(msg) - if ( n+1 < self.n_steps() ): - logger.info(" writing restarts at end of run") - logger.info(" short term archiving is on ") + logger.info(" spinup type: {}".format(self.spin[n])) + if __name__ != "__main__": + append_testlog(msg) + if n + 1 < self.n_steps(): + logger.info(" writing restarts at end of run") + logger.info(" short term archiving is on ") def n_steps(self): "Total number of steps" - return( len(self.steps) ) + return len(self.steps) def total_years(self): "Total number of years needed to do the full spinup" ysum = 0 for nyr in self.stop_n: - ysum = ysum + nyr + ysum = ysum + nyr - return( ysum ) + return ysum def append_user_nl(self, caseroot, n=0): "Append needed settings to the user_nl files" - self.check_n( n ) + self.check_n(n) # For all set output to yearly contents_to_append = "hist_nhtfrq = -8760" - contents_to_append = contents_to_append + ", hist_mfilt = "+str(self.nyr_forcing) + contents_to_append = ( + contents_to_append + ", hist_mfilt = " + str(self.nyr_forcing) + ) # For all but last step turn extra matrix output to off b4last = self.n_steps() - 1 - if ( n < b4last ): - contents_to_append = contents_to_append + ", hist_wrt_matrixcn_diag = .False." + if n < b4last: + contents_to_append = ( + contents_to_append + ", hist_wrt_matrixcn_diag = .False." + ) # For matrix spinup steps, set the matrix spinup and other variables associated with it - if ( self.spin[n] == "sasu" ): - contents_to_append = contents_to_append + ", nyr_forcing = "+str(self.nyr_forcing) - if ( self.sasu[n] != -999 ): - contents_to_append = contents_to_append + ", nyr_sasu = " + str(self.sasu[n]) - if ( self.iloop[n] != -999 ): - contents_to_append = contents_to_append + ", iloop_avg = " + str(self.iloop[n]) + if self.spin[n] == "sasu": + contents_to_append = ( + contents_to_append + ", nyr_forcing = " + str(self.nyr_forcing) + ) + if self.sasu[n] != -999: + contents_to_append = ( + contents_to_append + ", nyr_sasu = " + str(self.sasu[n]) + ) + if self.iloop[n] != -999: + contents_to_append = ( + contents_to_append + ", iloop_avg = " + str(self.iloop[n]) + ) # For cold start, run with matrix off - if ( self.cold[n] ): + if self.cold[n]: contents_to_append = contents_to_append + ", use_matrixcn = .False." contents_to_append = contents_to_append + ", use_soil_matrixcn = .False." # Always append to the end - user_nl_utils.append_to_user_nl_files(caseroot = caseroot, - component = self.comp, - contents = contents_to_append) + user_nl_utils.append_to_user_nl_files( + caseroot=caseroot, component=self.comp, contents=contents_to_append + ) def run_phase(self): "Run phase" @@ -156,77 +203,80 @@ def run_phase(self): orig_case = self._case orig_casevar = self._case.get_value("CASE") - # Get a clone of each step except the last one b4last = self.n_steps() - 1 for n in range(b4last): - # - # Clone the main case, and get it setup for the next step - # - clone_path = "{}.step{}".format(caseroot,self.steps[n]) - if os.path.exists(clone_path): - shutil.rmtree(clone_path) - if ( n > 0 ): - del clone - self._set_active_case(orig_case) - clone = self._case.create_clone(clone_path, keepexe=True) - os.chdir(clone_path) - self._set_active_case(clone) - - self.__logger__(n) - - with clone: - clone.set_value("RUN_TYPE", self.runtyp[n] ) - clone.set_value("STOP_N", self.stop_n[n] ) - - clone.set_value("CLM_ACCELERATED_SPINUP", self.spin[n] ) - - if ( self.cold[n] ): - clone.set_value("CLM_FORCE_COLDSTART", "on" ) - else: - clone.set_value("CLM_FORCE_COLDSTART", "off" ) - - self.append_user_nl( clone_path, n ) - - dout_sr = clone.get_value("DOUT_S_ROOT") - - self._skip_pnl = False - # - # Start up from the previous case - # - rundir = clone.get_value("RUNDIR") - with clone: - if ( n > 0 ): - clone.set_value("GET_REFCASE", False) - expect( "refcase" in locals(), "refcase was NOT previously set" ) - clone.set_value("RUN_REFCASE", refcase ) - expect( "refdate" in locals(), "refdate was NOT previously set" ) - clone.set_value("RUN_STARTDATE", refdate ) - clone.set_value("RUN_REFDATE", refdate ) - for item in glob.glob("{}/*{}*".format(rest_path, refdate)): - linkfile = os.path.join(rundir, os.path.basename(item)) - if os.path.exists(linkfile): - os.remove( linkfile ) - if not os.path.isdir(rundir): - os.makedirs(rundir) - os.symlink(item, linkfile ) - - for item in glob.glob("{}/*rpointer*".format(rest_path)): - shutil.copy(item, rundir) - - # - # Run the case (Archiving on) - # - self._case.flush() - self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True) - - # - # Get the reference case from this step for the next step - # - refcase = clone.get_value("CASE") - refdate = run_cmd_no_fail(r'ls -1dt {}/rest/*-00000* | head -1 | sed "s/-00000.*//" | sed "s/^.*rest\///"'.format(dout_sr)) - refsec = "00000" - rest_path = os.path.join(dout_sr, "rest", "{}-{}".format(refdate, refsec)) + # + # Clone the main case, and get it setup for the next step + # + clone_path = "{}.step{}".format(caseroot, self.steps[n]) + if os.path.exists(clone_path): + shutil.rmtree(clone_path) + if n > 0: + del clone + self._set_active_case(orig_case) + clone = self._case.create_clone(clone_path, keepexe=True) + os.chdir(clone_path) + self._set_active_case(clone) + + self.__logger__(n) + + with clone: + clone.set_value("RUN_TYPE", self.runtyp[n]) + clone.set_value("STOP_N", self.stop_n[n]) + + clone.set_value("CLM_ACCELERATED_SPINUP", self.spin[n]) + + if self.cold[n]: + clone.set_value("CLM_FORCE_COLDSTART", "on") + else: + clone.set_value("CLM_FORCE_COLDSTART", "off") + + self.append_user_nl(clone_path, n) + + dout_sr = clone.get_value("DOUT_S_ROOT") + + self._skip_pnl = False + # + # Start up from the previous case + # + rundir = clone.get_value("RUNDIR") + with clone: + if n > 0: + clone.set_value("GET_REFCASE", False) + expect("refcase" in locals(), "refcase was NOT previously set") + clone.set_value("RUN_REFCASE", refcase) + expect("refdate" in locals(), "refdate was NOT previously set") + clone.set_value("RUN_STARTDATE", refdate) + clone.set_value("RUN_REFDATE", refdate) + for item in glob.glob("{}/*{}*".format(rest_path, refdate)): + linkfile = os.path.join(rundir, os.path.basename(item)) + if os.path.exists(linkfile): + os.remove(linkfile) + if not os.path.isdir(rundir): + os.makedirs(rundir) + os.symlink(item, linkfile) + + for item in glob.glob("{}/*rpointer*".format(rest_path)): + shutil.copy(item, rundir) + + # + # Run the case (Archiving on) + # + self._case.flush() + self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=True) + + # + # Get the reference case from this step for the next step + # + refcase = clone.get_value("CASE") + refdate = run_cmd_no_fail( + r'ls -1dt {}/rest/*-00000* | head -1 | sed "s/-00000.*//" | sed "s/^.*rest\///"'.format( + dout_sr + ) + ) + refsec = "00000" + rest_path = os.path.join(dout_sr, "rest", "{}-{}".format(refdate, refsec)) # # Last step in original case @@ -239,25 +289,25 @@ def run_phase(self): self._set_active_case(orig_case) self.__logger__(n) self._case.set_value("DOUT_S", False) - self._case.set_value("RUN_TYPE", self.runtyp[n] ) - self._case.set_value("STOP_N", self.stop_n[n] ) + self._case.set_value("RUN_TYPE", self.runtyp[n]) + self._case.set_value("STOP_N", self.stop_n[n]) rundir = self._case.get_value("RUNDIR") self._case.set_value("GET_REFCASE", False) - expect( "refcase" in locals(), "refcase was NOT previously set" ) + expect("refcase" in locals(), "refcase was NOT previously set") self._case.set_value("RUN_REFCASE", refcase) - expect( "refdate" in locals(), "refdate was NOT previously set" ) + expect("refdate" in locals(), "refdate was NOT previously set") self._case.set_value("RUN_REFDATE", refdate) - self._case.set_value("RUN_STARTDATE", refdate ) + self._case.set_value("RUN_STARTDATE", refdate) for item in glob.glob("{}/*{}*".format(rest_path, refdate)): linkfile = os.path.join(rundir, os.path.basename(item)) if os.path.exists(linkfile): - os.remove( linkfile ) - os.symlink(item, linkfile ) + os.remove(linkfile) + os.symlink(item, linkfile) for item in glob.glob("{}/*rpointer*".format(rest_path)): shutil.copy(item, rundir) - self.append_user_nl( clone_path, n ) + self.append_user_nl(clone_path, n) # # Don't need to set COLDSTART or ACCEL_SPINUP # @@ -266,7 +316,8 @@ def run_phase(self): # Run the case (short term archiving is off) # self._case.flush() - self.run_indv( suffix="step{}".format(self.steps[n]), st_archive=False ) + self.run_indv(suffix="step{}".format(self.steps[n]), st_archive=False) + # # Unit testing for above @@ -274,59 +325,57 @@ def run_phase(self): import unittest from CIME.case import Case from CIME.utils import _LessThanFilter -from argparse import RawTextHelpFormatter +from argparse import RawTextHelpFormatter + class test_ssp_matrixcn(unittest.TestCase): + def setUp(self): + self.ssp = SSPMATRIXCN() + + def test_logger(self): + # Test the logger + stream_handler = logging.StreamHandler(sys.stdout) + logger.addHandler(stream_handler) + logger.level = logging.DEBUG + logger.info("nyr_forcing = {}".format(self.ssp.nyr_forcing)) + for n in range(self.ssp.n_steps()): + self.ssp.__logger__(n) + if self.ssp.spin[n] == "sasu": + logger.info(" SASU spinup is .true.") + if self.ssp.sasu[n] != -999: + logger.info(" nyr_sasu = {}".format(self.ssp.sasu[n])) + if self.ssp.iloop[n] != -999: + logger.info(" iloop_avg = {}".format(self.ssp.iloop[n])) + + logger.info("Total number of years {}".format(self.ssp.total_years())) + logger.removeHandler(stream_handler) + + def test_n_steps(self): + self.assertTrue(self.ssp.n_steps() == 3) + + def test_valid_n(self): + for n in range(self.ssp.n_steps()): + self.ssp.check_n(n) + + def test_negative_n(self): + self.assertRaises(SystemExit, self.ssp.check_n, -1) + + def test_n_too_big(self): + self.assertRaises(SystemExit, self.ssp.check_n, self.ssp.n_steps()) + + def test_append_user_nl_step2(self): + ufile = "user_nl_clm" + if not os.path.exists(ufile): + os.mknod(ufile) + else: + expect(0, ufile + " file already exists, not overwritting it") - def setUp( self ): - self.ssp = SSPMATRIXCN() - - def test_logger( self ): - # Test the logger - stream_handler = logging.StreamHandler(sys.stdout) - logger.addHandler(stream_handler) - logger.level = logging.DEBUG - logger.info( "nyr_forcing = {}".format(self.ssp.nyr_forcing) ) - for n in range(self.ssp.n_steps()): - self.ssp.__logger__(n) - if ( self.ssp.spin[n] == "sasu" ): - logger.info( " SASU spinup is .true." ) - if ( self.ssp.sasu[n] != -999 ): - logger.info( " nyr_sasu = {}".format(self.ssp.sasu[n]) ) - if ( self.ssp.iloop[n] != -999 ): - logger.info( " iloop_avg = {}".format(self.ssp.iloop[n]) ) - - logger.info( "Total number of years {}".format( self.ssp.total_years() ) ) - logger.removeHandler(stream_handler) - - def test_n_steps( self ): - self.assertTrue( self.ssp.n_steps() == 3) - - def test_valid_n( self ): - for n in range(self.ssp.n_steps()): - self.ssp.check_n(n) - - def test_negative_n( self ): - self.assertRaises(SystemExit, self.ssp.check_n, -1 ) - - def test_n_too_big( self ): - self.assertRaises(SystemExit, self.ssp.check_n, self.ssp.n_steps() ) - - def test_append_user_nl_step2( self ): - ufile = "user_nl_clm" - if not os.path.exists(ufile): - os.mknod(ufile) - else: - expect( 0, ufile+" file already exists, not overwritting it" ) - - self.ssp.append_user_nl( caseroot=".", n=2) - print( ufile+" for step 2" ) - log = open(ufile, "r").read() - print( log ) - os.remove(ufile) - - -if __name__ == '__main__': - unittest.main() + self.ssp.append_user_nl(caseroot=".", n=2) + print(ufile + " for step 2") + log = open(ufile, "r").read() + print(log) + os.remove(ufile) +if __name__ == "__main__": + unittest.main() diff --git a/cime_config/buildnml b/cime_config/buildnml index 11112b81f0..2f27473732 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -51,24 +51,24 @@ def buildnml(case, caseroot, compname): clm_accelerated_spinup = case.get_value("CLM_ACCELERATED_SPINUP") comp_interface = case.get_value("COMP_INTERFACE") lilac_mode = case.get_value("LILAC_MODE") - if ( comp_interface == "nuopc" ): - yr_start = case.get_value("DATM_YR_START") - yr_end = case.get_value("DATM_YR_END") + if comp_interface == "nuopc": + yr_start = case.get_value("DATM_YR_START") + yr_end = case.get_value("DATM_YR_END") else: - yr_start = case.get_value("DATM_CLMNCEP_YR_START") - yr_end = case.get_value("DATM_CLMNCEP_YR_END") + yr_start = case.get_value("DATM_CLMNCEP_YR_START") + yr_end = case.get_value("DATM_CLMNCEP_YR_END") - if ( yr_start != None and yr_start < 0 ): - yr_start = case.get_value("DATM_CPLHIST_YR_START") - yr_end = case.get_value("DATM_CPLHIST_YR_END") + if yr_start != None and yr_start < 0: + yr_start = case.get_value("DATM_CPLHIST_YR_START") + yr_end = case.get_value("DATM_CPLHIST_YR_END") # For LILAC - if ( yr_start == None or lilac_mode == "on" ): - yr_start = "0" - yr_end = "0" + if yr_start == None or lilac_mode == "on": + yr_start = "0" + yr_end = "0" yr_start = int(yr_start) - yr_end = int(yr_end) + yr_end = int(yr_end) comp_atm = case.get_value("COMP_ATM") lnd_grid = case.get_value("LND_GRID") @@ -117,7 +117,9 @@ def buildnml(case, caseroot, compname): clm_phys = case.get_value("CLM_PHYSICS_VERSION") config_cache_text = _config_cache_template.format(clm_phys=clm_phys) - config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml") + config_cache_path = os.path.join( + caseroot, "Buildconf", compname + "conf", "config_cache.xml" + ) with open(config_cache_path, "w") as config_cache_file: config_cache_file.write(config_cache_text) @@ -206,22 +208,28 @@ def buildnml(case, caseroot, compname): else: ignore = "-ignore_ic_date" - tuning = "-lnd_tuning_mode %s "%lnd_tuning_mode - + tuning = "-lnd_tuning_mode %s " % lnd_tuning_mode + # # Spinup settings and specifics for SASU spinup # - spinup = "-clm_accelerated_spinup %s "%clm_accelerated_spinup - if ( clm_accelerated_spinup == "sasu" ): - if ( (yr_start != None) and (yr_end != None) ): - nyr = yr_end - yr_start + 1 - if ( (yr_end <= 0) or (yr_start <= 0) ): - logger.error( "ERROR: Year start and end are both negative and should not be" ) - clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts) - else: - logger.warning( "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model" ) - logger.warning( " as it expects regular atmosphere forcing that is cycled over" ) - + spinup = "-clm_accelerated_spinup %s " % clm_accelerated_spinup + if clm_accelerated_spinup == "sasu": + if (yr_start != None) and (yr_end != None): + nyr = yr_end - yr_start + 1 + if (yr_end <= 0) or (yr_start <= 0): + logger.error( + "ERROR: Year start and end are both negative and should not be" + ) + clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts) + else: + logger.warning( + "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model" + ) + logger.warning( + " as it expects regular atmosphere forcing that is cycled over" + ) + infile = os.path.join(ctsmconf, "namelist") inputdata_file = os.path.join(caseroot, "Buildconf", "ctsm.input_data_list") @@ -234,7 +242,9 @@ def buildnml(case, caseroot, compname): lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file) lndfrac_setting = "-lnd_frac " + lndfrac_file - config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml") + config_cache_file = os.path.join( + caseroot, "Buildconf", compname + "conf", "config_cache.xml" + ) # ----------------------------------------------------- # Clear out old data @@ -297,7 +307,9 @@ def buildnml(case, caseroot, compname): break if not os.path.exists(os.path.join(rundir, clm_startfile)): - logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile) + logger.warning( + "WARNING: Could NOT find a start file to use using" + clm_startfile + ) clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile) else: clm_icfile = "" @@ -308,7 +320,9 @@ def buildnml(case, caseroot, compname): user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string) namelist_infile = os.path.join(ctsmconf, "namelist") - create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines)) + create_namelist_infile( + case, user_nl_file, namelist_infile, "\n".join(infile_lines) + ) cmd = os.path.join(lnd_root, "bld", "build-namelist") From 4cef2cc63b6282c1792ef45803cfad33f2dc3737 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Mar 2024 14:45:05 -0600 Subject: [PATCH 056/408] Update .git-blame-ignore-revs --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 4798c37853..2c92251e93 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -32,3 +32,4 @@ d866510188d26d51bcd6d37239283db690af7e82 6fccf682eaf718615407d9bacdd3903b8786a03d 2500534eb0a83cc3aff94b30fb62e915054030bf 78d05967c2b027dc9776a884716597db6ef7f57c +47839a77229c61555e3b8932927bb54cdc511b27 From e79364382b7f6a555a60070c6f84f52366c9c663 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 2 Apr 2024 18:08:20 -0600 Subject: [PATCH 057/408] testlist updates for LGRAIN2 and LREPRSTRUCT tests --- cime_config/testdefs/testlist_clm.xml | 67 ++------------------------- 1 file changed, 4 insertions(+), 63 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 04200b7271..f44a8e84ab 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3377,9 +3377,9 @@ - + - + @@ -3387,19 +3387,9 @@ - - - - - - - - - - - + - + @@ -3407,26 +3397,6 @@ - - - - - - - - - - - - - - - - - - - - @@ -3436,16 +3406,6 @@ - - - - - - - - - - @@ -3455,16 +3415,6 @@ - - - - - - - - - - @@ -3474,15 +3424,6 @@ - - - - - - - - - From 306d11a6dcb9c16f29fbc3937b1110110a5d436c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 3 Apr 2024 14:15:58 -0600 Subject: [PATCH 058/408] testlist updates for already existing matrixcn tests --- cime_config/testdefs/testlist_clm.xml | 30 ++++++--------------------- 1 file changed, 6 insertions(+), 24 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index f44a8e84ab..a47d74de5d 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -530,7 +530,7 @@ - + @@ -540,7 +540,7 @@ - + @@ -548,27 +548,9 @@ - - - - - - - - - - - - - - - - - - - + @@ -578,7 +560,7 @@ - + @@ -587,7 +569,7 @@ - + @@ -804,7 +786,7 @@ - + From 99ba6ced5d9fbfcfb42d3b4c4cd253ccc7d72c9c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 4 Apr 2024 18:05:23 -0600 Subject: [PATCH 059/408] Removed testmod directory not in use --- .../clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods | 2 -- 1 file changed, 2 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods deleted file mode 100644 index 442d7afb24..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_monthly_matrixcn_spinup/include_user_mods +++ /dev/null @@ -1,2 +0,0 @@ -../decStart -../ciso_monthly_matrixcn_spinup From 45dbe6247da94965e4c37593ca38592f3e25da9e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 4 Apr 2024 18:16:10 -0600 Subject: [PATCH 060/408] Adding matrixcnOn testmods --- .../testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods | 1 + cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm | 3 +++ 2 files changed, 4 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm new file mode 100644 index 0000000000..185d6a2410 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn/user_nl_clm @@ -0,0 +1,3 @@ +hist_wrt_matrixcn_diag = .true. +use_matrixcn = .true. +use_soil_matrixcn = .true. From fef58b6d383fd750233ab4fe64086a738a41f2e2 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 4 Apr 2024 20:23:43 -0600 Subject: [PATCH 061/408] Relax tolerance for truncating small snocan values in CanopyFluxes The default of 1e-13 was letting through some state updates that look like they should have been truncated to 0: each time step, snocan was decreasing by about 12 orders of magnitude. Addresses ESCOMP/CTSM#2444 --- src/biogeophys/CanopyFluxesMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 58334a70c0..a969dc0583 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1624,7 +1624,8 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! snocan < rel_epsilon * snocan_baseline will be set to zero ! See NumericsMod for rel_epsilon value call truncate_small_values(fn, filterp, begp, endp, & - snocan_baseline(begp:endp), snocan(begp:endp)) + snocan_baseline(begp:endp), snocan(begp:endp), & + custom_rel_epsilon=1.e-10_r8) if ( use_fates ) then From 0d07eb28518db409863bab811dbc3b7919f967c7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 8 Apr 2024 16:46:20 -0600 Subject: [PATCH 062/408] 45 new tests with matrixcnOn testmods --- cime_config/testdefs/testlist_clm.xml | 456 +++++++++++++++++++------- 1 file changed, 343 insertions(+), 113 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index a47d74de5d..6056439278 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2,17 +2,23 @@ - + + + + + + + + + - - @@ -21,6 +27,16 @@ + + + + + + + + + + @@ -139,13 +155,21 @@ - + + + + + + + + + @@ -350,13 +374,21 @@ - + + + + + + + + + @@ -378,13 +410,21 @@ - + + + + + + + + + @@ -396,8 +436,6 @@ - - @@ -405,6 +443,15 @@ + + + + + + + + + @@ -501,7 +548,6 @@ - @@ -509,9 +555,17 @@ + + + + + + + + + - @@ -519,15 +573,32 @@ + + + + + + + + + - + + + + + + + + + @@ -675,13 +746,13 @@ - + - + - - + + @@ -693,13 +764,13 @@ - + - + - + @@ -711,9 +782,17 @@ + + + + + + + + + - @@ -721,6 +800,15 @@ + + + + + + + + + @@ -759,12 +847,14 @@ - + - + + + @@ -775,13 +865,13 @@ - + - + - + @@ -820,36 +910,38 @@ - + - + - + + - + - + - + + @@ -961,6 +1053,16 @@ + + + + + + + + + + @@ -972,8 +1074,6 @@ - - @@ -981,6 +1081,15 @@ + + + + + + + + + @@ -1007,6 +1116,15 @@ + + + + + + + + + @@ -1035,6 +1153,15 @@ + + + + + + + + + @@ -1043,6 +1170,15 @@ + + + + + + + + + @@ -1051,27 +1187,26 @@ - + - + - + - + - @@ -1117,14 +1252,6 @@ - - - - - - - - @@ -1133,13 +1260,13 @@ - + - + - + @@ -1238,16 +1365,6 @@ - - - - - - - - - - @@ -1258,14 +1375,14 @@ - + - - + - - + + + @@ -1278,16 +1395,6 @@ - - - - - - - - - - @@ -1446,13 +1553,21 @@ - + + + + + + + + + @@ -1531,10 +1646,6 @@ - - - - @@ -1544,6 +1655,16 @@ + + + + + + + + + + @@ -1619,6 +1740,15 @@ + + + + + + + + + @@ -1647,6 +1777,16 @@ + + + + + + + + + + @@ -1666,15 +1806,6 @@ - - - - - - - - - @@ -1684,13 +1815,13 @@ - + - + - + @@ -1702,13 +1833,13 @@ - + - + - - + + @@ -1762,6 +1893,16 @@ + + + + + + + + + + @@ -1774,7 +1915,6 @@ - @@ -1782,13 +1922,13 @@ - + - + - + @@ -1800,6 +1940,15 @@ + + + + + + + + + @@ -1812,8 +1961,6 @@ - - @@ -1822,6 +1969,16 @@ + + + + + + + + + + @@ -1853,14 +2010,14 @@ - + - + + - - + @@ -1873,6 +2030,16 @@ + + + + + + + + + + @@ -1896,8 +2063,6 @@ - - @@ -1905,6 +2070,16 @@ + + + + + + + + + + @@ -2091,10 +2266,6 @@ - - - - @@ -2104,6 +2275,18 @@ + + + + + + + + + + + + @@ -2170,6 +2353,17 @@ + + + + + + + + + + + @@ -2255,7 +2449,6 @@ - @@ -2263,6 +2456,15 @@ + + + + + + + + + @@ -2427,6 +2629,15 @@ + + + + + + + + + @@ -2756,7 +2967,6 @@ - @@ -2765,6 +2975,16 @@ + + + + + + + + + + @@ -3312,7 +3532,6 @@ - @@ -3322,6 +3541,17 @@ + + + + + + + + + + + From a2fc12b8be573434ef95e23e00efecffc87a6c18 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 11 Apr 2024 12:44:38 -0600 Subject: [PATCH 063/408] Change matrixcnOn tests to Clm51 and remove redundant tests --- cime_config/testdefs/testlist_clm.xml | 95 ++++++++------------------- 1 file changed, 29 insertions(+), 66 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 6056439278..c3bda24655 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -27,7 +27,7 @@ - + @@ -161,7 +161,7 @@ - + @@ -380,7 +380,7 @@ - + @@ -555,7 +555,7 @@ - + @@ -573,7 +573,7 @@ - + @@ -590,7 +590,7 @@ - + @@ -800,7 +800,7 @@ - + @@ -847,10 +847,10 @@ - + - - + + @@ -918,7 +918,7 @@ - + @@ -935,7 +935,7 @@ - + @@ -1081,15 +1081,6 @@ - - - - - - - - - @@ -1116,15 +1107,6 @@ - - - - - - - - - @@ -1153,7 +1135,7 @@ - + @@ -1170,7 +1152,7 @@ - + @@ -1196,7 +1178,7 @@ - + @@ -1260,7 +1242,7 @@ - + @@ -1559,7 +1541,7 @@ - + @@ -1655,16 +1637,6 @@ - - - - - - - - - - @@ -1740,7 +1712,7 @@ - + @@ -1777,7 +1749,7 @@ - + @@ -1815,15 +1787,6 @@ - - - - - - - - - @@ -1893,7 +1856,7 @@ - + @@ -1922,7 +1885,7 @@ - + @@ -1940,7 +1903,7 @@ - + @@ -2030,7 +1993,7 @@ - + @@ -2070,7 +2033,7 @@ - + @@ -2275,7 +2238,7 @@ - + @@ -2456,7 +2419,7 @@ - + @@ -2629,7 +2592,7 @@ - + @@ -2975,7 +2938,7 @@ - + @@ -3541,7 +3504,7 @@ - + From bd7d031760665a5cdc920ef61c2a519bb5116b6e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 11 Apr 2024 14:51:17 -0600 Subject: [PATCH 064/408] Rename failing Clm51 tests back to Clm50 due to missing compsets --- cime_config/testdefs/testlist_clm.xml | 28 +++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index b730b62720..54c9d0fb62 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -27,7 +27,7 @@ - + @@ -199,7 +199,7 @@ - + @@ -418,7 +418,7 @@ - + @@ -611,7 +611,7 @@ - + @@ -628,7 +628,7 @@ - + @@ -956,7 +956,7 @@ - + @@ -973,7 +973,7 @@ - + @@ -1173,7 +1173,7 @@ - + @@ -1190,7 +1190,7 @@ - + @@ -1750,7 +1750,7 @@ - + @@ -1787,7 +1787,7 @@ - + @@ -1894,7 +1894,7 @@ - + @@ -2071,7 +2071,7 @@ - + @@ -2457,7 +2457,7 @@ - + From 5d0a037a71c8e97e6f7e4c12535715bfbc16722d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 11 Apr 2024 19:45:40 -0600 Subject: [PATCH 065/408] Remove a clm/FatesCold--clm/matrixcnOn test as invalid --- cime_config/testdefs/testlist_clm.xml | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 54c9d0fb62..aea06d7f1e 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2976,16 +2976,6 @@ - - - - - - - - - - From 7cc2965bef7a75966fdc69c52513bb88f027027a Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Wed, 17 Apr 2024 14:51:22 -0600 Subject: [PATCH 066/408] Fix to get correct urbantv streams file --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 0b9b161c20..0b4893dbb6 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3610,7 +3610,7 @@ sub setup_logic_urbantv_streams { 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_urbantv', 'phys'=>$nl_flags->{'phys'}, - 'hgrid'=>"0.9x1.25" ); + 'hgrid'=>"0.9x1.25", 'urban_explicit_ac'=>$nl->get_value('urban_explicit_ac') ); if ($opts->{'driver'} eq "nuopc" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_urbantv', 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>"0.9x1.25" ); From 48b52dc5179a4ba3388a911a8aea7f1c682ce62c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 17 Apr 2024 17:08:50 -0600 Subject: [PATCH 067/408] Point FATES external at Charlie's LUH2 branch. --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index dc1bc3f0e7..1494217277 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.70.0_api.32.0.0 +repo_url = https://github.com/ckoven/fates +hash = d37d9733b5970dfe67a required = True [externals_description] From 52962a5e9e5f9ada9119a0beb7bccc313c71d955 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 18 Apr 2024 16:46:42 -0500 Subject: [PATCH 068/408] Fix stream_varnames out of bounds error --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index e6ceed7173..b4bb592e91 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -288,8 +288,10 @@ subroutine urbantv_interp(this, bounds) if (stream_varnames((lun%itype(l)-6)) == stream_varnames(n)) then this%t_building_max(l) = dataptr2d(ig,n) end if - if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then - this%p_ac(l) = dataptr2d(ig,n) + if (urban_explicit_ac) then + if (stream_varnames((lun%itype(l)-3)) == stream_varnames(n)) then + this%p_ac(l) = dataptr2d(ig,n) + end if end if end do else From d9402b92d78b016603342dcff668ecef1435ce78 Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 18 Apr 2024 17:00:39 -0500 Subject: [PATCH 069/408] Add missing "use" statement --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index b4bb592e91..98d1d51989 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -231,6 +231,7 @@ subroutine urbantv_interp(this, bounds) use dshr_methods_mod , only : dshr_fldbun_getfldptr use dshr_strdata_mod , only : shr_strdata_advance use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + use UrbanParamsType , only : urban_explicit_ac ! ! !ARGUMENTS: class(urbantv_type) :: this From a1cb4db82f7709677fa7d1311358600cfe75a05a Mon Sep 17 00:00:00 2001 From: cathyxinchangli <55264121+cathyxinchangli@users.noreply.github.com> Date: Thu, 18 Apr 2024 23:22:02 -0500 Subject: [PATCH 070/408] Trying to fix "floating invalid" error Previous commit has "floating invalid" error if I try to output P_AC as an h0 history field. After P_AC is taken out from history field, it allows I2000Clm51Sp to run without an error under DEBUG mode, but leads to "floating invalid" error for I2000Clm50Sp run after 18-20mins. --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 98d1d51989..c8566dcc82 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -297,7 +297,8 @@ subroutine urbantv_interp(this, bounds) end do else this%t_building_max(l) = spval - this%p_ac(l) = nan ! set to nan for non-urban landunit + ! this%p_ac(l) = nan ! set to nan for non-urban landunit + this%p_ac(l) = 0._r8 end if end do deallocate(dataptr2d) From 496d0903ad5bea1c1935e93f9666450579abcfa2 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Tue, 23 Apr 2024 08:32:34 -0600 Subject: [PATCH 071/408] Only output P_AC if urban_explicit_ac is .true. --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index c8566dcc82..23e30f3909 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -89,10 +89,12 @@ subroutine Init(this, bounds, NLFilename) avgflag='A', long_name='prescribed maximum interior building temperature', & ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & l2g_scale_type='unity') - call hist_addfld1d (fname='P_AC', units='a fraction between 0 and 1', & - avgflag='A', long_name='prescribed air-conditioning ownership rate', & - ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & - l2g_scale_type='unity') + if (urban_explicit_ac) then + call hist_addfld1d (fname='P_AC', units='a fraction between 0 and 1', & + avgflag='A', long_name='prescribed air-conditioning ownership rate', & + ptr_lunit=this%p_ac, default='inactive', set_nourb=spval, & + l2g_scale_type='unity') + end if end subroutine Init From 1ae7a195ffcf5cbfe312d9e83497c36cd97876f2 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Tue, 23 Apr 2024 12:11:42 -0600 Subject: [PATCH 072/408] Make P_AC history output consistent with TBUILD_MAX, TSA_U, etc. and only check for valid p_ac data if urban_explicit_ac is .true. --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index 23e30f3909..01f37da564 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -78,7 +78,7 @@ subroutine Init(this, bounds, NLFilename) ! Allocate urbantv data structure allocate(this%t_building_max(begl:endl)); this%t_building_max(:) = nan - allocate(this%p_ac(begl:endl)); this%p_ac(:) = 0._r8 + allocate(this%p_ac(begl:endl)); this%p_ac(:) = nan allocate(stream_varnames(stream_varname_MIN:stream_varname_MAX)) call this%urbantv_init(bounds, NLFilename) @@ -299,8 +299,7 @@ subroutine urbantv_interp(this, bounds) end do else this%t_building_max(l) = spval - ! this%p_ac(l) = nan ! set to nan for non-urban landunit - this%p_ac(l) = 0._r8 + this%p_ac(l) = spval end if end do deallocate(dataptr2d) @@ -314,8 +313,13 @@ subroutine urbantv_interp(this, bounds) ig = ig+1 if (g == lun%gridcell(l)) exit end do - if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8) & - .or. (this%p_ac(l) < 0._r8) .or. (this%p_ac(l) > 1._r8)) then ! check if AC adoption rate is outside of range 0 to 1 + ! Check for valid urban data + if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then + found = .true. + gindx = g + lindx = l + exit + else if (urban_explicit_ac .and. (this%p_ac(l) < 0._r8 .or. this%p_ac(l) > 1._r8)) then found = .true. gindx = g lindx = l From 526bc19b068546e4d92828cf44c86596010e9482 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 17 Apr 2024 15:39:56 -0600 Subject: [PATCH 073/408] Update CTSM to work with FATES LUH2. Some issues remain. --- bld/CLMBuildNamelist.pm | 26 +- bld/namelist_files/namelist_defaults_ctsm.xml | 10 +- .../namelist_definition_ctsm.xml | 26 +- bld/unit_testers/build-namelist_test.pl | 1 + .../testmods_dirs/clm/Fates/user_nl_clm | 2 +- .../clm/FatesColdLogging/user_nl_clm | 1 + .../usermods_dirs/fates_sp/user_nl_clm | 2 +- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 80 +++++- src/main/clm_instMod.F90 | 3 +- src/main/clm_varctl.F90 | 4 +- src/main/controlMod.F90 | 14 +- src/utils/clmfates_interfaceMod.F90 | 227 ++++++++++++++++-- 12 files changed, 351 insertions(+), 45 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 4df42d5e74..bcf68a8d61 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -783,7 +783,7 @@ sub setup_cmdl_fates_mode { # dis-allow fates specific namelist items with non-fates runs my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", - "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging", + "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode", "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" ); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { @@ -4370,7 +4370,7 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", - "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" ); + "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" ); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); @@ -4426,6 +4426,28 @@ sub setup_logic_fates { } } } + + # Check fates_harvest_mode compatibility + my $var = "fates_harvest_mode"; + if ( defined($nl->get_value($var)) ) { + # using fates_harvest_mode with CLM landuse driver data - for user convienence + # if ( $nl->get_value($var) == 2) { + # # Make sure that do_harvest is set to true + # if ( ! &value_is_true($nl->get_value('do_harvest')) ) { + # fatal_error("do_harvest must be true when $var is equal to 2" ); + # } + # using fates_harvest mode with raw luh2 harvest data + if ( $nl->get_value($var) > 2) { + # Make sure that use_fates_luh is true when using raw fates luh2 harvest data + if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { + fatal_error("use_fates_luh is required to be true when $var is greater than 2" ); + } + # do_harvest can not be on if we are using the raw fates luh2 harvest data + if ( &value_is_true($nl->get_value('do_harvest')) ) { + fatal_error("do_harvest can not be true when $var is greater than 2" ); + } + } + } } } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 7891361238..bc962d1b0f 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1572,11 +1572,14 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/surfdata_map/release-clm5.0.18/landuse.timeseries_10x15_SSP5-3.4_16pfts_Irrig_CMIP6_simyr1850-2100_c190228.nc - + lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc + +lnd/clm2/surfdata_map/fates-sci.1.73.0_api.33.0.0/fates_landuse_pft_map_4x5_240206.nc + lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc @@ -2756,14 +2759,17 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 0 +0 .false. .false. .false. .false. .false. -.false. .false. .false. +.false. +.true. +.true. .false. 1 0 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index b672b43125..fa2d83a3c9 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -734,10 +734,15 @@ Toggle to turn on no competition mode (only relevant if FATES is being used). Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used). - -Toggle to turn on the logging module -(Only relevant if FATES is on) + +Set FATES harvesting mode by setting fates_harvest_mode > 0. +Allowed values are: + 0 : no fates harvesting of any kind + 1 : fates logging via fates logging event codes (see fates parameter file) only + 2 : fates harvest driven by CLM landuse timeseries data (dynHarvestMod) + 3 : fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod) + 4 : fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod) If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file. +This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harvest +data (fates_harvest_mode >= 3) (Also, only valid for use_fates = true and is incompatible with transient runs currently.) + +If TRUE, ignore the land-use state vector and transitions, and assert that all lands +are primary, and that there is no harvest. + + @@ -793,6 +806,11 @@ types to vary over time. (Only relevant if FATES is on). + +Full pathname of fates landuse x pft data map. + + Toggle to turn on the LUNA model, to effect Photosynthesis by leaf Nitrogen diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 9b579dd9ce..899bd10b9c 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1046,6 +1046,7 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, + # TODO SSR: Replace this with fates_harvest_mode "useloggingButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", namelst=>"use_fates_logging=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 406fb598f6..91df3e2e61 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -16,7 +16,7 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', 'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR', -'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE', +'FATES_HARVEST_WOODPROD_C_FLUX', 'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL', 'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP', 'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY', diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm index 3b74a4fd37..5f457f3f1c 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm @@ -1 +1,2 @@ +! TODO SSR: Replace this with fates_harvest_mode use_fates_logging= .true. diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/fates_sp/user_nl_clm index 093ecd7eda..37da8d1c67 100644 --- a/cime_config/usermods_dirs/fates_sp/user_nl_clm +++ b/cime_config/usermods_dirs/fates_sp/user_nl_clm @@ -22,7 +22,7 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLD 'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR', 'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL', - 'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY', + 'FATES_HARVEST_WOODPROD_C_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX', 'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY', 'FATES_DDBH_CANOPY_SZ', 'FATES_DDBH_USTORY_SZ', 'FATES_BASALAREA_SZ', diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index 45f4340d6a..4f326d82a5 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -26,13 +26,39 @@ module dynFATESLandUseChangeMod ! Landuse state at beginning of year (fraction of gridcell), landuse state name x gridcell real(r8), allocatable, public :: landuse_states(:,:) + ! TODO SSR: Ask Charlie for description to go here + real(r8), allocatable, public :: landuse_harvest(:,:) + ! Number of landuse transition and state names integer, public, parameter :: num_landuse_transition_vars = 108 integer, public, parameter :: num_landuse_state_vars = 12 + integer, public, parameter :: num_landuse_harvest_vars = 5 + + ! Define the fates landuse namelist mode switch values + integer, public, parameter :: fates_harvest_no_logging = 0 + integer, public, parameter :: fates_harvest_logging_only = 1 + integer, public, parameter :: fates_harvest_clmlanduse = 2 + integer, public, parameter :: fates_harvest_luh_area = 3 + integer, public, parameter :: fates_harvest_luh_mass = 4 + + ! Define landuse harvest unit integer representation + integer, public, parameter :: landuse_harvest_area_units = 1 + integer, public, parameter :: landuse_harvest_mass_units = 2 + integer, public :: landuse_harvest_units ! landuse filename type(dyn_file_type), target :: dynFatesLandUse_file + ! LUH2 raw wood harvest area fraction + character(len=10), target :: landuse_harvest_area_varnames(num_landuse_harvest_vars) = & + [character(len=10) :: 'primf_harv', 'primn_harv', 'secmf_harv', 'secyf_harv', 'secnf_harv'] + + ! LUH2 raw wood harvest biomass carbon + character(len=10), target :: landuse_harvest_mass_varnames(num_landuse_harvest_vars) = & + [character(len=10) :: 'primf_bioh', 'primn_bioh', 'secmf_bioh', 'secyf_bioh', 'secnf_bioh'] + + character(len=10), public, pointer :: landuse_harvest_varnames(:) => null() + ! Land use name arrays character(len=5), public, parameter :: landuse_state_varnames(num_landuse_state_vars) = & [character(len=5) :: 'primf','primn','secdf','secdn','pastr','range', & @@ -64,8 +90,9 @@ module dynFATESLandUseChangeMod 'c3nfx_to_c3ann','c3nfx_to_c4ann','c3nfx_to_c3per','c3nfx_to_c4per', & 'c3nfx_to_secdf','c3nfx_to_secdn','c3nfx_to_pastr','c3nfx_to_range','c3nfx_to_urban'] - type(dyn_var_time_uninterp_type) :: landuse_transition_vars(num_landuse_transition_vars) ! value of each landuse variable - type(dyn_var_time_uninterp_type) :: landuse_state_vars(num_landuse_state_vars) ! value of each landuse variable + type(dyn_var_time_uninterp_type) :: landuse_transition_vars(num_landuse_transition_vars) ! value of each transitions variable + type(dyn_var_time_uninterp_type) :: landuse_state_vars(num_landuse_state_vars) ! value of each state variable + type(dyn_var_time_uninterp_type) :: landuse_harvest_vars(num_landuse_harvest_vars) ! value of each harvest variable public :: dynFatesLandUseInit public :: dynFatesLandUseInterp @@ -79,14 +106,14 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) ! Initialize data structures for land use information. ! !USES: - use clm_varctl , only : use_cn, use_fates_luh + use clm_varctl , only : use_cn, use_fates_luh, fates_harvest_mode use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type use dynTimeInfoMod , only : YEAR_POSITION_START_OF_TIMESTEP use dynTimeInfoMod , only : YEAR_POSITION_END_OF_TIMESTEP ! !ARGUMENTS: type(bounds_type), intent(in) :: bounds ! proc-level bounds - character(len=*) , intent(in) :: landuse_filename ! name of file containing land use information + character(len=*) , intent(in) :: landuse_filename ! name of file containing landuse timeseries information (fates luh2) ! !LOCAL VARIABLES integer :: varnum, i ! counter for harvest variables @@ -111,17 +138,23 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) if (ier /= 0) then call endrun(msg=' allocation error for landuse_transitions'//errMsg(__FILE__, __LINE__)) end if + allocate(landuse_harvest(num_landuse_harvest_vars,bounds%begg:bounds%endg),stat=ier) + if (ier /= 0) then + call endrun(msg=' allocation error for landuse_harvest'//errMsg(__FILE__, __LINE__)) + end if + ! Initialize the states, transitions and harvest mapping percentages as zero by default landuse_states = 0._r8 landuse_transitions = 0._r8 + landuse_harvest = 0._r8 if (use_fates_luh) then - ! Generate the dyn_file_type object. Note that the land use data being read in is for the - ! transitions occuring within the current year + ! Generate the dyn_file_type object. + ! Start calls get_prev_date, whereas end calls get_curr_date dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP) - ! Get initial land use data + ! Get initial land use data from the fates luh2 timeseries dataset num_points = (bounds%endg - bounds%begg + 1) landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor? do varnum = 1, num_landuse_transition_vars @@ -136,6 +169,28 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) dim1name=grlnd, conversion_factor=1.0_r8, & do_check_sums_equal_1=.false., data_shape=landuse_shape) end do + + ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled + if (fates_harvest_mode .ge. fates_harvest_luh_area ) then + + ! change the harvest varnames being used depending on the mode selected + if (fates_harvest_mode .eq. fates_harvest_luh_area ) then + landuse_harvest_varnames => landuse_harvest_area_varnames + landuse_harvest_units = landuse_harvest_area_units + elseif (fates_harvest_mode .eq. fates_harvest_luh_mass ) then + landuse_harvest_varnames => landuse_harvest_mass_varnames + landuse_harvest_units = landuse_harvest_mass_units + else + call endrun(msg=' undefined fates harvest mode selected'//errMsg(__FILE__, __LINE__)) + end if + + do varnum = 1, num_landuse_harvest_vars + landuse_harvest_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_harvest_varnames(varnum), & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=landuse_shape) + end do + end if end if ! Since fates needs state data during initialization, make sure to call @@ -159,7 +214,7 @@ subroutine dynFatesLandUseInterp(bounds, init_state) ! !USES: use dynTimeInfoMod , only : time_info_type - use clm_varctl , only : use_cn + use clm_varctl , only : use_cn, fates_harvest_mode ! !ARGUMENTS: type(bounds_type), intent(in) :: bounds ! proc-level bounds @@ -181,13 +236,14 @@ subroutine dynFatesLandUseInterp(bounds, init_state) init_flag = init_state end if - ! Get the current year + ! Get the data for the current year call dynFatesLandUse_file%time_info%set_current_year() if (dynFatesLandUse_file%time_info%is_before_time_series() .and. .not.(init_flag)) then ! Reset the land use transitions to zero for safety landuse_transitions(1:num_landuse_transition_vars,bounds%begg:bounds%endg) = 0._r8 landuse_states(1:num_landuse_state_vars,bounds%begg:bounds%endg) = 0._r8 + landuse_harvest(1:num_landuse_harvest_vars,bounds%begg:bounds%endg) = 0._r8 else ! Loop through all variables on the data file and put data into the temporary array ! then update the global state and transitions array. @@ -200,6 +256,12 @@ subroutine dynFatesLandUseInterp(bounds, init_state) call landuse_state_vars(varnum)%get_current_data(this_data) landuse_states(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg) end do + if (fates_harvest_mode .ge. fates_harvest_luh_area ) then + do varnum = 1, num_landuse_harvest_vars + call landuse_harvest_vars(varnum)%get_current_data(this_data) + landuse_harvest(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg) + end do + end if deallocate(this_data) end if diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 1ca450b48d..830dcfcca7 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -200,6 +200,7 @@ subroutine clm_instInit(bounds) use SoilWaterRetentionCurveFactoryMod , only : create_soil_water_retention_curve use decompMod , only : get_proc_bounds use BalanceCheckMod , only : GetBalanceCheckSkipSteps + use clm_varctl , only : flandusepftdat ! ! !ARGUMENTS type(bounds_type), intent(in) :: bounds ! processor bounds @@ -436,7 +437,7 @@ subroutine clm_instInit(bounds) ! Initialize the Functionaly Assembled Terrestrial Ecosystem Simulator (FATES) ! if (use_fates) then - call clm_fates%Init(bounds) + call clm_fates%Init(bounds, flandusepftdat) end if deallocate (h2osno_col) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index e0d142bffd..9ab6c631c7 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -302,7 +302,7 @@ module clm_varctl ! > 1 for external data (lightning and/or anthropogenic ignitions) ! see bld/namelist_files/namelist_definition_clm4_5.xml for details logical, public :: use_fates_tree_damage = .false. ! true => turn on tree damage module - logical, public :: use_fates_logging = .false. ! true => turn on logging module + integer, public :: fates_harvest_mode = 0 ! 0 for no harvest/logging; 1-4 for harvest mode options logical, public :: use_fates_planthydro = .false. ! true => turn on fates hydro logical, public :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking logical, public :: use_fates_ed_st3 = .false. ! true => static stand structure @@ -311,7 +311,9 @@ module clm_varctl logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode logical, public :: use_fates_luh = .false. ! true => use FATES landuse data mode + logical, public :: use_fates_potentialveg = .false. ! true => FATES potential veg only character(len=256), public :: fluh_timeseries = '' ! filename for fates landuse timeseries data + character(len=256), public :: flandusepftdat = '' ! filename for fates landuse x pft data character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control ! FATES SP AND FATES BGC are MUTUTALLY EXCLUSIVE, THEY CAN'T BOTH BE ON diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 44efec4eeb..196bc141ff 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -222,7 +222,7 @@ subroutine control_init(dtime) ! FATES Flags namelist /clm_inparm/ fates_paramfile, use_fates, & - fates_spitfire_mode, use_fates_logging, & + fates_spitfire_mode, fates_harvest_mode, & use_fates_planthydro, use_fates_ed_st3, & use_fates_cohort_age_tracking, & use_fates_ed_prescribed_phys, & @@ -231,7 +231,9 @@ subroutine control_init(dtime) use_fates_nocomp, & use_fates_sp, & use_fates_luh, & + use_fates_potentialveg, & fluh_timeseries, & + flandusepftdat, & fates_inventory_ctrl_filename, & fates_parteh_mode, & fates_seeddisp_cadence, & @@ -772,7 +774,7 @@ subroutine control_spmd() call mpi_bcast (for_testing_allow_interp_non_ciso_to_ciso, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_spitfire_mode, 1, MPI_INTEGER, 0, mpicom, ier) - call mpi_bcast (use_fates_logging, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (fates_harvest_mode, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_tree_damage, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_cohort_age_tracking, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -783,10 +785,12 @@ subroutine control_spmd() call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_luh, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_fates_potentialveg, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) - call mpi_bcast (fluh_timeseries, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (fluh_timeseries, len(fluh_timeseries) , MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (flandusepftdat, len(flandusepftdat) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_parteh_mode, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (fates_seeddisp_cadence, 1, MPI_INTEGER, 0, mpicom, ier) @@ -1144,7 +1148,7 @@ subroutine control_print () write(iulog, *) ' use_fates = ', use_fates if (use_fates) then write(iulog, *) ' fates_spitfire_mode = ', fates_spitfire_mode - write(iulog, *) ' use_fates_logging = ', use_fates_logging + write(iulog, *) ' fates_harvest_mode = ', fates_harvest_mode write(iulog, *) ' fates_paramfile = ', fates_paramfile write(iulog, *) ' fates_parteh_mode = ', fates_parteh_mode write(iulog, *) ' use_fates_planthydro = ', use_fates_planthydro @@ -1157,7 +1161,9 @@ subroutine control_print () write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp write(iulog, *) ' use_fates_luh= ', use_fates_luh + write(iulog, *) ' use_fates_potentialveg = ', use_fates_potentialveg write(iulog, *) ' fluh_timeseries = ', trim(fluh_timeseries) + write(iulog, *) ' flandusepftdat = ', trim(flandusepftdat) write(iulog, *) ' fates_seeddisp_cadence = ', fates_seeddisp_cadence write(iulog, *) ' fates_seeddisp_cadence: 0, 1, 2, 3 => off, daily, monthly, or yearly dispersal' write(iulog, *) ' fates_inventory_ctrl_filename = ', trim(fates_inventory_ctrl_filename) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 83d7186021..3f84a28508 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -54,12 +54,14 @@ module CLMFatesInterfaceMod use clm_varctl , only : use_fates_cohort_age_tracking use clm_varctl , only : use_fates_ed_st3 use clm_varctl , only : use_fates_ed_prescribed_phys - use clm_varctl , only : use_fates_logging + use clm_varctl , only : fates_harvest_mode use clm_varctl , only : use_fates_inventory_init use clm_varctl , only : use_fates_fixed_biogeog use clm_varctl , only : use_fates_nocomp use clm_varctl , only : use_fates_sp use clm_varctl , only : use_fates_luh + use clm_varctl , only : use_fates_potentialveg + use clm_varctl , only : flandusepftdat use clm_varctl , only : fates_seeddisp_cadence use clm_varctl , only : fates_inventory_ctrl_filename use clm_varctl , only : use_nitrif_denitrif @@ -180,6 +182,12 @@ module CLMFatesInterfaceMod use dynFATESLandUseChangeMod, only : landuse_transitions, landuse_states use dynFATESLandUseChangeMod, only : landuse_transition_varnames, landuse_state_varnames use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp + use dynFATESLandUseChangeMod, only : num_landuse_harvest_vars + use dynFATESLandUseChangeMod, only : fates_harvest_no_logging + use dynFATESLandUseChangeMod, only : fates_harvest_luh_area + use dynFATESLandUseChangeMod, only : landuse_harvest + use dynFATESLandUseChangeMod, only : landuse_harvest_units + use dynFATESLandUseChangeMod, only : landuse_harvest_varnames implicit none @@ -272,6 +280,8 @@ module CLMFatesInterfaceMod character(len=*), parameter, private :: sourcefile = & __FILE__ + integer, parameter :: num_landuse_pft_vars = 4 + public :: CLMFatesGlobals1 public :: CLMFatesGlobals2 @@ -384,8 +394,10 @@ subroutine CLMFatesGlobals2() integer :: pass_cohort_age_tracking integer :: pass_tree_damage integer :: pass_use_luh + integer :: pass_use_potentialveg integer :: pass_num_luh_states integer :: pass_num_luh_transitions + integer :: pass_lupftdat call t_startf('fates_globals2') @@ -477,7 +489,7 @@ subroutine CLMFatesGlobals2() end if call set_fates_ctrlparms('use_ed_st3',ival=pass_ed_st3) - if(use_fates_logging) then + if (fates_harvest_mode > fates_harvest_no_logging) then pass_logging = 1 else pass_logging = 0 @@ -505,8 +517,8 @@ subroutine CLMFatesGlobals2() end if call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking) - ! check fates logging namelist value first because hlm harvest overrides it - if(use_fates_logging) then + ! check fates logging namelist value first because hlm harvest can override it + if (fates_harvest_mode > fates_harvest_no_logging) then pass_logging = 1 else pass_logging = 0 @@ -521,23 +533,53 @@ subroutine CLMFatesGlobals2() pass_num_lu_harvest_cats = 0 end if - call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest) - call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats) - call set_fates_ctrlparms('use_logging',ival=pass_logging) - if(use_fates_luh) then pass_use_luh = 1 pass_num_luh_states = num_landuse_state_vars pass_num_luh_transitions = num_landuse_transition_vars + + ! Do not set harvest passing variables to zero not in luh harvest modes + ! as the user may want to use the CLM landuse harvest with luh2 transitions + if(fates_harvest_mode >= fates_harvest_luh_area) then + ! End the run if do_harvest is true with this run mode. + ! This should be caught be the build namelist. + if(get_do_harvest()) then + call endrun(msg="do_harvest and fates_harvest_mode using luh2 harvest data are incompatible"//& + errmsg(sourcefile, __LINE__)) + else + pass_lu_harvest = 1 + end if + end if else pass_use_luh = 0 pass_num_luh_states = 0 pass_num_luh_transitions = 0 end if + call set_fates_ctrlparms('use_luh2',ival=pass_use_luh) call set_fates_ctrlparms('num_luh2_states',ival=pass_num_luh_states) call set_fates_ctrlparms('num_luh2_transitions',ival=pass_num_luh_transitions) + if ( use_fates_potentialveg ) then + pass_use_potentialveg = 1 + else + pass_use_potentialveg = 0 + end if + call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg) + + if(flandusepftdat /= '') then + pass_lupftdat = 1 + else + pass_lupftdat = 0 + end if + call set_fates_ctrlparms('use_landusepft_data',ival=pass_lupftdat) + + ! Wait to set the harvest and logging variables after checking get_do_harvest + ! and fates_harvest_modes + call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest) + call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats) + call set_fates_ctrlparms('use_logging',ival=pass_logging) + if(use_fates_inventory_init) then pass_inventory_init = 1 else @@ -585,7 +627,7 @@ end subroutine CLMFatesTimesteps ! ==================================================================================== - subroutine init(this, bounds_proc ) + subroutine init(this, bounds_proc, flandusepftdat) ! --------------------------------------------------------------------------------- ! This initializes the hlm_fates_interface_type @@ -614,6 +656,7 @@ subroutine init(this, bounds_proc ) ! Input Arguments class(hlm_fates_interface_type), intent(inout) :: this type(bounds_type),intent(in) :: bounds_proc + character(len=*), intent(in) :: flandusepftdat ! local variables integer :: nclumps ! Number of threads @@ -631,6 +674,9 @@ subroutine init(this, bounds_proc ) integer :: ndecomp integer :: numg + real(r8), allocatable :: landuse_pft_map(:,:,:) + real(r8), allocatable :: landuse_bareground(:) + ! Initialize the FATES communicators with the HLM ! This involves to stages ! 1) allocate the vectors @@ -663,6 +709,13 @@ subroutine init(this, bounds_proc ) write(iulog,*) 'clm_fates%init(): allocating for ',nclumps,' threads' end if + ! Retrieve the landuse x pft static data if the file is present + if (flandusepftdat /= '') then + call GetLandusePFTData(bounds_proc, flandusepftdat, landuse_pft_map, landuse_bareground) + end if + + nclumps = get_proc_clumps() + allocate(copy_fates_var(bounds_proc%begc:bounds_proc%endc)) copy_fates_var(:) = .false. @@ -767,18 +820,26 @@ subroutine init(this, bounds_proc ) this%fates(nc)%sites(s)%lat = grc%latdeg(g) this%fates(nc)%sites(s)%lon = grc%londeg(g) - this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8 - ! initialize static layers for reduced complexity FATES versions from HLM - ! maybe make this into a subroutine of it's own later. - do m = surfpft_lb,surfpft_ub - ft = m - surfpft_lb - this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m) - end do + ! Transfer the landuse x pft data to fates via bc_in if file is given + if (flandusepftdat /= '') then + this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars) + this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g) + end if - if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > sum_to_1_tol) then - write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)%pft_areafrac(:)) - 1.0_r8 - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if + if (flandusepftdat == '') then + ! initialize static layers for reduced complexity FATES versions from HLM + ! maybe make this into a subroutine of it's own later. + this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8 + do m = surfpft_lb,surfpft_ub + ft = m - surfpft_lb + this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m) + end do + + if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > sum_to_1_tol) then + write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s) %pft_areafrac(:)) - 1.0_r8 + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + end if end do !site ! Initialize site-level static quantities dictated by the HLM @@ -820,6 +881,12 @@ subroutine init(this, bounds_proc ) ! Fire data to send to FATES call create_fates_fire_data_method( this%fates_fire_data_method ) + ! deallocate the local landuse x pft array + if (flandusepftdat /= '') then + deallocate(landuse_pft_map) + deallocate(landuse_bareground) + end if + call t_stopf('fates_init') end subroutine init @@ -1087,6 +1154,12 @@ subroutine dynamics_driv(this, nc, bounds_clump, & this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g) this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames + + if (fates_harvest_mode >= fates_harvest_luh_area) then + this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g) + this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames + this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units + end if end if end do @@ -2033,6 +2106,12 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g) this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames + + if (fates_harvest_mode >= fates_harvest_luh_area ) then + this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g) + this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames + this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units + end if end if end do @@ -3646,6 +3725,114 @@ subroutine GetAndSetTime() end subroutine GetAndSetTime + ! ====================================================================================== + + subroutine GetLandusePFTData(bounds, landuse_pft_file, landuse_pft_map, landuse_bareground) + + ! !DESCRIPTION: + ! Read in static landuse x pft file + + ! !USES: + use fileutils , only : getfil + use ncdio_pio , only : file_desc_t, ncd_io, ncd_inqdlen + use ncdio_pio , only : ncd_pio_openfile, ncd_pio_closefile + use decompMod , only : BOUNDS_LEVEL_PROC + use clm_varcon, only : grlnd + use FatesConstantsMod, only : fates_unset_r8 + + + ! !ARGUMENTS: + type(bounds_type), intent(in) :: bounds ! proc-level bounds + character(len=*) , intent(in) :: landuse_pft_file ! name of file containing static landuse x pft information + real(r8), allocatable, intent(inout) :: landuse_pft_map(:,:,:) + real(r8), allocatable, intent(inout) :: landuse_bareground(:) + + ! !LOCAL VARIABLES + integer :: varnum ! variable number + integer :: dimid, dimlen ! dimension id number and length + integer :: ier ! error id + character(len=256) :: locfn ! local file name + type(file_desc_t) :: ncid ! netcdf id + real(r8), pointer :: arraylocal(:,:) ! local array for reading fraction data + real(r8), pointer :: arraylocal_bareground(:) ! local array for reading bareground data + logical :: readvar ! true => variable is on dataset + !character(len=16), parameter :: grlnd = 'lndgrid' ! name of lndgrid + + integer, parameter :: dim_landuse_pft = 14 + + ! Land use name arrays + character(len=10), parameter :: landuse_pft_map_varnames(num_landuse_pft_vars) = & + [character(len=10) :: 'frac_primr','frac_secnd','frac_pastr','frac_range'] !need to move 'frac_surf' to a different variable + + character(len=*), parameter :: subname = 'GetLandusePFTData' + + !----------------------------------------------------------------------- + + ! Check to see if the landuse file name has been provided + ! Note: getfile checks this as well + if (masterproc) then + write(iulog,*) 'Attempting to read landuse x pft data .....' + if (landuse_pft_file == ' ') then + write(iulog,*)'landuse_pft_file must be specified' + call endrun(msg=errMsg(__FILE__, __LINE__)) + endif + endif + + ! Initialize the landuse x pft arrays and initialize to unset + allocate(landuse_pft_map(bounds%begg:bounds%endg,dim_landuse_pft,num_landuse_pft_vars),stat=ier) + if (ier /= 0) then + call endrun(msg=' allocation error for landuse_pft_map'//errMsg(__FILE__, __LINE__)) + end if + landuse_pft_map = fates_unset_r8 + + allocate(landuse_bareground(bounds%begg:bounds%endg),stat=ier) + if (ier /= 0) then + call endrun(msg=' allocation error for landuse_bareground'//errMsg(__FILE__, __LINE__)) + end if + landuse_bareground = fates_unset_r8 + + + ! Get the local filename and open the file + call getfil(landuse_pft_file, locfn, 0) + call ncd_pio_openfile (ncid, trim(locfn), 0) + + ! Check that natpft dimension on the file matches the target array dimensions + call ncd_inqdlen(ncid, dimid, dimlen, 'natpft') + if (dimlen /= dim_landuse_pft) then + write(iulog,*) 'natpft dimensions on the landuse x pft file do not match target array size' + call endrun(msg=errMsg(__FILE__, __LINE__)) + end if + + ! Allocate a temporary array since ncdio expects a pointer + allocate(arraylocal(bounds%begg:bounds%endg,dim_landuse_pft)) + allocate(arraylocal_bareground(bounds%begg:bounds%endg)) + + ! Read the landuse x pft data from file + do varnum = 1, num_landuse_pft_vars + call ncd_io(ncid=ncid, varname=landuse_pft_map_varnames(varnum), flag='read', & + data=arraylocal, dim1name=grlnd, readvar=readvar) + if (.not. readvar) & + call endrun(msg='ERROR: '//trim(landuse_pft_map_varnames(varnum))// & + ' NOT on landuse x pft file'//errMsg(__FILE__, __LINE__)) + landuse_pft_map(bounds%begg:bounds%endg,:,varnum) = arraylocal(bounds%begg:bounds%endg,:) + end do + + ! Read the bareground data from file. This is per gridcell only. + call ncd_io(ncid=ncid, varname='frac_brgnd', flag='read', & + data=arraylocal_bareground, dim1name=grlnd, readvar=readvar) + if (.not. readvar) call endrun(msg='ERROR: frac_brgnd NOT on landuse x pft file'//errMsg(__FILE__, __LINE__)) + landuse_bareground(bounds%begg:bounds%endg) = arraylocal_bareground(bounds%begg:bounds%endg) + + ! Deallocate the temporary local array point and close the file + deallocate(arraylocal) + deallocate(arraylocal_bareground) + call ncd_pio_closefile(ncid) + + ! Check that sums equal to unity + + end subroutine GetLandusePFTData + + !----------------------------------------------------------------------- end module CLMFatesInterfaceMod From 46420cfb64f4ebb2b092daef9071a3f070b403bf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 18 Apr 2024 09:40:21 -0600 Subject: [PATCH 074/408] Add fates_landuse_v2 test suite. --- cime_config/testdefs/testlist_clm.xml | 36 +++++++++++++++++++ .../clm/FatesColdLUH2Mode1/include_user_mods | 1 + .../clm/FatesColdLUH2Mode1/user_nl_clm | 1 + .../clm/FatesColdLUH2Mode2/include_user_mods | 1 + .../clm/FatesColdLUH2Mode2/user_nl_clm | 1 + .../clm/FatesColdLUH2Mode3/include_user_mods | 1 + .../clm/FatesColdLUH2Mode3/user_nl_clm | 1 + .../clm/FatesColdLUH2Mode4/include_user_mods | 1 + .../clm/FatesColdLUH2Mode4/user_nl_clm | 1 + 9 files changed, 44 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index dec8cf49d8..4184cc7e1f 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2910,6 +2910,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods new file mode 100644 index 0000000000..7eb8bb1579 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods @@ -0,0 +1 @@ +../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm new file mode 100644 index 0000000000..dea75b71e7 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm @@ -0,0 +1 @@ +fates_harvest_mode = 1 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods new file mode 100644 index 0000000000..7eb8bb1579 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods @@ -0,0 +1 @@ +../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm new file mode 100644 index 0000000000..fd4c74fe57 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm @@ -0,0 +1 @@ +fates_harvest_mode = 2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods new file mode 100644 index 0000000000..7eb8bb1579 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods @@ -0,0 +1 @@ +../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm new file mode 100644 index 0000000000..3332e9e526 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm @@ -0,0 +1 @@ +fates_harvest_mode = 3 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods new file mode 100644 index 0000000000..7eb8bb1579 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods @@ -0,0 +1 @@ +../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm new file mode 100644 index 0000000000..13dae9efee --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm @@ -0,0 +1 @@ +fates_harvest_mode = 4 From e4c8b6a0f1dfd0392fc956cf5d3f41e197508ba5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 18 Apr 2024 11:32:05 -0600 Subject: [PATCH 075/408] Point FATES external to my repo: Nag array index fix. --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 1494217277..ef4406545e 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/ckoven/fates -hash = d37d9733b5970dfe67a +repo_url = https://github.com/samsrabin/fates +hash = c03a4ba64a7e59817658f1c3357ffff681d8b958 required = True [externals_description] From 7216006b1c2400d1ca2932899671f9bcec85b6af Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 18 Apr 2024 16:48:41 -0600 Subject: [PATCH 076/408] Apply relevant changes from rgknox/fates-auto-params. --- .../testdefs/testmods_dirs/clm/Fates/shell_commands | 5 +++++ .../testdefs/testmods_dirs/clm/Fates/user_nl_clm | 1 + .../testdefs/testmods_dirs/clm/_scripts/README | 2 ++ .../clm/_scripts/get_fates_shell_commands_vars.sh | 11 +++++++++++ 4 files changed, 19 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/_scripts/README create mode 100755 cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands index 41a2342a51..3443bacef0 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands @@ -1,2 +1,7 @@ ./xmlchange CLM_BLDNML_OPTS="-no-megan" --append ./xmlchange BFBFLAG="TRUE" + +SRCROOT=`./xmlquery SRCROOT --value` +. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh + +ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 91df3e2e61..57adea1ff6 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -4,6 +4,7 @@ hist_nhtfrq = -24 hist_empty_htapes = .true. hist_ndens = 1 fates_spitfire_mode = 1 +fates_paramfile='${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc' hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', 'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON', diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/README b/cime_config/testdefs/testmods_dirs/clm/_scripts/README new file mode 100644 index 0000000000..66eb22a375 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/_scripts/README @@ -0,0 +1,2 @@ +This directory contains scripts that can be called in +shell_commands of multiple testmods. diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh b/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh new file mode 100755 index 0000000000..382fb4e53e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh @@ -0,0 +1,11 @@ +# This script should be called in shell_commands with +# . "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh +# where the leading period ensures it's run in the same shell. + +CASE=`./xmlquery CASE --value` +FATESDIR="${SRCROOT}/src/fates" +FATESPARAMDIR="${SRCROOT}/src/fates/parameter_files/binaries" +mkdir -p "${FATESPARAMDIR}" +FATESPARAMFILE="${FATESPARAMDIR}/${CASE}-params.nc" + +# No exit status because it should be called in the same shell. From a7c21a752224c09361b4280a730e5c61273244fa Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 23 Apr 2024 12:26:35 -0600 Subject: [PATCH 077/408] Don't allow flandusepftdat to be set in non-FATES runs. --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index bcf68a8d61..e3ceedeccc 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -784,7 +784,7 @@ sub setup_cmdl_fates_mode { my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode", - "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries" ); + "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat"); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { From 90a40281134953f3d371a6454642773035efe137 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 23 Apr 2024 12:27:16 -0600 Subject: [PATCH 078/408] Actually set flandusepftdat in CLMBuildNamelist.pm. --- bld/CLMBuildNamelist.pm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index e3ceedeccc..0f7f6891c5 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4424,6 +4424,9 @@ sub setup_logic_fates { } elsif ( ! -f "$fname" ) { $log->fatal_error("$fname does NOT point to a valid filename" ); } + + $var = "flandusepftdat"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); } } From d88fda01ba5904e80cf432f609cc10d4392f2767 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 23 Apr 2024 12:27:43 -0600 Subject: [PATCH 079/408] Update path for default flandusepftdat. --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index bc962d1b0f..66c0f837e0 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1578,7 +1578,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc -lnd/clm2/surfdata_map/fates-sci.1.73.0_api.33.0.0/fates_landuse_pft_map_4x5_240206.nc +lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc Date: Sun, 28 Apr 2024 13:45:50 -0600 Subject: [PATCH 080/408] Point FATES external back at Charlie's branch. --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index ef4406545e..b689141aaf 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/samsrabin/fates -hash = c03a4ba64a7e59817658f1c3357ffff681d8b958 +repo_url = https://github.com/ckoven/fates +hash = c1a7453c8331277a156a0ee158a870c1b8598a9f required = True [externals_description] From 0191278f95a35f90c76b7922fb51d8e42d68b24e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 28 Apr 2024 13:48:21 -0600 Subject: [PATCH 081/408] Add missing potential veg to build list. Manually cherry-picked from Greg Lemieux's b33a722. --- bld/CLMBuildNamelist.pm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 0f7f6891c5..7e2e4294af 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -784,7 +784,8 @@ sub setup_cmdl_fates_mode { my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode", - "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat"); + "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat", + "use_fates_potentialveg"); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { From fffb79409b29ed741c119d9fb37496898a689cd9 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 1 May 2024 15:46:26 -0700 Subject: [PATCH 082/408] add use_fates_lupft switch --- bld/CLMBuildNamelist.pm | 25 +++++++++++++++++++ bld/namelist_files/namelist_defaults_ctsm.xml | 18 +++++++------ .../namelist_definition_ctsm.xml | 6 +++++ src/main/clm_varctl.F90 | 1 + src/main/controlMod.F90 | 3 +++ src/utils/clmfates_interfaceMod.F90 | 16 ++++-------- 6 files changed, 51 insertions(+), 18 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 7e2e4294af..021381a18e 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4414,6 +4414,31 @@ sub setup_logic_fates { } } } + # make sure that fates landuse x pft mode has the necessary run mode configurations + # and add the necessary landuse x pft static mapping data default if not defined + my $var = "use_fates_lupft"; + if ( defined($nl->get_value($var)) ) { + if ( &value_is_true($nl->get_value($var)) ) { + $var = "flandusepftdat"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + if ( ! defined($nl->get_value($var)) ) { + fatal_error("$var is required when use_fates_lupft is set" ); + } elsif ( ! -f "$fname" ) { + fatal_error("$fname does NOT point to a valid filename" ); + } + } + # make sure that nocomp and fbg mode are enabled as well as use_fates_luh + my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" ); + foreach my $var ( @list ) { + if ( ! &value_is_true($nl->get_value($var)) ) { + fatal_error("$var is required when use_fates_lupft is true" ); + } + } + } + # check that fates landuse change mode has the necessary luh2 landuse timeseries data + # and add the default if not defined my $var = "use_fates_luh"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 66c0f837e0..49109c6591 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2767,17 +2767,21 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. +.false. .false. -.true. -.true. -.false. +.true. +.true. +.true. +.false. 1 0 -.true. -.false. -.true. -.false. +.true. +.true. +.false. +.true. +.true. +.false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index fa2d83a3c9..a2df9b1d1e 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -791,6 +791,12 @@ data (fates_harvest_mode >= 3) (Also, only valid for use_fates = true and is incompatible with transient runs currently.) + +If TRUE, enable use of fates land use x pft mapping data file. +(Only valid for use_fates = true and is incompatible with transient runs currently.) + + If TRUE, ignore the land-use state vector and transitions, and assert that all lands diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 9ab6c631c7..64d6e15747 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -311,6 +311,7 @@ module clm_varctl logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode logical, public :: use_fates_luh = .false. ! true => use FATES landuse data mode + logical, public :: use_fates_lupft = .false. ! true => use FATES landuse x pft static mapping mode logical, public :: use_fates_potentialveg = .false. ! true => FATES potential veg only character(len=256), public :: fluh_timeseries = '' ! filename for fates landuse timeseries data character(len=256), public :: flandusepftdat = '' ! filename for fates landuse x pft data diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 196bc141ff..55dd92305d 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -231,6 +231,7 @@ subroutine control_init(dtime) use_fates_nocomp, & use_fates_sp, & use_fates_luh, & + use_fates_lupft, & use_fates_potentialveg, & fluh_timeseries, & flandusepftdat, & @@ -785,6 +786,7 @@ subroutine control_spmd() call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_luh, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_fates_lupft, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_potentialveg, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier) @@ -1161,6 +1163,7 @@ subroutine control_print () write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp write(iulog, *) ' use_fates_luh= ', use_fates_luh + write(iulog, *) ' use_fates_lupft= ', use_fates_lupft write(iulog, *) ' use_fates_potentialveg = ', use_fates_potentialveg write(iulog, *) ' fluh_timeseries = ', trim(fluh_timeseries) write(iulog, *) ' flandusepftdat = ', trim(flandusepftdat) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 3f84a28508..b0ae0044f3 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -60,6 +60,7 @@ module CLMFatesInterfaceMod use clm_varctl , only : use_fates_nocomp use clm_varctl , only : use_fates_sp use clm_varctl , only : use_fates_luh + use clm_varctl , only : use_fates_lupft use clm_varctl , only : use_fates_potentialveg use clm_varctl , only : flandusepftdat use clm_varctl , only : fates_seeddisp_cadence @@ -567,13 +568,6 @@ subroutine CLMFatesGlobals2() end if call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg) - if(flandusepftdat /= '') then - pass_lupftdat = 1 - else - pass_lupftdat = 0 - end if - call set_fates_ctrlparms('use_landusepft_data',ival=pass_lupftdat) - ! Wait to set the harvest and logging variables after checking get_do_harvest ! and fates_harvest_modes call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest) @@ -710,7 +704,7 @@ subroutine init(this, bounds_proc, flandusepftdat) end if ! Retrieve the landuse x pft static data if the file is present - if (flandusepftdat /= '') then + if (use_fates_lupft) then call GetLandusePFTData(bounds_proc, flandusepftdat, landuse_pft_map, landuse_bareground) end if @@ -821,12 +815,12 @@ subroutine init(this, bounds_proc, flandusepftdat) this%fates(nc)%sites(s)%lon = grc%londeg(g) ! Transfer the landuse x pft data to fates via bc_in if file is given - if (flandusepftdat /= '') then + if (use_fates_lupft) then this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars) this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g) end if - if (flandusepftdat == '') then + if (.not. use_fates_lupft) then ! initialize static layers for reduced complexity FATES versions from HLM ! maybe make this into a subroutine of it's own later. this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8 @@ -882,7 +876,7 @@ subroutine init(this, bounds_proc, flandusepftdat) call create_fates_fire_data_method( this%fates_fire_data_method ) ! deallocate the local landuse x pft array - if (flandusepftdat /= '') then + if (use_fates_lupft) then deallocate(landuse_pft_map) deallocate(landuse_bareground) end if From 5d11bcf5c1ad64bb8898e54f15852315439c5d57 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 1 May 2024 15:52:27 -0700 Subject: [PATCH 083/408] add fates use_potentialveg namelist defaults settings and checks --- bld/CLMBuildNamelist.pm | 13 ++++++++++++- bld/namelist_files/namelist_defaults_ctsm.xml | 9 +++++---- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 021381a18e..7999e9a31d 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4455,7 +4455,18 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); } } - + # check that fates landuse is on and harvest mode is off when potential veg switch is true + my $var = "use_potentialveg"; + if ( defined($nl->get_value($var)) ) { + if ( &value_is_true($nl->get_value($var)) ) { + if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { + fatal_error("use_fates_luh must be true when $var is true" ); + } + if ( $nl->get_value('fates_harvest_mode') > 0) { + fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" ); + } + } + } # Check fates_harvest_mode compatibility my $var = "fates_harvest_mode"; if ( defined($nl->get_value($var)) ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 49109c6591..68a122e9bc 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2769,10 +2769,11 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. -.true. -.true. -.true. -.false. +.true. +.true. +.true. +.true. +.false. 1 0 From f0f2b9e17c17cc095832e4439313192fdea28a75 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 1 May 2024 16:58:18 -0600 Subject: [PATCH 084/408] Additional conflict resolution in testlist_clm.xml --- cime_config/testdefs/testlist_clm.xml | 35 +-------------------------- 1 file changed, 1 insertion(+), 34 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index d3ee1eae35..ff3d113c53 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -955,14 +955,6 @@ - - - - - - - - @@ -981,14 +973,6 @@ - - - - - - - - @@ -1062,15 +1046,6 @@ - - - - - - - - - @@ -1088,14 +1063,6 @@ - - - - - - - - @@ -2875,7 +2842,7 @@ - + From 3cc33e59813be988d983cfca47f2e9ef99819f1d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 2 May 2024 12:24:55 -0600 Subject: [PATCH 085/408] Update test to use a valid compset --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index ff3d113c53..cfd81a5a2b 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -830,7 +830,7 @@ - + From 6bd7d37a956edb0fc2bb20f7d593c64e4fa6eb0c Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 2 May 2024 11:49:28 -0700 Subject: [PATCH 086/408] add use_fates_lupft to default namelist --- bld/CLMBuildNamelist.pm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 7999e9a31d..23505492bd 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -785,7 +785,7 @@ sub setup_cmdl_fates_mode { "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode", "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries","flandusepftdat", - "use_fates_potentialveg"); + "use_fates_potentialveg","use_fates_lupft"); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { @@ -4371,7 +4371,8 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", - "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" ); + "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage", + "use_fates_luh","use_fates_lupft" ); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); From bbfe2b4542fc56b08cfeeffefc1b4e54f9572181 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 2 May 2024 15:07:50 -0600 Subject: [PATCH 087/408] Correction to last commit (1850 should have been 2000) --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index cfd81a5a2b..bf20c1241a 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -830,7 +830,7 @@ - + From 57004d92e39e6f83393f6f7c74cf3e21062e18c3 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 3 May 2024 17:34:08 -0600 Subject: [PATCH 088/408] New conflict resolution in testlist_clm.xml, this time for an izumi test --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index bf20c1241a..c2bb819572 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1652,7 +1652,7 @@ - + From edae95a1013439e234e7d56d57c01efc74ce063f Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sat, 4 May 2024 13:08:16 -0600 Subject: [PATCH 089/408] manually revert defaults for use_fates_lupft and fix calls to fatal_error --- bld/CLMBuildNamelist.pm | 25 +++++++++++-------- bld/namelist_files/namelist_defaults_ctsm.xml | 7 ++---- 2 files changed, 17 insertions(+), 15 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 23505492bd..01d583eb16 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4371,12 +4371,16 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", - "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage", - "use_fates_luh","use_fates_lupft" ); + "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage"); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); } + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_fates_lupft'=>$nl_flags->{'use_fates_lupft'} ); + my $suplnitro = $nl->get_value('suplnitro'); my $parteh_mode = $nl->get_value('fates_parteh_mode'); if ( ($parteh_mode == 1) && ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) { @@ -4384,6 +4388,7 @@ sub setup_logic_fates { "but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" . "Change suplnitro back to ALL"); } + # # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set # And also check for other settings that can't be trigged on as well @@ -4425,16 +4430,16 @@ sub setup_logic_fates { 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { - fatal_error("$var is required when use_fates_lupft is set" ); + $log->fatal_error("$var is required when use_fates_lupft is set" ); } elsif ( ! -f "$fname" ) { - fatal_error("$fname does NOT point to a valid filename" ); + $log->fatal_error("$fname does NOT point to a valid filename" ); } } # make sure that nocomp and fbg mode are enabled as well as use_fates_luh my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" ); foreach my $var ( @list ) { if ( ! &value_is_true($nl->get_value($var)) ) { - fatal_error("$var is required when use_fates_lupft is true" ); + $log->fatal_error("$var is required when use_fates_lupft is true" ); } } } @@ -4461,10 +4466,10 @@ sub setup_logic_fates { if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { - fatal_error("use_fates_luh must be true when $var is true" ); + $log->fatal_error("use_fates_luh must be true when $var is true" ); } if ( $nl->get_value('fates_harvest_mode') > 0) { - fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" ); + $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" ); } } } @@ -4475,17 +4480,17 @@ sub setup_logic_fates { # if ( $nl->get_value($var) == 2) { # # Make sure that do_harvest is set to true # if ( ! &value_is_true($nl->get_value('do_harvest')) ) { - # fatal_error("do_harvest must be true when $var is equal to 2" ); + # $log->fatal_error("do_harvest must be true when $var is equal to 2" ); # } # using fates_harvest mode with raw luh2 harvest data if ( $nl->get_value($var) > 2) { # Make sure that use_fates_luh is true when using raw fates luh2 harvest data if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { - fatal_error("use_fates_luh is required to be true when $var is greater than 2" ); + $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" ); } # do_harvest can not be on if we are using the raw fates luh2 harvest data if ( &value_is_true($nl->get_value('do_harvest')) ) { - fatal_error("do_harvest can not be true when $var is greater than 2" ); + $log->fatal_error("do_harvest can not be true when $var is greater than 2" ); } } } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 68a122e9bc..1195ba5329 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2769,19 +2769,16 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. -.true. -.true. + .true. -.true. .false. + 1 0 .true. -.true. .false. .true. -.true. .false. From af6a1c0e87a4f3d03e3fe6976b00af3ac94398f1 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sat, 4 May 2024 13:37:22 -0600 Subject: [PATCH 090/408] remove old flandusepftdat add_default and fix use_fates_lupft check this also temporarily removes the use_fates_lupft check for the use_fates_luh namelist defaults --- bld/CLMBuildNamelist.pm | 17 +++++++---------- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +----- 2 files changed, 8 insertions(+), 15 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 01d583eb16..1cb14878e7 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4389,7 +4389,6 @@ sub setup_logic_fates { "Change suplnitro back to ALL"); } - # # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set # And also check for other settings that can't be trigged on as well # @@ -4434,12 +4433,13 @@ sub setup_logic_fates { } elsif ( ! -f "$fname" ) { $log->fatal_error("$fname does NOT point to a valid filename" ); } - } - # make sure that nocomp and fbg mode are enabled as well as use_fates_luh - my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" ); - foreach my $var ( @list ) { - if ( ! &value_is_true($nl->get_value($var)) ) { - $log->fatal_error("$var is required when use_fates_lupft is true" ); + + # make sure that nocomp and fbg mode are enabled as well as use_fates_luh + my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" ); + foreach my $var ( @list ) { + if ( ! &value_is_true($nl->get_value($var)) ) { + $log->fatal_error("$var is required when use_fates_lupft is true" ); + } } } } @@ -4456,9 +4456,6 @@ sub setup_logic_fates { } elsif ( ! -f "$fname" ) { $log->fatal_error("$fname does NOT point to a valid filename" ); } - - $var = "flandusepftdat"; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); } } # check that fates landuse is on and harvest mode is off when potential veg switch is true diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 1195ba5329..e6f6b736a6 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2769,13 +2769,9 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. - -.true. -.false. - +.false. 1 0 - .true. .false. .true. From d5575d5c31e0013b8e303b3bc6966f6c8e405f55 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sat, 4 May 2024 14:42:15 -0600 Subject: [PATCH 091/408] correct call to add_default for use_fates_lupft dependency with use_fates_luh --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 1cb14878e7..7ad35584aa 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4379,7 +4379,7 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_fates_lupft'=>$nl_flags->{'use_fates_lupft'} ); + 'use_fates_lupft'=>$nl->get_value('use_fates_lupft') ); my $suplnitro = $nl->get_value('suplnitro'); my $parteh_mode = $nl->get_value('fates_parteh_mode'); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index e6f6b736a6..38a0fe6493 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2769,7 +2769,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. -.false. +.true. +.false. 1 0 .true. From ea773e451b78b3b7011a534a73352693600be95e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sat, 4 May 2024 14:53:16 -0600 Subject: [PATCH 092/408] add use_fates_lupft dependencies for nocomp and fbg --- bld/CLMBuildNamelist.pm | 10 ++++++++-- bld/namelist_files/namelist_defaults_ctsm.xml | 2 ++ 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 7ad35584aa..261c775fbd 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4370,7 +4370,7 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", + "use_fates_inventory_init","fates_seeddisp_cadence", "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage"); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, @@ -4380,6 +4380,12 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_lupft'=>$nl->get_value('use_fates_lupft') ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), + 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), + 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); my $suplnitro = $nl->get_value('suplnitro'); my $parteh_mode = $nl->get_value('fates_parteh_mode'); @@ -4435,7 +4441,7 @@ sub setup_logic_fates { } # make sure that nocomp and fbg mode are enabled as well as use_fates_luh - my @list = ( "use_fates_nocomp", "use_fates_fixed_biogeog, use_fates_luh" ); + my @list = ( "use_fates_luh", "use_fates_nocomp", "use_fates_fixed_biogeog" ); foreach my $var ( @list ) { if ( ! &value_is_true($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_lupft is true" ); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 38a0fe6493..216ad74ca1 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2774,8 +2774,10 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 1 0 .true. +.true. .false. .true. +.true. .false. From a21181f1b3e4a89f426e4b9bdce52e76b06ffc39 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sun, 5 May 2024 12:24:05 -0600 Subject: [PATCH 093/408] add fates_harvest_mode to use_fates_luh check --- bld/CLMBuildNamelist.pm | 3 ++- bld/namelist_files/namelist_defaults_ctsm.xml | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 261c775fbd..8af5f035e9 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4379,7 +4379,8 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_fates_lupft'=>$nl->get_value('use_fates_lupft') ); + 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), + 'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 216ad74ca1..206ab7cd1b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2769,6 +2769,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. +.true. +.true. .true. .false. 1 From d8178e415a399f2f0fd61b15f92b4c43f9dd4484 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sun, 5 May 2024 12:54:52 -0600 Subject: [PATCH 094/408] add use_fates_potentialveg to use_fates_luh check --- bld/CLMBuildNamelist.pm | 4 +++- bld/namelist_files/namelist_defaults_ctsm.xml | 7 ++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 8af5f035e9..b450060736 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4377,9 +4377,11 @@ sub setup_logic_fates { 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_potentialveg', 'use_fates'=>$nl_flags->{'use_fates'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), + 'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'), 'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), @@ -4466,7 +4468,7 @@ sub setup_logic_fates { } } # check that fates landuse is on and harvest mode is off when potential veg switch is true - my $var = "use_potentialveg"; + my $var = "use_fates_potentialveg"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 206ab7cd1b..9d2a34b7bf 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2769,10 +2769,11 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. -.true. -.true. +.true. +.true. .true. -.false. +.true. +.false. 1 0 .true. From 9751fb68174903134e301472087edc263bc4822e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sun, 5 May 2024 13:01:20 -0600 Subject: [PATCH 095/408] add check to fates sp mode to make sure landuse isn't enabled --- bld/CLMBuildNamelist.pm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index b450060736..54f0c0c997 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4414,6 +4414,10 @@ sub setup_logic_fates { if ( $nl->get_value('fates_spitfire_mode') > 0 ) { $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true'); } + # fates landuse can't be on with FATES SP mode is active + if ( &value_is_true($nl->get_value('use_fates_luh')) ) { + $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true'); + } } } my $var = "use_fates_inventory_init"; From 75f9cc54227f39f7baabc430de7a12506b892192 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 6 May 2024 15:35:56 -0700 Subject: [PATCH 096/408] rename luh unit test that matched old test --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 899bd10b9c..0bf0ea5390 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1062,7 +1062,7 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, - "useinventorybutnotfile" =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan", + "useLUH2butnotfile" =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan", namelst=>"use_fates_luh=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", From ff3af55931b98e9cb7b9553717d10f2388954197 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 6 May 2024 16:24:30 -0700 Subject: [PATCH 097/408] add build namelist unit tests for fates landuse v2 --- bld/unit_testers/build-namelist_test.pl | 41 +++++++++++++++++++++++-- 1 file changed, 38 insertions(+), 3 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 0bf0ea5390..70243c5843 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1999; +my $ntests = 2006; if ( defined($opts{'compare'}) ) { - $ntests += 1353; + $ntests += 1360; } plan( tests=>$ntests ); @@ -1062,11 +1062,16 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, - "useLUH2butnotfile" =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan", + "useFATESLUH2butnotfile" =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan", namelst=>"use_fates_luh=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, + "useFATESLUPFTbutnotfile" =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan", + namelst=>"use_fates_lupft=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, "inventoryfileDNE" =>{ options=>"-bgc fates -envxml_dir . -no-megan", namelst=>"use_fates_luh=.true., fluh_timeseries='zztop'", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -1092,6 +1097,36 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, + "useFATESSPwithLUH" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_sp=T,use_fates_luh=T", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_potentialveg=T,fates_harvest_mode=1", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "useFATESHARVEST3WOLUH" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_luh=F,fates_harvest_mode=3", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "useFATESLUPFTWOLUH" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_lupft=T,use_fates_luh=F", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "useFATESLUPFTWONOCOMP" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_lupft=T,use_fates_nocomp=F", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "useFATESLUPFTWOFBG" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_lupft=T,use_fates_fixedbiogeog=F", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, "useFATESTRANSWdynPFT" =>{ options=>"-bgc fates -envxml_dir . -use_case 20thC_transient -no-megan", namelst=>"do_transient_pfts=T", GLC_TWO_WAY_COUPLING=>"FALSE", From 69154dab7b33706491bdabc634d9a80142bf0b35 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 6 May 2024 16:37:07 -0700 Subject: [PATCH 098/408] update fates logging unit test to use new fates harvest mode --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- bld/unit_testers/build-namelist_test.pl | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a2df9b1d1e..edcfa36d27 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -814,7 +814,7 @@ types to vary over time. -Full pathname of fates landuse x pft data map. +Full pathname of fates landuse x pft static data map. "FALSE", phys=>"clm4_5", }, - # TODO SSR: Replace this with fates_harvest_mode "useloggingButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", - namelst=>"use_fates_logging=.true.", + namelst=>"fates_harvest_mode=1", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, From 5c5ca6f8e40cc6fe69d9b9a7edf32ce5242a7629 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 6 May 2024 17:49:34 -0600 Subject: [PATCH 099/408] minor update --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 3b2dabd057..f674849b6f 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 2006; +my $ntests = 2007; if ( defined($opts{'compare'}) ) { $ntests += 1360; From 2a88002ea1a916d21da69b05c6621774cca74b39 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 7 May 2024 10:26:16 -0700 Subject: [PATCH 100/408] change lupft check to fbg + luh check to mirror fates-side logic --- src/utils/clmfates_interfaceMod.F90 | 37 ++++++++++++++--------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index b0ae0044f3..048824a83a 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -398,7 +398,6 @@ subroutine CLMFatesGlobals2() integer :: pass_use_potentialveg integer :: pass_num_luh_states integer :: pass_num_luh_transitions - integer :: pass_lupftdat call t_startf('fates_globals2') @@ -704,7 +703,7 @@ subroutine init(this, bounds_proc, flandusepftdat) end if ! Retrieve the landuse x pft static data if the file is present - if (use_fates_lupft) then + if (use_fates_fixed_biogeog .and. use_fates_luh) then call GetLandusePFTData(bounds_proc, flandusepftdat, landuse_pft_map, landuse_bareground) end if @@ -815,23 +814,23 @@ subroutine init(this, bounds_proc, flandusepftdat) this%fates(nc)%sites(s)%lon = grc%londeg(g) ! Transfer the landuse x pft data to fates via bc_in if file is given - if (use_fates_lupft) then - this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars) - this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g) - end if - - if (.not. use_fates_lupft) then - ! initialize static layers for reduced complexity FATES versions from HLM - ! maybe make this into a subroutine of it's own later. - this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8 - do m = surfpft_lb,surfpft_ub - ft = m - surfpft_lb - this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m) - end do + if (use_fates_fixed_biogeog) then + if (use_fates_luh) then + this%fates(nc)%bc_in(s)%pft_areafrac_lu(:,1:num_landuse_pft_vars) = landuse_pft_map(g,:,1:num_landuse_pft_vars) + this%fates(nc)%bc_in(s)%baregroundfrac = landuse_bareground(g) + else + ! initialize static layers for reduced complexity FATES versions from HLM + ! maybe make this into a subroutine of it's own later. + this%fates(nc)%bc_in(s)%pft_areafrac(:)=0._r8 + do m = surfpft_lb,surfpft_ub + ft = m - surfpft_lb + this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m) + end do - if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > sum_to_1_tol) then - write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s) %pft_areafrac(:)) - 1.0_r8 - call endrun(msg=errMsg(sourcefile, __LINE__)) + if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > sum_to_1_tol) then + write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s) %pft_areafrac(:)) - 1.0_r8 + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if end if end if end do !site @@ -876,7 +875,7 @@ subroutine init(this, bounds_proc, flandusepftdat) call create_fates_fire_data_method( this%fates_fire_data_method ) ! deallocate the local landuse x pft array - if (use_fates_lupft) then + if (use_fates_fixed_biogeog .and. use_fates_luh) then deallocate(landuse_pft_map) deallocate(landuse_bareground) end if From 0bcf80acea865f2df37d13911aa6b9d167622a66 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 1 May 2024 16:37:32 -0600 Subject: [PATCH 101/408] FatesColdLUH2 tests now use use_fates_nocomp false. --- cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm index 854c21407f..917ba314b3 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm @@ -1 +1,2 @@ use_fates_luh = .true. +use_fates_nocomp = .false. From 0edcb1b5b118c7029807a05e1ce3773396c6ec7f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 May 2024 10:22:47 -0600 Subject: [PATCH 102/408] Update FATES external to latest ckoven/luh2_nocomp_merge. --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index b689141aaf..e1bc1696af 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/ckoven/fates -hash = c1a7453c8331277a156a0ee158a870c1b8598a9f +hash = 153b0bda9c96f18e8d2a93887a082bc7a31b574b required = True [externals_description] From 92fb80687f707c1799cacea85bc64bc9c1cd9f89 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 May 2024 13:25:19 -0600 Subject: [PATCH 103/408] Update FatesColdLUH2 testdef. --- .../testmods_dirs/clm/FatesColdLUH2/user_nl_clm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm index 917ba314b3..970e7df7cd 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm @@ -1,2 +1,11 @@ + +! Run a transient case, with vegetation starting from bare ground, but land use starting from LUH state vector on starting date, in a nocomp configuration. +! From Charlie's list of valid FATES configurations: +! https://docs.google.com/spreadsheets/d/1eE3sRMYxfocZKbT8uIQhXpjjtfM2feXPRSWXJNoo4jM/edit#gid=0 +flandusepftdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc' use_fates_luh = .true. -use_fates_nocomp = .false. +use_fates_nocomp = .true. +use_fates_fixed_biogeog = .true. +use_fates_sp = .false. +use_fates_potentialveg = .false. +fluh_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc' From f6728017c7726f947492179f88031cccfa81181f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 May 2024 13:26:56 -0600 Subject: [PATCH 104/408] Add FatesColdLUH2Mode0 testdef. --- cime_config/testdefs/testlist_clm.xml | 9 +++++++++ .../clm/FatesColdLUH2Mode0/include_user_mods | 1 + .../testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm | 1 + 3 files changed, 11 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 4184cc7e1f..022bb9ad73 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2910,6 +2910,15 @@ + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods new file mode 100644 index 0000000000..7eb8bb1579 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods @@ -0,0 +1 @@ +../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm new file mode 100644 index 0000000000..929a8e6e14 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm @@ -0,0 +1 @@ +fates_harvest_mode = 0 From 05332fb117e7ed94abcc09c5c66f5db8d8885638 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 9 May 2024 10:53:59 -0700 Subject: [PATCH 105/408] Remove get_do_harvest dependency for fates harvest modes --- src/dyn_subgrid/dynSubgridDriverMod.F90 | 7 ++- src/utils/clmfates_interfaceMod.F90 | 71 +++++++++---------------- 2 files changed, 32 insertions(+), 46 deletions(-) diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90 index e5ca3f002e..b12b135b59 100644 --- a/src/dyn_subgrid/dynSubgridDriverMod.F90 +++ b/src/dyn_subgrid/dynSubgridDriverMod.F90 @@ -89,6 +89,11 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst) ! Note that dynpft_init needs to be called from outside any loops over clumps - so ! this routine needs to be called from outside any loops over clumps. ! + ! + ! !USES: + use clm_varctl , only : fates_harvest_mode + use dynFATESLandUseChangeMod , only : fates_harvest_clmlanduse + ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds_proc ! processor-level bounds type(glc_behavior_type) , intent(in) :: glc_behavior @@ -123,7 +128,7 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst) ! flanduse_timeseries file. However, this could theoretically be changed so that the ! harvest data were separated from the pftdyn data, allowing them to differ in the ! years over which they apply. - if (get_do_harvest()) then + if (get_do_harvest() .or. fates_harvest_mode >= fates_harvest_clmlanduse) then call dynHarvest_init(bounds_proc, harvest_filename=get_flanduse_timeseries()) end if diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 048824a83a..308d5cee8e 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -169,7 +169,6 @@ module CLMFatesInterfaceMod use FATESFireBase , only : fates_fire_base_type use FATESFireFactoryMod , only : no_fire, scalar_lightning, successful_ignitions,& anthro_ignitions, anthro_suppression - use dynSubgridControlMod , only : get_do_harvest use dynHarvestMod , only : num_harvest_inst, harvest_varnames use dynHarvestMod , only : harvest_units, mass_units, unitless_units use dynHarvestMod , only : dynHarvest_interp_resolve_harvesttypes @@ -185,6 +184,7 @@ module CLMFatesInterfaceMod use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp use dynFATESLandUseChangeMod, only : num_landuse_harvest_vars use dynFATESLandUseChangeMod, only : fates_harvest_no_logging + use dynFATESLandUseChangeMod, only : fates_harvest_clmlanduse use dynFATESLandUseChangeMod, only : fates_harvest_luh_area use dynFATESLandUseChangeMod, only : landuse_harvest use dynFATESLandUseChangeMod, only : landuse_harvest_units @@ -489,13 +489,6 @@ subroutine CLMFatesGlobals2() end if call set_fates_ctrlparms('use_ed_st3',ival=pass_ed_st3) - if (fates_harvest_mode > fates_harvest_no_logging) then - pass_logging = 1 - else - pass_logging = 0 - end if - call set_fates_ctrlparms('use_logging',ival=pass_logging) - if(use_fates_ed_prescribed_phys) then pass_ed_prescribed_phys = 1 else @@ -517,39 +510,28 @@ subroutine CLMFatesGlobals2() end if call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking) - ! check fates logging namelist value first because hlm harvest can override it + ! FATES logging and harvest modes if (fates_harvest_mode > fates_harvest_no_logging) then - pass_logging = 1 - else - pass_logging = 0 - end if - - if(get_do_harvest()) then - pass_logging = 1 - pass_num_lu_harvest_cats = num_harvest_inst - pass_lu_harvest = 1 - else - pass_lu_harvest = 0 - pass_num_lu_harvest_cats = 0 - end if + pass_logging = 1 ! Time driven logging, without landuse harvest + ! CLM landuse timeseries driven harvest rates + if (fates_harvest_mode == fates_harvest_clmlanduse) + pass_num_lu_harvest_cats = num_harvest_inst + pass_lu_harvest = 1 + + ! LUH2 landuse timeseries driven harvest rates + else if (fates_harvest_mode >= fates_harvest_luh_area) then + pass_lu_harvest = 1 + pass_num_lu_harvest_types = num_landuse_harvest_vars + else + pass_lu_harvest = 0 + pass_num_lu_harvest_cats = 0 + end if + ! FATES landuse modes if(use_fates_luh) then pass_use_luh = 1 pass_num_luh_states = num_landuse_state_vars pass_num_luh_transitions = num_landuse_transition_vars - - ! Do not set harvest passing variables to zero not in luh harvest modes - ! as the user may want to use the CLM landuse harvest with luh2 transitions - if(fates_harvest_mode >= fates_harvest_luh_area) then - ! End the run if do_harvest is true with this run mode. - ! This should be caught be the build namelist. - if(get_do_harvest()) then - call endrun(msg="do_harvest and fates_harvest_mode using luh2 harvest data are incompatible"//& - errmsg(sourcefile, __LINE__)) - else - pass_lu_harvest = 1 - end if - end if else pass_use_luh = 0 pass_num_luh_states = 0 @@ -567,8 +549,7 @@ subroutine CLMFatesGlobals2() end if call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg) - ! Wait to set the harvest and logging variables after checking get_do_harvest - ! and fates_harvest_modes + ! Wait to set the harvest and logging variables after checking fates_harvest_modes call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest) call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats) call set_fates_ctrlparms('use_logging',ival=pass_logging) @@ -996,7 +977,8 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! Set the FATES global time and date variables call GetAndSetTime - if (get_do_harvest()) then + ! Get harvest rates for CLM landuse timeseries driven rates + if (fates_harvest_mode == fates_harvest_clmlanduse) call dynHarvest_interp_resolve_harvesttypes(bounds_clump, & harvest_rates=harvest_rates(begg:endg,1:num_harvest_inst), & after_start_of_harvest_ts=after_start_of_harvest_ts) @@ -1122,7 +1104,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! for now there is one veg column per gridcell, so store all harvest data in each site ! this will eventually change ! today's hlm harvest flag needs to be set no matter what - if (get_do_harvest()) then + if (fates_harvest_mode == fates_harvest_clmlanduse) if (after_start_of_harvest_ts) then this%fates(nc)%bc_in(s)%hlm_harvest_rates(1:num_harvest_inst) = harvest_rates(g,1:num_harvest_inst) else @@ -1140,6 +1122,11 @@ subroutine dynamics_driv(this, nc, bounds_clump, & write(iulog,*) harvest_units call endrun(msg=errMsg(sourcefile, __LINE__)) end if + + else if (fates_harvest_mode >= fates_harvest_luh_area) then + this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g) + this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames + this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units endif if (use_fates_luh) then @@ -1147,12 +1134,6 @@ subroutine dynamics_driv(this, nc, bounds_clump, & this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g) this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames - - if (fates_harvest_mode >= fates_harvest_luh_area) then - this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g) - this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames - this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units - end if end if end do From a35f91d53444c2ac7af2ee1434ae0f85431208b4 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 9 May 2024 11:15:18 -0700 Subject: [PATCH 106/408] fix check to be only during use of clm landuse timeseries for fates --- src/dyn_subgrid/dynSubgridDriverMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90 index b12b135b59..162247a0ff 100644 --- a/src/dyn_subgrid/dynSubgridDriverMod.F90 +++ b/src/dyn_subgrid/dynSubgridDriverMod.F90 @@ -128,7 +128,7 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst) ! flanduse_timeseries file. However, this could theoretically be changed so that the ! harvest data were separated from the pftdyn data, allowing them to differ in the ! years over which they apply. - if (get_do_harvest() .or. fates_harvest_mode >= fates_harvest_clmlanduse) then + if (get_do_harvest() .or. fates_harvest_mode == fates_harvest_clmlanduse) then call dynHarvest_init(bounds_proc, harvest_filename=get_flanduse_timeseries()) end if From 74e86669d21c18043a057d955f55e17bd5e7913e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 9 May 2024 11:48:57 -0700 Subject: [PATCH 107/408] fix passing num landuse harvest vars to the fates landuse harvest categories --- src/utils/clmfates_interfaceMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 308d5cee8e..cd94b6a15c 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -521,7 +521,7 @@ subroutine CLMFatesGlobals2() ! LUH2 landuse timeseries driven harvest rates else if (fates_harvest_mode >= fates_harvest_luh_area) then pass_lu_harvest = 1 - pass_num_lu_harvest_types = num_landuse_harvest_vars + pass_num_lu_harvest_cats = num_landuse_harvest_vars else pass_lu_harvest = 0 pass_num_lu_harvest_cats = 0 From fd07890223b3e92d91caa1a034055d1184bcff2e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 9 May 2024 11:51:20 -0700 Subject: [PATCH 108/408] fix missing end if --- src/utils/clmfates_interfaceMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index cd94b6a15c..b9e9bf3031 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -526,6 +526,7 @@ subroutine CLMFatesGlobals2() pass_lu_harvest = 0 pass_num_lu_harvest_cats = 0 end if + end if ! FATES landuse modes if(use_fates_luh) then From 72ed62381b8312b0f0355b938d30c8b1a852cb31 Mon Sep 17 00:00:00 2001 From: loaner Date: Thu, 9 May 2024 16:25:53 -0700 Subject: [PATCH 109/408] update do_harvest to not be compatible with fates --- bld/CLMBuildNamelist.pm | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 54f0c0c997..e422109078 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2932,7 +2932,7 @@ sub setup_logic_do_harvest { $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; } - elsif (!&value_is_true($nl->get_value('use_cn')) && !&value_is_true($nl->get_value('use_fates'))) { + elsif (!&value_is_true($nl->get_value('use_cn')) && &value_is_true($nl->get_value('use_fates'))) { $cannot_be_true = "$var can only be set to true when running with either CN or FATES"; } @@ -4486,22 +4486,12 @@ sub setup_logic_fates { # Check fates_harvest_mode compatibility my $var = "fates_harvest_mode"; if ( defined($nl->get_value($var)) ) { - # using fates_harvest_mode with CLM landuse driver data - for user convienence - # if ( $nl->get_value($var) == 2) { - # # Make sure that do_harvest is set to true - # if ( ! &value_is_true($nl->get_value('do_harvest')) ) { - # $log->fatal_error("do_harvest must be true when $var is equal to 2" ); - # } # using fates_harvest mode with raw luh2 harvest data if ( $nl->get_value($var) > 2) { # Make sure that use_fates_luh is true when using raw fates luh2 harvest data if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" ); } - # do_harvest can not be on if we are using the raw fates luh2 harvest data - if ( &value_is_true($nl->get_value('do_harvest')) ) { - $log->fatal_error("do_harvest can not be true when $var is greater than 2" ); - } } } } From cf1a297864938fae60288ce742adfb2150e5caf8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 9 May 2024 17:28:23 -0600 Subject: [PATCH 110/408] Update Externals.cfg to cesm2_3_beta17 --- Externals.cfg | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index 185f412cab..80bfb45db8 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -8,7 +8,7 @@ required = True local_path = components/cism protocol = git repo_url = https://github.com/ESCOMP/CISM-wrapper -tag = cismwrap_2_1_99 +tag = cismwrap_2_1_100 externals = Externals_CISM.cfg required = True @@ -29,12 +29,12 @@ required = True [mizuRoute] local_path = components/mizuRoute protocol = git -repo_url = https://github.com/nmizukami/mizuRoute -hash = 34723c2 +repo_url = https://github.com/ESCOMP/mizuRoute +hash = 81c720c required = True [ccs_config] -tag = ccs_config_cesm0.0.92 +tag = ccs_config_cesm0.0.106 protocol = git repo_url = https://github.com/ESMCI/ccs_config_cesm.git local_path = ccs_config @@ -44,18 +44,18 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.217_httpsbranch03 +tag = cime6.0.238_httpsbranch01 required = True [cmeps] -tag = cmeps0.14.50 +tag = cmeps0.14.60 protocol = git repo_url = https://github.com/ESCOMP/CMEPS.git local_path = components/cmeps required = True [cdeps] -tag = cdeps1.0.28 +tag = cdeps1.0.33 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps From 2aa76c4b3f841d35d465a254285daeb075f9d7cc Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 9 May 2024 17:46:05 -0600 Subject: [PATCH 111/408] Remove mct from Externals.cfg --- Externals.cfg | 7 ------- 1 file changed, 7 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index 80bfb45db8..e8a2121df5 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -76,13 +76,6 @@ repo_url = https://github.com/ESCOMP/CESM_share local_path = share required = True -[mct] -tag = MCT_2.11.0 -protocol = git -repo_url = https://github.com/MCSclimate/MCT -local_path = libraries/mct -required = True - [parallelio] tag = pio2_6_2 protocol = git From ccce061987e7dc193aec37e53d7f46fa441d2147 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 9 May 2024 17:49:34 -0600 Subject: [PATCH 112/408] Remove cpl7 from Externals.cfg --- Externals.cfg | 7 ------- 1 file changed, 7 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index e8a2121df5..a8a77a40f1 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -62,13 +62,6 @@ local_path = components/cdeps externals = Externals_CDEPS.cfg required = True -[cpl7] -tag = cpl77.0.7 -protocol = git -repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps -local_path = components/cpl7 -required = True - [share] tag = share1.0.18 protocol = git From f00ba49d552a3dc3578012f1cf32e6925ac224f9 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 9 May 2024 17:58:07 -0600 Subject: [PATCH 113/408] remove fates from the do_harvest section altogether --- bld/CLMBuildNamelist.pm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index e422109078..aafc7739a3 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2932,8 +2932,8 @@ sub setup_logic_do_harvest { $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; } - elsif (!&value_is_true($nl->get_value('use_cn')) && &value_is_true($nl->get_value('use_fates'))) { - $cannot_be_true = "$var can only be set to true when running with either CN or FATES"; + elsif (!&value_is_true($nl->get_value('use_cn'))) { + $cannot_be_true = "$var can only be set to true when running with CN. Please set use_cn to true."; } if ($cannot_be_true) { From 278a901fc4821e0c6abef4e0c5ed9bbf41f64516 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 10 May 2024 10:43:41 -0700 Subject: [PATCH 114/408] fix if statements --- src/utils/clmfates_interfaceMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index b9e9bf3031..5c23f1c1dc 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -514,7 +514,7 @@ subroutine CLMFatesGlobals2() if (fates_harvest_mode > fates_harvest_no_logging) then pass_logging = 1 ! Time driven logging, without landuse harvest ! CLM landuse timeseries driven harvest rates - if (fates_harvest_mode == fates_harvest_clmlanduse) + if (fates_harvest_mode == fates_harvest_clmlanduse) then pass_num_lu_harvest_cats = num_harvest_inst pass_lu_harvest = 1 @@ -979,7 +979,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call GetAndSetTime ! Get harvest rates for CLM landuse timeseries driven rates - if (fates_harvest_mode == fates_harvest_clmlanduse) + if (fates_harvest_mode == fates_harvest_clmlanduse) then call dynHarvest_interp_resolve_harvesttypes(bounds_clump, & harvest_rates=harvest_rates(begg:endg,1:num_harvest_inst), & after_start_of_harvest_ts=after_start_of_harvest_ts) @@ -1105,7 +1105,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! for now there is one veg column per gridcell, so store all harvest data in each site ! this will eventually change ! today's hlm harvest flag needs to be set no matter what - if (fates_harvest_mode == fates_harvest_clmlanduse) + if (fates_harvest_mode == fates_harvest_clmlanduse) then if (after_start_of_harvest_ts) then this%fates(nc)%bc_in(s)%hlm_harvest_rates(1:num_harvest_inst) = harvest_rates(g,1:num_harvest_inst) else From 4861125a7a9c81008de5cb218755cd9792db0bb9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 13:11:58 -0600 Subject: [PATCH 115/408] Remove MCT from README and .config_files.xml --- .config_files.xml | 3 --- README | 5 ++--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/.config_files.xml b/.config_files.xml index d1a592e5db..7f0d6bb11a 100644 --- a/.config_files.xml +++ b/.config_files.xml @@ -19,11 +19,8 @@ $SRCROOT $SRCROOT/components/slim/ - $SRCROOT/components/cpl7/components/data_comps_$COMP_INTERFACE/dlnd $SRCROOT/components/cdeps/dlnd - $SRCROOT/components/cpl7/components/stub_comps_$COMP_INTERFACE/slnd $CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd - $SRCROOT/components/cpl7/components/xcpl_comps_$COMP_INTERFACE/xlnd $CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd case_comps diff --git a/README b/README index 18cc2b1458..4699fec858 100644 --- a/README +++ b/README @@ -57,7 +57,7 @@ python ------------ Python modules used in tools and testing and automated check Directory structure only for a CTSM checkout: components -------- Other active sub-components needed for CTSM to run (river routing and land-ice models) -libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO (deprecated) +libraries --------- CESM libraries: PIO (deprecated) share ------------- CESM shared code ccs_config -------- CIME configure files (for grids, compsets, and machines) for CESM @@ -68,7 +68,6 @@ components/cdeps -------------------- CESM top level data model shared code (for components/cism --------------------- CESM Community land Ice Sheet Model. components/mosart ------------------- Model for Scale Adaptive River Transport components/rtm ---------------------- CESM River Transport Model. -components/cpl7 --------------------- CESM top level driver for MCT driver (deprecated will be removed) Top level documentation ($CTSMROOT): @@ -154,7 +153,7 @@ Source code directory structure: src/biogeochem ---- Biogeochemisty src/main ---------- Main control and high level code -src/cpl ----------- Land model high level caps for NUOPC driver (and MCT and LILAC) +src/cpl ----------- Land model high level caps for NUOPC driver (and LILAC) src/biogeophys ---- Biogeophysics (Hydrology) src/dyn_subgrid --- Dynamic land unit change src/init_interp --- Online interpolation From db147cd616ea8a52e4bc64e88299c8fe76036396 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 13:57:37 -0600 Subject: [PATCH 116/408] Remove MCT from CLMBuildNamelist.pm --- bld/CLMBuildNamelist.pm | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index fb44023cd5..731589289c 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -71,7 +71,7 @@ REQUIRED OPTIONS (if read they allow user_nl_clm and CLM_BLDNML_OPTS to expand variables [for example to use \$DIN_LOC_ROOT]) (default current directory) - -lnd_frac "domainfile" Land fraction file (the input domain file) (needed for MCT driver and LILAC) + -lnd_frac "domainfile" Land fraction file (the input domain file) (needed for LILAC) -res "resolution" Specify horizontal grid. Use nlatxnlon for spectral grids; dlatxdlon for fv grids (dlat and dlon are the grid cell size in degrees for latitude and longitude respectively) @@ -83,7 +83,7 @@ REQUIRED OPTIONS (default 2000) -structure "structure" The overall structure being used [ standard | fast ] OPTIONS - -driver "value" CESM driver type you will run with [ mct | nuopc ] + -driver "value" CESM driver type you will run with [ nuopc ] -bgc "value" Build CLM with BGC package [ sp | bgc | fates ] (default is sp). CLM Biogeochemistry mode @@ -1893,10 +1893,10 @@ sub setup_logic_lnd_frac { my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_; # - # fatmlndfrc is required for the MCT driver (or LILAC), but uneeded for NUOPC + # fatmlndfrc is required for LILAC but uneeded for NUOPC # my $var = "lnd_frac"; - if ( ($opts->{'driver'} eq "mct") || $opts->{'lilac'} ) { + if ( $opts->{'lilac'} ) { if ( defined($opts->{$var}) ) { if ( defined($nl->get_value('fatmlndfrc')) ) { $log->fatal_error("Can NOT set both -lnd_frac option (set via LND_DOMAIN_PATH/LND_DOMAIN_FILE " . @@ -3838,9 +3838,7 @@ sub setup_logic_popd_streams { } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_popdens', 'phys'=>$nl_flags->{'phys'}, 'cnfireson'=>$nl_flags->{'cnfireson'}, 'hgrid'=>"0.5x0.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'} ); - # - # TODO (mvertens, 2021-06-22) the following is needed for MCT since a use case enforces this - so for now stream_meshfile_popdens will be added to the mct - # stream namelist but simply not used + if ($opts->{'driver'} eq "nuopc" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_popdens', 'hgrid'=>"0.5x0.5"); my $inputdata_rootdir = $nl_flags->{'inputdata_rootdir'}; @@ -3854,12 +3852,6 @@ sub setup_logic_popd_streams { $val = "e_string( $val ); $nl->set_variable_value($group, $var, $val); } - } else { - my $var = 'stream_meshfile_popdens'; - my $group = $definition->get_group_name($var); - my $val = "none"; - $val = "e_string( $val ); - $nl->set_variable_value($group, $var, $val); } } else { # If bgc is NOT CN/CNDV or fire_method==nofire then make sure none of the popdens settings are set From 68d46b68f92ebe08ce04d61527638d6997275b38 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 14:03:49 -0600 Subject: [PATCH 117/408] Remove MCT from build-namelist_test.pl --- bld/unit_testers/build-namelist_test.pl | 30 ++----------------------- 1 file changed, 2 insertions(+), 28 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 7b654337af..12a5f4bd38 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -314,7 +314,7 @@ sub cat_and_create_namelistinfile { print "=================================================================================\n"; my $startfile = "clmrun.clm2.r.1964-05-27-00000.nc"; -foreach my $driver ( "mct", "nuopc" ) { +foreach my $driver ( "nuopc" ) { print " For $driver driver\n\n"; # configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case foreach my $options ( "-res 0.9x1.25 -configuration nwp", @@ -335,13 +335,7 @@ sub cat_and_create_namelistinfile { my $file = $startfile; &make_env_run(); my $base_options = "-envxml_dir . -driver $driver"; - if ( $driver eq "mct" ) { - $base_options = "$base_options -lnd_frac $DOMFILE"; - # Skip the MCT test for excess ice streams - if ( $options =~ /use_excess_ice_streams=.true./ ) { - next; - } - } else { + if ( $driver eq "nuopc" ) { $base_options = "$base_options -namelist '&a force_send_to_atm = .false./'"; } eval{ system( "$bldnml $base_options $options > $tempfile 2>&1 " ); }; @@ -548,11 +542,6 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "exice stream on, but mct" =>{ options=>"--res 0.9x1.25 --envxml_dir . --driver mct --lnd_frac $DOMFILE ", - namelst=>"use_excess_ice=.true., use_excess_ice_streams=.true.", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm5_0", - }, "clm50CNDVwtransient" =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -898,16 +887,6 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "both lnd_frac and on nml" =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .", - namelst=>"fatmlndfrc='frac.nc'", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm5_0", - }, - "lnd_frac set to UNSET" =>{ options=>"-driver mct -lnd_frac UNSET -envxml_dir .", - namelst=>"", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm6_0", - }, "lnd_frac set but nuopc" =>{ options=>"-driver nuopc -lnd_frac $DOMFILE -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -923,11 +902,6 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm6_0", }, - "force_send but not nuopc" =>{ options=>"-driver mct -lnd_frac $DOMFILE -envxml_dir .", - namelst=>"force_send_to_atm = .false.", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm6_0", - }, "branch but NO nrevsn" =>{ options=>"-clm_start_type branch -envxml_dir .", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", From f3386bcd5c0ec78d6d2be660aaa7b4c257910030 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 15:58:49 -0600 Subject: [PATCH 118/408] Remove MCT from config_definition_ctsm.xml --- bld/config_files/config_definition_ctsm.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/config_files/config_definition_ctsm.xml b/bld/config_files/config_definition_ctsm.xml index dfe6378f17..e6628b1d94 100644 --- a/bld/config_files/config_definition_ctsm.xml +++ b/bld/config_files/config_definition_ctsm.xml @@ -18,11 +18,11 @@ Root directory of CLM source distribution (directory above CLM configure). Component framework interface to use -(Model Coupling Toolkit, or Earth System Modeling Framework) +(Earth System Modeling Framework) Date: Fri, 10 May 2024 16:08:42 -0600 Subject: [PATCH 119/408] Remove MCT from ExpectedTestFails.xml and update README.NUOPC_driver.md --- README.NUOPC_driver.md | 5 +---- cime_config/testdefs/ExpectedTestFails.xml | 7 ------- 2 files changed, 1 insertion(+), 11 deletions(-) diff --git a/README.NUOPC_driver.md b/README.NUOPC_driver.md index ba0b70c2c0..9eb5d5b2cb 100644 --- a/README.NUOPC_driver.md +++ b/README.NUOPC_driver.md @@ -43,9 +43,6 @@ by having an updated copy in your case directory. ## What if I want to use the MCT driver? -The MCT driver is now deprecated, and will be removed. So at this point we don't -suggest using it anymore. - -For more notes see: +The MCT driver is now removed. For more notes see: https://docs.google.com/presentation/d/1yjiKSEV53JDAJbYxhpY2T9GTxlWFzQAn diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 8ee60cf4b8..f600444547 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -51,13 +51,6 @@ - - - FAIL - #1887 - - - FAIL From 629961c2afa8d86be3101b90dfe040a8d9603ac2 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 16:11:33 -0600 Subject: [PATCH 120/408] Remove reference to MCT in fsurdat_modifier.py --- python/ctsm/modify_input_files/fsurdat_modifier.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index bd060cb9dc..1a45590872 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -254,8 +254,8 @@ def modify_optional( """Modify the dataset according to the optional settings""" # Set fsurdat variables in a rectangle that could be global (default). - # Note that the land/ocean mask gets specified in the domain file for - # MCT or the ocean mesh files for NUOPC. Here the user may specify + # Note that the land/ocean mask gets specified in + # the ocean mesh files. Here the user may specify # fsurdat variables inside a box but cannot change which points will # run as land and which as ocean. if idealized: From fb5b6310be60477a7c4cb67656a68a9c71cb8b6e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 16:15:09 -0600 Subject: [PATCH 121/408] Remove src/unit_test_stubs/csm_share/CMakeLists.txt --- src/unit_test_stubs/csm_share/CMakeLists.txt | 5 ----- 1 file changed, 5 deletions(-) delete mode 100644 src/unit_test_stubs/csm_share/CMakeLists.txt diff --git a/src/unit_test_stubs/csm_share/CMakeLists.txt b/src/unit_test_stubs/csm_share/CMakeLists.txt deleted file mode 100644 index 33ddbfb342..0000000000 --- a/src/unit_test_stubs/csm_share/CMakeLists.txt +++ /dev/null @@ -1,5 +0,0 @@ -list(APPEND share_sources - shr_mpi_mod_stub.F90 - ) - -sourcelist_to_parent(share_sources) From 3d1ab9be7da02a53107786a952582462049611db Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 16:18:43 -0600 Subject: [PATCH 122/408] Remove MCT from test_driver.sh --- test/tools/test_driver.sh | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh index f93301a530..307d1accf8 100755 --- a/test/tools/test_driver.sh +++ b/test/tools/test_driver.sh @@ -463,8 +463,7 @@ if [ ! -d \$CLM_TESTDIR ]; then fi fi -## MCT and PIO build directorys -export MCT_LIBDIR=\$CLM_TESTDIR/mct +## PIO build directory export PIO_LIBDIR=\$CLM_TESTDIR/pio ##set our own environment vars From 371f093e02a7820e8beec823c97dd23b94277c05 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 16:20:13 -0600 Subject: [PATCH 123/408] Remove the src/cpl/mct directory --- src/cpl/mct/ExcessIceStreamType.F90 | 144 ----- src/cpl/mct/FireDataBaseType.F90 | 561 ------------------- src/cpl/mct/SoilMoistureStreamMod.F90 | 418 -------------- src/cpl/mct/UrbanTimeVarType.F90 | 314 ----------- src/cpl/mct/ch4FInundatedStreamType.F90 | 389 ------------- src/cpl/mct/clm_cpl_indices.F90 | 330 ----------- src/cpl/mct/laiStreamMod.F90 | 241 --------- src/cpl/mct/lnd_comp_mct.F90 | 632 ---------------------- src/cpl/mct/lnd_import_export.F90 | 354 ------------ src/cpl/mct/lnd_set_decomp_and_domain.F90 | 352 ------------ src/cpl/mct/ndepStreamMod.F90 | 376 ------------- 11 files changed, 4111 deletions(-) delete mode 100644 src/cpl/mct/ExcessIceStreamType.F90 delete mode 100644 src/cpl/mct/FireDataBaseType.F90 delete mode 100644 src/cpl/mct/SoilMoistureStreamMod.F90 delete mode 100644 src/cpl/mct/UrbanTimeVarType.F90 delete mode 100644 src/cpl/mct/ch4FInundatedStreamType.F90 delete mode 100644 src/cpl/mct/clm_cpl_indices.F90 delete mode 100644 src/cpl/mct/laiStreamMod.F90 delete mode 100644 src/cpl/mct/lnd_comp_mct.F90 delete mode 100644 src/cpl/mct/lnd_import_export.F90 delete mode 100644 src/cpl/mct/lnd_set_decomp_and_domain.F90 delete mode 100644 src/cpl/mct/ndepStreamMod.F90 diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90 deleted file mode 100644 index 5c5394233c..0000000000 --- a/src/cpl/mct/ExcessIceStreamType.F90 +++ /dev/null @@ -1,144 +0,0 @@ -module ExcessIceStreamType - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Stub for ExcessIceStreams for the MCT driver. So that MCT can be used - ! without excess ice streams. - ! - ! !USES - use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL - use shr_log_mod , only : errMsg => shr_log_errMsg - use spmdMod , only : mpicom, masterproc - use clm_varctl , only : iulog - use abortutils , only : endrun - use decompMod , only : bounds_type - - ! !PUBLIC TYPES: - implicit none - private - - public :: UseExcessIceStreams ! If streams will be used - - type, public :: excessicestream_type - contains - - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: Init ! Initialize and read data in - procedure, public :: CalcExcessIce ! Calculate excess ice ammount - - ! !PRIVATE MEMBER FUNCTIONS: - procedure, private :: ReadNML ! Read in namelist - - end type excessicestream_type - ! ! PRIVATE DATA: - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -!============================================================================== -contains -!============================================================================== - - subroutine Init(this, bounds, NLFilename) - ! - ! - ! arguments - implicit none - class(excessicestream_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - - ! - ! local variables - - call this%ReadNML( bounds, NLFileName ) - end subroutine Init - - subroutine CalcExcessIce(this,bounds,exice_bulk_init) - - ! only transfers grid values to columns - implicit none - class(excessicestream_type) :: this - type(bounds_type), intent(in) :: bounds - real(r8) , intent(inout) :: exice_bulk_init(bounds%begc:bounds%endc) - ! - ! !LOCAL VARIABLES: - - end subroutine CalcExcessIce - - logical function UseExcessIceStreams() - ! - ! !DESCRIPTION: - ! Return true if - ! - ! !USES: - ! - ! !ARGUMENTS: - implicit none - ! - ! !LOCAL VARIABLES: - UseExcessIceStreams = .false. -end function UseExcessIceStreams - -subroutine ReadNML(this, bounds, NLFilename) - ! - ! Read the namelist data stream information. - ! - ! Uses: - use shr_nl_mod , only : shr_nl_find_group_name - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_mpi_mod , only : shr_mpi_bcast - ! - ! arguments - implicit none - class(excessicestream_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - logical :: use_excess_ice_streams = .false. ! logical to turn on use of excess ice streams - character(len=CL) :: stream_fldFileName_exice = ' ' - character(len=CL) :: stream_mapalgo_exice = 'none' - character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read - character(len=*), parameter :: subName = "('exice_streams::ReadNML')" - !----------------------------------------------------------------------- - - namelist /exice_streams/ & ! MUST agree with namelist_name above - stream_mapalgo_exice, stream_fldFileName_exice, use_excess_ice_streams - !----------------------------------------------------------------------- - ! Default values for namelist - - ! Read excess ice namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=exice_streams,iostat=nml_error) ! MUST agree with namelist_name above - if (nml_error /= 0) then - call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - else - call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - close(nu_nml) - endif - - call shr_mpi_bcast(use_excess_ice_streams , mpicom) - - if (masterproc) then - if ( use_excess_ice_streams ) then - call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__)) - end if - if ( trim(stream_fldFileName_exice) /= '' ) then - call endrun(msg=' ERROR stream_fldFileName_exice can NOT be set for the MCT driver'//errMsg(sourcefile, __LINE__)) - end if - if ( trim(stream_mapalgo_exice) /= 'none' ) then - call endrun(msg=' ERROR stream_mapalgo_exice can only be none for the MCT driver'//errMsg(sourcefile, __LINE__)) - end if - endif - -end subroutine ReadNML - -end module ExcessIceStreamType diff --git a/src/cpl/mct/FireDataBaseType.F90 b/src/cpl/mct/FireDataBaseType.F90 deleted file mode 100644 index 0ee635b2fa..0000000000 --- a/src/cpl/mct/FireDataBaseType.F90 +++ /dev/null @@ -1,561 +0,0 @@ -module FireDataBaseType - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! module for handling of fire data - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create, shr_strdata_print - use shr_strdata_mod , only : shr_strdata_advance - use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog, inst_name - use spmdMod , only : masterproc, mpicom, comp_id - use fileutils , only : getavu, relavu - use domainMod , only : ldomain - use abortutils , only : endrun - use decompMod , only : bounds_type - use FireMethodType , only : fire_method_type - use lnd_set_decomp_and_domain, only : gsmap_global - use mct_mod - ! - implicit none - private - ! - ! !PUBLIC TYPES: - public :: fire_base_type - - ! - type, abstract, extends(fire_method_type) :: fire_base_type - private - ! !PRIVATE MEMBER DATA: - - real(r8), public, pointer :: forc_lnfm(:) ! Lightning frequency - real(r8), public, pointer :: forc_hdm(:) ! Human population density - - real(r8), public, pointer :: gdp_lf_col(:) ! col global real gdp data (k US$/capita) - real(r8), public, pointer :: peatf_lf_col(:) ! col global peatland fraction data (0-1) - integer , public, pointer :: abm_lf_col(:) ! col global peak month of crop fire emissions - - type(shr_strdata_type) :: sdat_hdm ! Human population density input data stream - type(shr_strdata_type) :: sdat_lnfm ! Lightning input data stream - - contains - ! - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: FireInit => BaseFireInit ! Initialization of Fire - procedure, public :: BaseFireInit ! Initialization of Fire - procedure(FireReadNML_interface), public, deferred :: FireReadNML ! Read in namelist for Fire - procedure, public :: FireInterp ! Interpolate fire data - procedure(need_lightning_and_popdens_interface), public, deferred :: & - need_lightning_and_popdens ! Returns true if need lightning & popdens - ! - ! !PRIVATE MEMBER FUNCTIONS: - procedure, private :: hdm_init ! position datasets for dynamic human population density - procedure, private :: hdm_interp ! interpolates between two years of human pop. density file data - procedure, private :: lnfm_init ! position datasets for Lightning - procedure, private :: lnfm_interp ! interpolates between two years of Lightning file data - procedure, private :: surfdataread ! read fire related data from surface data set - end type fire_base_type - !----------------------------------------------------------------------- - - abstract interface - !----------------------------------------------------------------------- - function need_lightning_and_popdens_interface(this) result(need_lightning_and_popdens) - ! - ! !DESCRIPTION: - ! Returns true if need lightning and popdens, false otherwise - ! - ! USES - import :: fire_base_type - ! - ! !ARGUMENTS: - class(fire_base_type), intent(in) :: this - logical :: need_lightning_and_popdens ! function result - !----------------------------------------------------------------------- - end function need_lightning_and_popdens_interface - end interface - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -contains - - !----------------------------------------------------------------------- - subroutine FireReadNML_interface( this, NLFilename ) - ! - ! !DESCRIPTION: - ! Read the namelist for Fire - ! - ! !USES: - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - character(len=*), intent(in) :: NLFilename ! Namelist filename - end subroutine FireReadNML_interface - - !----------------------------------------------------------------------- - subroutine BaseFireInit( this, bounds, NLFilename ) - ! - ! !DESCRIPTION: - ! Initialize CN Fire module - ! !USES: - use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename - !----------------------------------------------------------------------- - - if ( this%need_lightning_and_popdens() ) then - ! Allocate lightning forcing data - allocate( this%forc_lnfm(bounds%begg:bounds%endg) ) - this%forc_lnfm(bounds%begg:) = nan - ! Allocate pop dens forcing data - allocate( this%forc_hdm(bounds%begg:bounds%endg) ) - this%forc_hdm(bounds%begg:) = nan - - ! Allocate real gdp data - allocate(this%gdp_lf_col(bounds%begc:bounds%endc)) - ! Allocate peatland fraction data - allocate(this%peatf_lf_col(bounds%begc:bounds%endc)) - ! Allocates peak month of crop fire emissions - allocate(this%abm_lf_col(bounds%begc:bounds%endc)) - - - call this%hdm_init(bounds, NLFilename) - call this%hdm_interp(bounds) - call this%lnfm_init(bounds, NLFilename) - call this%lnfm_interp(bounds) - call this%surfdataread(bounds) - end if - - end subroutine BaseFireInit - - !----------------------------------------------------------------------- - subroutine FireInterp(this,bounds) - ! - ! !DESCRIPTION: - ! Interpolate CN Fire datasets - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - !----------------------------------------------------------------------- - - if ( this%need_lightning_and_popdens() ) then - call this%hdm_interp(bounds) - call this%lnfm_interp(bounds) - end if - - end subroutine FireInterp - - !----------------------------------------------------------------------- - subroutine hdm_init( this, bounds, NLFilename ) - ! - ! !DESCRIPTION: - ! Initialize data stream information for population density. - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use histFileMod , only : hist_addfld1d - ! - ! !ARGUMENTS: - implicit none - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! !LOCAL VARIABLES: - integer :: stream_year_first_popdens ! first year in pop. dens. stream to use - integer :: stream_year_last_popdens ! last year in pop. dens. stream to use - integer :: model_year_align_popdens ! align stream_year_first_hdm with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_popdens ! population density streams filename - character(len=CL) :: popdensmapalgo = 'bilinear' ! mapping alogrithm for population density - character(len=CL) :: popdens_tintalgo = 'nearest'! time interpolation alogrithm for population density - character(len=CL) :: stream_meshfile_popdens ! not used - character(*), parameter :: subName = "('hdmdyn_init')" - character(*), parameter :: F00 = "('(hdmdyn_init) ',4a)" - !----------------------------------------------------------------------- - - namelist /popd_streams/ & - stream_year_first_popdens, & - stream_year_last_popdens, & - model_year_align_popdens, & - popdensmapalgo, & - stream_fldFileName_popdens, & - stream_meshfile_popdens , & - popdens_tintalgo - - ! Default values for namelist - stream_year_first_popdens = 1 ! first year in stream to use - stream_year_last_popdens = 1 ! last year in stream to use - model_year_align_popdens = 1 ! align stream_year_first_popdens with this model year - stream_fldFileName_popdens = ' ' - - ! Read popd_streams namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'popd_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=popd_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg='ERROR reading popd_streams namelist'//errMsg(sourcefile, __LINE__)) - end if - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_year_first_popdens, mpicom) - call shr_mpi_bcast(stream_year_last_popdens, mpicom) - call shr_mpi_bcast(model_year_align_popdens, mpicom) - call shr_mpi_bcast(stream_fldFileName_popdens, mpicom) - call shr_mpi_bcast(popdens_tintalgo, mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'popdens_streams settings:' - write(iulog,*) ' stream_year_first_popdens = ',stream_year_first_popdens - write(iulog,*) ' stream_year_last_popdens = ',stream_year_last_popdens - write(iulog,*) ' model_year_align_popdens = ',model_year_align_popdens - write(iulog,*) ' stream_fldFileName_popdens = ',stream_fldFileName_popdens - write(iulog,*) ' popdens_tintalgo = ',popdens_tintalgo - write(iulog,*) ' ' - endif - - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(this%sdat_hdm,name="clmhdm", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_popdens, & - yearLast=stream_year_last_popdens, & - yearAlign=model_year_align_popdens, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_popdens), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/trim(stream_fldFileName_popdens)/) , & - fldListFile='hdm', & - fldListModel='hdm', & - fillalgo='none', & - mapalgo=popdensmapalgo, & - calendar=get_calendar(), & - tintalgo=popdens_tintalgo, & - taxmode='extend' ) - - if (masterproc) then - call shr_strdata_print(this%sdat_hdm,'population density data') - endif - - ! Add history fields - call hist_addfld1d (fname='HDM', units='counts/km^2', & - avgflag='A', long_name='human population density', & - ptr_lnd=this%forc_hdm, default='inactive') - - end subroutine hdm_init - - !----------------------------------------------------------------------- - subroutine hdm_interp( this, bounds) - ! - ! !DESCRIPTION: - ! Interpolate data stream information for population density. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g, ig - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(this%sdat_hdm, mcdate, sec, mpicom, 'hdmdyn') - - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - this%forc_hdm(g) = this%sdat_hdm%avs(1)%rAttr(1,ig) - end do - - end subroutine hdm_interp - - !----------------------------------------------------------------------- - subroutine lnfm_init( this, bounds, NLFilename ) - ! - ! !DESCRIPTION: - ! - ! Initialize data stream information for Lightning. - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use histFileMod , only : hist_addfld1d - ! - ! !ARGUMENTS: - implicit none - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename - ! - ! !LOCAL VARIABLES: - integer :: stream_year_first_lightng ! first year in Lightning stream to use - integer :: stream_year_last_lightng ! last year in Lightning stream to use - integer :: model_year_align_lightng ! align stream_year_first_lnfm with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_lightng ! lightning stream filename to read - character(len=CL) :: lightng_tintalgo = 'linear'! time interpolation alogrithm - character(len=CL) :: lightngmapalgo = 'bilinear'! Mapping alogrithm - character(*), parameter :: subName = "('lnfmdyn_init')" - character(*), parameter :: F00 = "('(lnfmdyn_init) ',4a)" - !----------------------------------------------------------------------- - - namelist /light_streams/ & - stream_year_first_lightng, & - stream_year_last_lightng, & - model_year_align_lightng, & - lightngmapalgo, & - stream_fldFileName_lightng, & - lightng_tintalgo - - ! Default values for namelist - stream_year_first_lightng = 1 ! first year in stream to use - stream_year_last_lightng = 1 ! last year in stream to use - model_year_align_lightng = 1 ! align stream_year_first_lnfm with this model year - stream_fldFileName_lightng = ' ' - - ! Read light_streams namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'light_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=light_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg='ERROR reading light_streams namelist'//errMsg(sourcefile, __LINE__)) - end if - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_year_first_lightng, mpicom) - call shr_mpi_bcast(stream_year_last_lightng, mpicom) - call shr_mpi_bcast(model_year_align_lightng, mpicom) - call shr_mpi_bcast(stream_fldFileName_lightng, mpicom) - call shr_mpi_bcast(lightng_tintalgo, mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'light_stream settings:' - write(iulog,*) ' stream_year_first_lightng = ',stream_year_first_lightng - write(iulog,*) ' stream_year_last_lightng = ',stream_year_last_lightng - write(iulog,*) ' model_year_align_lightng = ',model_year_align_lightng - write(iulog,*) ' stream_fldFileName_lightng = ',stream_fldFileName_lightng - write(iulog,*) ' lightng_tintalgo = ',lightng_tintalgo - write(iulog,*) ' ' - endif - - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(this%sdat_lnfm,name="clmlnfm", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_lightng, & - yearLast=stream_year_last_lightng, & - yearAlign=model_year_align_lightng, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_lightng), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/trim(stream_fldFileName_lightng)/), & - fldListFile='lnfm', & - fldListModel='lnfm', & - fillalgo='none', & - tintalgo=lightng_tintalgo, & - mapalgo=lightngmapalgo, & - calendar=get_calendar(), & - taxmode='cycle' ) - - if (masterproc) then - call shr_strdata_print(this%sdat_lnfm,'Lightning data') - endif - - ! Add history fields - call hist_addfld1d (fname='LNFM', units='counts/km^2/hr', & - avgflag='A', long_name='Lightning frequency', & - ptr_lnd=this%forc_lnfm, default='inactive') - - end subroutine lnfm_init - - !----------------------------------------------------------------------- - subroutine lnfm_interp(this, bounds ) - ! - ! !DESCRIPTION: - ! Interpolate data stream information for Lightning. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g, ig - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(this%sdat_lnfm, mcdate, sec, mpicom, 'lnfmdyn') - - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - this%forc_lnfm(g) = this%sdat_lnfm%avs(1)%rAttr(1,ig) - end do - - end subroutine lnfm_interp - - !----------------------------------------------------------------------- - subroutine surfdataread(this, bounds) - ! - ! !DESCRIPTION: - ! Read surface data set to populate relevant fire-related variables - ! - ! !USES: - use spmdMod , only : masterproc - use clm_varctl , only : nsrest, nsrStartup, fsurdat - use clm_varcon , only : grlnd - use ColumnType , only : col - use fileutils , only : getfil - use ncdio_pio - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g,c ! indices - type(file_desc_t) :: ncid ! netcdf id - logical :: readvar ! true => variable is on initial dataset - character(len=256) :: locfn ! local filename - real(r8), pointer :: gdp(:) ! global gdp data (needs to be a pointer for use in ncdio) - real(r8), pointer :: peatf(:) ! global peatf data (needs to be a pointer for use in ncdio) - integer, pointer :: abm(:) ! global abm data (needs to be a pointer for use in ncdio) - !----------------------------------------------------------------------- - - ! -------------------------------------------------------------------- - ! Open surface dataset - ! -------------------------------------------------------------------- - - call getfil (fsurdat, locfn, 0) - call ncd_pio_openfile (ncid, locfn, 0) - - ! -------------------------------------------------------------------- - ! Read in GDP data - ! -------------------------------------------------------------------- - - allocate(gdp(bounds%begg:bounds%endg)) - call ncd_io(ncid=ncid, varname='gdp', flag='read', data=gdp, dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun(msg=' ERROR: gdp NOT on surfdata file'//errMsg(sourcefile, __LINE__)) - end if - do c = bounds%begc, bounds%endc - g = col%gridcell(c) - this%gdp_lf_col(c) = gdp(g) - end do - deallocate(gdp) - - ! -------------------------------------------------------------------- - ! Read in peatf data - ! -------------------------------------------------------------------- - - allocate(peatf(bounds%begg:bounds%endg)) - call ncd_io(ncid=ncid, varname='peatf', flag='read', data=peatf, dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun(msg=' ERROR: peatf NOT on surfdata file'//errMsg(sourcefile, __LINE__)) - end if - do c = bounds%begc, bounds%endc - g = col%gridcell(c) - this%peatf_lf_col(c) = peatf(g) - end do - deallocate(peatf) - - ! -------------------------------------------------------------------- - ! Read in ABM data - ! -------------------------------------------------------------------- - - allocate(abm(bounds%begg:bounds%endg)) - call ncd_io(ncid=ncid, varname='abm', flag='read', data=abm, dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun(msg=' ERROR: abm NOT on surfdata file'//errMsg(sourcefile, __LINE__)) - end if - do c = bounds%begc, bounds%endc - g = col%gridcell(c) - this%abm_lf_col(c) = abm(g) - end do - deallocate(abm) - - ! Close file - - call ncd_pio_closefile(ncid) - - if (masterproc) then - write(iulog,*) 'Successfully read fmax, soil color, sand and clay boundary data' - write(iulog,*) - endif - - end subroutine surfdataread - - -end module FireDataBaseType diff --git a/src/cpl/mct/SoilMoistureStreamMod.F90 b/src/cpl/mct/SoilMoistureStreamMod.F90 deleted file mode 100644 index 8b366d6c8e..0000000000 --- a/src/cpl/mct/SoilMoistureStreamMod.F90 +++ /dev/null @@ -1,418 +0,0 @@ -module SoilMoistureStreamMod - - ! ********************************************************************** - ! --------------------------- IMPORTANT NOTE --------------------------- - ! - ! In cases using the NUOPC driver/mediator, we use a different version of this module, - ! based on CDEPS, which resides in src/cpl/nuopc/. Changes to the science here should - ! also be made in the similar file in src/cpl/nuopc. Once we start using CDEPS by - ! default, we can remove this version and move the CDEPS-based version into its place. - ! ********************************************************************** - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Read in soil moisture from data stream - ! - ! !USES: - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create - use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance - use shr_kind_mod , only : r8 => shr_kind_r8 - use shr_kind_mod , only : CL => shr_kind_CL, CXX => shr_kind_CXX - use shr_log_mod , only : errMsg => shr_log_errMsg - use decompMod , only : bounds_type, subgrid_level_column - use abortutils , only : endrun - use clm_varctl , only : iulog, use_soil_moisture_streams, inst_name - use clm_varcon , only : grlnd - use controlMod , only : NLFilename - use domainMod , only : ldomain - use LandunitType , only : lun - use ColumnType , only : col - use SoilStateType , only : soilstate_type - use WaterStateBulkType , only : waterstatebulk_type - use perf_mod , only : t_startf, t_stopf - use spmdMod , only : masterproc, mpicom, comp_id - use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo - use mct_mod - use ncdio_pio - ! - ! !PUBLIC TYPES: - implicit none - private - ! - ! !PUBLIC MEMBER FUNCTIONS: - public :: PrescribedSoilMoistureInit ! position datasets for soil moisture - public :: PrescribedSoilMoistureAdvance ! Advance the soil moisture stream (outside of Open-MP loops) - public :: PrescribedSoilMoistureInterp ! interpolates between two periods of soil moisture data - - ! !PRIVATE MEMBER DATA: - type(shr_strdata_type) :: sdat_soilm ! soil moisture input data stream - integer :: ism ! Soil moisture steram index - integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - logical :: soilm_ignore_data_if_missing ! If should ignore overridding a point with soil moisture data - ! from the streams file, if the streams file shows that point - ! as missing (namelist item) - ! - ! !PRIVATE TYPES: - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - !----------------------------------------------------------------------- - -contains - - !----------------------------------------------------------------------- - ! - ! soil_moisture_init - ! - !----------------------------------------------------------------------- - subroutine PrescribedSoilMoistureInit(bounds) - ! - ! Initialize data stream information for soil moisture. - ! - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use shr_stream_mod , only : shr_stream_file_null - use shr_string_mod , only : shr_string_listCreateField - use clm_varpar , only : nlevsoi - ! - ! !ARGUMENTS: - implicit none - type(bounds_type), intent(in) :: bounds ! bounds - ! - ! !LOCAL VARIABLES: - integer :: i ! index - integer :: stream_year_first_soilm ! first year in Ustar stream to use - integer :: stream_year_last_soilm ! last year in Ustar stream to use - integer :: model_year_align_soilm ! align stream_year_first_soilm with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - integer :: soilm_offset ! Offset in time for dataset (sec) - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldfilename_soilm ! ustar stream filename to read - character(len=CL) :: soilm_tintalgo = 'linear' ! Time interpolation alogrithm - - character(*), parameter :: subName = "('PrescribedSoilMoistureInit')" - character(*), parameter :: F00 = "('(PrescribedSoilMoistureInit) ',4a)" - character(*), parameter :: soilmString = "H2OSOI" ! base string for field string - character(CXX) :: fldList ! field string - !----------------------------------------------------------------------- - ! - ! deal with namelist variables here in init - ! - namelist /soil_moisture_streams/ & - stream_year_first_soilm, & - stream_year_last_soilm, & - model_year_align_soilm, & - soilm_tintalgo, & - soilm_offset, & - soilm_ignore_data_if_missing, & - stream_fldfilename_soilm - - ! Default values for namelist - stream_year_first_soilm = 1 ! first year in stream to use - stream_year_last_soilm = 1 ! last year in stream to use - model_year_align_soilm = 1 ! align stream_year_first_soilm with this model year - stream_fldfilename_soilm = shr_stream_file_null - soilm_offset = 0 - soilm_ignore_data_if_missing = .false. - - ! Read soilm_streams namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'soil_moisture_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=soil_moisture_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(subname // ':: ERROR reading soil_moisture_streams namelist') - end if - else - call endrun(subname // ':: ERROR finding soilm_streams namelist') - end if - close(nu_nml) - endif - - call shr_mpi_bcast(stream_year_first_soilm, mpicom) - call shr_mpi_bcast(stream_year_last_soilm, mpicom) - call shr_mpi_bcast(model_year_align_soilm, mpicom) - call shr_mpi_bcast(stream_fldfilename_soilm, mpicom) - call shr_mpi_bcast(soilm_tintalgo, mpicom) - call shr_mpi_bcast(soilm_offset, mpicom) - call shr_mpi_bcast(soilm_ignore_data_if_missing, mpicom) - - if (masterproc) then - - write(iulog,*) ' ' - write(iulog,*) 'soil_moisture_stream settings:' - write(iulog,*) ' stream_year_first_soilm = ',stream_year_first_soilm - write(iulog,*) ' stream_year_last_soilm = ',stream_year_last_soilm - write(iulog,*) ' model_year_align_soilm = ',model_year_align_soilm - write(iulog,*) ' stream_fldfilename_soilm = ',trim(stream_fldfilename_soilm) - write(iulog,*) ' soilm_tintalgo = ',trim(soilm_tintalgo) - write(iulog,*) ' soilm_offset = ',soilm_offset - if ( soilm_ignore_data_if_missing )then - write(iulog,*) ' Do NOT override a point with streams data if the streams data is missing' - else - write(iulog,*) ' Abort, if you find a model point where the input streams data is set to missing value' - end if - - endif - - call clm_domain_mct (bounds, dom_clm, nlevels=nlevsoi) - - ! create the field list for these fields...use in shr_strdata_create - fldList = trim(soilmString) - if (masterproc) write(iulog,*) 'fieldlist: ', trim(fldList) - - call shr_strdata_create(sdat_soilm,name="soil_moisture", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsMap_lnd2Dsoi_gdc2glo, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - nzg=nlevsoi, & - yearFirst=stream_year_first_soilm, & - yearLast=stream_year_last_soilm, & - yearAlign=model_year_align_soilm, & - offset=soilm_offset, & - domFilePath='', & - domFileName=trim(stream_fldFileName_soilm), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domZvarName='levsoi' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/stream_fldFileName_soilm/), & - fldListFile=fldList, & - fldListModel=fldList, & - fillalgo='none', & - mapalgo='none', & - tintalgo=soilm_tintalgo, & - calendar=get_calendar(), & - dtlimit = 15._r8, & - taxmode='cycle' ) - - if (masterproc) then - call shr_strdata_print(sdat_soilm,'soil moisture data') - endif - - end subroutine PrescribedSoilMoistureInit - - - !----------------------------------------------------------------------- - ! - ! PrescribedSoilMoistureAdvance - ! - !----------------------------------------------------------------------- - subroutine PrescribedSoilMoistureAdvance( bounds ) - ! - ! Advanace the prescribed soil moisture stream - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - type(bounds_type) , intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - character(len=CL) :: stream_var_name - integer :: g, ig - integer :: ier ! error code - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - stream_var_name = 'H2OSOI' - - ! Determine variable index - ism = mct_aVect_indexRA(sdat_soilm%avs(1),trim(stream_var_name)) - - call shr_strdata_advance(sdat_soilm, mcdate, sec, mpicom, trim(stream_var_name)) - - ! Map gridcell to AV index - ier = 0 - if ( .not. allocated(g_to_ig) )then - allocate (g_to_ig(bounds%begg:bounds%endg), stat=ier) - if (ier /= 0) then - write(iulog,*) 'Prescribed soil moisture allocation error' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - g_to_ig(g) = ig - end do - end if - - end subroutine PrescribedSoilMoistureAdvance - - !----------------------------------------------------------------------- - ! - ! PrescribedSoilMoistureInterp - ! - !----------------------------------------------------------------------- - subroutine PrescribedSoilMoistureInterp(bounds, soilstate_inst, & - waterstatebulk_inst) - ! - ! Assign data stream information for prescribed soil moisture. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - use clm_varpar , only : nlevsoi - use clm_varcon , only : denh2o, denice, watmin, spval - use landunit_varcon , only : istsoil, istcrop - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - type(soilstate_type) , intent(in) :: soilstate_inst - type(waterstatebulk_type) , intent(inout) :: waterstatebulk_inst - ! - ! !LOCAL VARIABLES: - integer :: c, g, j, ig, n - real(r8) :: soilm_liq_frac ! liquid fraction of soil moisture - real(r8) :: soilm_ice_frac ! ice fraction of soil moisture - real(r8) :: moisture_increment ! soil moisture adjustment increment - real(r8) :: h2osoi_vol_initial ! initial vwc value - character(*), parameter :: subName = "('PrescribedSoilMoistureInterp')" - - !----------------------------------------------------------------------- - - SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,2) >= g_to_ig(bounds%endg)+(nlevsoi-1)*size(g_to_ig) ), sourcefile, __LINE__) - associate( & - dz => col%dz , & ! Input: [real(r8) (:,:) ] layer depth (m) - watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] volumetric soil water at saturation (porosity) - h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input/Output: [real(r8) (:,:) ] liquid water (kg/m2) - h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input/Output: [real(r8) (:,:) ] ice water (kg/m2) - h2osoi_vol => waterstatebulk_inst%h2osoi_vol_col , & ! Output: volumetric soil water (m3/m3) - h2osoi_vol_prs => waterstatebulk_inst%h2osoi_vol_prs_grc & ! Output: prescribed volumetric soil water (m3/m3) - ) - SHR_ASSERT_FL( (lbound(h2osoi_vol,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_vol,2) == 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(dz,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(dz,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(dz,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(dz,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(watsat,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(watsat,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(watsat,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(watsat,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_liq,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_liq,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_liq,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_liq,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_ice,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_ice,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_ice,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_ice,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,1) >= bounds%endg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,2) == 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,2) >= nlevsoi ), sourcefile, __LINE__) - ! - ! Set the prescribed soil moisture read from the file everywhere - ! - do g = bounds%begg, bounds%endg - ig = g_to_ig(g) - do j = 1, nlevsoi - - !n = ig + (j-1)*size(g_to_ig) - n = ig + (j-1)*size(g_to_ig) - - h2osoi_vol_prs(g,j) = sdat_soilm%avs(1)%rAttr(ism,n) - - ! If soil moiture is being interpolated in time and the result is - ! large that probably means one of the two data points is missing (set to spval) - if ( h2osoi_vol_prs(g,j) > 10.0_r8 .and. (h2osoi_vol_prs(g,j) /= spval) )then - h2osoi_vol_prs(g,j) = spval - end if - - end do - end do - - do c = bounds%begc, bounds%endc - ! - ! Set variable for each gridcell/column combination - ! - g = col%gridcell(c) - ig = g_to_ig(g) - - ! EBK Jan/2020, also check weights on gridcell (See https://github.com/ESCOMP/CTSM/issues/847) - if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) .and. & - (col%wtgcell(c) /= 0._r8) ) then - ! this is a 2d field (gridcell/nlevsoi) ! - do j = 1, nlevsoi - - n = ig + (j-1)*size(g_to_ig) - - ! if soil water is zero, liq/ice fractions cannot be calculated - if((h2osoi_liq(c, j) + h2osoi_ice(c, j)) > 0._r8) then - - ! save original soil moisture value - h2osoi_vol_initial = h2osoi_vol(c,j) - - ! Check if the vegetated land mask from the dataset on the - ! file is different - if ( (h2osoi_vol_prs(g,j) == spval) .and. (h2osoi_vol_initial /= spval) )then - if ( soilm_ignore_data_if_missing )then - cycle - else - write(iulog,*) 'Input soil moisture dataset is not vegetated as expected: gridcell=', & - g, ' active = ', col%active(c) - call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, & - msg = subname // & - ' ERROR:: The input soil moisture stream is NOT vegetated for one of the land points' ) - end if - end if - - ! update volumetric soil moisture from data prescribed from the file - h2osoi_vol(c,j) = h2osoi_vol_prs(g,j) - - - ! calculate liq/ice mass fractions - soilm_liq_frac = h2osoi_liq(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j)) - soilm_ice_frac = h2osoi_ice(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j)) - - ! calculate moisture increment - moisture_increment = h2osoi_vol(c,j) - h2osoi_vol_initial - ! add limitation check - moisture_increment = min((watsat(c,j) - h2osoi_vol_initial),max(-(h2osoi_vol_initial-watmin),moisture_increment)) - - ! update liq/ice water mass due to (volumetric) moisture increment - h2osoi_liq(c,j) = h2osoi_liq(c,j) + (soilm_liq_frac * moisture_increment * dz(c, j) * denh2o) - h2osoi_ice(c,j) = h2osoi_ice(c,j) + (soilm_ice_frac * moisture_increment * dz(c, j) * denice) - - else - call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, & - msg = subname // ':: ERROR h2osoil liquid plus ice is zero') - endif - enddo - endif - end do - - end associate - - end subroutine PrescribedSoilMoistureInterp - -end module SoilMoistureStreamMod diff --git a/src/cpl/mct/UrbanTimeVarType.F90 b/src/cpl/mct/UrbanTimeVarType.F90 deleted file mode 100644 index 805ac47fbf..0000000000 --- a/src/cpl/mct/UrbanTimeVarType.F90 +++ /dev/null @@ -1,314 +0,0 @@ -module UrbanTimeVarType - - !------------------------------------------------------------------------------ - ! !DESCRIPTION: - ! Urban Time Varying Data - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL - use shr_log_mod , only : errMsg => shr_log_errMsg - use abortutils , only : endrun - use decompMod , only : bounds_type, subgrid_level_landunit - use clm_varctl , only : iulog, inst_name - use landunit_varcon , only : isturb_MIN, isturb_MAX - use clm_varcon , only : spval - use LandunitType , only : lun - use GridcellType , only : grc - use mct_mod - use shr_strdata_mod , only : shr_strdata_type - ! - implicit none - save - private - ! - ! - - ! !PUBLIC TYPE - type, public :: urbantv_type - - real(r8), public, pointer :: t_building_max(:) ! lun maximum internal building air temperature (K) - type(shr_strdata_type) :: sdat_urbantv ! urban time varying input data stream - contains - - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: Init ! Allocate and initialize urbantv - procedure, public :: urbantv_init ! Initialize urban time varying stream - procedure, public :: urbantv_interp ! Interpolate urban time varying stream - - end type urbantv_type - - !----------------------------------------------------------------------- - character(15), private :: stream_var_name(isturb_MIN:isturb_MAX) - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -contains - - !----------------------------------------------------------------------- - subroutine Init(this, bounds, NLFilename) - ! - ! Allocate module variables and data structures - ! - ! !USES: - use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) - use histFileMod , only : hist_addfld1d - ! - ! !ARGUMENTS: - class(urbantv_type) :: this - type(bounds_type) , intent(in) :: bounds - character(len=*) , intent(in) :: NLFilename ! Namelist filename - ! - ! !LOCAL VARIABLES: - integer :: begl, endl - !--------------------------------------------------------------------- - - begl = bounds%begl; endl = bounds%endl - - ! Allocate urbantv data structure - - allocate(this%t_building_max (begl:endl)) ; this%t_building_max (:) = nan - - call this%urbantv_init(bounds, NLFilename) - call this%urbantv_interp(bounds) - - ! Add history fields - call hist_addfld1d (fname='TBUILD_MAX', units='K', & - avgflag='A', long_name='prescribed maximum interior building temperature', & - ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & - l2g_scale_type='unity') - - - end subroutine Init - - !----------------------------------------------------------------------- - - !----------------------------------------------------------------------- - subroutine urbantv_init(this, bounds, NLFilename) - ! - ! !DESCRIPTION: - ! Initialize data stream information for urban time varying data - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use spmdMod , only : masterproc, mpicom, comp_id - use fileutils , only : getavu, relavu - use shr_mpi_mod , only : shr_mpi_bcast - use shr_string_mod , only : shr_string_listAppend - use shr_strdata_mod , only : shr_strdata_create, shr_strdata_print - use domainMod , only : ldomain - use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) - use landunit_varcon , only : isturb_TBD, isturb_HD, isturb_MD - use lnd_set_decomp_and_domain , only : gsmap_global - ! - ! !ARGUMENTS: - implicit none - class(urbantv_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! !LOCAL VARIABLES: - integer :: begl, endl ! landunits - integer :: ifield ! field index - integer :: stream_year_first_urbantv ! first year in urban tv stream to use - integer :: stream_year_last_urbantv ! last year in urban tv stream to use - integer :: model_year_align_urbantv ! align stream_year_first_urbantv - ! with this model year - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_urbantv ! urban tv streams filename - character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac - character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm - character(len=CL) :: fldList ! field string - character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string - character(*), parameter :: subName = "('urbantv_init')" - character(*), parameter :: F00 = "('(urbantv_init) ',4a)" - !----------------------------------------------------------------------- - namelist /urbantv_streams/ & - stream_year_first_urbantv, & - stream_year_last_urbantv, & - model_year_align_urbantv, & - urbantvmapalgo, & - stream_fldFileName_urbantv, & - urbantv_tintalgo - !----------------------------------------------------------------------- - - begl = bounds%begl; endl = bounds%endl - - ! Default values for namelist - stream_year_first_urbantv = 1 ! first year in stream to use - stream_year_last_urbantv = 1 ! last year in stream to use - model_year_align_urbantv = 1 ! align stream_year_first_urbantv with this model year - stream_fldFileName_urbantv = ' ' - - ! Read urbantv_streams namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'urbantv_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=urbantv_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg='ERROR reading urbantv_streams namelist'//errMsg(sourcefile, __LINE__)) - end if - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_year_first_urbantv, mpicom) - call shr_mpi_bcast(stream_year_last_urbantv, mpicom) - call shr_mpi_bcast(model_year_align_urbantv, mpicom) - call shr_mpi_bcast(stream_fldFileName_urbantv, mpicom) - call shr_mpi_bcast(urbantv_tintalgo, mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'urbantv_streams settings:' - write(iulog,*) ' stream_year_first_urbantv = ',stream_year_first_urbantv - write(iulog,*) ' stream_year_last_urbantv = ',stream_year_last_urbantv - write(iulog,*) ' model_year_align_urbantv = ',model_year_align_urbantv - write(iulog,*) ' stream_fldFileName_urbantv = ',stream_fldFileName_urbantv - write(iulog,*) ' urbantv_tintalgo = ',urbantv_tintalgo - write(iulog,*) ' ' - endif - - call clm_domain_mct (bounds, dom_clm) - - ! create the field list for these urbantv fields...use in shr_strdata_create - stream_var_name(:) = "NOT_SET" - stream_var_name(isturb_TBD) = urbantvString//"TBD" - stream_var_name(isturb_HD) = urbantvString//"HD" - stream_var_name(isturb_MD) = urbantvString//"MD" - fldList = "" - do ifield = isturb_MIN, isturb_MAX - call shr_string_listAppend( fldList, stream_var_name(ifield) ) - end do - - call shr_strdata_create(this%sdat_urbantv,name="clmurbantv", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_urbantv, & - yearLast=stream_year_last_urbantv, & - yearAlign=model_year_align_urbantv, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_urbantv), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='LANDMASK', & - filePath='', & - filename=(/trim(stream_fldFileName_urbantv)/) , & - fldListFile=fldList, & - fldListModel=fldList, & - fillalgo='none', & - mapalgo=urbantvmapalgo, & - calendar=get_calendar(), & - tintalgo=urbantv_tintalgo, & - taxmode='extend' ) - - if (masterproc) then - call shr_strdata_print(this%sdat_urbantv,'urban time varying data') - endif - - - end subroutine urbantv_init - - !----------------------------------------------------------------------- - subroutine urbantv_interp(this, bounds) - ! - ! !DESCRIPTION: - ! Interpolate data stream information for urban time varying data. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - use spmdMod , only : mpicom - use shr_strdata_mod , only : shr_strdata_advance - use clm_instur , only : urban_valid - ! - ! !ARGUMENTS: - class(urbantv_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - logical :: found - integer :: l, glun, ig, g, ip - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - integer :: lindx ! landunit index - integer :: gindx ! gridcell index - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(this%sdat_urbantv, mcdate, sec, mpicom, 'urbantvdyn') - - do l = bounds%begl,bounds%endl - if (lun%urbpoi(l)) then - glun = lun%gridcell(l) - ip = mct_aVect_indexRA(this%sdat_urbantv%avs(1),trim(stream_var_name(lun%itype(l)))) - ! - ! Determine vector index corresponding to glun - ! - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - if (g == glun) exit - end do - - this%t_building_max(l) = this%sdat_urbantv%avs(1)%rAttr(ip,ig) - else - this%t_building_max(l) = spval - end if - end do - - found = .false. - do l = bounds%begl,bounds%endl - if (lun%urbpoi(l)) then - glun = lun%gridcell(l) - ! - ! Determine vector index corresponding to glun - ! - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - if (g == glun) exit - end do - - if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then - found = .true. - gindx = g - lindx = l - exit - end if - end if - end do - if ( found ) then - write(iulog,*)'ERROR: no valid urban data for g= ',gindx - write(iulog,*)'landunit type: ',lun%itype(lindx) - write(iulog,*)'urban_valid: ',urban_valid(gindx) - write(iulog,*)'t_building_max: ',this%t_building_max(lindx) - call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, & - msg=errmsg(sourcefile, __LINE__)) - end if - - - end subroutine urbantv_interp - - !----------------------------------------------------------------------- - -end module UrbanTimeVarType diff --git a/src/cpl/mct/ch4FInundatedStreamType.F90 b/src/cpl/mct/ch4FInundatedStreamType.F90 deleted file mode 100644 index 3c26f4d109..0000000000 --- a/src/cpl/mct/ch4FInundatedStreamType.F90 +++ /dev/null @@ -1,389 +0,0 @@ -module ch4FInundatedStreamType - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Contains methods for reading in finundated streams file for methane code. - ! - ! !USES - use shr_kind_mod , only: r8 => shr_kind_r8, CL => shr_kind_cl - use spmdMod , only: mpicom, masterproc - use clm_varctl , only: iulog, inst_name - use abortutils , only: endrun - use decompMod , only: bounds_type - use ch4varcon , only: finundation_mtd - - ! !PUBLIC TYPES: - implicit none - private - save - - type, public :: ch4finundatedstream_type - real(r8), pointer, private :: zwt0_gdc (:) ! col coefficient for determining finundated (m) - real(r8), pointer, private :: f0_gdc (:) ! col maximum inundated fraction for a gridcell (for methane code) - real(r8), pointer, private :: p3_gdc (:) ! col coefficient for determining finundated (m) - real(r8), pointer, private :: fws_slope_gdc (:) ! col slope in fws = slope * tws + intercept (A coefficient) - real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient) - contains - - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: Init ! Initialize and read data in - procedure, public :: CalcFinundated ! Calculate finundated based on input streams - procedure, public :: UseStreams ! If streams will be used - - ! !PRIVATE MEMBER FUNCTIONS: - procedure, private :: InitAllocate ! Allocate data - - end type ch4finundatedstream_type - - - ! ! PRIVATE DATA: - - type, private :: streamcontrol_type - character(len=CL) :: stream_fldFileName_ch4finundated ! Filename - character(len=CL) :: ch4finundatedmapalgo ! map algo - character(len=CL) :: fldList ! List of fields to read - contains - procedure, private :: ReadNML ! Read in namelist - end type streamcontrol_type - - type(streamcontrol_type), private :: control ! Stream control data - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - !============================================================================== - -contains - - !============================================================================== - - subroutine Init(this, bounds, NLFilename) - ! - ! Initialize the ch4 finundated stream object - ! - ! Uses: - use clm_time_manager , only : get_calendar, get_curr_date - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_nl_mod , only : shr_nl_find_group_name - use shr_mpi_mod , only : shr_mpi_bcast - use ndepStreamMod , only : clm_domain_mct - use domainMod , only : ldomain - use decompMod , only : bounds_type - use mct_mod , only : mct_ggrid, mct_avect_indexra - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create - use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance - use spmdMod , only : comp_id, iam - use ch4varcon , only : finundation_mtd_h2osfc - use ch4varcon , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion - use lnd_set_decomp_and_domain , only : gsmap_global - ! - ! arguments - implicit none - class(ch4finundatedstream_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: ig, g ! Indices - type(mct_ggrid) :: dom_clm ! domain information - type(shr_strdata_type) :: sdat ! input data stream - integer :: index_ZWT0 = 0 ! Index of ZWT0 field - integer :: index_F0 = 0 ! Index of F0 field - integer :: index_P3 = 0 ! Index of P3 field - integer :: index_FWS_TWS_A = 0 ! Index of FWS_TWS_A field - integer :: index_FWS_TWS_B = 0 ! Index of FWS_TWS_B field - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - character(len=*), parameter :: stream_name = 'ch4finundated' - character(*), parameter :: subName = "('ch4finundatedstream::Init')" - !----------------------------------------------------------------------- - if ( finundation_mtd /= finundation_mtd_h2osfc )then - call this%InitAllocate( bounds ) - call control%ReadNML( bounds, NLFileName ) - - if ( this%useStreams() )then - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(sdat,name=stream_name, & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=1996, & - yearLast=1996, & - yearAlign=1, & - offset=0, & - domFilePath='', & - domFileName=trim(control%stream_fldFileName_ch4finundated), & - domTvarName='time', & - domXvarName='LONGXY' , & - domYvarName='LATIXY' , & - domAreaName='AREA', & - domMaskName='LANDMASK', & - filePath='', & - filename=(/trim(control%stream_fldFileName_ch4finundated)/), & - fldListFile=control%fldList, & - fldListModel=control%fldList, & - fillalgo='none', & - mapalgo=control%ch4finundatedmapalgo, & - calendar=get_calendar(), & - taxmode='extend' ) - - if (masterproc) then - call shr_strdata_print(sdat,'CLM '//stream_name//' data') - endif - - if( finundation_mtd == finundation_mtd_ZWT_inversion )then - index_ZWT0 = mct_avect_indexra(sdat%avs(1),'ZWT0') - index_F0 = mct_avect_indexra(sdat%avs(1),'F0' ) - index_P3 = mct_avect_indexra(sdat%avs(1),'P3' ) - else if( finundation_mtd == finundation_mtd_TWS_inversion )then - index_FWS_TWS_A = mct_avect_indexra(sdat%avs(1),'FWS_TWS_A') - index_FWS_TWS_B = mct_avect_indexra(sdat%avs(1),'FWS_TWS_B') - end if - - - ! Explicitly set current date to a hardcoded constant value. Otherwise - ! using the real date can cause roundoff differences that are - ! detrected as issues with exact restart. EBK M05/20/2017 - !call get_curr_date(year, mon, day, sec) - year = 1996 - mon = 12 - day = 31 - sec = 0 - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ch4finundated') - - ! Get the data - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - if ( index_ZWT0 > 0 )then - this%zwt0_gdc(g) = sdat%avs(1)%rAttr(index_ZWT0,ig) - end if - if ( index_F0 > 0 )then - this%f0_gdc(g) = sdat%avs(1)%rAttr(index_F0,ig) - end if - if ( index_P3 > 0 )then - this%p3_gdc(g) = sdat%avs(1)%rAttr(index_P3,ig) - end if - if ( index_FWS_TWS_A > 0 )then - this%fws_slope_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_A,ig) - end if - if ( index_FWS_TWS_B > 0 )then - this%fws_intercept_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_B,ig) - end if - end do - end if - end if - - end subroutine Init - - !----------------------------------------------------------------------- - logical function UseStreams(this) - ! - ! !DESCRIPTION: - ! Return true if - ! - ! !USES: - ! - ! !ARGUMENTS: - implicit none - class(ch4finundatedstream_type) :: this - ! - ! !LOCAL VARIABLES: - if ( trim(control%stream_fldFileName_ch4finundated) == '' )then - UseStreams = .false. - else - UseStreams = .true. - end if - end function UseStreams - - !----------------------------------------------------------------------- - subroutine InitAllocate(this, bounds) - ! - ! !DESCRIPTION: - ! Allocate module variables and data structures - ! - ! !USES: - use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=) - use ch4varcon , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion - ! - ! !ARGUMENTS: - implicit none - class(ch4finundatedstream_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: begc, endc - integer :: begg, endg - !--------------------------------------------------------------------- - - begc = bounds%begc; endc = bounds%endc - begg = bounds%begg; endg = bounds%endg - - if( finundation_mtd == finundation_mtd_ZWT_inversion )then - allocate(this%zwt0_gdc (begg:endg)) ; this%zwt0_gdc (:) = nan - allocate(this%f0_gdc (begg:endg)) ; this%f0_gdc (:) = nan - allocate(this%p3_gdc (begg:endg)) ; this%p3_gdc (:) = nan - else if( finundation_mtd == finundation_mtd_TWS_inversion )then - allocate(this%fws_slope_gdc (begg:endg)) ; this%fws_slope_gdc (:) = nan - allocate(this%fws_intercept_gdc(begg:endg)) ; this%fws_intercept_gdc(:) = nan - end if - - end subroutine InitAllocate - - !----------------------------------------------------------------------- - subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, & - waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated ) - ! - ! !DESCRIPTION: - ! - ! Calculate finundated according to the appropriate methodology - ! - ! !USES: - use ColumnType , only : col - use ch4varcon , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion - use ch4varcon , only : finundation_mtd_TWS_inversion - use clm_varpar , only : nlevsoi - use SoilHydrologyType, only : soilhydrology_type - use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type - ! - ! !ARGUMENTS: - implicit none - class(ch4finundatedstream_type) :: this - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of column soil points in column filter - integer , intent(in) :: filter_soilc(:) ! column filter for soil points - type(soilhydrology_type) , intent(in) :: soilhydrology_inst - type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst - real(r8) , intent(in) :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s) - real(r8) , intent(inout) :: finundated(bounds%begc:) ! fractional inundated area in soil column (excluding dedicated wetland columns) - ! - ! !LOCAL VARIABLES: - integer :: g, c, fc ! Indices - real(r8) :: zwt_actual ! Total water storage (ZWT) to use either perched or total depending on conditions - - SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(finundated) == (/bounds%endc/)), sourcefile, __LINE__) - - associate( & - z => col%z , & ! Input: [real(r8) (:,:) ] layer depth (m) (-nlevsno+1:nlevsoi) - zwt => soilhydrology_inst%zwt_col , & ! Input: [real(r8) (:) ] water table depth (m) - zwt_perched => soilhydrology_inst%zwt_perched_col , & ! Input: [real(r8) (:) ] perched water table depth (m) - tws => waterdiagnosticbulk_inst%tws_grc , & ! Input: [real(r8) (:) ] total water storage (kg m-2) - frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) - ) - - ! Calculate finundated - do fc = 1, num_soilc - c = filter_soilc(fc) - g = col%gridcell(c) - select case( finundation_mtd ) - case ( finundation_mtd_h2osfc ) - finundated(c) = frac_h2osfc(c) - case ( finundation_mtd_ZWT_inversion ) - if (this%zwt0_gdc(g) > 0._r8) then - if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then - zwt_actual = zwt_perched(c) - else - zwt_actual = zwt(c) - end if - finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c) - else - finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c) - end if - case ( finundation_mtd_TWS_inversion ) - finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g) - end select - finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) ) - end do - end associate - - end subroutine CalcFinundated - !============================================================================== - - subroutine ReadNML(this, bounds, NLFilename) - ! - ! Read the namelist data stream information. - ! - ! Uses: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_nl_mod , only : shr_nl_find_group_name - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_mpi_mod , only : shr_mpi_bcast - use fileutils , only : getavu, relavu - use ch4varcon , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion - ! - ! arguments - implicit none - class(streamcontrol_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - character(len=CL) :: stream_fldFileName_ch4finundated = ' ' - character(len=CL) :: ch4finundatedmapalgo = 'bilinear' - character(len=*), parameter :: namelist_name = 'ch4finundated' ! MUST agree with name in namelist and read - character(len=*), parameter :: shr_strdata_unset = 'NOT_SET' - character(len=*), parameter :: subName = "('ch4finundated::ReadNML')" - character(len=*), parameter :: F00 = "('(ch4finundated_readnml) ',4a)" - !----------------------------------------------------------------------- - - namelist /ch4finundated/ & ! MUST agree with namelist_name above - ch4finundatedmapalgo, stream_fldFileName_ch4finundated - - ! Default values for namelist - - ! Read ch4finundated namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=ch4finundated,iostat=nml_error) ! MUST agree with namelist_name above - if (nml_error /= 0) then - call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - else - call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_fldFileName_ch4finundated, mpicom) - call shr_mpi_bcast(ch4finundatedmapalgo , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) namelist_name, ' stream settings:' - write(iulog,*) ' stream_fldFileName_ch4finundated = ',stream_fldFileName_ch4finundated - write(iulog,*) ' ch4finundatedmapalgo = ',ch4finundatedmapalgo - write(iulog,*) ' ' - endif - this%stream_fldFileName_ch4finundated = stream_fldFileName_ch4finundated - this%ch4finundatedmapalgo = ch4finundatedmapalgo - if ( finundation_mtd == finundation_mtd_ZWT_inversion )then - this%fldList = "ZWT0:F0:P3" - else if ( finundation_mtd == finundation_mtd_TWS_inversion )then - this%fldList = "FWS_TWS_A:FWS_TWS_B" - else - call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// & - errMsg(sourcefile, __LINE__)) - end if - - end subroutine ReadNML - -end module ch4FInundatedStreamType diff --git a/src/cpl/mct/clm_cpl_indices.F90 b/src/cpl/mct/clm_cpl_indices.F90 deleted file mode 100644 index 09ed89e92d..0000000000 --- a/src/cpl/mct/clm_cpl_indices.F90 +++ /dev/null @@ -1,330 +0,0 @@ -module clm_cpl_indices - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Module containing the indices for the fields passed between CLM and - ! the driver. Includes the River Transport Model fields (RTM) and the - ! fields needed by the land-ice component (sno). - ! - ! !USES: - - use shr_sys_mod, only : shr_sys_abort - implicit none - - SAVE - private ! By default make data private - ! - ! !PUBLIC MEMBER FUNCTIONS: - public :: clm_cpl_indices_set ! Set the coupler indices - ! - ! !PUBLIC DATA MEMBERS: - ! - integer , public :: glc_nec ! number of elevation classes for glacier_mec landunits - ! (from coupler) - must equal maxpatch_glc from namelist - - ! lnd -> drv (required) - - integer, public ::index_l2x_Flrl_rofsur ! lnd->rtm input liquid surface fluxes - integer, public ::index_l2x_Flrl_rofgwl ! lnd->rtm input liquid gwl fluxes - integer, public ::index_l2x_Flrl_rofsub ! lnd->rtm input liquid subsurface fluxes - integer, public ::index_l2x_Flrl_rofi ! lnd->rtm input frozen fluxes - integer, public ::index_l2x_Flrl_irrig ! irrigation withdrawal - - integer, public ::index_l2x_Sl_t ! temperature - integer, public ::index_l2x_Sl_tref ! 2m reference temperature - integer, public ::index_l2x_Sl_qref ! 2m reference specific humidity - integer, public ::index_l2x_Sl_avsdr ! albedo: direct , visible - integer, public ::index_l2x_Sl_anidr ! albedo: direct , near-ir - integer, public ::index_l2x_Sl_avsdf ! albedo: diffuse, visible - integer, public ::index_l2x_Sl_anidf ! albedo: diffuse, near-ir - integer, public ::index_l2x_Sl_snowh ! snow height - integer, public ::index_l2x_Sl_u10 ! 10m wind - integer, public ::index_l2x_Sl_ddvel ! dry deposition velocities (optional) - integer, public ::index_l2x_Sl_fv ! friction velocity - integer, public ::index_l2x_Sl_ram1 ! aerodynamical resistance - integer, public ::index_l2x_Sl_soilw ! volumetric soil water - integer, public ::index_l2x_Fall_taux ! wind stress, zonal - integer, public ::index_l2x_Fall_tauy ! wind stress, meridional - integer, public ::index_l2x_Fall_lat ! latent heat flux - integer, public ::index_l2x_Fall_sen ! sensible heat flux - integer, public ::index_l2x_Fall_lwup ! upward longwave heat flux - integer, public ::index_l2x_Fall_evap ! evaporation water flux - integer, public ::index_l2x_Fall_swnet ! heat flux shortwave net - integer, public ::index_l2x_Fall_fco2_lnd ! co2 flux **For testing set to 0 - integer, public ::index_l2x_Fall_flxdst1 ! dust flux size bin 1 - integer, public ::index_l2x_Fall_flxdst2 ! dust flux size bin 2 - integer, public ::index_l2x_Fall_flxdst3 ! dust flux size bin 3 - integer, public ::index_l2x_Fall_flxdst4 ! dust flux size bin 4 - integer, public ::index_l2x_Fall_flxvoc ! MEGAN fluxes - integer, public ::index_l2x_Fall_flxfire ! Fire fluxes - integer, public ::index_l2x_Sl_ztopfire ! Top of fire emissions (m) - - ! In the following, index 0 is bare land, other indices are glc elevation classes - integer, allocatable, public ::index_l2x_Sl_tsrf(:) ! glc MEC temperature - integer, allocatable, public ::index_l2x_Sl_topo(:) ! glc MEC topo height - integer, allocatable, public ::index_l2x_Flgl_qice(:) ! glc MEC ice flux - - integer, public ::index_x2l_Sa_methane - integer, public ::index_l2x_Fall_methane - - integer, public :: nflds_l2x = 0 - - ! drv -> lnd (required) - - integer, public ::index_x2l_Sa_z ! bottom atm level height - integer, public ::index_x2l_Sa_topo ! atm surface height (m) - integer, public ::index_x2l_Sa_u ! bottom atm level zon wind - integer, public ::index_x2l_Sa_v ! bottom atm level mer wind - integer, public ::index_x2l_Sa_ptem ! bottom atm level pot temp - integer, public ::index_x2l_Sa_shum ! bottom atm level spec hum - integer, public ::index_x2l_Sa_pbot ! bottom atm level pressure - integer, public ::index_x2l_Sa_tbot ! bottom atm level temp - integer, public ::index_x2l_Faxa_lwdn ! downward lw heat flux - integer, public ::index_x2l_Faxa_rainc ! prec: liquid "convective" - integer, public ::index_x2l_Faxa_rainl ! prec: liquid "large scale" - integer, public ::index_x2l_Faxa_snowc ! prec: frozen "convective" - integer, public ::index_x2l_Faxa_snowl ! prec: frozen "large scale" - integer, public ::index_x2l_Faxa_swndr ! sw: nir direct downward - integer, public ::index_x2l_Faxa_swvdr ! sw: vis direct downward - integer, public ::index_x2l_Faxa_swndf ! sw: nir diffuse downward - integer, public ::index_x2l_Faxa_swvdf ! sw: vis diffuse downward - integer, public ::index_x2l_Sa_co2prog ! bottom atm level prognostic co2 - integer, public ::index_x2l_Sa_co2diag ! bottom atm level diagnostic co2 - integer, public ::index_x2l_Faxa_bcphidry ! flux: Black Carbon hydrophilic dry deposition - integer, public ::index_x2l_Faxa_bcphodry ! flux: Black Carbon hydrophobic dry deposition - integer, public ::index_x2l_Faxa_bcphiwet ! flux: Black Carbon hydrophilic wet deposition - integer, public ::index_x2l_Faxa_ocphidry ! flux: Organic Carbon hydrophilic dry deposition - integer, public ::index_x2l_Faxa_ocphodry ! flux: Organic Carbon hydrophobic dry deposition - integer, public ::index_x2l_Faxa_ocphiwet ! flux: Organic Carbon hydrophilic dry deposition - integer, public ::index_x2l_Faxa_dstwet1 ! flux: Size 1 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstwet2 ! flux: Size 2 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstwet3 ! flux: Size 3 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstwet4 ! flux: Size 4 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstdry1 ! flux: Size 1 dust -- dry deposition - integer, public ::index_x2l_Faxa_dstdry2 ! flux: Size 2 dust -- dry deposition - integer, public ::index_x2l_Faxa_dstdry3 ! flux: Size 3 dust -- dry deposition - integer, public ::index_x2l_Faxa_dstdry4 ! flux: Size 4 dust -- dry deposition - - integer, public ::index_x2l_Faxa_nhx ! flux nhx from atm - integer, public ::index_x2l_Faxa_noy ! flux noy from atm - - integer, public ::index_x2l_Flrr_flood ! rtm->lnd rof flood flux - integer, public ::index_x2l_Flrr_volr ! rtm->lnd rof volr total volume - integer, public ::index_x2l_Flrr_volrmch ! rtm->lnd rof volr main channel volume - - ! In the following, index 0 is bare land, other indices are glc elevation classes - integer, allocatable, public ::index_x2l_Sg_ice_covered(:) ! Fraction of glacier from glc model - integer, allocatable, public ::index_x2l_Sg_topo(:) ! Topo height from glc model - integer, allocatable, public ::index_x2l_Flgg_hflx(:) ! Heat flux from glc model - - integer, public ::index_x2l_Sg_icemask - integer, public ::index_x2l_Sg_icemask_coupled_fluxes - - integer, public :: nflds_x2l = 0 - - !----------------------------------------------------------------------- - -contains - - !----------------------------------------------------------------------- - subroutine clm_cpl_indices_set( ) - ! - ! !DESCRIPTION: - ! Set the coupler indices needed by the land model coupler - ! interface. - ! - ! !USES: - use seq_flds_mod , only: seq_flds_x2l_fields, seq_flds_l2x_fields - use mct_mod , only: mct_aVect, mct_aVect_init, mct_avect_indexra - use mct_mod , only: mct_aVect_clean, mct_avect_nRattr - use shr_drydep_mod , only: drydep_fields_token, n_drydep - use shr_megan_mod , only: shr_megan_fields_token, shr_megan_mechcomps_n - use shr_fire_emis_mod,only: shr_fire_emis_fields_token, shr_fire_emis_ztop_token, shr_fire_emis_mechcomps_n - use clm_varctl , only: ndep_from_cpl - use glc_elevclass_mod, only: glc_get_num_elevation_classes, glc_elevclass_as_string - ! - ! !ARGUMENTS: - implicit none - ! - ! !REVISION HISTORY: - ! Author: Mariana Vertenstein - ! 01/2011, Erik Kluzek: Added protex headers - ! - ! !LOCAL VARIABLES: - type(mct_aVect) :: l2x ! temporary, land to coupler - type(mct_aVect) :: x2l ! temporary, coupler to land - integer :: num - character(len=:), allocatable :: nec_str ! string version of glc elev. class number - character(len=64) :: name - character(len=32) :: subname = 'clm_cpl_indices_set' ! subroutine name - !----------------------------------------------------------------------- - - ! Determine attribute vector indices - - ! create temporary attribute vectors - call mct_aVect_init(x2l, rList=seq_flds_x2l_fields, lsize=1) - nflds_x2l = mct_avect_nRattr(x2l) - - call mct_aVect_init(l2x, rList=seq_flds_l2x_fields, lsize=1) - nflds_l2x = mct_avect_nRattr(l2x) - - !------------------------------------------------------------- - ! clm -> drv - !------------------------------------------------------------- - - index_l2x_Flrl_rofsur = mct_avect_indexra(l2x,'Flrl_rofsur') - index_l2x_Flrl_rofgwl = mct_avect_indexra(l2x,'Flrl_rofgwl') - index_l2x_Flrl_rofsub = mct_avect_indexra(l2x,'Flrl_rofsub') - index_l2x_Flrl_rofi = mct_avect_indexra(l2x,'Flrl_rofi') - index_l2x_Flrl_irrig = mct_avect_indexra(l2x,'Flrl_irrig') - - index_l2x_Sl_t = mct_avect_indexra(l2x,'Sl_t') - index_l2x_Sl_snowh = mct_avect_indexra(l2x,'Sl_snowh') - index_l2x_Sl_avsdr = mct_avect_indexra(l2x,'Sl_avsdr') - index_l2x_Sl_anidr = mct_avect_indexra(l2x,'Sl_anidr') - index_l2x_Sl_avsdf = mct_avect_indexra(l2x,'Sl_avsdf') - index_l2x_Sl_anidf = mct_avect_indexra(l2x,'Sl_anidf') - index_l2x_Sl_tref = mct_avect_indexra(l2x,'Sl_tref') - index_l2x_Sl_qref = mct_avect_indexra(l2x,'Sl_qref') - index_l2x_Sl_u10 = mct_avect_indexra(l2x,'Sl_u10') - index_l2x_Sl_ram1 = mct_avect_indexra(l2x,'Sl_ram1') - index_l2x_Sl_fv = mct_avect_indexra(l2x,'Sl_fv') - index_l2x_Sl_soilw = mct_avect_indexra(l2x,'Sl_soilw',perrwith='quiet') - - if ( n_drydep>0 )then - index_l2x_Sl_ddvel = mct_avect_indexra(l2x, trim(drydep_fields_token)) - else - index_l2x_Sl_ddvel = 0 - end if - - index_l2x_Fall_taux = mct_avect_indexra(l2x,'Fall_taux') - index_l2x_Fall_tauy = mct_avect_indexra(l2x,'Fall_tauy') - index_l2x_Fall_lat = mct_avect_indexra(l2x,'Fall_lat') - index_l2x_Fall_sen = mct_avect_indexra(l2x,'Fall_sen') - index_l2x_Fall_lwup = mct_avect_indexra(l2x,'Fall_lwup') - index_l2x_Fall_evap = mct_avect_indexra(l2x,'Fall_evap') - index_l2x_Fall_swnet = mct_avect_indexra(l2x,'Fall_swnet') - index_l2x_Fall_flxdst1 = mct_avect_indexra(l2x,'Fall_flxdst1') - index_l2x_Fall_flxdst2 = mct_avect_indexra(l2x,'Fall_flxdst2') - index_l2x_Fall_flxdst3 = mct_avect_indexra(l2x,'Fall_flxdst3') - index_l2x_Fall_flxdst4 = mct_avect_indexra(l2x,'Fall_flxdst4') - - index_l2x_Fall_fco2_lnd = mct_avect_indexra(l2x,'Fall_fco2_lnd',perrwith='quiet') - - index_l2x_Fall_methane = mct_avect_indexra(l2x,'Fall_methane',perrWith='quiet') - - ! MEGAN fluxes - if (shr_megan_mechcomps_n>0) then - index_l2x_Fall_flxvoc = mct_avect_indexra(l2x,trim(shr_megan_fields_token)) - else - index_l2x_Fall_flxvoc = 0 - endif - - ! Fire fluxes - if (shr_fire_emis_mechcomps_n>0) then - index_l2x_Fall_flxfire = mct_avect_indexra(l2x,trim(shr_fire_emis_fields_token)) - index_l2x_Sl_ztopfire = mct_avect_indexra(l2x,trim(shr_fire_emis_ztop_token)) - else - index_l2x_Fall_flxfire = 0 - index_l2x_Sl_ztopfire = 0 - endif - - !------------------------------------------------------------- - ! drv -> clm - !------------------------------------------------------------- - - index_x2l_Sa_z = mct_avect_indexra(x2l,'Sa_z') - index_x2l_Sa_topo = mct_avect_indexra(x2l,'Sa_topo') - index_x2l_Sa_u = mct_avect_indexra(x2l,'Sa_u') - index_x2l_Sa_v = mct_avect_indexra(x2l,'Sa_v') - index_x2l_Sa_ptem = mct_avect_indexra(x2l,'Sa_ptem') - index_x2l_Sa_pbot = mct_avect_indexra(x2l,'Sa_pbot') - index_x2l_Sa_tbot = mct_avect_indexra(x2l,'Sa_tbot') - index_x2l_Sa_shum = mct_avect_indexra(x2l,'Sa_shum') - index_x2l_Sa_co2prog = mct_avect_indexra(x2l,'Sa_co2prog',perrwith='quiet') - index_x2l_Sa_co2diag = mct_avect_indexra(x2l,'Sa_co2diag',perrwith='quiet') - - index_x2l_Sa_methane = mct_avect_indexra(x2l,'Sa_methane',perrWith='quiet') - - index_x2l_Flrr_volr = mct_avect_indexra(x2l,'Flrr_volr') - index_x2l_Flrr_volrmch = mct_avect_indexra(x2l,'Flrr_volrmch') - - index_x2l_Faxa_lwdn = mct_avect_indexra(x2l,'Faxa_lwdn') - index_x2l_Faxa_rainc = mct_avect_indexra(x2l,'Faxa_rainc') - index_x2l_Faxa_rainl = mct_avect_indexra(x2l,'Faxa_rainl') - index_x2l_Faxa_snowc = mct_avect_indexra(x2l,'Faxa_snowc') - index_x2l_Faxa_snowl = mct_avect_indexra(x2l,'Faxa_snowl') - index_x2l_Faxa_swndr = mct_avect_indexra(x2l,'Faxa_swndr') - index_x2l_Faxa_swvdr = mct_avect_indexra(x2l,'Faxa_swvdr') - index_x2l_Faxa_swndf = mct_avect_indexra(x2l,'Faxa_swndf') - index_x2l_Faxa_swvdf = mct_avect_indexra(x2l,'Faxa_swvdf') - index_x2l_Faxa_bcphidry = mct_avect_indexra(x2l,'Faxa_bcphidry') - index_x2l_Faxa_bcphodry = mct_avect_indexra(x2l,'Faxa_bcphodry') - index_x2l_Faxa_bcphiwet = mct_avect_indexra(x2l,'Faxa_bcphiwet') - index_x2l_Faxa_ocphidry = mct_avect_indexra(x2l,'Faxa_ocphidry') - index_x2l_Faxa_ocphodry = mct_avect_indexra(x2l,'Faxa_ocphodry') - index_x2l_Faxa_ocphiwet = mct_avect_indexra(x2l,'Faxa_ocphiwet') - index_x2l_Faxa_dstdry1 = mct_avect_indexra(x2l,'Faxa_dstdry1') - index_x2l_Faxa_dstdry2 = mct_avect_indexra(x2l,'Faxa_dstdry2') - index_x2l_Faxa_dstdry3 = mct_avect_indexra(x2l,'Faxa_dstdry3') - index_x2l_Faxa_dstdry4 = mct_avect_indexra(x2l,'Faxa_dstdry4') - index_x2l_Faxa_dstwet1 = mct_avect_indexra(x2l,'Faxa_dstwet1') - index_x2l_Faxa_dstwet2 = mct_avect_indexra(x2l,'Faxa_dstwet2') - index_x2l_Faxa_dstwet3 = mct_avect_indexra(x2l,'Faxa_dstwet3') - index_x2l_Faxa_dstwet4 = mct_avect_indexra(x2l,'Faxa_dstwet4') - - index_x2l_Faxa_nhx = mct_avect_indexra(x2l,'Faxa_nhx', perrWith='quiet') - index_x2l_Faxa_noy = mct_avect_indexra(x2l,'Faxa_noy', perrWith='quiet') - - if (index_x2l_Faxa_nhx > 0 .and. index_x2l_Faxa_noy > 0) then - ndep_from_cpl = .true. - end if - - index_x2l_Flrr_flood = mct_avect_indexra(x2l,'Flrr_flood') - - !------------------------------------------------------------- - ! glc coupling - !------------------------------------------------------------- - - index_x2l_Sg_icemask = mct_avect_indexra(x2l,'Sg_icemask') - index_x2l_Sg_icemask_coupled_fluxes = mct_avect_indexra(x2l,'Sg_icemask_coupled_fluxes') - - glc_nec = glc_get_num_elevation_classes() - if (glc_nec < 1) then - call shr_sys_abort('ERROR: In CLM4.5 and later, glc_nec must be at least 1.') - end if - - ! Create coupling fields for all glc elevation classes (1:glc_nec) plus bare land - ! (index 0). - allocate(index_l2x_Sl_tsrf(0:glc_nec)) - allocate(index_l2x_Sl_topo(0:glc_nec)) - allocate(index_l2x_Flgl_qice(0:glc_nec)) - allocate(index_x2l_Sg_ice_covered(0:glc_nec)) - allocate(index_x2l_Sg_topo(0:glc_nec)) - allocate(index_x2l_Flgg_hflx(0:glc_nec)) - - do num = 0,glc_nec - nec_str = glc_elevclass_as_string(num) - - name = 'Sg_ice_covered' // nec_str - index_x2l_Sg_ice_covered(num) = mct_avect_indexra(x2l,trim(name)) - name = 'Sg_topo' // nec_str - index_x2l_Sg_topo(num) = mct_avect_indexra(x2l,trim(name)) - name = 'Flgg_hflx' // nec_str - index_x2l_Flgg_hflx(num) = mct_avect_indexra(x2l,trim(name)) - - name = 'Sl_tsrf' // nec_str - index_l2x_Sl_tsrf(num) = mct_avect_indexra(l2x,trim(name)) - name = 'Sl_topo' // nec_str - index_l2x_Sl_topo(num) = mct_avect_indexra(l2x,trim(name)) - name = 'Flgl_qice' // nec_str - index_l2x_Flgl_qice(num) = mct_avect_indexra(l2x,trim(name)) - end do - - call mct_aVect_clean(x2l) - call mct_aVect_clean(l2x) - - end subroutine clm_cpl_indices_set - -!======================================================================= - -end module clm_cpl_indices diff --git a/src/cpl/mct/laiStreamMod.F90 b/src/cpl/mct/laiStreamMod.F90 deleted file mode 100644 index 47d25287b7..0000000000 --- a/src/cpl/mct/laiStreamMod.F90 +++ /dev/null @@ -1,241 +0,0 @@ -module laiStreamMod - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Read LAI from stream - ! - ! !USES: - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create - use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance - use shr_kind_mod , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX - use shr_log_mod , only : errMsg => shr_log_errMsg - use decompMod , only : bounds_type - use abortutils , only : endrun - use clm_varctl , only : iulog, inst_name - use perf_mod , only : t_startf, t_stopf - use spmdMod , only : masterproc, mpicom, comp_id - use ncdio_pio - use mct_mod - ! - ! !PUBLIC TYPES: - implicit none - private - - ! !PUBLIC MEMBER FUNCTIONS: - public :: lai_init ! position datasets for LAI - public :: lai_advance ! Advance the LAI streams (outside of a Open-MP threading loop) - public :: lai_interp ! interpolates between two years of LAI data (when LAI streams - - ! !PRIVATE MEMBER DATA: - integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - type(shr_strdata_type) :: sdat_lai ! LAI input data stream - - character(len=*), parameter :: sourcefile = & - __FILE__ - -!============================================================================== -contains -!============================================================================== - - subroutine lai_init(bounds) - ! - ! Initialize data stream information for LAI. - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_stream_mod , only : shr_stream_file_null - use shr_string_mod , only : shr_string_listCreateField - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use histFileMod , only : hist_addfld1d - use domainMod , only : ldomain - use controlMod , only : NLFilename - use lnd_set_decomp_and_domain , only : gsmap_global - ! - ! !ARGUMENTS: - implicit none - type(bounds_type), intent(in) :: bounds ! bounds - ! - ! !LOCAL VARIABLES: - integer :: stream_year_first_lai ! first year in Lai stream to use - integer :: stream_year_last_lai ! last year in Lai stream to use - integer :: model_year_align_lai ! align stream_year_first_lai with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_lai ! lai stream filename to read - character(len=CL) :: lai_mapalgo = 'bilinear' ! Mapping alogrithm - character(len=CL) :: lai_tintalgo = 'linear' ! Time interpolation alogrithm - character(len=CXX) :: fldList ! field string - character(*), parameter :: laiString = "LAI" ! base string for field string - integer , parameter :: numLaiFields = 16 ! number of fields to build field string - character(*), parameter :: subName = "('laidyn_init')" - !----------------------------------------------------------------------- - ! - ! deal with namelist variables here in init - ! - namelist /lai_streams/ & - stream_year_first_lai, & - stream_year_last_lai, & - model_year_align_lai, & - lai_mapalgo, & - stream_fldFileName_lai, & - lai_tintalgo - - ! Default values for namelist - stream_year_first_lai = 1 ! first year in stream to use - stream_year_last_lai = 1 ! last year in stream to use - model_year_align_lai = 1 ! align stream_year_first_lai with this model year - stream_fldFileName_lai = shr_stream_file_null - - ! Read lai_streams namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'lai_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=lai_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(subname // ':: ERROR reading lai_streams namelist') - end if - else - call endrun(subname // ':: ERROR finding lai_streams namelist') - end if - close(nu_nml) - endif - call shr_mpi_bcast(stream_year_first_lai , mpicom) - call shr_mpi_bcast(stream_year_last_lai , mpicom) - call shr_mpi_bcast(model_year_align_lai , mpicom) - call shr_mpi_bcast(stream_fldFileName_lai , mpicom) - call shr_mpi_bcast(lai_tintalgo , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'lai_stream settings:' - write(iulog,*) ' stream_year_first_lai = ',stream_year_first_lai - write(iulog,*) ' stream_year_last_lai = ',stream_year_last_lai - write(iulog,*) ' model_year_align_lai = ',model_year_align_lai - write(iulog,*) ' stream_fldFileName_lai = ',trim(stream_fldFileName_lai) - write(iulog,*) ' lai_tintalgo = ',trim(lai_tintalgo) - endif - - call clm_domain_mct (bounds, dom_clm) - - ! create the field list for these lai fields...use in shr_strdata_create - fldList = shr_string_listCreateField( numLaiFields, laiString ) - - call shr_strdata_create(sdat_lai,name="laidyn", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_lai, & - yearLast=stream_year_last_lai, & - yearAlign=model_year_align_lai, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_lai), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/stream_fldFileName_lai/), & - fldListFile=fldList, & - fldListModel=fldList, & - fillalgo='none', & - mapalgo=lai_mapalgo, & - tintalgo=lai_tintalgo, & - calendar=get_calendar(), & - taxmode='cycle' ) - - if (masterproc) then - call shr_strdata_print(sdat_lai,'LAI data') - endif - - end subroutine lai_init - - !============================================================================== - subroutine lai_advance( bounds ) - ! - ! Advance LAI streams - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g, ig ! Indices - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(sdat_lai, mcdate, sec, mpicom, 'laidyn') - if ( .not. allocated(g_to_ig) )then - allocate (g_to_ig(bounds%begg:bounds%endg) ) - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - g_to_ig(g) = ig - end do - end if - - end subroutine lai_advance - - !============================================================================== - subroutine lai_interp(bounds, canopystate_inst) - ! - ! Interpolate data stream information for Lai. - ! - ! !USES: - use pftconMod , only : noveg - use CanopyStateType , only : canopystate_type - use PatchType , only : patch - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - type(canopystate_type) , intent(inout) :: canopystate_inst - ! - ! !LOCAL VARIABLES: - integer :: ivt, p, ip, ig - character(len=CL) :: stream_var_name - !----------------------------------------------------------------------- - SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(sdat_lai%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_lai%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - - do p = bounds%begp, bounds%endp - ivt = patch%itype(p) - ! Set lai for each gridcell/patch combination - if (ivt /= noveg) then - ! vegetated pft - write(stream_var_name,"(i6)") ivt - stream_var_name = 'LAI_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_lai%avs(1),trim(stream_var_name)) - ig = g_to_ig(patch%gridcell(p)) - canopystate_inst%tlai_patch(p) = sdat_lai%avs(1)%rAttr(ip,ig) - else - ! non-vegetated pft - canopystate_inst%tlai_patch(p) = 0._r8 - endif - end do - - end subroutine lai_interp - -end module LaiStreamMod diff --git a/src/cpl/mct/lnd_comp_mct.F90 b/src/cpl/mct/lnd_comp_mct.F90 deleted file mode 100644 index e50602a378..0000000000 --- a/src/cpl/mct/lnd_comp_mct.F90 +++ /dev/null @@ -1,632 +0,0 @@ -module lnd_comp_mct - - !--------------------------------------------------------------------------- - ! !DESCRIPTION: - ! Interface of the active land model component of CESM the CLM (Community Land Model) - ! with the main CESM driver. This is a thin interface taking CESM driver information - ! in MCT (Model Coupling Toolkit) format and converting it to use by CLM. - ! - ! !uses: - use shr_kind_mod , only : r8 => shr_kind_r8 - use shr_sys_mod , only : shr_sys_flush - use shr_log_mod , only : errMsg => shr_log_errMsg - use mct_mod , only : mct_avect, mct_gsmap, mct_gGrid - use decompmod , only : bounds_type - use lnd_import_export, only : lnd_import, lnd_export - ! - ! !public member functions: - implicit none - private ! by default make data private - ! - ! !public member functions: - public :: lnd_init_mct ! clm initialization - public :: lnd_run_mct ! clm run phase - public :: lnd_final_mct ! clm finalization/cleanup - ! - ! !private member functions: - private :: lnd_domain_mct ! set the land model domain information - private :: lnd_handle_resume ! handle pause/resume signals from the coupler - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -!==================================================================================== -contains -!==================================================================================== - - subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename ) - ! - ! !DESCRIPTION: - ! Initialize land surface model and obtain relevant atmospheric model arrays - ! back from (i.e. albedos, surface temperature and snow cover over land). - ! - ! !USES: - use shr_kind_mod , only : shr_kind_cl - use abortutils , only : endrun - use clm_time_manager , only : get_nstep, set_timemgr_init - use clm_initializeMod, only : initialize1, initialize2 - use clm_instMod , only : water_inst, lnd2atm_inst, lnd2glc_inst - use clm_varctl , only : finidat, single_column, clm_varctl_set, iulog - use clm_varctl , only : inst_index, inst_suffix, inst_name - use clm_varorb , only : eccen, obliqr, lambm0, mvelpp - use controlMod , only : control_setNL - use decompMod , only : get_proc_bounds - use domainMod , only : ldomain - use shr_file_mod , only : shr_file_setLogUnit, shr_file_setLogLevel - use shr_file_mod , only : shr_file_getLogUnit, shr_file_getLogLevel - use shr_file_mod , only : shr_file_getUnit, shr_file_setIO - use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs - use seq_timemgr_mod , only : seq_timemgr_EClockGetData - use seq_infodata_mod , only : seq_infodata_type, seq_infodata_GetData, seq_infodata_PutData, & - seq_infodata_start_type_start, seq_infodata_start_type_cont, & - seq_infodata_start_type_brnch - use seq_comm_mct , only : seq_comm_suffix, seq_comm_inst, seq_comm_name - use seq_flds_mod , only : seq_flds_x2l_fields, seq_flds_l2x_fields - use spmdMod , only : masterproc, spmd_init - use clm_varctl , only : nsrStartup, nsrContinue, nsrBranch - use clm_cpl_indices , only : clm_cpl_indices_set - use mct_mod , only : mct_aVect_init, mct_aVect_zero, mct_gsMap, mct_gsMap_init - use decompMod , only : gindex_global - use lnd_set_decomp_and_domain, only : lnd_set_decomp_and_domain_from_surfrd, gsmap_global - use ESMF - ! - ! !ARGUMENTS: - type(ESMF_Clock), intent(inout) :: EClock ! Input synchronization clock - type(seq_cdata), intent(inout) :: cdata_l ! Input land-model driver data - type(mct_aVect), intent(inout) :: x2l_l, l2x_l ! land model import and export states - character(len=*), optional, intent(in) :: NLFilename ! Namelist filename to read - ! - ! !LOCAL VARIABLES: - integer :: LNDID ! Land identifyer - integer :: mpicom_lnd ! MPI communicator - type(mct_gsMap), pointer :: GSMap_lnd ! Land model MCT GS map - type(mct_gGrid), pointer :: dom_l ! Land model domain - type(seq_infodata_type), pointer :: infodata ! CESM driver level info data - integer :: lsize ! size of attribute vector - integer :: gsize ! global size - integer :: g,i,j ! indices - integer :: dtime_sync ! coupling time-step from the input synchronization clock - logical :: exists ! true if file exists - logical :: atm_aero ! Flag if aerosol data sent from atm model - real(r8) :: scmlat ! single-column latitude - real(r8) :: scmlon ! single-column longitude - character(len=SHR_KIND_CL) :: caseid ! case identifier name - character(len=SHR_KIND_CL) :: ctitle ! case description title - character(len=SHR_KIND_CL) :: starttype ! start-type (startup, continue, branch, hybrid) - character(len=SHR_KIND_CL) :: calendar ! calendar type name - character(len=SHR_KIND_CL) :: hostname ! hostname of machine running on - character(len=SHR_KIND_CL) :: version ! Model version - character(len=SHR_KIND_CL) :: username ! user running the model - integer :: nsrest ! clm restart type - integer :: ref_ymd ! reference date (YYYYMMDD) - integer :: ref_tod ! reference time of day (sec) - integer :: start_ymd ! start date (YYYYMMDD) - integer :: start_tod ! start time of day (sec) - logical :: brnch_retain_casename ! flag if should retain the case name on a branch start type - integer :: lbnum ! input to memory diagnostic - integer :: shrlogunit,shrloglev ! old values for log unit and log level - type(bounds_type) :: bounds ! bounds - logical :: noland - integer :: ni,nj - real(r8) , parameter :: rundef = -9999999._r8 - character(len=32), parameter :: sub = 'lnd_init_mct' - character(len=*), parameter :: format = "('("//trim(sub)//") :',A)" - !----------------------------------------------------------------------- - - ! Set cdata data - call seq_cdata_setptrs(cdata_l, ID=LNDID, mpicom=mpicom_lnd, & - gsMap=GSMap_lnd, dom=dom_l, infodata=infodata) - - ! Determine attriute vector indices - call clm_cpl_indices_set() - - ! Initialize clm MPI communicator - call spmd_init( mpicom_lnd, LNDID ) - -#if (defined _MEMTRACE) - if(masterproc) then - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_init_mct:start::',lbnum) - endif -#endif - - inst_name = seq_comm_name(LNDID) - inst_index = seq_comm_inst(LNDID) - inst_suffix = seq_comm_suffix(LNDID) - ! Initialize io log unit - - call shr_file_getLogUnit (shrlogunit) - if (masterproc) then - inquire(file='lnd_modelio.nml'//trim(inst_suffix),exist=exists) - if (exists) then - iulog = shr_file_getUnit() - call shr_file_setIO('lnd_modelio.nml'//trim(inst_suffix),iulog) - end if - write(iulog,format) "CLM land model initialization" - else - iulog = shrlogunit - end if - - call shr_file_getLogLevel(shrloglev) - call shr_file_setLogUnit (iulog) - - ! Use infodata to set orbital values - call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, & - orb_lambm0=lambm0, orb_obliqr=obliqr ) - - ! Consistency check on namelist filename - call control_setNL("lnd_in"//trim(inst_suffix)) - - ! Initialize clm - ! initialize1 reads namelists - ! decomp and domain are set in lnd_set_decomp_and_domain_from_surfrd - ! initialize2 performs the rest of initialization - call seq_timemgr_EClockGetData(EClock, & - start_ymd=start_ymd, & - start_tod=start_tod, ref_ymd=ref_ymd, & - ref_tod=ref_tod, & - calendar=calendar, & - dtime=dtime_sync) - if (masterproc) then - write(iulog,*)'dtime = ',dtime_sync - end if - call seq_infodata_GetData(infodata, case_name=caseid, & - case_desc=ctitle, single_column=single_column, & - scmlat=scmlat, scmlon=scmlon, & - brnch_retain_casename=brnch_retain_casename, & - start_type=starttype, model_version=version, & - hostname=hostname, username=username ) - - ! Single Column - if ( single_column .and. (scmlat == rundef .or. scmlon == rundef ) ) then - call endrun(msg=' ERROR:: single column mode on -- but scmlat and scmlon are NOT set'//& - errMsg(sourcefile, __LINE__)) - end if - - ! Note that we assume that CTSM's internal dtime matches the coupling time step. - ! i.e., we currently do NOT allow sub-cycling within a coupling time step. - call set_timemgr_init( calendar_in=calendar, start_ymd_in=start_ymd, start_tod_in=start_tod, & - ref_ymd_in=ref_ymd, ref_tod_in=ref_tod, dtime_in=dtime_sync) - - if ( trim(starttype) == trim(seq_infodata_start_type_start)) then - nsrest = nsrStartup - else if (trim(starttype) == trim(seq_infodata_start_type_cont) ) then - nsrest = nsrContinue - else if (trim(starttype) == trim(seq_infodata_start_type_brnch)) then - nsrest = nsrBranch - else - call endrun( sub//' ERROR: unknown starttype' ) - end if - - ! set default values for run control variables - call clm_varctl_set(caseid_in=caseid, ctitle_in=ctitle, & - brnch_retain_casename_in=brnch_retain_casename, & - single_column_in=single_column, scmlat_in=scmlat, & - scmlon_in=scmlon, nsrest_in=nsrest, version_in=version, & - hostname_in=hostname, username_in=username) - - ! Read namelists - call initialize1(dtime=dtime_sync) - - ! Initialize decomposition and domain (ldomain) type - call lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj) - - ! If no land then exit out of initialization - if ( noland ) then - - call seq_infodata_PutData( infodata, lnd_present =.false.) - call seq_infodata_PutData( infodata, lnd_prognostic=.false.) - - else - - ! Determine if aerosol and dust deposition come from atmosphere component - call seq_infodata_GetData(infodata, atm_aero=atm_aero ) - if ( .not. atm_aero )then - call endrun( sub//' ERROR: atmosphere model MUST send aerosols to CLM' ) - end if - - ! Initialize clm gsMap, clm domain and clm attribute vectors - call get_proc_bounds( bounds ) - lsize = bounds%endg - bounds%begg + 1 - gsize = ldomain%ni * ldomain%nj - call mct_gsMap_init( gsMap_lnd, gindex_global, mpicom_lnd, LNDID, lsize, gsize ) - gsmap_global => gsmap_lnd ! module variable in lnd_set_decomp_and_domain - call lnd_domain_mct( bounds, lsize, gsMap_lnd, dom_l ) - call mct_aVect_init(x2l_l, rList=seq_flds_x2l_fields, lsize=lsize) - call mct_aVect_zero(x2l_l) - call mct_aVect_init(l2x_l, rList=seq_flds_l2x_fields, lsize=lsize) - call mct_aVect_zero(l2x_l) - - ! Finish initializing clm - call initialize2(ni,nj) - - ! Create land export state - call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr) - - ! Fill in infodata settings - call seq_infodata_PutData(infodata, lnd_prognostic=.true.) - call seq_infodata_PutData(infodata, lnd_nx=ldomain%ni, lnd_ny=ldomain%nj) - call lnd_handle_resume( cdata_l ) - - ! Reset shr logging to original values - call shr_file_setLogUnit (shrlogunit) - call shr_file_setLogLevel(shrloglev) - -#if (defined _MEMTRACE) - if(masterproc) then - write(iulog,*) TRIM(Sub) // ':end::' - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_int_mct:end::',lbnum) - call memmon_reset_addr() - endif -#endif - end if - - end subroutine lnd_init_mct - - !==================================================================================== - subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l) - ! - ! !DESCRIPTION: - ! Run clm model - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_instMod , only : water_inst, lnd2atm_inst, atm2lnd_inst, lnd2glc_inst, glc2lnd_inst - use clm_driver , only : clm_drv - use clm_time_manager, only : get_curr_date, get_nstep, get_curr_calday, get_step_size - use clm_time_manager, only : advance_timestep, update_rad_dtime - use decompMod , only : get_proc_bounds - use abortutils , only : endrun - use clm_varctl , only : iulog - use clm_varorb , only : eccen, obliqr, lambm0, mvelpp - use shr_file_mod , only : shr_file_setLogUnit, shr_file_setLogLevel - use shr_file_mod , only : shr_file_getLogUnit, shr_file_getLogLevel - use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs - use seq_timemgr_mod , only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn - use seq_timemgr_mod , only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync - use seq_infodata_mod, only : seq_infodata_type, seq_infodata_GetData - use spmdMod , only : masterproc, mpicom - use perf_mod , only : t_startf, t_stopf, t_barrierf - use shr_orb_mod , only : shr_orb_decl - use ESMF - ! - ! !ARGUMENTS: - type(ESMF_Clock) , intent(inout) :: EClock ! Input synchronization clock from driver - type(seq_cdata) , intent(inout) :: cdata_l ! Input driver data for land model - type(mct_aVect) , intent(inout) :: x2l_l ! Import state to land model - type(mct_aVect) , intent(inout) :: l2x_l ! Export state from land model - ! - ! !LOCAL VARIABLES: - integer :: ymd_sync ! Sync date (YYYYMMDD) - integer :: yr_sync ! Sync current year - integer :: mon_sync ! Sync current month - integer :: day_sync ! Sync current day - integer :: tod_sync ! Sync current time of day (sec) - integer :: ymd ! CLM current date (YYYYMMDD) - integer :: yr ! CLM current year - integer :: mon ! CLM current month - integer :: day ! CLM current day - integer :: tod ! CLM current time of day (sec) - integer :: dtime ! time step increment (sec) - integer :: nstep ! time step index - logical :: rstwr_sync ! .true. ==> write restart file before returning - logical :: rstwr ! .true. ==> write restart file before returning - logical :: nlend_sync ! Flag signaling last time-step - logical :: nlend ! .true. ==> last time-step - logical :: dosend ! true => send data back to driver - logical :: doalb ! .true. ==> do albedo calculation on this time step - logical :: rof_prognostic ! .true. => running with a prognostic ROF model - logical :: glc_present ! .true. => running with a non-stub GLC model - real(r8) :: nextsw_cday ! calday from clock of next radiation computation - real(r8) :: caldayp1 ! clm calday plus dtime offset - integer :: shrlogunit,shrloglev ! old values for share log unit and log level - integer :: lbnum ! input to memory diagnostic - integer :: g,i,lsize ! counters - real(r8) :: calday ! calendar day for nstep - real(r8) :: declin ! solar declination angle in radians for nstep - real(r8) :: declinp1 ! solar declination angle in radians for nstep+1 - real(r8) :: eccf ! earth orbit eccentricity factor - real(r8) :: recip ! reciprical - logical,save :: first_call = .true. ! first call work - type(seq_infodata_type),pointer :: infodata ! CESM information from the driver - type(mct_gGrid), pointer :: dom_l ! Land model domain data - type(bounds_type) :: bounds ! bounds - character(len=32) :: rdate ! date char string for restart file names - character(len=32), parameter :: sub = "lnd_run_mct" - !--------------------------------------------------------------------------- - - ! Determine processor bounds - - call get_proc_bounds(bounds) - -#if (defined _MEMTRACE) - if(masterproc) then - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_run_mct:start::',lbnum) - endif -#endif - - ! Reset shr logging to my log file - call shr_file_getLogUnit (shrlogunit) - call shr_file_getLogLevel(shrloglev) - call shr_file_setLogUnit (iulog) - - ! Determine time of next atmospheric shortwave calculation - call seq_cdata_setptrs(cdata_l, infodata=infodata, dom=dom_l) - call seq_timemgr_EClockGetData(EClock, & - curr_ymd=ymd, curr_tod=tod_sync, & - curr_yr=yr_sync, curr_mon=mon_sync, curr_day=day_sync) - call seq_infodata_GetData(infodata, nextsw_cday=nextsw_cday ) - - dtime = get_step_size() - - ! Handle pause/resume signals from coupler - call lnd_handle_resume( cdata_l ) - - write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync,mon_sync,day_sync,tod_sync - nlend_sync = seq_timemgr_StopAlarmIsOn( EClock ) - rstwr_sync = seq_timemgr_RestartAlarmIsOn( EClock ) - - ! Determine if we're running with a prognostic ROF model, and if we're running with a - ! non-stub GLC model. These won't change throughout the run, but we can't count on - ! their being set in initialization, so need to get them in the run method. - - call seq_infodata_GetData( infodata, & - rof_prognostic=rof_prognostic, & - glc_present=glc_present) - - ! Map MCT to land data type - ! Perform downscaling if appropriate - - - ! Map to clm (only when state and/or fluxes need to be updated) - - call t_startf ('lc_lnd_import') - call lnd_import( bounds, & - x2l = x2l_l%rattr, & - glc_present = glc_present, & - atm2lnd_inst = atm2lnd_inst, & - glc2lnd_inst = glc2lnd_inst, & - wateratm2lndbulk_inst = water_inst%wateratm2lndbulk_inst) - call t_stopf ('lc_lnd_import') - - ! Use infodata to set orbital values if updated mid-run - - call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, & - orb_lambm0=lambm0, orb_obliqr=obliqr ) - - ! Loop over time steps in coupling interval - - dosend = .false. - do while(.not. dosend) - - ! Determine if dosend - ! When time is not updated at the beginning of the loop - then return only if - ! are in sync with clock before time is updated - ! - ! NOTE(wjs, 2020-03-09) I think the do while (.not. dosend) loop only is important - ! for the first time step (when we run 2 steps). After that, we now assume that we - ! run one time step per coupling interval (based on setting the model's dtime from - ! the driver). (According to Mariana Vertenstein, sub-cycling (running multiple - ! land model time steps per coupling interval) used to be supported, but hasn't - ! been fully supported for a long time.) We may want to rework this logic to make - ! this more explicit, or - ideally - get rid of this extra time step at the start - ! of the run, at which point I think we could do away with this looping entirely. - - call get_curr_date( yr, mon, day, tod ) - ymd = yr*10000 + mon*100 + day - tod = tod - dosend = (seq_timemgr_EClockDateInSync( EClock, ymd, tod)) - - ! Determine doalb based on nextsw_cday sent from atm model - - nstep = get_nstep() - caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.) - if (nstep == 0) then - doalb = .false. - else if (nstep == 1) then - doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8) - else - doalb = (nextsw_cday >= -0.5_r8) - end if - call update_rad_dtime(doalb) - - ! Determine if time to write restart and stop - - rstwr = .false. - if (rstwr_sync .and. dosend) rstwr = .true. - nlend = .false. - if (nlend_sync .and. dosend) nlend = .true. - - ! Run clm - - call t_barrierf('sync_clm_run1', mpicom) - call t_startf ('clm_run') - call t_startf ('shr_orb_decl') - calday = get_curr_calday(reuse_day_365_for_day_366=.true.) - call shr_orb_decl( calday , eccen, mvelpp, lambm0, obliqr, declin , eccf ) - call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf ) - call t_stopf ('shr_orb_decl') - call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic) - call t_stopf ('clm_run') - - ! Create l2x_l export state - add river runoff input to l2x_l if appropriate - - call t_startf ('lc_lnd_export') - call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr) - call t_stopf ('lc_lnd_export') - - ! Advance clm time step - - call t_startf ('lc_clm2_adv_timestep') - call advance_timestep() - call t_stopf ('lc_clm2_adv_timestep') - - end do - - ! Check that internal clock is in sync with master clock - - call get_curr_date( yr, mon, day, tod, offset=-dtime ) - ymd = yr*10000 + mon*100 + day - tod = tod - if ( .not. seq_timemgr_EClockDateInSync( EClock, ymd, tod ) )then - call seq_timemgr_EclockGetData( EClock, curr_ymd=ymd_sync, curr_tod=tod_sync ) - write(iulog,*)' clm ymd=',ymd ,' clm tod= ',tod - write(iulog,*)'sync ymd=',ymd_sync,' sync tod= ',tod_sync - call endrun( sub//":: CLM clock not in sync with Master Sync clock" ) - end if - - ! Reset shr logging to my original values - - call shr_file_setLogUnit (shrlogunit) - call shr_file_setLogLevel(shrloglev) - -#if (defined _MEMTRACE) - if(masterproc) then - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_run_mct:end::',lbnum) - call memmon_reset_addr() - endif -#endif - - first_call = .false. - - end subroutine lnd_run_mct - - !==================================================================================== - subroutine lnd_final_mct( EClock, cdata_l, x2l_l, l2x_l) - ! - ! !DESCRIPTION: - ! Finalize land surface model - - use seq_cdata_mod ,only : seq_cdata, seq_cdata_setptrs - use seq_timemgr_mod ,only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn - use seq_timemgr_mod ,only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync - use esmf - ! - ! !ARGUMENTS: - type(ESMF_Clock) , intent(inout) :: EClock ! Input synchronization clock from driver - type(seq_cdata) , intent(inout) :: cdata_l ! Input driver data for land model - type(mct_aVect) , intent(inout) :: x2l_l ! Import state to land model - type(mct_aVect) , intent(inout) :: l2x_l ! Export state from land model - !--------------------------------------------------------------------------- - - ! fill this in - end subroutine lnd_final_mct - - !==================================================================================== - subroutine lnd_domain_mct( bounds, lsize, gsMap_l, dom_l ) - ! - ! !DESCRIPTION: - ! Send the land model domain information to the coupler - ! - ! !USES: - use clm_varcon , only: re - use domainMod , only: ldomain - use spmdMod , only: iam - use mct_mod , only: mct_gGrid_importIAttr - use mct_mod , only: mct_gGrid_importRAttr, mct_gGrid_init, mct_gsMap_orderedPoints - use seq_flds_mod, only: seq_flds_dom_coord, seq_flds_dom_other - ! - ! !ARGUMENTS: - type(bounds_type), intent(in) :: bounds ! bounds - integer , intent(in) :: lsize ! land model domain data size - type(mct_gsMap), intent(inout) :: gsMap_l ! Output land model MCT GS map - type(mct_ggrid), intent(out) :: dom_l ! Output domain information for land model - ! - ! Local Variables - integer :: g,i,j ! index - real(r8), pointer :: data(:) ! temporary - integer , pointer :: idata(:) ! temporary - !--------------------------------------------------------------------------- - ! - ! Initialize mct domain type - ! lat/lon in degrees, area in radians^2, mask is 1 (land), 0 (non-land) - ! Note that in addition land carries around landfrac for the purposes of domain checking - ! - call mct_gGrid_init( GGrid=dom_l, CoordChars=trim(seq_flds_dom_coord), & - OtherChars=trim(seq_flds_dom_other), lsize=lsize ) - ! - ! Allocate memory - ! - allocate(data(lsize)) - ! - ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT - ! - call mct_gsMap_orderedPoints(gsMap_l, iam, idata) - call mct_gGrid_importIAttr(dom_l,'GlobGridNum',idata,lsize) - ! - ! Determine domain (numbering scheme is: West to East and South to North to South pole) - ! Initialize attribute vector with special value - ! - data(:) = -9999.0_R8 - call mct_gGrid_importRAttr(dom_l,"lat" ,data,lsize) - call mct_gGrid_importRAttr(dom_l,"lon" ,data,lsize) - call mct_gGrid_importRAttr(dom_l,"area" ,data,lsize) - call mct_gGrid_importRAttr(dom_l,"aream",data,lsize) - data(:) = 0.0_R8 - call mct_gGrid_importRAttr(dom_l,"mask" ,data,lsize) - ! - ! Fill in correct values for domain components - ! Note aream will be filled in in the atm-lnd mapper - ! - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%lonc(g) - end do - call mct_gGrid_importRattr(dom_l,"lon",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%latc(g) - end do - call mct_gGrid_importRattr(dom_l,"lat",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%area(g)/(re*re) - end do - call mct_gGrid_importRattr(dom_l,"area",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%mask(g), r8) - end do - call mct_gGrid_importRattr(dom_l,"mask",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%frac(g), r8) - end do - call mct_gGrid_importRattr(dom_l,"frac",data,lsize) - - deallocate(data) - deallocate(idata) - - end subroutine lnd_domain_mct - - !==================================================================================== - subroutine lnd_handle_resume( cdata_l ) - ! - ! !DESCRIPTION: - ! Handle resume signals for Data Assimilation (DA) - ! - ! !USES: - use clm_time_manager , only : update_DA_nstep - use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs - implicit none - ! !ARGUMENTS: - type(seq_cdata), intent(inout) :: cdata_l ! Input land-model driver data - ! !LOCAL VARIABLES: - logical :: resume_from_data_assim ! flag if we are resuming after data assimulation was done - !--------------------------------------------------------------------------- - - ! Check to see if restart was modified and we are resuming from data - ! assimilation - call seq_cdata_setptrs(cdata_l, post_assimilation=resume_from_data_assim) - if ( resume_from_data_assim ) call update_DA_nstep() - - end subroutine lnd_handle_resume - -end module lnd_comp_mct diff --git a/src/cpl/mct/lnd_import_export.F90 b/src/cpl/mct/lnd_import_export.F90 deleted file mode 100644 index 537abd49d9..0000000000 --- a/src/cpl/mct/lnd_import_export.F90 +++ /dev/null @@ -1,354 +0,0 @@ -module lnd_import_export - - use shr_kind_mod , only: r8 => shr_kind_r8, cl=>shr_kind_cl - use abortutils , only: endrun - use decompmod , only: bounds_type, subgrid_level_gridcell - use lnd2atmType , only: lnd2atm_type - use lnd2glcMod , only: lnd2glc_type - use atm2lndType , only: atm2lnd_type - use glc2lndMod , only: glc2lnd_type - use Waterlnd2atmBulkType , only: waterlnd2atmbulk_type - use Wateratm2lndBulkType , only: wateratm2lndbulk_type - use clm_cpl_indices - use GridcellType , only : grc - ! - implicit none - !=============================================================================== - -contains - - !=============================================================================== - subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst, wateratm2lndbulk_inst) - - !--------------------------------------------------------------------------- - ! !DESCRIPTION: - ! Convert the input data from the coupler to the land model - ! - ! !USES: - use seq_flds_mod , only: seq_flds_x2l_fields - use clm_varctl , only: co2_type, co2_ppmv, iulog, use_c13 - use clm_varctl , only: ndep_from_cpl - use clm_varcon , only: c13ratio - use domainMod , only: ldomain - use lnd_import_export_utils, only : derive_quantities, check_for_errors, check_for_nans - ! - ! !ARGUMENTS: - type(bounds_type) , intent(in) :: bounds ! bounds - real(r8) , intent(in) :: x2l(:,:) ! driver import state to land model - logical , intent(in) :: glc_present ! .true. => running with a non-stub GLC model - type(atm2lnd_type) , intent(inout) :: atm2lnd_inst ! clm internal input data type - type(glc2lnd_type) , intent(inout) :: glc2lnd_inst ! clm internal input data type - type(wateratm2lndbulk_type), intent(inout) :: wateratm2lndbulk_inst ! clm internal input data type - ! - ! !LOCAL VARIABLES: - integer :: begg, endg ! bounds - integer :: g,i,k,nstep,ier ! indices, number of steps, and error code - real(r8) :: qsat_kg_kg ! saturation specific humidity (kg/kg) - real(r8) :: forc_pbot ! atmospheric pressure (Pa) - real(r8) :: forc_rainc(bounds%begg:bounds%endg) ! rainxy Atm flux mm/s - real(r8) :: forc_rainl(bounds%begg:bounds%endg) ! rainxy Atm flux mm/s - real(r8) :: forc_snowc(bounds%begg:bounds%endg) ! snowfxy Atm flux mm/s - real(r8) :: forc_snowl(bounds%begg:bounds%endg) ! snowfxl Atm flux mm/s - real(r8) :: co2_ppmv_diag ! temporary - real(r8) :: co2_ppmv_prog ! temporary - real(r8) :: co2_ppmv_val ! temporary - integer :: co2_type_idx ! integer flag for co2_type options - character(len=32) :: fname ! name of field that is NaN - character(len=32), parameter :: sub = 'lnd_import' - - !--------------------------------------------------------------------------- - - ! Set bounds - begg = bounds%begg; endg = bounds%endg - - co2_type_idx = 0 - if (co2_type == 'prognostic') then - co2_type_idx = 1 - else if (co2_type == 'diagnostic') then - co2_type_idx = 2 - end if - if (co2_type == 'prognostic' .and. index_x2l_Sa_co2prog == 0) then - call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2prog for co2_type equal to prognostic' ) - else if (co2_type == 'diagnostic' .and. index_x2l_Sa_co2diag == 0) then - call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2diag for co2_type equal to diagnostic' ) - end if - - ! Note that the precipitation fluxes received from the coupler - ! are in units of kg/s/m^2. To convert these precipitation rates - ! in units of mm/sec, one must divide by 1000 kg/m^3 and multiply - ! by 1000 mm/m resulting in an overall factor of unity. - ! Below the units are therefore given in mm/s. - - do g = begg,endg - i = 1 + (g - begg) - - ! Determine flooding input, sign convention is positive downward and - ! hierarchy is atm/glc/lnd/rof/ice/ocn. so water sent from rof to land is negative, - ! change the sign to indicate addition of water to system. - - wateratm2lndbulk_inst%forc_flood_grc(g) = -x2l(index_x2l_Flrr_flood,i) - - wateratm2lndbulk_inst%volr_grc(g) = x2l(index_x2l_Flrr_volr,i) * (ldomain%area(g) * 1.e6_r8) - wateratm2lndbulk_inst%volrmch_grc(g)= x2l(index_x2l_Flrr_volrmch,i) * (ldomain%area(g) * 1.e6_r8) - - ! Determine required receive fields - - atm2lnd_inst%forc_hgt_grc(g) = x2l(index_x2l_Sa_z,i) ! zgcmxy Atm state m - atm2lnd_inst%forc_topo_grc(g) = x2l(index_x2l_Sa_topo,i) ! Atm surface height (m) - atm2lnd_inst%forc_u_grc(g) = x2l(index_x2l_Sa_u,i) ! forc_uxy Atm state m/s - atm2lnd_inst%forc_v_grc(g) = x2l(index_x2l_Sa_v,i) ! forc_vxy Atm state m/s - atm2lnd_inst%forc_solad_not_downscaled_grc(g,2) = x2l(index_x2l_Faxa_swndr,i) ! forc_sollxy Atm flux W/m^2 - atm2lnd_inst%forc_solad_not_downscaled_grc(g,1) = x2l(index_x2l_Faxa_swvdr,i) ! forc_solsxy Atm flux W/m^2 - atm2lnd_inst%forc_solai_grc(g,2) = x2l(index_x2l_Faxa_swndf,i) ! forc_solldxy Atm flux W/m^2 - atm2lnd_inst%forc_solai_grc(g,1) = x2l(index_x2l_Faxa_swvdf,i) ! forc_solsdxy Atm flux W/m^2 - - atm2lnd_inst%forc_th_not_downscaled_grc(g) = x2l(index_x2l_Sa_ptem,i) ! forc_thxy Atm state K - wateratm2lndbulk_inst%forc_q_not_downscaled_grc(g) = x2l(index_x2l_Sa_shum,i) ! forc_qxy Atm state kg/kg - atm2lnd_inst%forc_pbot_not_downscaled_grc(g) = x2l(index_x2l_Sa_pbot,i) ! ptcmxy Atm state Pa - atm2lnd_inst%forc_t_not_downscaled_grc(g) = x2l(index_x2l_Sa_tbot,i) ! forc_txy Atm state K - atm2lnd_inst%forc_lwrad_not_downscaled_grc(g) = x2l(index_x2l_Faxa_lwdn,i) ! flwdsxy Atm flux W/m^2 - - forc_rainc(g) = x2l(index_x2l_Faxa_rainc,i) ! mm/s - forc_rainl(g) = x2l(index_x2l_Faxa_rainl,i) ! mm/s - forc_snowc(g) = x2l(index_x2l_Faxa_snowc,i) ! mm/s - forc_snowl(g) = x2l(index_x2l_Faxa_snowl,i) ! mm/s - - ! atmosphere coupling, for prognostic/prescribed aerosols - atm2lnd_inst%forc_aer_grc(g,1) = x2l(index_x2l_Faxa_bcphidry,i) - atm2lnd_inst%forc_aer_grc(g,2) = x2l(index_x2l_Faxa_bcphodry,i) - atm2lnd_inst%forc_aer_grc(g,3) = x2l(index_x2l_Faxa_bcphiwet,i) - atm2lnd_inst%forc_aer_grc(g,4) = x2l(index_x2l_Faxa_ocphidry,i) - atm2lnd_inst%forc_aer_grc(g,5) = x2l(index_x2l_Faxa_ocphodry,i) - atm2lnd_inst%forc_aer_grc(g,6) = x2l(index_x2l_Faxa_ocphiwet,i) - atm2lnd_inst%forc_aer_grc(g,7) = x2l(index_x2l_Faxa_dstwet1,i) - atm2lnd_inst%forc_aer_grc(g,8) = x2l(index_x2l_Faxa_dstdry1,i) - atm2lnd_inst%forc_aer_grc(g,9) = x2l(index_x2l_Faxa_dstwet2,i) - atm2lnd_inst%forc_aer_grc(g,10) = x2l(index_x2l_Faxa_dstdry2,i) - atm2lnd_inst%forc_aer_grc(g,11) = x2l(index_x2l_Faxa_dstwet3,i) - atm2lnd_inst%forc_aer_grc(g,12) = x2l(index_x2l_Faxa_dstdry3,i) - atm2lnd_inst%forc_aer_grc(g,13) = x2l(index_x2l_Faxa_dstwet4,i) - atm2lnd_inst%forc_aer_grc(g,14) = x2l(index_x2l_Faxa_dstdry4,i) - - if (index_x2l_Sa_methane /= 0) then - atm2lnd_inst%forc_pch4_grc(g) = x2l(index_x2l_Sa_methane,i) - endif - - !-------------------------- - ! Check for nans from coupler - !-------------------------- - - call check_for_nans(x2l(:,i), fname, begg, "x2l") - - end do - - !-------------------------- - ! Derived quantities for required fields - ! and corresponding error checks - !-------------------------- - - call derive_quantities(bounds, atm2lnd_inst, wateratm2lndbulk_inst, & - forc_rainc, forc_rainl, forc_snowc, forc_snowl) - - call check_for_errors(bounds, atm2lnd_inst, wateratm2lndbulk_inst) - - ! Determine derived quantities for optional fields - ! Note that the following does unit conversions from ppmv to partial pressures (Pa) - ! Note that forc_pbot is in Pa - - do g = begg,endg - i = 1 + (g - begg) - - forc_pbot = atm2lnd_inst%forc_pbot_not_downscaled_grc(g) - - ! Determine optional receive fields - if (index_x2l_Sa_co2prog /= 0) then - co2_ppmv_prog = x2l(index_x2l_Sa_co2prog,i) ! co2 atm state prognostic - else - co2_ppmv_prog = co2_ppmv - end if - if (index_x2l_Sa_co2diag /= 0) then - co2_ppmv_diag = x2l(index_x2l_Sa_co2diag,i) ! co2 atm state diagnostic - else - co2_ppmv_diag = co2_ppmv - end if - - if (co2_type_idx == 1) then - co2_ppmv_val = co2_ppmv_prog - else if (co2_type_idx == 2) then - co2_ppmv_val = co2_ppmv_diag - else - co2_ppmv_val = co2_ppmv - end if - if ( (co2_ppmv_val < 10.0_r8) .or. (co2_ppmv_val > 15000.0_r8) )then - call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, & - msg = sub//' ERROR: CO2 is outside of an expected range' ) - end if - atm2lnd_inst%forc_pco2_grc(g) = co2_ppmv_val * 1.e-6_r8 * forc_pbot - if (use_c13) then - atm2lnd_inst%forc_pc13o2_grc(g) = co2_ppmv_val * c13ratio * 1.e-6_r8 * forc_pbot - end if - - if (ndep_from_cpl) then - ! The coupler is sending ndep in units if kgN/m2/s - and clm uses units of gN/m2/sec - so the - ! following conversion needs to happen - atm2lnd_inst%forc_ndep_grc(g) = (x2l(index_x2l_Faxa_nhx, i) + x2l(index_x2l_faxa_noy, i))*1000._r8 - end if - - end do - - call glc2lnd_inst%set_glc2lnd_fields_mct( & - bounds = bounds, & - glc_present = glc_present, & - ! NOTE(wjs, 2017-12-13) the x2l argument doesn't have the typical bounds - ! subsetting (bounds%begg:bounds%endg). This mirrors the lack of these bounds in - ! the call to lnd_import from lnd_run_mct. This is okay as long as this code is - ! outside a clump loop. - x2l = x2l, & - index_x2l_Sg_ice_covered = index_x2l_Sg_ice_covered, & - index_x2l_Sg_topo = index_x2l_Sg_topo, & - index_x2l_Flgg_hflx = index_x2l_Flgg_hflx, & - index_x2l_Sg_icemask = index_x2l_Sg_icemask, & - index_x2l_Sg_icemask_coupled_fluxes = index_x2l_Sg_icemask_coupled_fluxes) - - end subroutine lnd_import - - !=============================================================================== - - subroutine lnd_export( bounds, waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x) - - !--------------------------------------------------------------------------- - ! !DESCRIPTION: - ! Convert the data to be sent from the clm model to the coupler - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 - use seq_flds_mod , only : seq_flds_l2x_fields - use clm_varctl , only : iulog - use shr_drydep_mod , only : n_drydep - use shr_megan_mod , only : shr_megan_mechcomps_n - use shr_fire_emis_mod , only : shr_fire_emis_mechcomps_n - use lnd_import_export_utils, only : check_for_nans - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds ! bounds - type(lnd2atm_type), intent(inout) :: lnd2atm_inst ! clm land to atmosphere exchange data type - type(lnd2glc_type), intent(inout) :: lnd2glc_inst ! clm land to atmosphere exchange data type - type(waterlnd2atmbulk_type), intent(in) :: waterlnd2atmbulk_inst - real(r8) , intent(out) :: l2x(:,:)! land to coupler export state on land grid - ! - ! !LOCAL VARIABLES: - integer :: begg, endg ! bounds - integer :: g,i,k ! indices - integer :: ier ! error status - integer :: nstep ! time step index - integer :: dtime ! time step - integer :: num ! counter - character(len=32) :: fname ! name of field that is NaN - character(len=32), parameter :: sub = 'lnd_export' - !--------------------------------------------------------------------------- - - ! Set bounds - begg = bounds%begg; endg = bounds%endg - - ! cesm sign convention is that fluxes are positive downward - - l2x(:,:) = 0.0_r8 - - do g = begg,endg - i = 1 + (g-begg) - l2x(index_l2x_Sl_t,i) = lnd2atm_inst%t_rad_grc(g) - l2x(index_l2x_Sl_snowh,i) = waterlnd2atmbulk_inst%h2osno_grc(g) - l2x(index_l2x_Sl_avsdr,i) = lnd2atm_inst%albd_grc(g,1) - l2x(index_l2x_Sl_anidr,i) = lnd2atm_inst%albd_grc(g,2) - l2x(index_l2x_Sl_avsdf,i) = lnd2atm_inst%albi_grc(g,1) - l2x(index_l2x_Sl_anidf,i) = lnd2atm_inst%albi_grc(g,2) - l2x(index_l2x_Sl_tref,i) = lnd2atm_inst%t_ref2m_grc(g) - l2x(index_l2x_Sl_qref,i) = waterlnd2atmbulk_inst%q_ref2m_grc(g) - l2x(index_l2x_Sl_u10,i) = lnd2atm_inst%u_ref10m_grc(g) - l2x(index_l2x_Fall_taux,i) = -lnd2atm_inst%taux_grc(g) - l2x(index_l2x_Fall_tauy,i) = -lnd2atm_inst%tauy_grc(g) - l2x(index_l2x_Fall_lat,i) = -lnd2atm_inst%eflx_lh_tot_grc(g) - l2x(index_l2x_Fall_sen,i) = -lnd2atm_inst%eflx_sh_tot_grc(g) - l2x(index_l2x_Fall_lwup,i) = -lnd2atm_inst%eflx_lwrad_out_grc(g) - l2x(index_l2x_Fall_evap,i) = -waterlnd2atmbulk_inst%qflx_evap_tot_grc(g) - l2x(index_l2x_Fall_swnet,i) = lnd2atm_inst%fsa_grc(g) - if (index_l2x_Fall_fco2_lnd /= 0) then - l2x(index_l2x_Fall_fco2_lnd,i) = -lnd2atm_inst%net_carbon_exchange_grc(g) - end if - - ! Additional fields for DUST, PROGSSLT, dry-deposition and VOC - ! These are now standard fields, but the check on the index makes sure the driver handles them - if (index_l2x_Sl_ram1 /= 0 ) l2x(index_l2x_Sl_ram1,i) = lnd2atm_inst%ram1_grc(g) - if (index_l2x_Sl_fv /= 0 ) l2x(index_l2x_Sl_fv,i) = lnd2atm_inst%fv_grc(g) - if (index_l2x_Sl_soilw /= 0 ) l2x(index_l2x_Sl_soilw,i) = waterlnd2atmbulk_inst%h2osoi_vol_grc(g,1) - if (index_l2x_Fall_flxdst1 /= 0 ) l2x(index_l2x_Fall_flxdst1,i)= -lnd2atm_inst%flxdst_grc(g,1) - if (index_l2x_Fall_flxdst2 /= 0 ) l2x(index_l2x_Fall_flxdst2,i)= -lnd2atm_inst%flxdst_grc(g,2) - if (index_l2x_Fall_flxdst3 /= 0 ) l2x(index_l2x_Fall_flxdst3,i)= -lnd2atm_inst%flxdst_grc(g,3) - if (index_l2x_Fall_flxdst4 /= 0 ) l2x(index_l2x_Fall_flxdst4,i)= -lnd2atm_inst%flxdst_grc(g,4) - - - ! for dry dep velocities - if (index_l2x_Sl_ddvel /= 0 ) then - l2x(index_l2x_Sl_ddvel:index_l2x_Sl_ddvel+n_drydep-1,i) = & - lnd2atm_inst%ddvel_grc(g,:n_drydep) - end if - - ! for MEGAN VOC emis fluxes - if (index_l2x_Fall_flxvoc /= 0 ) then - l2x(index_l2x_Fall_flxvoc:index_l2x_Fall_flxvoc+shr_megan_mechcomps_n-1,i) = & - -lnd2atm_inst%flxvoc_grc(g,:shr_megan_mechcomps_n) - end if - - - ! for fire emis fluxes - if (index_l2x_Fall_flxfire /= 0 ) then - l2x(index_l2x_Fall_flxfire:index_l2x_Fall_flxfire+shr_fire_emis_mechcomps_n-1,i) = & - -lnd2atm_inst%fireflx_grc(g,:shr_fire_emis_mechcomps_n) - l2x(index_l2x_Sl_ztopfire,i) = lnd2atm_inst%fireztop_grc(g) - end if - - if (index_l2x_Fall_methane /= 0) then - l2x(index_l2x_Fall_methane,i) = -lnd2atm_inst%ch4_surf_flux_tot_grc(g) - endif - - ! sign convention is positive downward with - ! hierarchy of atm/glc/lnd/rof/ice/ocn. - ! I.e. water sent from land to rof is positive - - l2x(index_l2x_Flrl_rofsur,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsur_grc(g) - - ! subsurface runoff is the sum of qflx_drain and qflx_perched_drain - l2x(index_l2x_Flrl_rofsub,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsub_grc(g) & - + waterlnd2atmbulk_inst%qflx_rofliq_drain_perched_grc(g) - - ! qgwl sent individually to coupler - l2x(index_l2x_Flrl_rofgwl,i) = waterlnd2atmbulk_inst%qflx_rofliq_qgwl_grc(g) - - ! ice sent individually to coupler - l2x(index_l2x_Flrl_rofi,i) = waterlnd2atmbulk_inst%qflx_rofice_grc(g) - - ! irrigation flux to be removed from main channel storage (negative) - l2x(index_l2x_Flrl_irrig,i) = - waterlnd2atmbulk_inst%qirrig_grc(g) - - ! glc coupling - ! We could avoid setting these fields if glc_present is .false., if that would - ! help with performance. (The downside would be that we wouldn't have these fields - ! available for diagnostic purposes or to force a later T compset with dlnd.) - do num = 0,glc_nec - l2x(index_l2x_Sl_tsrf(num),i) = lnd2glc_inst%tsrf_grc(g,num) - l2x(index_l2x_Sl_topo(num),i) = lnd2glc_inst%topo_grc(g,num) - l2x(index_l2x_Flgl_qice(num),i) = lnd2glc_inst%qice_grc(g,num) - end do - - !-------------------------- - ! Check for nans to coupler - !-------------------------- - - call check_for_nans(l2x(:,i), fname, begg, "l2x") - - end do - - end subroutine lnd_export - -end module lnd_import_export diff --git a/src/cpl/mct/lnd_set_decomp_and_domain.F90 b/src/cpl/mct/lnd_set_decomp_and_domain.F90 deleted file mode 100644 index 0a37554313..0000000000 --- a/src/cpl/mct/lnd_set_decomp_and_domain.F90 +++ /dev/null @@ -1,352 +0,0 @@ -module lnd_set_decomp_and_domain - - use shr_kind_mod , only : r8 => shr_kind_r8 - use spmdMod , only : masterproc - use clm_varctl , only : iulog - use mct_mod , only : mct_gsMap - - implicit none - private ! except - - ! public member routines - public :: lnd_set_decomp_and_domain_from_surfrd - - ! private member routines - private :: surfrd_get_globmask ! Reads global land mask (needed for setting domain decomp) - private :: surfrd_get_grid ! Read grid/ladnfrac data into domain (after domain decomp) - - ! translation between local and global indices at gridcell level - type(mct_gsmap), pointer, public :: gsmap_global - - ! translation between local and global indices at gridcell level for multiple levels - ! needed for 3d soil moisture stream - type(mct_gsmap), target , public :: gsMap_lnd2Dsoi_gdc2glo - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -!=============================================================================== -contains -!=============================================================================== - - subroutine lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj) - - ! Initialize ldomain data types - - use clm_varpar , only: nlevsoi - use clm_varctl , only: fatmlndfrc, use_soil_moisture_streams - use decompInitMod , only: decompInit_lnd - use decompMod , only: bounds_type, get_proc_bounds - use domainMod , only: ldomain, domain_check - - ! input/output variables - logical, intent(out) :: noland - integer, intent(out) :: ni, nj ! global grid sizes - - ! local variables - integer ,pointer :: amask(:) ! global land mask - integer :: begg, endg ! processor bounds - type(bounds_type) :: bounds ! bounds - character(len=32) :: subname = 'lnd_set_decomp_and_domain_from_surfrd' - !----------------------------------------------------------------------- - - ! Read in global land grid and land mask (amask)- needed to set decomposition - ! global memory for amask is allocate in surfrd_get_glomask - must be deallocated below - if (masterproc) then - write(iulog,*) 'Attempting to read global land mask from ',trim(fatmlndfrc) - endif - - ! Get global mask, ni and nj - call surfrd_get_globmask(filename=fatmlndfrc, mask=amask, ni=ni, nj=nj) - - ! Exit early if no valid land points - if ( all(amask == 0) )then - if (masterproc) write(iulog,*) trim(subname)//': no valid land points do NOT run clm' - noland = .true. - return - else - noland = .false. - end if - - ! Determine ctsm gridcell decomposition and processor bounds for gridcells - call decompInit_lnd(ni, nj, amask) - deallocate(amask) - if (use_soil_moisture_streams) call decompInit_lnd3D(ni, nj, nlevsoi) - - ! Initialize bounds for just gridcells - ! Remaining bounds (landunits, columns, patches) will be determined - ! after the call to decompInit_glcp - so get_proc_bounds is called - ! twice and the gridcell information is just filled in twice - call get_proc_bounds(bounds) - - ! Get grid cell bounds values - begg = bounds%begg - endg = bounds%endg - - ! Initialize ldomain data type - if (masterproc) then - write(iulog,*) 'Attempting to read ldomain from ',trim(fatmlndfrc) - endif - call surfrd_get_grid(begg, endg, ldomain, fatmlndfrc) - if (masterproc) then - call domain_check(ldomain) - endif - ldomain%mask = 1 !!! TODO - is this needed? - - end subroutine lnd_set_decomp_and_domain_from_surfrd - - !----------------------------------------------------------------------- - subroutine surfrd_get_globmask(filename, mask, ni, nj) - - ! Read the surface dataset grid related information - ! This is used to set the domain decomposition - so global data is read here - - use fileutils , only : getfil - use ncdio_pio , only : ncd_io, ncd_pio_openfile, ncd_pio_closefile, ncd_inqfdims, file_desc_t - use abortutils , only : endrun - use shr_log_mod, only : errMsg => shr_log_errMsg - - ! input/output variables - character(len=*), intent(in) :: filename ! grid filename - integer , pointer :: mask(:) ! grid mask - integer , intent(out) :: ni, nj ! global grid sizes - - ! local variables - logical :: isgrid2d - integer :: dimid,varid ! netCDF id's - integer :: ns ! size of grid on file - integer :: n,i,j ! index - integer :: ier ! error status - type(file_desc_t) :: ncid ! netcdf id - character(len=256) :: locfn ! local file name - logical :: readvar ! read variable in or not - integer , allocatable :: idata2d(:,:) - character(len=32) :: subname = 'surfrd_get_globmask' ! subroutine name - !----------------------------------------------------------------------- - - if (filename == ' ') then - mask(:) = 1 - else - ! Check if file exists - if (masterproc) then - if (filename == ' ') then - write(iulog,*) trim(subname),' ERROR: filename must be specified ' - call endrun(msg=errMsg(sourcefile, __LINE__)) - endif - end if - - ! Open file - call getfil( filename, locfn, 0 ) - call ncd_pio_openfile (ncid, trim(locfn), 0) - - ! Determine dimensions and if grid file is 2d or 1d - call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns) - if (masterproc) then - write(iulog,*)'lat/lon grid flag (isgrid2d) is ',isgrid2d - end if - allocate(mask(ns)) - mask(:) = 1 - if (isgrid2d) then - ! Grid is 2d - allocate(idata2d(ni,nj)) - idata2d(:,:) = 1 - call ncd_io(ncid=ncid, varname='LANDMASK', data=idata2d, flag='read', readvar=readvar) - if (.not. readvar) then - call ncd_io(ncid=ncid, varname='mask', data=idata2d, flag='read', readvar=readvar) - end if - if (readvar) then - do j = 1,nj - do i = 1,ni - n = (j-1)*ni + i - mask(n) = idata2d(i,j) - enddo - enddo - end if - deallocate(idata2d) - else - ! Grid is not 2d - call ncd_io(ncid=ncid, varname='LANDMASK', data=mask, flag='read', readvar=readvar) - if (.not. readvar) then - call ncd_io(ncid=ncid, varname='mask', data=mask, flag='read', readvar=readvar) - end if - end if - if (.not. readvar) call endrun( msg=' ERROR: landmask not on fatmlndfrc file'//errMsg(sourcefile, __LINE__)) - - ! Close file - call ncd_pio_closefile(ncid) - end if - - end subroutine surfrd_get_globmask - - !----------------------------------------------------------------------- - subroutine surfrd_get_grid(begg, endg, ldomain, filename) - - ! Read the surface dataset grid related information: - ! This is called after the domain decomposition has been created - ! - real latitude of grid cell (degrees) - ! - real longitude of grid cell (degrees) - - use clm_varcon , only : spval, re, grlnd - use domainMod , only : domain_type, lon1d, lat1d, domain_init - use fileutils , only : getfil - use abortutils , only : endrun - use shr_log_mod , only : errMsg => shr_log_errMsg - use ncdio_pio , only : file_desc_t, ncd_pio_openfile, ncd_pio_closefile - use ncdio_pio , only : ncd_io, check_var, ncd_inqfdims, check_dim_size - use pio - - ! input/output variables - integer , intent(in) :: begg, endg - type(domain_type) , intent(inout) :: ldomain ! domain to init - character(len=*) , intent(in) :: filename ! grid filename - - ! local variables - type(file_desc_t) :: ncid ! netcdf id - integer :: beg ! local beg index - integer :: end ! local end index - integer :: ni,nj,ns ! size of grid on file - logical :: readvar ! true => variable is on input file - logical :: isgrid2d ! true => file is 2d lat/lon - logical :: istype_domain ! true => input file is of type domain - real(r8), allocatable :: rdata2d(:,:) ! temporary - character(len=16) :: vname ! temporary - character(len=256) :: locfn ! local file name - integer :: n ! indices - character(len=32) :: subname = 'surfrd_get_grid' ! subroutine name - !----------------------------------------------------------------------- - - if (masterproc) then - if (filename == ' ') then - write(iulog,*) trim(subname),' ERROR: filename must be specified ' - call endrun(msg=errMsg(sourcefile, __LINE__)) - endif - end if - - call getfil( filename, locfn, 0 ) - call ncd_pio_openfile (ncid, trim(locfn), 0) - - ! Determine dimensions - call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns) - - ! Determine isgrid2d flag for domain - call domain_init(ldomain, isgrid2d=isgrid2d, ni=ni, nj=nj, nbeg=begg, nend=endg) - - ! Determine type of file - old style grid file or new style domain file - call check_var(ncid=ncid, varname='xc', readvar=readvar) - if (readvar)then - istype_domain = .true. - else - istype_domain = .false. - end if - - ! Read in area, lon, lat - if (istype_domain) then - call ncd_io(ncid=ncid, varname= 'area', flag='read', data=ldomain%area, & - dim1name=grlnd, readvar=readvar) - ! convert from radians**2 to km**2 - ldomain%area = ldomain%area * (re**2) - if (.not. readvar) call endrun( msg=' ERROR: area NOT on file'//errMsg(sourcefile, __LINE__)) - call ncd_io(ncid=ncid, varname= 'xc', flag='read', data=ldomain%lonc, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) call endrun( msg=' ERROR: xc NOT on file'//errMsg(sourcefile, __LINE__)) - call ncd_io(ncid=ncid, varname= 'yc', flag='read', data=ldomain%latc, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) call endrun( msg=' ERROR: yc NOT on file'//errMsg(sourcefile, __LINE__)) - else - call endrun( msg=" ERROR: can no longer read non domain files" ) - end if - - if (isgrid2d) then - allocate(rdata2d(ni,nj), lon1d(ni), lat1d(nj)) - if (istype_domain) vname = 'xc' - call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar) - lon1d(:) = rdata2d(:,1) - if (istype_domain) vname = 'yc' - call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar) - lat1d(:) = rdata2d(1,:) - deallocate(rdata2d) - end if - - ! Check lat limited to -90,90 - if (minval(ldomain%latc) < -90.0_r8 .or. & - maxval(ldomain%latc) > 90.0_r8) then - write(iulog,*) trim(subname),' WARNING: lat/lon min/max is ', & - minval(ldomain%latc),maxval(ldomain%latc) - endif - if ( any(ldomain%lonc < 0.0_r8) )then - call endrun( msg=' ERROR: lonc is negative (see https://github.com/ESCOMP/ctsm/issues/507)' & - //errMsg(sourcefile, __LINE__)) - endif - call ncd_io(ncid=ncid, varname='mask', flag='read', data=ldomain%mask, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun( msg=' ERROR: LANDMASK NOT on fracdata file'//errMsg(sourcefile, __LINE__)) - end if - call ncd_io(ncid=ncid, varname='frac', flag='read', data=ldomain%frac, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun( msg=' ERROR: LANDFRAC NOT on fracdata file'//errMsg(sourcefile, __LINE__)) - end if - - call ncd_pio_closefile(ncid) - - end subroutine surfrd_get_grid - - !------------------------------------------------------------------------------ - subroutine decompInit_lnd3D(lni,lnj,lnk) - ! - ! !DESCRIPTION: - ! Create a 3D decomposition gsmap for the global 2D grid with soil levels - ! as the 3rd dimesnion. - ! - ! !USES: - use decompMod, only : gindex_global, bounds_type, get_proc_bounds - use spmdMod , only : comp_id, mpicom - use mct_mod , only : mct_gsmap_init - ! - ! !ARGUMENTS: - integer , intent(in) :: lni,lnj,lnk ! domain global size - ! - ! !LOCAL VARIABLES: - integer :: m,n,k ! indices - integer :: begg,endg,lsize,gsize ! used for gsmap init - integer :: begg3d,endg3d - integer, pointer :: gindex(:) ! global index for gsmap init - type(bounds_type) :: bounds - !------------------------------------------------------------------------------ - - ! Initialize gsmap_lnd2dsoi_gdc2glo - call get_proc_bounds(bounds) - begg = bounds%begg; endg=bounds%endg - - begg3d = (begg-1)*lnk + 1 - endg3d = endg*lnk - lsize = (endg3d - begg3d + 1 ) - allocate(gindex(begg3d:endg3d)) - do k = 1, lnk - do n = begg,endg - m = (begg-1)*lnk + (k-1)*(endg-begg+1) + (n-begg+1) - gindex(m) = gindex_global(n-begg+1) + (k-1)*(lni*lnj) - enddo - enddo - gsize = lni * lnj * lnk - call mct_gsMap_init(gsMap_lnd2Dsoi_gdc2glo, gindex, mpicom, comp_id, lsize, gsize) - - ! Diagnostic output - - if (masterproc) then - write(iulog,*)' 3D GSMap' - write(iulog,*)' longitude points = ',lni - write(iulog,*)' latitude points = ',lnj - write(iulog,*)' soil levels = ',lnk - write(iulog,*)' gsize = ',gsize - write(iulog,*)' lsize = ',lsize - write(iulog,*)' bounds(gindex) = ',size(gindex) - write(iulog,*) - end if - - deallocate(gindex) - - end subroutine decompInit_lnd3D - -end module lnd_set_decomp_and_domain diff --git a/src/cpl/mct/ndepStreamMod.F90 b/src/cpl/mct/ndepStreamMod.F90 deleted file mode 100644 index d26ff7c95e..0000000000 --- a/src/cpl/mct/ndepStreamMod.F90 +++ /dev/null @@ -1,376 +0,0 @@ -module ndepStreamMod - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Contains methods for reading in nitrogen deposition data file - ! Also includes functions for dynamic ndep file handling and - ! interpolation. - ! - ! !USES - use shr_kind_mod, only: r8 => shr_kind_r8, CL => shr_kind_cl - use shr_strdata_mod, only: shr_strdata_type, shr_strdata_create - use shr_strdata_mod, only: shr_strdata_print, shr_strdata_advance - use mct_mod , only: mct_ggrid - use spmdMod , only: mpicom, masterproc, comp_id, iam - use clm_varctl , only: iulog, inst_name - use abortutils , only: endrun - use decompMod , only: bounds_type - use domainMod , only: ldomain - - ! !PUBLIC TYPES: - implicit none - private - - ! !PUBLIC MEMBER FUNCTIONS: - public :: ndep_init ! position datasets for dynamic ndep - public :: ndep_interp ! interpolates between two years of ndep file data - public :: clm_domain_mct ! Sets up MCT domain for this resolution - - ! !PRIVATE MEMBER FUNCTIONS: - private :: check_units ! Check the units and make sure they can be used - - ! ! PRIVATE TYPES - type(shr_strdata_type) :: sdat ! input data stream - integer :: stream_year_first_ndep ! first year in stream to use - integer :: stream_year_last_ndep ! last year in stream to use - integer :: model_year_align_ndep ! align stream_year_firstndep with - logical :: divide_by_secs_per_yr = .true. ! divide by the number of seconds per year - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - !============================================================================== - -contains - - !============================================================================== - - subroutine ndep_init(bounds, NLFilename) - ! - ! Initialize data stream information. - ! - ! Uses: - use shr_kind_mod , only : CS => shr_kind_cs - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_nl_mod , only : shr_nl_find_group_name - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_mpi_mod , only : shr_mpi_bcast - use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global - ! - ! arguments - implicit none - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_ndep - character(len=CL) :: ndepmapalgo = 'bilinear' - character(len=CL) :: ndep_tintalgo = 'linear' - character(len=CS) :: ndep_taxmode = 'extend' - character(len=CL) :: ndep_varlist = 'NDEP_year' - character(*), parameter :: shr_strdata_unset = 'NOT_SET' - character(*), parameter :: subName = "('ndepdyn_init')" - character(*), parameter :: F00 = "('(ndepdyn_init) ',4a)" - !----------------------------------------------------------------------- - - namelist /ndepdyn_nml/ & - stream_year_first_ndep, & - stream_year_last_ndep, & - model_year_align_ndep, & - ndepmapalgo, ndep_taxmode, & - ndep_varlist, & - stream_fldFileName_ndep, & - ndep_tintalgo - - ! Default values for namelist - stream_year_first_ndep = 1 ! first year in stream to use - stream_year_last_ndep = 1 ! last year in stream to use - model_year_align_ndep = 1 ! align stream_year_first_ndep with this model year - stream_fldFileName_ndep = ' ' - - ! Read ndepdyn_nml namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call shr_nl_find_group_name(nu_nml, 'ndepdyn_nml', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=ndepdyn_nml,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg=' ERROR reading ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__)) - end if - else - call endrun(msg=' ERROR finding ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__)) - end if - close(nu_nml) - endif - - call shr_mpi_bcast(stream_year_first_ndep , mpicom) - call shr_mpi_bcast(stream_year_last_ndep , mpicom) - call shr_mpi_bcast(model_year_align_ndep , mpicom) - call shr_mpi_bcast(stream_fldFileName_ndep, mpicom) - call shr_mpi_bcast(ndep_varlist , mpicom) - call shr_mpi_bcast(ndep_taxmode , mpicom) - call shr_mpi_bcast(ndep_tintalgo , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'ndepdyn stream settings:' - write(iulog,*) ' stream_year_first_ndep = ',stream_year_first_ndep - write(iulog,*) ' stream_year_last_ndep = ',stream_year_last_ndep - write(iulog,*) ' model_year_align_ndep = ',model_year_align_ndep - write(iulog,*) ' stream_fldFileName_ndep = ',stream_fldFileName_ndep - write(iulog,*) ' ndep_varList = ',ndep_varList - write(iulog,*) ' ndep_taxmode = ',ndep_taxmode - write(iulog,*) ' ndep_tintalgo = ',ndep_tintalgo - write(iulog,*) ' ' - endif - ! Read in units - call check_units( stream_fldFileName_ndep, ndep_varList ) - - ! Set domain and create streams - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(sdat,name="clmndep", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_ndep, & - yearLast=stream_year_last_ndep, & - yearAlign=model_year_align_ndep, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_ndep), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/trim(stream_fldFileName_ndep)/),& - fldListFile=ndep_varlist, & - fldListModel=ndep_varlist, & - fillalgo='none', & - mapalgo=ndepmapalgo, & - tintalgo=ndep_tintalgo, & - calendar=get_calendar(), & - taxmode=ndep_taxmode ) - - - if (masterproc) then - call shr_strdata_print(sdat,'CLMNDEP data') - endif - - end subroutine ndep_init - !================================================================ - - subroutine check_units( stream_fldFileName_ndep, ndep_varList ) - !------------------------------------------------------------------- - ! Check that units are correct on the file and if need any conversion - use ncdio_pio , only : ncd_pio_openfile, ncd_inqvid, ncd_getatt, ncd_pio_closefile, ncd_nowrite - use ncdio_pio , only : file_desc_t, var_desc_t - use shr_kind_mod , only : CS => shr_kind_cs - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_string_mod, only : shr_string_listGetName - implicit none - - !----------------------------------------------------------------------- - ! - ! Arguments - character(len=*), intent(IN) :: stream_fldFileName_ndep ! ndep filename - character(len=*), intent(IN) :: ndep_varList ! ndep variable list to examine - ! - ! Local variables - type(file_desc_t) :: ncid ! NetCDF filehandle for ndep file - type(var_desc_t) :: vardesc ! variable descriptor - integer :: varid ! variable index - logical :: readvar ! If variable was read - character(len=CS) :: ndepunits! ndep units - character(len=CS) :: fname ! ndep field name - !----------------------------------------------------------------------- - call ncd_pio_openfile( ncid, trim(stream_fldFileName_ndep), ncd_nowrite ) - call shr_string_listGetName( ndep_varList, 1, fname ) - call ncd_inqvid( ncid, fname, varid, vardesc, readvar=readvar ) - if ( readvar ) then - call ncd_getatt( ncid, varid, "units", ndepunits ) - else - call endrun(msg=' ERROR finding variable: '//trim(fname)//" in file: "// & - trim(stream_fldFileName_ndep)//errMsg(sourcefile, __LINE__)) - end if - call ncd_pio_closefile( ncid ) - - ! Now check to make sure they are correct - if ( trim(ndepunits) == "g(N)/m2/s" )then - divide_by_secs_per_yr = .false. - else if ( trim(ndepunits) == "g(N)/m2/yr" )then - divide_by_secs_per_yr = .true. - else - call endrun(msg=' ERROR in units for nitrogen deposition equal to: '//trim(ndepunits)//" not units expected"// & - errMsg(sourcefile, __LINE__)) - end if - - end subroutine check_units - - !================================================================ - subroutine ndep_interp(bounds, atm2lnd_inst) - - !----------------------------------------------------------------------- - use clm_time_manager, only : get_curr_date, get_curr_days_per_year - use clm_varcon , only : secspday - use atm2lndType , only : atm2lnd_type - ! - ! Arguments - type(bounds_type) , intent(in) :: bounds - type(atm2lnd_type), intent(inout) :: atm2lnd_inst - ! - ! Local variables - integer :: g, ig - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - integer :: dayspyr ! days per year - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ndepdyn') - - if ( divide_by_secs_per_yr )then - ig = 0 - dayspyr = get_curr_days_per_year( ) - do g = bounds%begg,bounds%endg - ig = ig+1 - atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) / (secspday * dayspyr) - end do - else - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) - end do - end if - - end subroutine ndep_interp - - !============================================================================== - subroutine clm_domain_mct(bounds, dom_clm, nlevels) - - !------------------------------------------------------------------- - ! Set domain data type for internal clm grid - use clm_varcon , only : re - use domainMod , only : ldomain - use mct_mod , only : mct_ggrid, mct_gsMap_lsize, mct_gGrid_init - use mct_mod , only : mct_gsMap_orderedPoints, mct_gGrid_importIAttr - use mct_mod , only : mct_gGrid_importRAttr, mct_gsMap - use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global - implicit none - ! - ! arguments - type(bounds_type), intent(in) :: bounds - type(mct_ggrid), intent(out) :: dom_clm ! Output domain information for land model - integer, intent(in), optional :: nlevels ! Number of levels if this is a 3D field - ! - ! local variables - integer :: g,i,j,k ! index - integer :: lsize ! land model domain data size - real(r8), pointer :: data(:) ! temporary - integer , pointer :: idata(:) ! temporary - integer :: nlevs ! Number of vertical levels - type(mct_gsMap), pointer :: gsmap => null() ! MCT GS map - !------------------------------------------------------------------- - ! SEt number of levels, and get the GS map for either the 2D or 3D grid - nlevs = 1 - if ( present(nlevels) ) nlevs = nlevels - if ( nlevs == 1 ) then - gsmap => gsmap_global - else - gsmap => gsMap_lnd2Dsoi_gdc2glo - end if - ! - ! Initialize mct domain type - ! lat/lon in degrees, area in radians^2, mask is 1 (land), 0 (non-land) - ! Note that in addition land carries around landfrac for the purposes of domain checking - ! - lsize = mct_gsMap_lsize(gsmap, mpicom) - call mct_gGrid_init( GGrid=dom_clm, & - CoordChars='lat:lon:hgt', OtherChars='area:aream:mask:frac', lsize=lsize ) - ! - ! Allocate memory - ! - allocate(data(lsize)) - ! - ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT - ! - call mct_gsMap_orderedPoints(gsmap, iam, idata) - gsmap => null() - call mct_gGrid_importIAttr(dom_clm,'GlobGridNum',idata,lsize) - ! - ! Determine domain (numbering scheme is: West to East and South to North to South pole) - ! Initialize attribute vector with special value - ! - data(:) = -9999.0_R8 - call mct_gGrid_importRAttr(dom_clm,"lat" ,data,lsize) - call mct_gGrid_importRAttr(dom_clm,"lon" ,data,lsize) - call mct_gGrid_importRAttr(dom_clm,"area" ,data,lsize) - call mct_gGrid_importRAttr(dom_clm,"aream",data,lsize) - data(:) = 0.0_R8 - call mct_gGrid_importRAttr(dom_clm,"mask" ,data,lsize) - ! - ! Determine bounds - ! - ! Fill in correct values for domain components - ! Note aream will be filled in in the atm-lnd mapper - ! - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%lonc(g) - end do - end do - call mct_gGrid_importRattr(dom_clm,"lon",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%latc(g) - end do - end do - call mct_gGrid_importRattr(dom_clm,"lat",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%area(g)/(re*re) - end do - end do - call mct_gGrid_importRattr(dom_clm,"area",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%mask(g), r8) - end do - end do - call mct_gGrid_importRattr(dom_clm,"mask",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%frac(g), r8) - end do - end do - call mct_gGrid_importRattr(dom_clm,"frac",data,lsize) - - deallocate(data) - deallocate(idata) - - end subroutine clm_domain_mct - -end module ndepStreamMod From 788f4996c12dda3873af80d9875c4a6feda340c9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 16:35:53 -0600 Subject: [PATCH 124/408] Remove a couple more references to MCT --- .../customizing-the-clm-configuration.rst | 2 +- src/main/clm_varctl.F90 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst index f8b5fee002..e76a9cc6f0 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst @@ -638,7 +638,7 @@ The output to the above command is as follows: -vichydro Turn VIC hydrologic parameterizations : [on | off] (default is off) -crop Toggle for prognostic crop model. [on | off] (default is off) (can ONLY be turned on when BGC type is CN or CNDV) - -comp_intf Component interface to use (ESMF or MCT) (default MCT) + -comp_intf Component interface to use (default ESMF, currently no other option) -defaults Specify full path to a configuration file which will be used to supply defaults instead of the defaults in bld/config_files. This file is used to specify model configuration parameters only. diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 7d0b2b55ad..0daedbbb1f 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -115,7 +115,7 @@ module clm_varctl character(len=fname_len), public :: fsnowaging = ' ' ! snow aging parameters file name character(len=fname_len), public :: fatmlndfrc = ' ' ! lnd frac file on atm grid - ! only needed for LILAC and MCT drivers + ! only needed for LILAC !---------------------------------------------------------- ! Flag to read ndep rather than obtain it from coupler From cc0e04dafe87cb878a8d3333c7a16d1b41a8c7e0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 10 May 2024 17:21:55 -0600 Subject: [PATCH 125/408] Update ntests in build-namelist_test.pl --- bld/unit_testers/build-namelist_test.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 12a5f4bd38..ec370749bb 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 2513; +my $ntests = 2454; if ( defined($opts{'compare'}) ) { - $ntests += 1545; + $ntests += 1486; } plan( tests=>$ntests ); From d66ddff54439bd192b9ed8b07419a17cd3282656 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 13 May 2024 11:21:08 -0700 Subject: [PATCH 126/408] update fates_harvest_mode to use chars to set namelist options initial commit --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 10 ++++++---- src/main/clm_varctl.F90 | 2 +- src/main/controlMod.F90 | 2 +- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index 4f326d82a5..d9bd0352ca 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -171,13 +171,14 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) end do ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled - if (fates_harvest_mode .ge. fates_harvest_luh_area ) then + if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. & + trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then ! change the harvest varnames being used depending on the mode selected - if (fates_harvest_mode .eq. fates_harvest_luh_area ) then + if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area ) then landuse_harvest_varnames => landuse_harvest_area_varnames landuse_harvest_units = landuse_harvest_area_units - elseif (fates_harvest_mode .eq. fates_harvest_luh_mass ) then + elseif (trim(fates_harvest_mode) .eq. fates_harvest_luh_mass ) then landuse_harvest_varnames => landuse_harvest_mass_varnames landuse_harvest_units = landuse_harvest_mass_units else @@ -256,7 +257,8 @@ subroutine dynFatesLandUseInterp(bounds, init_state) call landuse_state_vars(varnum)%get_current_data(this_data) landuse_states(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg) end do - if (fates_harvest_mode .ge. fates_harvest_luh_area ) then + if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. & + trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then do varnum = 1, num_landuse_harvest_vars call landuse_harvest_vars(varnum)%get_current_data(this_data) landuse_harvest(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 64d6e15747..59b72c8e74 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -302,7 +302,7 @@ module clm_varctl ! > 1 for external data (lightning and/or anthropogenic ignitions) ! see bld/namelist_files/namelist_definition_clm4_5.xml for details logical, public :: use_fates_tree_damage = .false. ! true => turn on tree damage module - integer, public :: fates_harvest_mode = 0 ! 0 for no harvest/logging; 1-4 for harvest mode options + character(len=256), public :: fates_harvest_mode = '' ! five different harvest modes; see namelist definition logical, public :: use_fates_planthydro = .false. ! true => turn on fates hydro logical, public :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking logical, public :: use_fates_ed_st3 = .false. ! true => static stand structure diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 55dd92305d..1dd432bb7e 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -775,7 +775,7 @@ subroutine control_spmd() call mpi_bcast (for_testing_allow_interp_non_ciso_to_ciso, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_spitfire_mode, 1, MPI_INTEGER, 0, mpicom, ier) - call mpi_bcast (fates_harvest_mode, 1, MPI_INTEGER, 0, mpicom, ier) + call mpi_bcast (fates_harvest_mode, len(fates_harvest_mode) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_tree_damage, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_cohort_age_tracking, 1, MPI_LOGICAL, 0, mpicom, ier) From 458c788eb6b7ca8b6351a5c3e4ebfae7d8364e21 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 13 May 2024 15:07:05 -0700 Subject: [PATCH 127/408] add default pass values for logging and harvest --- src/utils/clmfates_interfaceMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 5c23f1c1dc..ba6c59143f 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -511,6 +511,9 @@ subroutine CLMFatesGlobals2() call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking) ! FATES logging and harvest modes + pass_logging = 0 + pass_lu_harvest = 0 + pass_num_lu_harvest_cats = 0 if (fates_harvest_mode > fates_harvest_no_logging) then pass_logging = 1 ! Time driven logging, without landuse harvest ! CLM landuse timeseries driven harvest rates @@ -522,9 +525,6 @@ subroutine CLMFatesGlobals2() else if (fates_harvest_mode >= fates_harvest_luh_area) then pass_lu_harvest = 1 pass_num_lu_harvest_cats = num_landuse_harvest_vars - else - pass_lu_harvest = 0 - pass_num_lu_harvest_cats = 0 end if end if From 28f5bc36108af5281f3fdfd286b43bac5a849786 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 13 May 2024 15:25:00 -0700 Subject: [PATCH 128/408] update fates_harvest_mode to accept strings --- bld/CLMBuildNamelist.pm | 4 +-- bld/namelist_files/namelist_defaults_ctsm.xml | 6 ++--- .../namelist_definition_ctsm.xml | 17 ++++++------ bld/unit_testers/build-namelist_test.pl | 6 ++--- .../clm/FatesColdLUH2Mode0/user_nl_clm | 2 +- .../clm/FatesColdLUH2Mode1/user_nl_clm | 2 +- .../clm/FatesColdLUH2Mode2/user_nl_clm | 2 +- .../clm/FatesColdLUH2Mode3/user_nl_clm | 2 +- .../clm/FatesColdLUH2Mode4/user_nl_clm | 2 +- src/dyn_subgrid/dynSubgridDriverMod.F90 | 2 +- src/utils/clmfates_interfaceMod.F90 | 27 ++++++++++--------- 11 files changed, 37 insertions(+), 35 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index aafc7739a3..456447925c 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4478,7 +4478,7 @@ sub setup_logic_fates { if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { $log->fatal_error("use_fates_luh must be true when $var is true" ); } - if ( $nl->get_value('fates_harvest_mode') > 0) { + if ( $nl->get_value('fates_harvest_mode') ne 'no_harvest') { $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" ); } } @@ -4487,7 +4487,7 @@ sub setup_logic_fates { my $var = "fates_harvest_mode"; if ( defined($nl->get_value($var)) ) { # using fates_harvest mode with raw luh2 harvest data - if ( $nl->get_value($var) > 2) { + if ( $nl->get_value($var) eq 'luhdata_area' || $nl->get_value($var) eq 'luhdata_mass' ) { # Make sure that use_fates_luh is true when using raw fates luh2 harvest data if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" ); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 9d2a34b7bf..5da9cb22bf 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2759,7 +2759,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 0 -0 +no_harvest .false. .false. .false. @@ -2769,8 +2769,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. -.true. -.true. +.true. +.true. .true. .true. .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index edcfa36d27..03b1e9e64d 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -735,14 +735,14 @@ Toggle to turn on FATES satellite phenology mode (only relevant if FATES is bein -Set FATES harvesting mode by setting fates_harvest_mode > 0. + group="clm_inparm" valid_values="no_harvest_event_code,surfdata_file,luhdata_area,luhdata_mass"> +Set FATES harvesting mode by setting fates_harvest_mode to a valid string option. Allowed values are: - 0 : no fates harvesting of any kind - 1 : fates logging via fates logging event codes (see fates parameter file) only - 2 : fates harvest driven by CLM landuse timeseries data (dynHarvestMod) - 3 : fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod) - 4 : fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod) + no_harvest: no fates harvesting of any kind + event_code: fates logging via fates logging event codes (see fates parameter file) only + surfdata_file: fates harvest driven by CLM landuse timeseries data (dynHarvestMod) + luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod) + luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod) If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file. -This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harvest -data (fates_harvest_mode >= 3) +This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harvest data (Also, only valid for use_fates = true and is incompatible with transient runs currently.) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index f674849b6f..973fdffd16 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1047,7 +1047,7 @@ sub cat_and_create_namelistinfile { phys=>"clm4_5", }, "useloggingButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", - namelst=>"fates_harvest_mode=1", + namelst=>"fates_harvest_mode=event_code", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, @@ -1102,12 +1102,12 @@ sub cat_and_create_namelistinfile { phys=>"clm5_0", }, "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan", - namelst=>"use_fates_potentialveg=T,fates_harvest_mode=1", + namelst=>"use_fates_potentialveg=T,fates_harvest_mode=event_code", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, "useFATESHARVEST3WOLUH" =>{ options=>"-bgc fates -envxml_dir . -no-megan", - namelst=>"use_fates_luh=F,fates_harvest_mode=3", + namelst=>"use_fates_luh=F,fates_harvest_mode=luhdata_area", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm index 929a8e6e14..b3b338e232 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = 0 +fates_harvest_mode = no_harvest diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm index dea75b71e7..c0e1c476be 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = 1 +fates_harvest_mode = event_code diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm index fd4c74fe57..61e1daaa93 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = 2 +fates_harvest_mode = surfdata_file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm index 3332e9e526..d760105e68 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = 3 +fates_harvest_mode = luhdata_area diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm index 13dae9efee..bb5f30f75d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = 4 +fates_harvest_mode = luhdata_mass diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90 index 162247a0ff..faef029b40 100644 --- a/src/dyn_subgrid/dynSubgridDriverMod.F90 +++ b/src/dyn_subgrid/dynSubgridDriverMod.F90 @@ -128,7 +128,7 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst) ! flanduse_timeseries file. However, this could theoretically be changed so that the ! harvest data were separated from the pftdyn data, allowing them to differ in the ! years over which they apply. - if (get_do_harvest() .or. fates_harvest_mode == fates_harvest_clmlanduse) then + if (get_do_harvest() .or. trim(fates_harvest_mode) == fates_harvest_clmlanduse) then call dynHarvest_init(bounds_proc, harvest_filename=get_flanduse_timeseries()) end if diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index ba6c59143f..4205802088 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -186,6 +186,7 @@ module CLMFatesInterfaceMod use dynFATESLandUseChangeMod, only : fates_harvest_no_logging use dynFATESLandUseChangeMod, only : fates_harvest_clmlanduse use dynFATESLandUseChangeMod, only : fates_harvest_luh_area + use dynFATESLandUseChangeMod, only : fates_harvest_luh_mass use dynFATESLandUseChangeMod, only : landuse_harvest use dynFATESLandUseChangeMod, only : landuse_harvest_units use dynFATESLandUseChangeMod, only : landuse_harvest_varnames @@ -514,20 +515,25 @@ subroutine CLMFatesGlobals2() pass_logging = 0 pass_lu_harvest = 0 pass_num_lu_harvest_cats = 0 - if (fates_harvest_mode > fates_harvest_no_logging) then + if (trim(fates_harvest_mode) /= fates_harvest_no_logging) then pass_logging = 1 ! Time driven logging, without landuse harvest ! CLM landuse timeseries driven harvest rates - if (fates_harvest_mode == fates_harvest_clmlanduse) then + if (trim(fates_harvest_mode) == fates_harvest_clmlanduse) then pass_num_lu_harvest_cats = num_harvest_inst pass_lu_harvest = 1 ! LUH2 landuse timeseries driven harvest rates - else if (fates_harvest_mode >= fates_harvest_luh_area) then + else if (trim(fates_harvest_mode)== fates_harvest_luh_area .or. & + trim(fates_harvest_mode)== fates_harvest_luh_mass) then pass_lu_harvest = 1 pass_num_lu_harvest_cats = num_landuse_harvest_vars end if end if + call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest) + call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats) + call set_fates_ctrlparms('use_logging',ival=pass_logging) + ! FATES landuse modes if(use_fates_luh) then pass_use_luh = 1 @@ -550,11 +556,6 @@ subroutine CLMFatesGlobals2() end if call set_fates_ctrlparms('use_fates_potentialveg',ival=pass_use_potentialveg) - ! Wait to set the harvest and logging variables after checking fates_harvest_modes - call set_fates_ctrlparms('use_lu_harvest',ival=pass_lu_harvest) - call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats) - call set_fates_ctrlparms('use_logging',ival=pass_logging) - if(use_fates_inventory_init) then pass_inventory_init = 1 else @@ -979,7 +980,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call GetAndSetTime ! Get harvest rates for CLM landuse timeseries driven rates - if (fates_harvest_mode == fates_harvest_clmlanduse) then + if (trim(fates_harvest_mode) == fates_harvest_clmlanduse) then call dynHarvest_interp_resolve_harvesttypes(bounds_clump, & harvest_rates=harvest_rates(begg:endg,1:num_harvest_inst), & after_start_of_harvest_ts=after_start_of_harvest_ts) @@ -1105,7 +1106,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! for now there is one veg column per gridcell, so store all harvest data in each site ! this will eventually change ! today's hlm harvest flag needs to be set no matter what - if (fates_harvest_mode == fates_harvest_clmlanduse) then + if (trim(fates_harvest_mode) == fates_harvest_clmlanduse) then if (after_start_of_harvest_ts) then this%fates(nc)%bc_in(s)%hlm_harvest_rates(1:num_harvest_inst) = harvest_rates(g,1:num_harvest_inst) else @@ -1124,7 +1125,8 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call endrun(msg=errMsg(sourcefile, __LINE__)) end if - else if (fates_harvest_mode >= fates_harvest_luh_area) then + else if (trim(fates_harvest_mode) == fates_harvest_luh_area .or. & + trim(fates_harvest_mode) == fates_harvest_luh_mass) then this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g) this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units @@ -2082,7 +2084,8 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g) this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames - if (fates_harvest_mode >= fates_harvest_luh_area ) then + if (trim(fates_harvest_mode) == fates_harvest_luh_area .or. & + trim(fates_harvest_mode) == fates_harvest_luh_mass) then this%fates(nc)%bc_in(s)%hlm_harvest_rates = landuse_harvest(:,g) this%fates(nc)%bc_in(s)%hlm_harvest_catnames = landuse_harvest_varnames this%fates(nc)%bc_in(s)%hlm_harvest_units = landuse_harvest_units From 4715afef8db5cade7e3a2835ee6044bd711b21e3 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 15 May 2024 14:33:34 -0600 Subject: [PATCH 129/408] Bring back src/unit_test_stubs/csm_share/CMakeLists.txt for FUNIT test --- src/unit_test_stubs/csm_share/CMakeLists.txt | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 src/unit_test_stubs/csm_share/CMakeLists.txt diff --git a/src/unit_test_stubs/csm_share/CMakeLists.txt b/src/unit_test_stubs/csm_share/CMakeLists.txt new file mode 100644 index 0000000000..33ddbfb342 --- /dev/null +++ b/src/unit_test_stubs/csm_share/CMakeLists.txt @@ -0,0 +1,5 @@ +list(APPEND share_sources + shr_mpi_mod_stub.F90 + ) + +sourcelist_to_parent(share_sources) From f19a080721f5fffa96b580da51a170cbe80d4244 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 15 May 2024 17:59:34 -0600 Subject: [PATCH 130/408] add more landuse graceful failures If luh + fbg are present fail if flandusepftdat isn't valid. Don't allow fluh_timeseries to be defined if in potential veg mode to avoid confusing users that it is needed. --- bld/CLMBuildNamelist.pm | 71 ++++++++++++++++++++++++----------------- 1 file changed, 42 insertions(+), 29 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index aafc7739a3..0d8ca732b4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4433,21 +4433,9 @@ sub setup_logic_fates { } } # make sure that fates landuse x pft mode has the necessary run mode configurations - # and add the necessary landuse x pft static mapping data default if not defined my $var = "use_fates_lupft"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { - $var = "flandusepftdat"; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); - my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); - if ( ! defined($nl->get_value($var)) ) { - $log->fatal_error("$var is required when use_fates_lupft is set" ); - } elsif ( ! -f "$fname" ) { - $log->fatal_error("$fname does NOT point to a valid filename" ); - } - - # make sure that nocomp and fbg mode are enabled as well as use_fates_luh my @list = ( "use_fates_luh", "use_fates_nocomp", "use_fates_fixed_biogeog" ); foreach my $var ( @list ) { if ( ! &value_is_true($nl->get_value($var)) ) { @@ -4457,31 +4445,56 @@ sub setup_logic_fates { } } # check that fates landuse change mode has the necessary luh2 landuse timeseries data - # and add the default if not defined + # and add the default if not defined. Do not add default if use_fates_potentialveg is true. + # If fixed biogeography is on, make sure that flandusepftdat is avilable. my $var = "use_fates_luh"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { - $var = "fluh_timeseries"; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); - my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); - if ( ! defined($nl->get_value($var)) ) { - $log->fatal_error("$var is required when use_fates_luh is set" ); - } elsif ( ! -f "$fname" ) { - $log->fatal_error("$fname does NOT point to a valid filename" ); - } + $var = "use_fates_potentialveg"; + if ( defined($nl->get_value($var)) ) { + if ( ! &value_is_true($nl->get_value($var)) ) { + $var = "fluh_timeseries"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, + 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + if ( ! defined($nl->get_value($var)) ) { + $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$var does NOT point to a valid filename" ); + } + } + } + $var = "use_fates_fixed_biogeog"; + if ( defined($nl->get_value($var)) ) { + if ( &value_is_true($nl->get_value($var)) ) { + $var = "flandusepftdat"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + if ( ! defined($nl->get_value($var)) ) { + $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$var does NOT point to a valid filename" ); + } + } + } } } # check that fates landuse is on and harvest mode is off when potential veg switch is true my $var = "use_fates_potentialveg"; if ( defined($nl->get_value($var)) ) { - if ( &value_is_true($nl->get_value($var)) ) { - if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { - $log->fatal_error("use_fates_luh must be true when $var is true" ); - } - if ( $nl->get_value('fates_harvest_mode') > 0) { - $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" ); - } - } + if ( &value_is_true($nl->get_value($var)) ) { + if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { + $log->fatal_error("use_fates_luh must be true when $var is true" ); + } + if ( $nl->get_value('fates_harvest_mode') > 0) { + $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" ); + } + my $var = "fluh_timeseries"; + if ( defined($nl->get_value($var)) ) { + $log->fatal_error("fluh_timeseries can not be defined when use_fates_potentialveg is true" ); + } + } } # Check fates_harvest_mode compatibility my $var = "fates_harvest_mode"; From 39dc01e6f31f72246a5c3c781b5c83ab6e2a2598 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 16 May 2024 11:39:30 -0600 Subject: [PATCH 131/408] Revert "Remove the src/cpl/mct directory" This reverts commit 371f093e02a7820e8beec823c97dd23b94277c05. Jim Edwards posted the following in my PR: "although you can remove cpl7 you cannot yet remove mct. However I don't expect you to remove any externals in this tag, I will remove them in the next tag." --- src/cpl/mct/ExcessIceStreamType.F90 | 144 +++++ src/cpl/mct/FireDataBaseType.F90 | 561 +++++++++++++++++++ src/cpl/mct/SoilMoistureStreamMod.F90 | 418 ++++++++++++++ src/cpl/mct/UrbanTimeVarType.F90 | 314 +++++++++++ src/cpl/mct/ch4FInundatedStreamType.F90 | 389 +++++++++++++ src/cpl/mct/clm_cpl_indices.F90 | 330 +++++++++++ src/cpl/mct/laiStreamMod.F90 | 241 +++++++++ src/cpl/mct/lnd_comp_mct.F90 | 632 ++++++++++++++++++++++ src/cpl/mct/lnd_import_export.F90 | 354 ++++++++++++ src/cpl/mct/lnd_set_decomp_and_domain.F90 | 352 ++++++++++++ src/cpl/mct/ndepStreamMod.F90 | 376 +++++++++++++ 11 files changed, 4111 insertions(+) create mode 100644 src/cpl/mct/ExcessIceStreamType.F90 create mode 100644 src/cpl/mct/FireDataBaseType.F90 create mode 100644 src/cpl/mct/SoilMoistureStreamMod.F90 create mode 100644 src/cpl/mct/UrbanTimeVarType.F90 create mode 100644 src/cpl/mct/ch4FInundatedStreamType.F90 create mode 100644 src/cpl/mct/clm_cpl_indices.F90 create mode 100644 src/cpl/mct/laiStreamMod.F90 create mode 100644 src/cpl/mct/lnd_comp_mct.F90 create mode 100644 src/cpl/mct/lnd_import_export.F90 create mode 100644 src/cpl/mct/lnd_set_decomp_and_domain.F90 create mode 100644 src/cpl/mct/ndepStreamMod.F90 diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90 new file mode 100644 index 0000000000..5c5394233c --- /dev/null +++ b/src/cpl/mct/ExcessIceStreamType.F90 @@ -0,0 +1,144 @@ +module ExcessIceStreamType + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Stub for ExcessIceStreams for the MCT driver. So that MCT can be used + ! without excess ice streams. + ! + ! !USES + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL + use shr_log_mod , only : errMsg => shr_log_errMsg + use spmdMod , only : mpicom, masterproc + use clm_varctl , only : iulog + use abortutils , only : endrun + use decompMod , only : bounds_type + + ! !PUBLIC TYPES: + implicit none + private + + public :: UseExcessIceStreams ! If streams will be used + + type, public :: excessicestream_type + contains + + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Init ! Initialize and read data in + procedure, public :: CalcExcessIce ! Calculate excess ice ammount + + ! !PRIVATE MEMBER FUNCTIONS: + procedure, private :: ReadNML ! Read in namelist + + end type excessicestream_type + ! ! PRIVATE DATA: + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine Init(this, bounds, NLFilename) + ! + ! + ! arguments + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + + ! + ! local variables + + call this%ReadNML( bounds, NLFileName ) + end subroutine Init + + subroutine CalcExcessIce(this,bounds,exice_bulk_init) + + ! only transfers grid values to columns + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + real(r8) , intent(inout) :: exice_bulk_init(bounds%begc:bounds%endc) + ! + ! !LOCAL VARIABLES: + + end subroutine CalcExcessIce + + logical function UseExcessIceStreams() + ! + ! !DESCRIPTION: + ! Return true if + ! + ! !USES: + ! + ! !ARGUMENTS: + implicit none + ! + ! !LOCAL VARIABLES: + UseExcessIceStreams = .false. +end function UseExcessIceStreams + +subroutine ReadNML(this, bounds, NLFilename) + ! + ! Read the namelist data stream information. + ! + ! Uses: + use shr_nl_mod , only : shr_nl_find_group_name + use shr_log_mod , only : errMsg => shr_log_errMsg + use shr_mpi_mod , only : shr_mpi_bcast + ! + ! arguments + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! local variables + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + logical :: use_excess_ice_streams = .false. ! logical to turn on use of excess ice streams + character(len=CL) :: stream_fldFileName_exice = ' ' + character(len=CL) :: stream_mapalgo_exice = 'none' + character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read + character(len=*), parameter :: subName = "('exice_streams::ReadNML')" + !----------------------------------------------------------------------- + + namelist /exice_streams/ & ! MUST agree with namelist_name above + stream_mapalgo_exice, stream_fldFileName_exice, use_excess_ice_streams + !----------------------------------------------------------------------- + ! Default values for namelist + + ! Read excess ice namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=exice_streams,iostat=nml_error) ! MUST agree with namelist_name above + if (nml_error /= 0) then + call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + else + call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + close(nu_nml) + endif + + call shr_mpi_bcast(use_excess_ice_streams , mpicom) + + if (masterproc) then + if ( use_excess_ice_streams ) then + call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__)) + end if + if ( trim(stream_fldFileName_exice) /= '' ) then + call endrun(msg=' ERROR stream_fldFileName_exice can NOT be set for the MCT driver'//errMsg(sourcefile, __LINE__)) + end if + if ( trim(stream_mapalgo_exice) /= 'none' ) then + call endrun(msg=' ERROR stream_mapalgo_exice can only be none for the MCT driver'//errMsg(sourcefile, __LINE__)) + end if + endif + +end subroutine ReadNML + +end module ExcessIceStreamType diff --git a/src/cpl/mct/FireDataBaseType.F90 b/src/cpl/mct/FireDataBaseType.F90 new file mode 100644 index 0000000000..0ee635b2fa --- /dev/null +++ b/src/cpl/mct/FireDataBaseType.F90 @@ -0,0 +1,561 @@ +module FireDataBaseType + +#include "shr_assert.h" + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! module for handling of fire data + ! + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL + use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create, shr_strdata_print + use shr_strdata_mod , only : shr_strdata_advance + use shr_log_mod , only : errMsg => shr_log_errMsg + use clm_varctl , only : iulog, inst_name + use spmdMod , only : masterproc, mpicom, comp_id + use fileutils , only : getavu, relavu + use domainMod , only : ldomain + use abortutils , only : endrun + use decompMod , only : bounds_type + use FireMethodType , only : fire_method_type + use lnd_set_decomp_and_domain, only : gsmap_global + use mct_mod + ! + implicit none + private + ! + ! !PUBLIC TYPES: + public :: fire_base_type + + ! + type, abstract, extends(fire_method_type) :: fire_base_type + private + ! !PRIVATE MEMBER DATA: + + real(r8), public, pointer :: forc_lnfm(:) ! Lightning frequency + real(r8), public, pointer :: forc_hdm(:) ! Human population density + + real(r8), public, pointer :: gdp_lf_col(:) ! col global real gdp data (k US$/capita) + real(r8), public, pointer :: peatf_lf_col(:) ! col global peatland fraction data (0-1) + integer , public, pointer :: abm_lf_col(:) ! col global peak month of crop fire emissions + + type(shr_strdata_type) :: sdat_hdm ! Human population density input data stream + type(shr_strdata_type) :: sdat_lnfm ! Lightning input data stream + + contains + ! + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: FireInit => BaseFireInit ! Initialization of Fire + procedure, public :: BaseFireInit ! Initialization of Fire + procedure(FireReadNML_interface), public, deferred :: FireReadNML ! Read in namelist for Fire + procedure, public :: FireInterp ! Interpolate fire data + procedure(need_lightning_and_popdens_interface), public, deferred :: & + need_lightning_and_popdens ! Returns true if need lightning & popdens + ! + ! !PRIVATE MEMBER FUNCTIONS: + procedure, private :: hdm_init ! position datasets for dynamic human population density + procedure, private :: hdm_interp ! interpolates between two years of human pop. density file data + procedure, private :: lnfm_init ! position datasets for Lightning + procedure, private :: lnfm_interp ! interpolates between two years of Lightning file data + procedure, private :: surfdataread ! read fire related data from surface data set + end type fire_base_type + !----------------------------------------------------------------------- + + abstract interface + !----------------------------------------------------------------------- + function need_lightning_and_popdens_interface(this) result(need_lightning_and_popdens) + ! + ! !DESCRIPTION: + ! Returns true if need lightning and popdens, false otherwise + ! + ! USES + import :: fire_base_type + ! + ! !ARGUMENTS: + class(fire_base_type), intent(in) :: this + logical :: need_lightning_and_popdens ! function result + !----------------------------------------------------------------------- + end function need_lightning_and_popdens_interface + end interface + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +contains + + !----------------------------------------------------------------------- + subroutine FireReadNML_interface( this, NLFilename ) + ! + ! !DESCRIPTION: + ! Read the namelist for Fire + ! + ! !USES: + ! + ! !ARGUMENTS: + class(fire_base_type) :: this + character(len=*), intent(in) :: NLFilename ! Namelist filename + end subroutine FireReadNML_interface + + !----------------------------------------------------------------------- + subroutine BaseFireInit( this, bounds, NLFilename ) + ! + ! !DESCRIPTION: + ! Initialize CN Fire module + ! !USES: + use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + ! + ! !ARGUMENTS: + class(fire_base_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename + !----------------------------------------------------------------------- + + if ( this%need_lightning_and_popdens() ) then + ! Allocate lightning forcing data + allocate( this%forc_lnfm(bounds%begg:bounds%endg) ) + this%forc_lnfm(bounds%begg:) = nan + ! Allocate pop dens forcing data + allocate( this%forc_hdm(bounds%begg:bounds%endg) ) + this%forc_hdm(bounds%begg:) = nan + + ! Allocate real gdp data + allocate(this%gdp_lf_col(bounds%begc:bounds%endc)) + ! Allocate peatland fraction data + allocate(this%peatf_lf_col(bounds%begc:bounds%endc)) + ! Allocates peak month of crop fire emissions + allocate(this%abm_lf_col(bounds%begc:bounds%endc)) + + + call this%hdm_init(bounds, NLFilename) + call this%hdm_interp(bounds) + call this%lnfm_init(bounds, NLFilename) + call this%lnfm_interp(bounds) + call this%surfdataread(bounds) + end if + + end subroutine BaseFireInit + + !----------------------------------------------------------------------- + subroutine FireInterp(this,bounds) + ! + ! !DESCRIPTION: + ! Interpolate CN Fire datasets + ! + ! !ARGUMENTS: + class(fire_base_type) :: this + type(bounds_type), intent(in) :: bounds + !----------------------------------------------------------------------- + + if ( this%need_lightning_and_popdens() ) then + call this%hdm_interp(bounds) + call this%lnfm_interp(bounds) + end if + + end subroutine FireInterp + + !----------------------------------------------------------------------- + subroutine hdm_init( this, bounds, NLFilename ) + ! + ! !DESCRIPTION: + ! Initialize data stream information for population density. + ! + ! !USES: + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use clm_nlUtilsMod , only : find_nlgroup_name + use ndepStreamMod , only : clm_domain_mct + use histFileMod , only : hist_addfld1d + ! + ! !ARGUMENTS: + implicit none + class(fire_base_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! !LOCAL VARIABLES: + integer :: stream_year_first_popdens ! first year in pop. dens. stream to use + integer :: stream_year_last_popdens ! last year in pop. dens. stream to use + integer :: model_year_align_popdens ! align stream_year_first_hdm with + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + type(mct_ggrid) :: dom_clm ! domain information + character(len=CL) :: stream_fldFileName_popdens ! population density streams filename + character(len=CL) :: popdensmapalgo = 'bilinear' ! mapping alogrithm for population density + character(len=CL) :: popdens_tintalgo = 'nearest'! time interpolation alogrithm for population density + character(len=CL) :: stream_meshfile_popdens ! not used + character(*), parameter :: subName = "('hdmdyn_init')" + character(*), parameter :: F00 = "('(hdmdyn_init) ',4a)" + !----------------------------------------------------------------------- + + namelist /popd_streams/ & + stream_year_first_popdens, & + stream_year_last_popdens, & + model_year_align_popdens, & + popdensmapalgo, & + stream_fldFileName_popdens, & + stream_meshfile_popdens , & + popdens_tintalgo + + ! Default values for namelist + stream_year_first_popdens = 1 ! first year in stream to use + stream_year_last_popdens = 1 ! last year in stream to use + model_year_align_popdens = 1 ! align stream_year_first_popdens with this model year + stream_fldFileName_popdens = ' ' + + ! Read popd_streams namelist + if (masterproc) then + nu_nml = getavu() + open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'popd_streams', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=popd_streams,iostat=nml_error) + if (nml_error /= 0) then + call endrun(msg='ERROR reading popd_streams namelist'//errMsg(sourcefile, __LINE__)) + end if + end if + close(nu_nml) + call relavu( nu_nml ) + endif + + call shr_mpi_bcast(stream_year_first_popdens, mpicom) + call shr_mpi_bcast(stream_year_last_popdens, mpicom) + call shr_mpi_bcast(model_year_align_popdens, mpicom) + call shr_mpi_bcast(stream_fldFileName_popdens, mpicom) + call shr_mpi_bcast(popdens_tintalgo, mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) 'popdens_streams settings:' + write(iulog,*) ' stream_year_first_popdens = ',stream_year_first_popdens + write(iulog,*) ' stream_year_last_popdens = ',stream_year_last_popdens + write(iulog,*) ' model_year_align_popdens = ',model_year_align_popdens + write(iulog,*) ' stream_fldFileName_popdens = ',stream_fldFileName_popdens + write(iulog,*) ' popdens_tintalgo = ',popdens_tintalgo + write(iulog,*) ' ' + endif + + call clm_domain_mct (bounds, dom_clm) + + call shr_strdata_create(this%sdat_hdm,name="clmhdm", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_popdens, & + yearLast=stream_year_last_popdens, & + yearAlign=model_year_align_popdens, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_popdens), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/trim(stream_fldFileName_popdens)/) , & + fldListFile='hdm', & + fldListModel='hdm', & + fillalgo='none', & + mapalgo=popdensmapalgo, & + calendar=get_calendar(), & + tintalgo=popdens_tintalgo, & + taxmode='extend' ) + + if (masterproc) then + call shr_strdata_print(this%sdat_hdm,'population density data') + endif + + ! Add history fields + call hist_addfld1d (fname='HDM', units='counts/km^2', & + avgflag='A', long_name='human population density', & + ptr_lnd=this%forc_hdm, default='inactive') + + end subroutine hdm_init + + !----------------------------------------------------------------------- + subroutine hdm_interp( this, bounds) + ! + ! !DESCRIPTION: + ! Interpolate data stream information for population density. + ! + ! !USES: + use clm_time_manager, only : get_curr_date + ! + ! !ARGUMENTS: + class(fire_base_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: g, ig + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + !----------------------------------------------------------------------- + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + + call shr_strdata_advance(this%sdat_hdm, mcdate, sec, mpicom, 'hdmdyn') + + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + this%forc_hdm(g) = this%sdat_hdm%avs(1)%rAttr(1,ig) + end do + + end subroutine hdm_interp + + !----------------------------------------------------------------------- + subroutine lnfm_init( this, bounds, NLFilename ) + ! + ! !DESCRIPTION: + ! + ! Initialize data stream information for Lightning. + ! + ! !USES: + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use clm_nlUtilsMod , only : find_nlgroup_name + use ndepStreamMod , only : clm_domain_mct + use histFileMod , only : hist_addfld1d + ! + ! !ARGUMENTS: + implicit none + class(fire_base_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename + ! + ! !LOCAL VARIABLES: + integer :: stream_year_first_lightng ! first year in Lightning stream to use + integer :: stream_year_last_lightng ! last year in Lightning stream to use + integer :: model_year_align_lightng ! align stream_year_first_lnfm with + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + type(mct_ggrid) :: dom_clm ! domain information + character(len=CL) :: stream_fldFileName_lightng ! lightning stream filename to read + character(len=CL) :: lightng_tintalgo = 'linear'! time interpolation alogrithm + character(len=CL) :: lightngmapalgo = 'bilinear'! Mapping alogrithm + character(*), parameter :: subName = "('lnfmdyn_init')" + character(*), parameter :: F00 = "('(lnfmdyn_init) ',4a)" + !----------------------------------------------------------------------- + + namelist /light_streams/ & + stream_year_first_lightng, & + stream_year_last_lightng, & + model_year_align_lightng, & + lightngmapalgo, & + stream_fldFileName_lightng, & + lightng_tintalgo + + ! Default values for namelist + stream_year_first_lightng = 1 ! first year in stream to use + stream_year_last_lightng = 1 ! last year in stream to use + model_year_align_lightng = 1 ! align stream_year_first_lnfm with this model year + stream_fldFileName_lightng = ' ' + + ! Read light_streams namelist + if (masterproc) then + nu_nml = getavu() + open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'light_streams', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=light_streams,iostat=nml_error) + if (nml_error /= 0) then + call endrun(msg='ERROR reading light_streams namelist'//errMsg(sourcefile, __LINE__)) + end if + end if + close(nu_nml) + call relavu( nu_nml ) + endif + + call shr_mpi_bcast(stream_year_first_lightng, mpicom) + call shr_mpi_bcast(stream_year_last_lightng, mpicom) + call shr_mpi_bcast(model_year_align_lightng, mpicom) + call shr_mpi_bcast(stream_fldFileName_lightng, mpicom) + call shr_mpi_bcast(lightng_tintalgo, mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) 'light_stream settings:' + write(iulog,*) ' stream_year_first_lightng = ',stream_year_first_lightng + write(iulog,*) ' stream_year_last_lightng = ',stream_year_last_lightng + write(iulog,*) ' model_year_align_lightng = ',model_year_align_lightng + write(iulog,*) ' stream_fldFileName_lightng = ',stream_fldFileName_lightng + write(iulog,*) ' lightng_tintalgo = ',lightng_tintalgo + write(iulog,*) ' ' + endif + + call clm_domain_mct (bounds, dom_clm) + + call shr_strdata_create(this%sdat_lnfm,name="clmlnfm", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_lightng, & + yearLast=stream_year_last_lightng, & + yearAlign=model_year_align_lightng, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_lightng), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/trim(stream_fldFileName_lightng)/), & + fldListFile='lnfm', & + fldListModel='lnfm', & + fillalgo='none', & + tintalgo=lightng_tintalgo, & + mapalgo=lightngmapalgo, & + calendar=get_calendar(), & + taxmode='cycle' ) + + if (masterproc) then + call shr_strdata_print(this%sdat_lnfm,'Lightning data') + endif + + ! Add history fields + call hist_addfld1d (fname='LNFM', units='counts/km^2/hr', & + avgflag='A', long_name='Lightning frequency', & + ptr_lnd=this%forc_lnfm, default='inactive') + + end subroutine lnfm_init + + !----------------------------------------------------------------------- + subroutine lnfm_interp(this, bounds ) + ! + ! !DESCRIPTION: + ! Interpolate data stream information for Lightning. + ! + ! !USES: + use clm_time_manager, only : get_curr_date + ! + ! !ARGUMENTS: + class(fire_base_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: g, ig + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + !----------------------------------------------------------------------- + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + + call shr_strdata_advance(this%sdat_lnfm, mcdate, sec, mpicom, 'lnfmdyn') + + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + this%forc_lnfm(g) = this%sdat_lnfm%avs(1)%rAttr(1,ig) + end do + + end subroutine lnfm_interp + + !----------------------------------------------------------------------- + subroutine surfdataread(this, bounds) + ! + ! !DESCRIPTION: + ! Read surface data set to populate relevant fire-related variables + ! + ! !USES: + use spmdMod , only : masterproc + use clm_varctl , only : nsrest, nsrStartup, fsurdat + use clm_varcon , only : grlnd + use ColumnType , only : col + use fileutils , only : getfil + use ncdio_pio + ! + ! !ARGUMENTS: + class(fire_base_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: g,c ! indices + type(file_desc_t) :: ncid ! netcdf id + logical :: readvar ! true => variable is on initial dataset + character(len=256) :: locfn ! local filename + real(r8), pointer :: gdp(:) ! global gdp data (needs to be a pointer for use in ncdio) + real(r8), pointer :: peatf(:) ! global peatf data (needs to be a pointer for use in ncdio) + integer, pointer :: abm(:) ! global abm data (needs to be a pointer for use in ncdio) + !----------------------------------------------------------------------- + + ! -------------------------------------------------------------------- + ! Open surface dataset + ! -------------------------------------------------------------------- + + call getfil (fsurdat, locfn, 0) + call ncd_pio_openfile (ncid, locfn, 0) + + ! -------------------------------------------------------------------- + ! Read in GDP data + ! -------------------------------------------------------------------- + + allocate(gdp(bounds%begg:bounds%endg)) + call ncd_io(ncid=ncid, varname='gdp', flag='read', data=gdp, dim1name=grlnd, readvar=readvar) + if (.not. readvar) then + call endrun(msg=' ERROR: gdp NOT on surfdata file'//errMsg(sourcefile, __LINE__)) + end if + do c = bounds%begc, bounds%endc + g = col%gridcell(c) + this%gdp_lf_col(c) = gdp(g) + end do + deallocate(gdp) + + ! -------------------------------------------------------------------- + ! Read in peatf data + ! -------------------------------------------------------------------- + + allocate(peatf(bounds%begg:bounds%endg)) + call ncd_io(ncid=ncid, varname='peatf', flag='read', data=peatf, dim1name=grlnd, readvar=readvar) + if (.not. readvar) then + call endrun(msg=' ERROR: peatf NOT on surfdata file'//errMsg(sourcefile, __LINE__)) + end if + do c = bounds%begc, bounds%endc + g = col%gridcell(c) + this%peatf_lf_col(c) = peatf(g) + end do + deallocate(peatf) + + ! -------------------------------------------------------------------- + ! Read in ABM data + ! -------------------------------------------------------------------- + + allocate(abm(bounds%begg:bounds%endg)) + call ncd_io(ncid=ncid, varname='abm', flag='read', data=abm, dim1name=grlnd, readvar=readvar) + if (.not. readvar) then + call endrun(msg=' ERROR: abm NOT on surfdata file'//errMsg(sourcefile, __LINE__)) + end if + do c = bounds%begc, bounds%endc + g = col%gridcell(c) + this%abm_lf_col(c) = abm(g) + end do + deallocate(abm) + + ! Close file + + call ncd_pio_closefile(ncid) + + if (masterproc) then + write(iulog,*) 'Successfully read fmax, soil color, sand and clay boundary data' + write(iulog,*) + endif + + end subroutine surfdataread + + +end module FireDataBaseType diff --git a/src/cpl/mct/SoilMoistureStreamMod.F90 b/src/cpl/mct/SoilMoistureStreamMod.F90 new file mode 100644 index 0000000000..8b366d6c8e --- /dev/null +++ b/src/cpl/mct/SoilMoistureStreamMod.F90 @@ -0,0 +1,418 @@ +module SoilMoistureStreamMod + + ! ********************************************************************** + ! --------------------------- IMPORTANT NOTE --------------------------- + ! + ! In cases using the NUOPC driver/mediator, we use a different version of this module, + ! based on CDEPS, which resides in src/cpl/nuopc/. Changes to the science here should + ! also be made in the similar file in src/cpl/nuopc. Once we start using CDEPS by + ! default, we can remove this version and move the CDEPS-based version into its place. + ! ********************************************************************** + +#include "shr_assert.h" + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Read in soil moisture from data stream + ! + ! !USES: + use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create + use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_kind_mod , only : CL => shr_kind_CL, CXX => shr_kind_CXX + use shr_log_mod , only : errMsg => shr_log_errMsg + use decompMod , only : bounds_type, subgrid_level_column + use abortutils , only : endrun + use clm_varctl , only : iulog, use_soil_moisture_streams, inst_name + use clm_varcon , only : grlnd + use controlMod , only : NLFilename + use domainMod , only : ldomain + use LandunitType , only : lun + use ColumnType , only : col + use SoilStateType , only : soilstate_type + use WaterStateBulkType , only : waterstatebulk_type + use perf_mod , only : t_startf, t_stopf + use spmdMod , only : masterproc, mpicom, comp_id + use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo + use mct_mod + use ncdio_pio + ! + ! !PUBLIC TYPES: + implicit none + private + ! + ! !PUBLIC MEMBER FUNCTIONS: + public :: PrescribedSoilMoistureInit ! position datasets for soil moisture + public :: PrescribedSoilMoistureAdvance ! Advance the soil moisture stream (outside of Open-MP loops) + public :: PrescribedSoilMoistureInterp ! interpolates between two periods of soil moisture data + + ! !PRIVATE MEMBER DATA: + type(shr_strdata_type) :: sdat_soilm ! soil moisture input data stream + integer :: ism ! Soil moisture steram index + integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index + logical :: soilm_ignore_data_if_missing ! If should ignore overridding a point with soil moisture data + ! from the streams file, if the streams file shows that point + ! as missing (namelist item) + ! + ! !PRIVATE TYPES: + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + !----------------------------------------------------------------------- + +contains + + !----------------------------------------------------------------------- + ! + ! soil_moisture_init + ! + !----------------------------------------------------------------------- + subroutine PrescribedSoilMoistureInit(bounds) + ! + ! Initialize data stream information for soil moisture. + ! + ! + ! !USES: + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use clm_nlUtilsMod , only : find_nlgroup_name + use ndepStreamMod , only : clm_domain_mct + use shr_stream_mod , only : shr_stream_file_null + use shr_string_mod , only : shr_string_listCreateField + use clm_varpar , only : nlevsoi + ! + ! !ARGUMENTS: + implicit none + type(bounds_type), intent(in) :: bounds ! bounds + ! + ! !LOCAL VARIABLES: + integer :: i ! index + integer :: stream_year_first_soilm ! first year in Ustar stream to use + integer :: stream_year_last_soilm ! last year in Ustar stream to use + integer :: model_year_align_soilm ! align stream_year_first_soilm with + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + integer :: soilm_offset ! Offset in time for dataset (sec) + type(mct_ggrid) :: dom_clm ! domain information + character(len=CL) :: stream_fldfilename_soilm ! ustar stream filename to read + character(len=CL) :: soilm_tintalgo = 'linear' ! Time interpolation alogrithm + + character(*), parameter :: subName = "('PrescribedSoilMoistureInit')" + character(*), parameter :: F00 = "('(PrescribedSoilMoistureInit) ',4a)" + character(*), parameter :: soilmString = "H2OSOI" ! base string for field string + character(CXX) :: fldList ! field string + !----------------------------------------------------------------------- + ! + ! deal with namelist variables here in init + ! + namelist /soil_moisture_streams/ & + stream_year_first_soilm, & + stream_year_last_soilm, & + model_year_align_soilm, & + soilm_tintalgo, & + soilm_offset, & + soilm_ignore_data_if_missing, & + stream_fldfilename_soilm + + ! Default values for namelist + stream_year_first_soilm = 1 ! first year in stream to use + stream_year_last_soilm = 1 ! last year in stream to use + model_year_align_soilm = 1 ! align stream_year_first_soilm with this model year + stream_fldfilename_soilm = shr_stream_file_null + soilm_offset = 0 + soilm_ignore_data_if_missing = .false. + + ! Read soilm_streams namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'soil_moisture_streams', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=soil_moisture_streams,iostat=nml_error) + if (nml_error /= 0) then + call endrun(subname // ':: ERROR reading soil_moisture_streams namelist') + end if + else + call endrun(subname // ':: ERROR finding soilm_streams namelist') + end if + close(nu_nml) + endif + + call shr_mpi_bcast(stream_year_first_soilm, mpicom) + call shr_mpi_bcast(stream_year_last_soilm, mpicom) + call shr_mpi_bcast(model_year_align_soilm, mpicom) + call shr_mpi_bcast(stream_fldfilename_soilm, mpicom) + call shr_mpi_bcast(soilm_tintalgo, mpicom) + call shr_mpi_bcast(soilm_offset, mpicom) + call shr_mpi_bcast(soilm_ignore_data_if_missing, mpicom) + + if (masterproc) then + + write(iulog,*) ' ' + write(iulog,*) 'soil_moisture_stream settings:' + write(iulog,*) ' stream_year_first_soilm = ',stream_year_first_soilm + write(iulog,*) ' stream_year_last_soilm = ',stream_year_last_soilm + write(iulog,*) ' model_year_align_soilm = ',model_year_align_soilm + write(iulog,*) ' stream_fldfilename_soilm = ',trim(stream_fldfilename_soilm) + write(iulog,*) ' soilm_tintalgo = ',trim(soilm_tintalgo) + write(iulog,*) ' soilm_offset = ',soilm_offset + if ( soilm_ignore_data_if_missing )then + write(iulog,*) ' Do NOT override a point with streams data if the streams data is missing' + else + write(iulog,*) ' Abort, if you find a model point where the input streams data is set to missing value' + end if + + endif + + call clm_domain_mct (bounds, dom_clm, nlevels=nlevsoi) + + ! create the field list for these fields...use in shr_strdata_create + fldList = trim(soilmString) + if (masterproc) write(iulog,*) 'fieldlist: ', trim(fldList) + + call shr_strdata_create(sdat_soilm,name="soil_moisture", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsMap_lnd2Dsoi_gdc2glo, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + nzg=nlevsoi, & + yearFirst=stream_year_first_soilm, & + yearLast=stream_year_last_soilm, & + yearAlign=model_year_align_soilm, & + offset=soilm_offset, & + domFilePath='', & + domFileName=trim(stream_fldFileName_soilm), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domZvarName='levsoi' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/stream_fldFileName_soilm/), & + fldListFile=fldList, & + fldListModel=fldList, & + fillalgo='none', & + mapalgo='none', & + tintalgo=soilm_tintalgo, & + calendar=get_calendar(), & + dtlimit = 15._r8, & + taxmode='cycle' ) + + if (masterproc) then + call shr_strdata_print(sdat_soilm,'soil moisture data') + endif + + end subroutine PrescribedSoilMoistureInit + + + !----------------------------------------------------------------------- + ! + ! PrescribedSoilMoistureAdvance + ! + !----------------------------------------------------------------------- + subroutine PrescribedSoilMoistureAdvance( bounds ) + ! + ! Advanace the prescribed soil moisture stream + ! + ! !USES: + use clm_time_manager, only : get_curr_date + ! + ! !ARGUMENTS: + type(bounds_type) , intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + character(len=CL) :: stream_var_name + integer :: g, ig + integer :: ier ! error code + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + + stream_var_name = 'H2OSOI' + + ! Determine variable index + ism = mct_aVect_indexRA(sdat_soilm%avs(1),trim(stream_var_name)) + + call shr_strdata_advance(sdat_soilm, mcdate, sec, mpicom, trim(stream_var_name)) + + ! Map gridcell to AV index + ier = 0 + if ( .not. allocated(g_to_ig) )then + allocate (g_to_ig(bounds%begg:bounds%endg), stat=ier) + if (ier /= 0) then + write(iulog,*) 'Prescribed soil moisture allocation error' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + g_to_ig(g) = ig + end do + end if + + end subroutine PrescribedSoilMoistureAdvance + + !----------------------------------------------------------------------- + ! + ! PrescribedSoilMoistureInterp + ! + !----------------------------------------------------------------------- + subroutine PrescribedSoilMoistureInterp(bounds, soilstate_inst, & + waterstatebulk_inst) + ! + ! Assign data stream information for prescribed soil moisture. + ! + ! !USES: + use clm_time_manager, only : get_curr_date + use clm_varpar , only : nlevsoi + use clm_varcon , only : denh2o, denice, watmin, spval + use landunit_varcon , only : istsoil, istcrop + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds + type(soilstate_type) , intent(in) :: soilstate_inst + type(waterstatebulk_type) , intent(inout) :: waterstatebulk_inst + ! + ! !LOCAL VARIABLES: + integer :: c, g, j, ig, n + real(r8) :: soilm_liq_frac ! liquid fraction of soil moisture + real(r8) :: soilm_ice_frac ! ice fraction of soil moisture + real(r8) :: moisture_increment ! soil moisture adjustment increment + real(r8) :: h2osoi_vol_initial ! initial vwc value + character(*), parameter :: subName = "('PrescribedSoilMoistureInterp')" + + !----------------------------------------------------------------------- + + SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,2) >= g_to_ig(bounds%endg)+(nlevsoi-1)*size(g_to_ig) ), sourcefile, __LINE__) + associate( & + dz => col%dz , & ! Input: [real(r8) (:,:) ] layer depth (m) + watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] volumetric soil water at saturation (porosity) + h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input/Output: [real(r8) (:,:) ] liquid water (kg/m2) + h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input/Output: [real(r8) (:,:) ] ice water (kg/m2) + h2osoi_vol => waterstatebulk_inst%h2osoi_vol_col , & ! Output: volumetric soil water (m3/m3) + h2osoi_vol_prs => waterstatebulk_inst%h2osoi_vol_prs_grc & ! Output: prescribed volumetric soil water (m3/m3) + ) + SHR_ASSERT_FL( (lbound(h2osoi_vol,1) <= bounds%begc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_vol,1) >= bounds%endc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(h2osoi_vol,2) == 1 ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_vol,2) >= nlevsoi ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(dz,1) <= bounds%begc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(dz,1) >= bounds%endc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(dz,2) <= 1 ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(dz,2) >= nlevsoi ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(watsat,1) <= bounds%begc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(watsat,1) >= bounds%endc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(watsat,2) <= 1 ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(watsat,2) >= nlevsoi ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(h2osoi_liq,1) <= bounds%begc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_liq,1) >= bounds%endc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(h2osoi_liq,2) <= 1 ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_liq,2) >= nlevsoi ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(h2osoi_ice,1) <= bounds%begc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_ice,1) >= bounds%endc ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(h2osoi_ice,2) <= 1 ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_ice,2) >= nlevsoi ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,1) <= bounds%begg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,1) >= bounds%endg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,2) == 1 ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,2) >= nlevsoi ), sourcefile, __LINE__) + ! + ! Set the prescribed soil moisture read from the file everywhere + ! + do g = bounds%begg, bounds%endg + ig = g_to_ig(g) + do j = 1, nlevsoi + + !n = ig + (j-1)*size(g_to_ig) + n = ig + (j-1)*size(g_to_ig) + + h2osoi_vol_prs(g,j) = sdat_soilm%avs(1)%rAttr(ism,n) + + ! If soil moiture is being interpolated in time and the result is + ! large that probably means one of the two data points is missing (set to spval) + if ( h2osoi_vol_prs(g,j) > 10.0_r8 .and. (h2osoi_vol_prs(g,j) /= spval) )then + h2osoi_vol_prs(g,j) = spval + end if + + end do + end do + + do c = bounds%begc, bounds%endc + ! + ! Set variable for each gridcell/column combination + ! + g = col%gridcell(c) + ig = g_to_ig(g) + + ! EBK Jan/2020, also check weights on gridcell (See https://github.com/ESCOMP/CTSM/issues/847) + if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) .and. & + (col%wtgcell(c) /= 0._r8) ) then + ! this is a 2d field (gridcell/nlevsoi) ! + do j = 1, nlevsoi + + n = ig + (j-1)*size(g_to_ig) + + ! if soil water is zero, liq/ice fractions cannot be calculated + if((h2osoi_liq(c, j) + h2osoi_ice(c, j)) > 0._r8) then + + ! save original soil moisture value + h2osoi_vol_initial = h2osoi_vol(c,j) + + ! Check if the vegetated land mask from the dataset on the + ! file is different + if ( (h2osoi_vol_prs(g,j) == spval) .and. (h2osoi_vol_initial /= spval) )then + if ( soilm_ignore_data_if_missing )then + cycle + else + write(iulog,*) 'Input soil moisture dataset is not vegetated as expected: gridcell=', & + g, ' active = ', col%active(c) + call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, & + msg = subname // & + ' ERROR:: The input soil moisture stream is NOT vegetated for one of the land points' ) + end if + end if + + ! update volumetric soil moisture from data prescribed from the file + h2osoi_vol(c,j) = h2osoi_vol_prs(g,j) + + + ! calculate liq/ice mass fractions + soilm_liq_frac = h2osoi_liq(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j)) + soilm_ice_frac = h2osoi_ice(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j)) + + ! calculate moisture increment + moisture_increment = h2osoi_vol(c,j) - h2osoi_vol_initial + ! add limitation check + moisture_increment = min((watsat(c,j) - h2osoi_vol_initial),max(-(h2osoi_vol_initial-watmin),moisture_increment)) + + ! update liq/ice water mass due to (volumetric) moisture increment + h2osoi_liq(c,j) = h2osoi_liq(c,j) + (soilm_liq_frac * moisture_increment * dz(c, j) * denh2o) + h2osoi_ice(c,j) = h2osoi_ice(c,j) + (soilm_ice_frac * moisture_increment * dz(c, j) * denice) + + else + call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, & + msg = subname // ':: ERROR h2osoil liquid plus ice is zero') + endif + enddo + endif + end do + + end associate + + end subroutine PrescribedSoilMoistureInterp + +end module SoilMoistureStreamMod diff --git a/src/cpl/mct/UrbanTimeVarType.F90 b/src/cpl/mct/UrbanTimeVarType.F90 new file mode 100644 index 0000000000..805ac47fbf --- /dev/null +++ b/src/cpl/mct/UrbanTimeVarType.F90 @@ -0,0 +1,314 @@ +module UrbanTimeVarType + + !------------------------------------------------------------------------------ + ! !DESCRIPTION: + ! Urban Time Varying Data + ! + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL + use shr_log_mod , only : errMsg => shr_log_errMsg + use abortutils , only : endrun + use decompMod , only : bounds_type, subgrid_level_landunit + use clm_varctl , only : iulog, inst_name + use landunit_varcon , only : isturb_MIN, isturb_MAX + use clm_varcon , only : spval + use LandunitType , only : lun + use GridcellType , only : grc + use mct_mod + use shr_strdata_mod , only : shr_strdata_type + ! + implicit none + save + private + ! + ! + + ! !PUBLIC TYPE + type, public :: urbantv_type + + real(r8), public, pointer :: t_building_max(:) ! lun maximum internal building air temperature (K) + type(shr_strdata_type) :: sdat_urbantv ! urban time varying input data stream + contains + + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Init ! Allocate and initialize urbantv + procedure, public :: urbantv_init ! Initialize urban time varying stream + procedure, public :: urbantv_interp ! Interpolate urban time varying stream + + end type urbantv_type + + !----------------------------------------------------------------------- + character(15), private :: stream_var_name(isturb_MIN:isturb_MAX) + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +contains + + !----------------------------------------------------------------------- + subroutine Init(this, bounds, NLFilename) + ! + ! Allocate module variables and data structures + ! + ! !USES: + use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + use histFileMod , only : hist_addfld1d + ! + ! !ARGUMENTS: + class(urbantv_type) :: this + type(bounds_type) , intent(in) :: bounds + character(len=*) , intent(in) :: NLFilename ! Namelist filename + ! + ! !LOCAL VARIABLES: + integer :: begl, endl + !--------------------------------------------------------------------- + + begl = bounds%begl; endl = bounds%endl + + ! Allocate urbantv data structure + + allocate(this%t_building_max (begl:endl)) ; this%t_building_max (:) = nan + + call this%urbantv_init(bounds, NLFilename) + call this%urbantv_interp(bounds) + + ! Add history fields + call hist_addfld1d (fname='TBUILD_MAX', units='K', & + avgflag='A', long_name='prescribed maximum interior building temperature', & + ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & + l2g_scale_type='unity') + + + end subroutine Init + + !----------------------------------------------------------------------- + + !----------------------------------------------------------------------- + subroutine urbantv_init(this, bounds, NLFilename) + ! + ! !DESCRIPTION: + ! Initialize data stream information for urban time varying data + ! + ! !USES: + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use clm_nlUtilsMod , only : find_nlgroup_name + use ndepStreamMod , only : clm_domain_mct + use spmdMod , only : masterproc, mpicom, comp_id + use fileutils , only : getavu, relavu + use shr_mpi_mod , only : shr_mpi_bcast + use shr_string_mod , only : shr_string_listAppend + use shr_strdata_mod , only : shr_strdata_create, shr_strdata_print + use domainMod , only : ldomain + use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + use landunit_varcon , only : isturb_TBD, isturb_HD, isturb_MD + use lnd_set_decomp_and_domain , only : gsmap_global + ! + ! !ARGUMENTS: + implicit none + class(urbantv_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! !LOCAL VARIABLES: + integer :: begl, endl ! landunits + integer :: ifield ! field index + integer :: stream_year_first_urbantv ! first year in urban tv stream to use + integer :: stream_year_last_urbantv ! last year in urban tv stream to use + integer :: model_year_align_urbantv ! align stream_year_first_urbantv + ! with this model year + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + type(mct_ggrid) :: dom_clm ! domain information + character(len=CL) :: stream_fldFileName_urbantv ! urban tv streams filename + character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac + character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm + character(len=CL) :: fldList ! field string + character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string + character(*), parameter :: subName = "('urbantv_init')" + character(*), parameter :: F00 = "('(urbantv_init) ',4a)" + !----------------------------------------------------------------------- + namelist /urbantv_streams/ & + stream_year_first_urbantv, & + stream_year_last_urbantv, & + model_year_align_urbantv, & + urbantvmapalgo, & + stream_fldFileName_urbantv, & + urbantv_tintalgo + !----------------------------------------------------------------------- + + begl = bounds%begl; endl = bounds%endl + + ! Default values for namelist + stream_year_first_urbantv = 1 ! first year in stream to use + stream_year_last_urbantv = 1 ! last year in stream to use + model_year_align_urbantv = 1 ! align stream_year_first_urbantv with this model year + stream_fldFileName_urbantv = ' ' + + ! Read urbantv_streams namelist + if (masterproc) then + nu_nml = getavu() + open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'urbantv_streams', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=urbantv_streams,iostat=nml_error) + if (nml_error /= 0) then + call endrun(msg='ERROR reading urbantv_streams namelist'//errMsg(sourcefile, __LINE__)) + end if + end if + close(nu_nml) + call relavu( nu_nml ) + endif + + call shr_mpi_bcast(stream_year_first_urbantv, mpicom) + call shr_mpi_bcast(stream_year_last_urbantv, mpicom) + call shr_mpi_bcast(model_year_align_urbantv, mpicom) + call shr_mpi_bcast(stream_fldFileName_urbantv, mpicom) + call shr_mpi_bcast(urbantv_tintalgo, mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) 'urbantv_streams settings:' + write(iulog,*) ' stream_year_first_urbantv = ',stream_year_first_urbantv + write(iulog,*) ' stream_year_last_urbantv = ',stream_year_last_urbantv + write(iulog,*) ' model_year_align_urbantv = ',model_year_align_urbantv + write(iulog,*) ' stream_fldFileName_urbantv = ',stream_fldFileName_urbantv + write(iulog,*) ' urbantv_tintalgo = ',urbantv_tintalgo + write(iulog,*) ' ' + endif + + call clm_domain_mct (bounds, dom_clm) + + ! create the field list for these urbantv fields...use in shr_strdata_create + stream_var_name(:) = "NOT_SET" + stream_var_name(isturb_TBD) = urbantvString//"TBD" + stream_var_name(isturb_HD) = urbantvString//"HD" + stream_var_name(isturb_MD) = urbantvString//"MD" + fldList = "" + do ifield = isturb_MIN, isturb_MAX + call shr_string_listAppend( fldList, stream_var_name(ifield) ) + end do + + call shr_strdata_create(this%sdat_urbantv,name="clmurbantv", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_urbantv, & + yearLast=stream_year_last_urbantv, & + yearAlign=model_year_align_urbantv, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_urbantv), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='LANDMASK', & + filePath='', & + filename=(/trim(stream_fldFileName_urbantv)/) , & + fldListFile=fldList, & + fldListModel=fldList, & + fillalgo='none', & + mapalgo=urbantvmapalgo, & + calendar=get_calendar(), & + tintalgo=urbantv_tintalgo, & + taxmode='extend' ) + + if (masterproc) then + call shr_strdata_print(this%sdat_urbantv,'urban time varying data') + endif + + + end subroutine urbantv_init + + !----------------------------------------------------------------------- + subroutine urbantv_interp(this, bounds) + ! + ! !DESCRIPTION: + ! Interpolate data stream information for urban time varying data. + ! + ! !USES: + use clm_time_manager, only : get_curr_date + use spmdMod , only : mpicom + use shr_strdata_mod , only : shr_strdata_advance + use clm_instur , only : urban_valid + ! + ! !ARGUMENTS: + class(urbantv_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + logical :: found + integer :: l, glun, ig, g, ip + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + integer :: lindx ! landunit index + integer :: gindx ! gridcell index + !----------------------------------------------------------------------- + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + + call shr_strdata_advance(this%sdat_urbantv, mcdate, sec, mpicom, 'urbantvdyn') + + do l = bounds%begl,bounds%endl + if (lun%urbpoi(l)) then + glun = lun%gridcell(l) + ip = mct_aVect_indexRA(this%sdat_urbantv%avs(1),trim(stream_var_name(lun%itype(l)))) + ! + ! Determine vector index corresponding to glun + ! + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + if (g == glun) exit + end do + + this%t_building_max(l) = this%sdat_urbantv%avs(1)%rAttr(ip,ig) + else + this%t_building_max(l) = spval + end if + end do + + found = .false. + do l = bounds%begl,bounds%endl + if (lun%urbpoi(l)) then + glun = lun%gridcell(l) + ! + ! Determine vector index corresponding to glun + ! + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + if (g == glun) exit + end do + + if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then + found = .true. + gindx = g + lindx = l + exit + end if + end if + end do + if ( found ) then + write(iulog,*)'ERROR: no valid urban data for g= ',gindx + write(iulog,*)'landunit type: ',lun%itype(lindx) + write(iulog,*)'urban_valid: ',urban_valid(gindx) + write(iulog,*)'t_building_max: ',this%t_building_max(lindx) + call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, & + msg=errmsg(sourcefile, __LINE__)) + end if + + + end subroutine urbantv_interp + + !----------------------------------------------------------------------- + +end module UrbanTimeVarType diff --git a/src/cpl/mct/ch4FInundatedStreamType.F90 b/src/cpl/mct/ch4FInundatedStreamType.F90 new file mode 100644 index 0000000000..3c26f4d109 --- /dev/null +++ b/src/cpl/mct/ch4FInundatedStreamType.F90 @@ -0,0 +1,389 @@ +module ch4FInundatedStreamType + +#include "shr_assert.h" + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Contains methods for reading in finundated streams file for methane code. + ! + ! !USES + use shr_kind_mod , only: r8 => shr_kind_r8, CL => shr_kind_cl + use spmdMod , only: mpicom, masterproc + use clm_varctl , only: iulog, inst_name + use abortutils , only: endrun + use decompMod , only: bounds_type + use ch4varcon , only: finundation_mtd + + ! !PUBLIC TYPES: + implicit none + private + save + + type, public :: ch4finundatedstream_type + real(r8), pointer, private :: zwt0_gdc (:) ! col coefficient for determining finundated (m) + real(r8), pointer, private :: f0_gdc (:) ! col maximum inundated fraction for a gridcell (for methane code) + real(r8), pointer, private :: p3_gdc (:) ! col coefficient for determining finundated (m) + real(r8), pointer, private :: fws_slope_gdc (:) ! col slope in fws = slope * tws + intercept (A coefficient) + real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient) + contains + + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Init ! Initialize and read data in + procedure, public :: CalcFinundated ! Calculate finundated based on input streams + procedure, public :: UseStreams ! If streams will be used + + ! !PRIVATE MEMBER FUNCTIONS: + procedure, private :: InitAllocate ! Allocate data + + end type ch4finundatedstream_type + + + ! ! PRIVATE DATA: + + type, private :: streamcontrol_type + character(len=CL) :: stream_fldFileName_ch4finundated ! Filename + character(len=CL) :: ch4finundatedmapalgo ! map algo + character(len=CL) :: fldList ! List of fields to read + contains + procedure, private :: ReadNML ! Read in namelist + end type streamcontrol_type + + type(streamcontrol_type), private :: control ! Stream control data + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + !============================================================================== + +contains + + !============================================================================== + + subroutine Init(this, bounds, NLFilename) + ! + ! Initialize the ch4 finundated stream object + ! + ! Uses: + use clm_time_manager , only : get_calendar, get_curr_date + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use shr_nl_mod , only : shr_nl_find_group_name + use shr_mpi_mod , only : shr_mpi_bcast + use ndepStreamMod , only : clm_domain_mct + use domainMod , only : ldomain + use decompMod , only : bounds_type + use mct_mod , only : mct_ggrid, mct_avect_indexra + use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create + use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance + use spmdMod , only : comp_id, iam + use ch4varcon , only : finundation_mtd_h2osfc + use ch4varcon , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion + use lnd_set_decomp_and_domain , only : gsmap_global + ! + ! arguments + implicit none + class(ch4finundatedstream_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! local variables + integer :: ig, g ! Indices + type(mct_ggrid) :: dom_clm ! domain information + type(shr_strdata_type) :: sdat ! input data stream + integer :: index_ZWT0 = 0 ! Index of ZWT0 field + integer :: index_F0 = 0 ! Index of F0 field + integer :: index_P3 = 0 ! Index of P3 field + integer :: index_FWS_TWS_A = 0 ! Index of FWS_TWS_A field + integer :: index_FWS_TWS_B = 0 ! Index of FWS_TWS_B field + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + character(len=*), parameter :: stream_name = 'ch4finundated' + character(*), parameter :: subName = "('ch4finundatedstream::Init')" + !----------------------------------------------------------------------- + if ( finundation_mtd /= finundation_mtd_h2osfc )then + call this%InitAllocate( bounds ) + call control%ReadNML( bounds, NLFileName ) + + if ( this%useStreams() )then + call clm_domain_mct (bounds, dom_clm) + + call shr_strdata_create(sdat,name=stream_name, & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=1996, & + yearLast=1996, & + yearAlign=1, & + offset=0, & + domFilePath='', & + domFileName=trim(control%stream_fldFileName_ch4finundated), & + domTvarName='time', & + domXvarName='LONGXY' , & + domYvarName='LATIXY' , & + domAreaName='AREA', & + domMaskName='LANDMASK', & + filePath='', & + filename=(/trim(control%stream_fldFileName_ch4finundated)/), & + fldListFile=control%fldList, & + fldListModel=control%fldList, & + fillalgo='none', & + mapalgo=control%ch4finundatedmapalgo, & + calendar=get_calendar(), & + taxmode='extend' ) + + if (masterproc) then + call shr_strdata_print(sdat,'CLM '//stream_name//' data') + endif + + if( finundation_mtd == finundation_mtd_ZWT_inversion )then + index_ZWT0 = mct_avect_indexra(sdat%avs(1),'ZWT0') + index_F0 = mct_avect_indexra(sdat%avs(1),'F0' ) + index_P3 = mct_avect_indexra(sdat%avs(1),'P3' ) + else if( finundation_mtd == finundation_mtd_TWS_inversion )then + index_FWS_TWS_A = mct_avect_indexra(sdat%avs(1),'FWS_TWS_A') + index_FWS_TWS_B = mct_avect_indexra(sdat%avs(1),'FWS_TWS_B') + end if + + + ! Explicitly set current date to a hardcoded constant value. Otherwise + ! using the real date can cause roundoff differences that are + ! detrected as issues with exact restart. EBK M05/20/2017 + !call get_curr_date(year, mon, day, sec) + year = 1996 + mon = 12 + day = 31 + sec = 0 + mcdate = year*10000 + mon*100 + day + + call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ch4finundated') + + ! Get the data + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + if ( index_ZWT0 > 0 )then + this%zwt0_gdc(g) = sdat%avs(1)%rAttr(index_ZWT0,ig) + end if + if ( index_F0 > 0 )then + this%f0_gdc(g) = sdat%avs(1)%rAttr(index_F0,ig) + end if + if ( index_P3 > 0 )then + this%p3_gdc(g) = sdat%avs(1)%rAttr(index_P3,ig) + end if + if ( index_FWS_TWS_A > 0 )then + this%fws_slope_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_A,ig) + end if + if ( index_FWS_TWS_B > 0 )then + this%fws_intercept_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_B,ig) + end if + end do + end if + end if + + end subroutine Init + + !----------------------------------------------------------------------- + logical function UseStreams(this) + ! + ! !DESCRIPTION: + ! Return true if + ! + ! !USES: + ! + ! !ARGUMENTS: + implicit none + class(ch4finundatedstream_type) :: this + ! + ! !LOCAL VARIABLES: + if ( trim(control%stream_fldFileName_ch4finundated) == '' )then + UseStreams = .false. + else + UseStreams = .true. + end if + end function UseStreams + + !----------------------------------------------------------------------- + subroutine InitAllocate(this, bounds) + ! + ! !DESCRIPTION: + ! Allocate module variables and data structures + ! + ! !USES: + use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=) + use ch4varcon , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion + ! + ! !ARGUMENTS: + implicit none + class(ch4finundatedstream_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: begc, endc + integer :: begg, endg + !--------------------------------------------------------------------- + + begc = bounds%begc; endc = bounds%endc + begg = bounds%begg; endg = bounds%endg + + if( finundation_mtd == finundation_mtd_ZWT_inversion )then + allocate(this%zwt0_gdc (begg:endg)) ; this%zwt0_gdc (:) = nan + allocate(this%f0_gdc (begg:endg)) ; this%f0_gdc (:) = nan + allocate(this%p3_gdc (begg:endg)) ; this%p3_gdc (:) = nan + else if( finundation_mtd == finundation_mtd_TWS_inversion )then + allocate(this%fws_slope_gdc (begg:endg)) ; this%fws_slope_gdc (:) = nan + allocate(this%fws_intercept_gdc(begg:endg)) ; this%fws_intercept_gdc(:) = nan + end if + + end subroutine InitAllocate + + !----------------------------------------------------------------------- + subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, & + waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated ) + ! + ! !DESCRIPTION: + ! + ! Calculate finundated according to the appropriate methodology + ! + ! !USES: + use ColumnType , only : col + use ch4varcon , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion + use ch4varcon , only : finundation_mtd_TWS_inversion + use clm_varpar , only : nlevsoi + use SoilHydrologyType, only : soilhydrology_type + use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type + ! + ! !ARGUMENTS: + implicit none + class(ch4finundatedstream_type) :: this + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_soilc ! number of column soil points in column filter + integer , intent(in) :: filter_soilc(:) ! column filter for soil points + type(soilhydrology_type) , intent(in) :: soilhydrology_inst + type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst + real(r8) , intent(in) :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s) + real(r8) , intent(inout) :: finundated(bounds%begc:) ! fractional inundated area in soil column (excluding dedicated wetland columns) + ! + ! !LOCAL VARIABLES: + integer :: g, c, fc ! Indices + real(r8) :: zwt_actual ! Total water storage (ZWT) to use either perched or total depending on conditions + + SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__) + SHR_ASSERT_ALL_FL((ubound(finundated) == (/bounds%endc/)), sourcefile, __LINE__) + + associate( & + z => col%z , & ! Input: [real(r8) (:,:) ] layer depth (m) (-nlevsno+1:nlevsoi) + zwt => soilhydrology_inst%zwt_col , & ! Input: [real(r8) (:) ] water table depth (m) + zwt_perched => soilhydrology_inst%zwt_perched_col , & ! Input: [real(r8) (:) ] perched water table depth (m) + tws => waterdiagnosticbulk_inst%tws_grc , & ! Input: [real(r8) (:) ] total water storage (kg m-2) + frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) + ) + + ! Calculate finundated + do fc = 1, num_soilc + c = filter_soilc(fc) + g = col%gridcell(c) + select case( finundation_mtd ) + case ( finundation_mtd_h2osfc ) + finundated(c) = frac_h2osfc(c) + case ( finundation_mtd_ZWT_inversion ) + if (this%zwt0_gdc(g) > 0._r8) then + if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then + zwt_actual = zwt_perched(c) + else + zwt_actual = zwt(c) + end if + finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c) + else + finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c) + end if + case ( finundation_mtd_TWS_inversion ) + finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g) + end select + finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) ) + end do + end associate + + end subroutine CalcFinundated + !============================================================================== + + subroutine ReadNML(this, bounds, NLFilename) + ! + ! Read the namelist data stream information. + ! + ! Uses: + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use shr_nl_mod , only : shr_nl_find_group_name + use shr_log_mod , only : errMsg => shr_log_errMsg + use shr_mpi_mod , only : shr_mpi_bcast + use fileutils , only : getavu, relavu + use ch4varcon , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion + ! + ! arguments + implicit none + class(streamcontrol_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! local variables + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + character(len=CL) :: stream_fldFileName_ch4finundated = ' ' + character(len=CL) :: ch4finundatedmapalgo = 'bilinear' + character(len=*), parameter :: namelist_name = 'ch4finundated' ! MUST agree with name in namelist and read + character(len=*), parameter :: shr_strdata_unset = 'NOT_SET' + character(len=*), parameter :: subName = "('ch4finundated::ReadNML')" + character(len=*), parameter :: F00 = "('(ch4finundated_readnml) ',4a)" + !----------------------------------------------------------------------- + + namelist /ch4finundated/ & ! MUST agree with namelist_name above + ch4finundatedmapalgo, stream_fldFileName_ch4finundated + + ! Default values for namelist + + ! Read ch4finundated namelist + if (masterproc) then + nu_nml = getavu() + open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=ch4finundated,iostat=nml_error) ! MUST agree with namelist_name above + if (nml_error /= 0) then + call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + else + call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + close(nu_nml) + call relavu( nu_nml ) + endif + + call shr_mpi_bcast(stream_fldFileName_ch4finundated, mpicom) + call shr_mpi_bcast(ch4finundatedmapalgo , mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) namelist_name, ' stream settings:' + write(iulog,*) ' stream_fldFileName_ch4finundated = ',stream_fldFileName_ch4finundated + write(iulog,*) ' ch4finundatedmapalgo = ',ch4finundatedmapalgo + write(iulog,*) ' ' + endif + this%stream_fldFileName_ch4finundated = stream_fldFileName_ch4finundated + this%ch4finundatedmapalgo = ch4finundatedmapalgo + if ( finundation_mtd == finundation_mtd_ZWT_inversion )then + this%fldList = "ZWT0:F0:P3" + else if ( finundation_mtd == finundation_mtd_TWS_inversion )then + this%fldList = "FWS_TWS_A:FWS_TWS_B" + else + call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// & + errMsg(sourcefile, __LINE__)) + end if + + end subroutine ReadNML + +end module ch4FInundatedStreamType diff --git a/src/cpl/mct/clm_cpl_indices.F90 b/src/cpl/mct/clm_cpl_indices.F90 new file mode 100644 index 0000000000..09ed89e92d --- /dev/null +++ b/src/cpl/mct/clm_cpl_indices.F90 @@ -0,0 +1,330 @@ +module clm_cpl_indices + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Module containing the indices for the fields passed between CLM and + ! the driver. Includes the River Transport Model fields (RTM) and the + ! fields needed by the land-ice component (sno). + ! + ! !USES: + + use shr_sys_mod, only : shr_sys_abort + implicit none + + SAVE + private ! By default make data private + ! + ! !PUBLIC MEMBER FUNCTIONS: + public :: clm_cpl_indices_set ! Set the coupler indices + ! + ! !PUBLIC DATA MEMBERS: + ! + integer , public :: glc_nec ! number of elevation classes for glacier_mec landunits + ! (from coupler) - must equal maxpatch_glc from namelist + + ! lnd -> drv (required) + + integer, public ::index_l2x_Flrl_rofsur ! lnd->rtm input liquid surface fluxes + integer, public ::index_l2x_Flrl_rofgwl ! lnd->rtm input liquid gwl fluxes + integer, public ::index_l2x_Flrl_rofsub ! lnd->rtm input liquid subsurface fluxes + integer, public ::index_l2x_Flrl_rofi ! lnd->rtm input frozen fluxes + integer, public ::index_l2x_Flrl_irrig ! irrigation withdrawal + + integer, public ::index_l2x_Sl_t ! temperature + integer, public ::index_l2x_Sl_tref ! 2m reference temperature + integer, public ::index_l2x_Sl_qref ! 2m reference specific humidity + integer, public ::index_l2x_Sl_avsdr ! albedo: direct , visible + integer, public ::index_l2x_Sl_anidr ! albedo: direct , near-ir + integer, public ::index_l2x_Sl_avsdf ! albedo: diffuse, visible + integer, public ::index_l2x_Sl_anidf ! albedo: diffuse, near-ir + integer, public ::index_l2x_Sl_snowh ! snow height + integer, public ::index_l2x_Sl_u10 ! 10m wind + integer, public ::index_l2x_Sl_ddvel ! dry deposition velocities (optional) + integer, public ::index_l2x_Sl_fv ! friction velocity + integer, public ::index_l2x_Sl_ram1 ! aerodynamical resistance + integer, public ::index_l2x_Sl_soilw ! volumetric soil water + integer, public ::index_l2x_Fall_taux ! wind stress, zonal + integer, public ::index_l2x_Fall_tauy ! wind stress, meridional + integer, public ::index_l2x_Fall_lat ! latent heat flux + integer, public ::index_l2x_Fall_sen ! sensible heat flux + integer, public ::index_l2x_Fall_lwup ! upward longwave heat flux + integer, public ::index_l2x_Fall_evap ! evaporation water flux + integer, public ::index_l2x_Fall_swnet ! heat flux shortwave net + integer, public ::index_l2x_Fall_fco2_lnd ! co2 flux **For testing set to 0 + integer, public ::index_l2x_Fall_flxdst1 ! dust flux size bin 1 + integer, public ::index_l2x_Fall_flxdst2 ! dust flux size bin 2 + integer, public ::index_l2x_Fall_flxdst3 ! dust flux size bin 3 + integer, public ::index_l2x_Fall_flxdst4 ! dust flux size bin 4 + integer, public ::index_l2x_Fall_flxvoc ! MEGAN fluxes + integer, public ::index_l2x_Fall_flxfire ! Fire fluxes + integer, public ::index_l2x_Sl_ztopfire ! Top of fire emissions (m) + + ! In the following, index 0 is bare land, other indices are glc elevation classes + integer, allocatable, public ::index_l2x_Sl_tsrf(:) ! glc MEC temperature + integer, allocatable, public ::index_l2x_Sl_topo(:) ! glc MEC topo height + integer, allocatable, public ::index_l2x_Flgl_qice(:) ! glc MEC ice flux + + integer, public ::index_x2l_Sa_methane + integer, public ::index_l2x_Fall_methane + + integer, public :: nflds_l2x = 0 + + ! drv -> lnd (required) + + integer, public ::index_x2l_Sa_z ! bottom atm level height + integer, public ::index_x2l_Sa_topo ! atm surface height (m) + integer, public ::index_x2l_Sa_u ! bottom atm level zon wind + integer, public ::index_x2l_Sa_v ! bottom atm level mer wind + integer, public ::index_x2l_Sa_ptem ! bottom atm level pot temp + integer, public ::index_x2l_Sa_shum ! bottom atm level spec hum + integer, public ::index_x2l_Sa_pbot ! bottom atm level pressure + integer, public ::index_x2l_Sa_tbot ! bottom atm level temp + integer, public ::index_x2l_Faxa_lwdn ! downward lw heat flux + integer, public ::index_x2l_Faxa_rainc ! prec: liquid "convective" + integer, public ::index_x2l_Faxa_rainl ! prec: liquid "large scale" + integer, public ::index_x2l_Faxa_snowc ! prec: frozen "convective" + integer, public ::index_x2l_Faxa_snowl ! prec: frozen "large scale" + integer, public ::index_x2l_Faxa_swndr ! sw: nir direct downward + integer, public ::index_x2l_Faxa_swvdr ! sw: vis direct downward + integer, public ::index_x2l_Faxa_swndf ! sw: nir diffuse downward + integer, public ::index_x2l_Faxa_swvdf ! sw: vis diffuse downward + integer, public ::index_x2l_Sa_co2prog ! bottom atm level prognostic co2 + integer, public ::index_x2l_Sa_co2diag ! bottom atm level diagnostic co2 + integer, public ::index_x2l_Faxa_bcphidry ! flux: Black Carbon hydrophilic dry deposition + integer, public ::index_x2l_Faxa_bcphodry ! flux: Black Carbon hydrophobic dry deposition + integer, public ::index_x2l_Faxa_bcphiwet ! flux: Black Carbon hydrophilic wet deposition + integer, public ::index_x2l_Faxa_ocphidry ! flux: Organic Carbon hydrophilic dry deposition + integer, public ::index_x2l_Faxa_ocphodry ! flux: Organic Carbon hydrophobic dry deposition + integer, public ::index_x2l_Faxa_ocphiwet ! flux: Organic Carbon hydrophilic dry deposition + integer, public ::index_x2l_Faxa_dstwet1 ! flux: Size 1 dust -- wet deposition + integer, public ::index_x2l_Faxa_dstwet2 ! flux: Size 2 dust -- wet deposition + integer, public ::index_x2l_Faxa_dstwet3 ! flux: Size 3 dust -- wet deposition + integer, public ::index_x2l_Faxa_dstwet4 ! flux: Size 4 dust -- wet deposition + integer, public ::index_x2l_Faxa_dstdry1 ! flux: Size 1 dust -- dry deposition + integer, public ::index_x2l_Faxa_dstdry2 ! flux: Size 2 dust -- dry deposition + integer, public ::index_x2l_Faxa_dstdry3 ! flux: Size 3 dust -- dry deposition + integer, public ::index_x2l_Faxa_dstdry4 ! flux: Size 4 dust -- dry deposition + + integer, public ::index_x2l_Faxa_nhx ! flux nhx from atm + integer, public ::index_x2l_Faxa_noy ! flux noy from atm + + integer, public ::index_x2l_Flrr_flood ! rtm->lnd rof flood flux + integer, public ::index_x2l_Flrr_volr ! rtm->lnd rof volr total volume + integer, public ::index_x2l_Flrr_volrmch ! rtm->lnd rof volr main channel volume + + ! In the following, index 0 is bare land, other indices are glc elevation classes + integer, allocatable, public ::index_x2l_Sg_ice_covered(:) ! Fraction of glacier from glc model + integer, allocatable, public ::index_x2l_Sg_topo(:) ! Topo height from glc model + integer, allocatable, public ::index_x2l_Flgg_hflx(:) ! Heat flux from glc model + + integer, public ::index_x2l_Sg_icemask + integer, public ::index_x2l_Sg_icemask_coupled_fluxes + + integer, public :: nflds_x2l = 0 + + !----------------------------------------------------------------------- + +contains + + !----------------------------------------------------------------------- + subroutine clm_cpl_indices_set( ) + ! + ! !DESCRIPTION: + ! Set the coupler indices needed by the land model coupler + ! interface. + ! + ! !USES: + use seq_flds_mod , only: seq_flds_x2l_fields, seq_flds_l2x_fields + use mct_mod , only: mct_aVect, mct_aVect_init, mct_avect_indexra + use mct_mod , only: mct_aVect_clean, mct_avect_nRattr + use shr_drydep_mod , only: drydep_fields_token, n_drydep + use shr_megan_mod , only: shr_megan_fields_token, shr_megan_mechcomps_n + use shr_fire_emis_mod,only: shr_fire_emis_fields_token, shr_fire_emis_ztop_token, shr_fire_emis_mechcomps_n + use clm_varctl , only: ndep_from_cpl + use glc_elevclass_mod, only: glc_get_num_elevation_classes, glc_elevclass_as_string + ! + ! !ARGUMENTS: + implicit none + ! + ! !REVISION HISTORY: + ! Author: Mariana Vertenstein + ! 01/2011, Erik Kluzek: Added protex headers + ! + ! !LOCAL VARIABLES: + type(mct_aVect) :: l2x ! temporary, land to coupler + type(mct_aVect) :: x2l ! temporary, coupler to land + integer :: num + character(len=:), allocatable :: nec_str ! string version of glc elev. class number + character(len=64) :: name + character(len=32) :: subname = 'clm_cpl_indices_set' ! subroutine name + !----------------------------------------------------------------------- + + ! Determine attribute vector indices + + ! create temporary attribute vectors + call mct_aVect_init(x2l, rList=seq_flds_x2l_fields, lsize=1) + nflds_x2l = mct_avect_nRattr(x2l) + + call mct_aVect_init(l2x, rList=seq_flds_l2x_fields, lsize=1) + nflds_l2x = mct_avect_nRattr(l2x) + + !------------------------------------------------------------- + ! clm -> drv + !------------------------------------------------------------- + + index_l2x_Flrl_rofsur = mct_avect_indexra(l2x,'Flrl_rofsur') + index_l2x_Flrl_rofgwl = mct_avect_indexra(l2x,'Flrl_rofgwl') + index_l2x_Flrl_rofsub = mct_avect_indexra(l2x,'Flrl_rofsub') + index_l2x_Flrl_rofi = mct_avect_indexra(l2x,'Flrl_rofi') + index_l2x_Flrl_irrig = mct_avect_indexra(l2x,'Flrl_irrig') + + index_l2x_Sl_t = mct_avect_indexra(l2x,'Sl_t') + index_l2x_Sl_snowh = mct_avect_indexra(l2x,'Sl_snowh') + index_l2x_Sl_avsdr = mct_avect_indexra(l2x,'Sl_avsdr') + index_l2x_Sl_anidr = mct_avect_indexra(l2x,'Sl_anidr') + index_l2x_Sl_avsdf = mct_avect_indexra(l2x,'Sl_avsdf') + index_l2x_Sl_anidf = mct_avect_indexra(l2x,'Sl_anidf') + index_l2x_Sl_tref = mct_avect_indexra(l2x,'Sl_tref') + index_l2x_Sl_qref = mct_avect_indexra(l2x,'Sl_qref') + index_l2x_Sl_u10 = mct_avect_indexra(l2x,'Sl_u10') + index_l2x_Sl_ram1 = mct_avect_indexra(l2x,'Sl_ram1') + index_l2x_Sl_fv = mct_avect_indexra(l2x,'Sl_fv') + index_l2x_Sl_soilw = mct_avect_indexra(l2x,'Sl_soilw',perrwith='quiet') + + if ( n_drydep>0 )then + index_l2x_Sl_ddvel = mct_avect_indexra(l2x, trim(drydep_fields_token)) + else + index_l2x_Sl_ddvel = 0 + end if + + index_l2x_Fall_taux = mct_avect_indexra(l2x,'Fall_taux') + index_l2x_Fall_tauy = mct_avect_indexra(l2x,'Fall_tauy') + index_l2x_Fall_lat = mct_avect_indexra(l2x,'Fall_lat') + index_l2x_Fall_sen = mct_avect_indexra(l2x,'Fall_sen') + index_l2x_Fall_lwup = mct_avect_indexra(l2x,'Fall_lwup') + index_l2x_Fall_evap = mct_avect_indexra(l2x,'Fall_evap') + index_l2x_Fall_swnet = mct_avect_indexra(l2x,'Fall_swnet') + index_l2x_Fall_flxdst1 = mct_avect_indexra(l2x,'Fall_flxdst1') + index_l2x_Fall_flxdst2 = mct_avect_indexra(l2x,'Fall_flxdst2') + index_l2x_Fall_flxdst3 = mct_avect_indexra(l2x,'Fall_flxdst3') + index_l2x_Fall_flxdst4 = mct_avect_indexra(l2x,'Fall_flxdst4') + + index_l2x_Fall_fco2_lnd = mct_avect_indexra(l2x,'Fall_fco2_lnd',perrwith='quiet') + + index_l2x_Fall_methane = mct_avect_indexra(l2x,'Fall_methane',perrWith='quiet') + + ! MEGAN fluxes + if (shr_megan_mechcomps_n>0) then + index_l2x_Fall_flxvoc = mct_avect_indexra(l2x,trim(shr_megan_fields_token)) + else + index_l2x_Fall_flxvoc = 0 + endif + + ! Fire fluxes + if (shr_fire_emis_mechcomps_n>0) then + index_l2x_Fall_flxfire = mct_avect_indexra(l2x,trim(shr_fire_emis_fields_token)) + index_l2x_Sl_ztopfire = mct_avect_indexra(l2x,trim(shr_fire_emis_ztop_token)) + else + index_l2x_Fall_flxfire = 0 + index_l2x_Sl_ztopfire = 0 + endif + + !------------------------------------------------------------- + ! drv -> clm + !------------------------------------------------------------- + + index_x2l_Sa_z = mct_avect_indexra(x2l,'Sa_z') + index_x2l_Sa_topo = mct_avect_indexra(x2l,'Sa_topo') + index_x2l_Sa_u = mct_avect_indexra(x2l,'Sa_u') + index_x2l_Sa_v = mct_avect_indexra(x2l,'Sa_v') + index_x2l_Sa_ptem = mct_avect_indexra(x2l,'Sa_ptem') + index_x2l_Sa_pbot = mct_avect_indexra(x2l,'Sa_pbot') + index_x2l_Sa_tbot = mct_avect_indexra(x2l,'Sa_tbot') + index_x2l_Sa_shum = mct_avect_indexra(x2l,'Sa_shum') + index_x2l_Sa_co2prog = mct_avect_indexra(x2l,'Sa_co2prog',perrwith='quiet') + index_x2l_Sa_co2diag = mct_avect_indexra(x2l,'Sa_co2diag',perrwith='quiet') + + index_x2l_Sa_methane = mct_avect_indexra(x2l,'Sa_methane',perrWith='quiet') + + index_x2l_Flrr_volr = mct_avect_indexra(x2l,'Flrr_volr') + index_x2l_Flrr_volrmch = mct_avect_indexra(x2l,'Flrr_volrmch') + + index_x2l_Faxa_lwdn = mct_avect_indexra(x2l,'Faxa_lwdn') + index_x2l_Faxa_rainc = mct_avect_indexra(x2l,'Faxa_rainc') + index_x2l_Faxa_rainl = mct_avect_indexra(x2l,'Faxa_rainl') + index_x2l_Faxa_snowc = mct_avect_indexra(x2l,'Faxa_snowc') + index_x2l_Faxa_snowl = mct_avect_indexra(x2l,'Faxa_snowl') + index_x2l_Faxa_swndr = mct_avect_indexra(x2l,'Faxa_swndr') + index_x2l_Faxa_swvdr = mct_avect_indexra(x2l,'Faxa_swvdr') + index_x2l_Faxa_swndf = mct_avect_indexra(x2l,'Faxa_swndf') + index_x2l_Faxa_swvdf = mct_avect_indexra(x2l,'Faxa_swvdf') + index_x2l_Faxa_bcphidry = mct_avect_indexra(x2l,'Faxa_bcphidry') + index_x2l_Faxa_bcphodry = mct_avect_indexra(x2l,'Faxa_bcphodry') + index_x2l_Faxa_bcphiwet = mct_avect_indexra(x2l,'Faxa_bcphiwet') + index_x2l_Faxa_ocphidry = mct_avect_indexra(x2l,'Faxa_ocphidry') + index_x2l_Faxa_ocphodry = mct_avect_indexra(x2l,'Faxa_ocphodry') + index_x2l_Faxa_ocphiwet = mct_avect_indexra(x2l,'Faxa_ocphiwet') + index_x2l_Faxa_dstdry1 = mct_avect_indexra(x2l,'Faxa_dstdry1') + index_x2l_Faxa_dstdry2 = mct_avect_indexra(x2l,'Faxa_dstdry2') + index_x2l_Faxa_dstdry3 = mct_avect_indexra(x2l,'Faxa_dstdry3') + index_x2l_Faxa_dstdry4 = mct_avect_indexra(x2l,'Faxa_dstdry4') + index_x2l_Faxa_dstwet1 = mct_avect_indexra(x2l,'Faxa_dstwet1') + index_x2l_Faxa_dstwet2 = mct_avect_indexra(x2l,'Faxa_dstwet2') + index_x2l_Faxa_dstwet3 = mct_avect_indexra(x2l,'Faxa_dstwet3') + index_x2l_Faxa_dstwet4 = mct_avect_indexra(x2l,'Faxa_dstwet4') + + index_x2l_Faxa_nhx = mct_avect_indexra(x2l,'Faxa_nhx', perrWith='quiet') + index_x2l_Faxa_noy = mct_avect_indexra(x2l,'Faxa_noy', perrWith='quiet') + + if (index_x2l_Faxa_nhx > 0 .and. index_x2l_Faxa_noy > 0) then + ndep_from_cpl = .true. + end if + + index_x2l_Flrr_flood = mct_avect_indexra(x2l,'Flrr_flood') + + !------------------------------------------------------------- + ! glc coupling + !------------------------------------------------------------- + + index_x2l_Sg_icemask = mct_avect_indexra(x2l,'Sg_icemask') + index_x2l_Sg_icemask_coupled_fluxes = mct_avect_indexra(x2l,'Sg_icemask_coupled_fluxes') + + glc_nec = glc_get_num_elevation_classes() + if (glc_nec < 1) then + call shr_sys_abort('ERROR: In CLM4.5 and later, glc_nec must be at least 1.') + end if + + ! Create coupling fields for all glc elevation classes (1:glc_nec) plus bare land + ! (index 0). + allocate(index_l2x_Sl_tsrf(0:glc_nec)) + allocate(index_l2x_Sl_topo(0:glc_nec)) + allocate(index_l2x_Flgl_qice(0:glc_nec)) + allocate(index_x2l_Sg_ice_covered(0:glc_nec)) + allocate(index_x2l_Sg_topo(0:glc_nec)) + allocate(index_x2l_Flgg_hflx(0:glc_nec)) + + do num = 0,glc_nec + nec_str = glc_elevclass_as_string(num) + + name = 'Sg_ice_covered' // nec_str + index_x2l_Sg_ice_covered(num) = mct_avect_indexra(x2l,trim(name)) + name = 'Sg_topo' // nec_str + index_x2l_Sg_topo(num) = mct_avect_indexra(x2l,trim(name)) + name = 'Flgg_hflx' // nec_str + index_x2l_Flgg_hflx(num) = mct_avect_indexra(x2l,trim(name)) + + name = 'Sl_tsrf' // nec_str + index_l2x_Sl_tsrf(num) = mct_avect_indexra(l2x,trim(name)) + name = 'Sl_topo' // nec_str + index_l2x_Sl_topo(num) = mct_avect_indexra(l2x,trim(name)) + name = 'Flgl_qice' // nec_str + index_l2x_Flgl_qice(num) = mct_avect_indexra(l2x,trim(name)) + end do + + call mct_aVect_clean(x2l) + call mct_aVect_clean(l2x) + + end subroutine clm_cpl_indices_set + +!======================================================================= + +end module clm_cpl_indices diff --git a/src/cpl/mct/laiStreamMod.F90 b/src/cpl/mct/laiStreamMod.F90 new file mode 100644 index 0000000000..47d25287b7 --- /dev/null +++ b/src/cpl/mct/laiStreamMod.F90 @@ -0,0 +1,241 @@ +module laiStreamMod + +#include "shr_assert.h" + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Read LAI from stream + ! + ! !USES: + use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create + use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance + use shr_kind_mod , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX + use shr_log_mod , only : errMsg => shr_log_errMsg + use decompMod , only : bounds_type + use abortutils , only : endrun + use clm_varctl , only : iulog, inst_name + use perf_mod , only : t_startf, t_stopf + use spmdMod , only : masterproc, mpicom, comp_id + use ncdio_pio + use mct_mod + ! + ! !PUBLIC TYPES: + implicit none + private + + ! !PUBLIC MEMBER FUNCTIONS: + public :: lai_init ! position datasets for LAI + public :: lai_advance ! Advance the LAI streams (outside of a Open-MP threading loop) + public :: lai_interp ! interpolates between two years of LAI data (when LAI streams + + ! !PRIVATE MEMBER DATA: + integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index + type(shr_strdata_type) :: sdat_lai ! LAI input data stream + + character(len=*), parameter :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine lai_init(bounds) + ! + ! Initialize data stream information for LAI. + ! + ! !USES: + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use shr_stream_mod , only : shr_stream_file_null + use shr_string_mod , only : shr_string_listCreateField + use clm_nlUtilsMod , only : find_nlgroup_name + use ndepStreamMod , only : clm_domain_mct + use histFileMod , only : hist_addfld1d + use domainMod , only : ldomain + use controlMod , only : NLFilename + use lnd_set_decomp_and_domain , only : gsmap_global + ! + ! !ARGUMENTS: + implicit none + type(bounds_type), intent(in) :: bounds ! bounds + ! + ! !LOCAL VARIABLES: + integer :: stream_year_first_lai ! first year in Lai stream to use + integer :: stream_year_last_lai ! last year in Lai stream to use + integer :: model_year_align_lai ! align stream_year_first_lai with + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + type(mct_ggrid) :: dom_clm ! domain information + character(len=CL) :: stream_fldFileName_lai ! lai stream filename to read + character(len=CL) :: lai_mapalgo = 'bilinear' ! Mapping alogrithm + character(len=CL) :: lai_tintalgo = 'linear' ! Time interpolation alogrithm + character(len=CXX) :: fldList ! field string + character(*), parameter :: laiString = "LAI" ! base string for field string + integer , parameter :: numLaiFields = 16 ! number of fields to build field string + character(*), parameter :: subName = "('laidyn_init')" + !----------------------------------------------------------------------- + ! + ! deal with namelist variables here in init + ! + namelist /lai_streams/ & + stream_year_first_lai, & + stream_year_last_lai, & + model_year_align_lai, & + lai_mapalgo, & + stream_fldFileName_lai, & + lai_tintalgo + + ! Default values for namelist + stream_year_first_lai = 1 ! first year in stream to use + stream_year_last_lai = 1 ! last year in stream to use + model_year_align_lai = 1 ! align stream_year_first_lai with this model year + stream_fldFileName_lai = shr_stream_file_null + + ! Read lai_streams namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'lai_streams', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=lai_streams,iostat=nml_error) + if (nml_error /= 0) then + call endrun(subname // ':: ERROR reading lai_streams namelist') + end if + else + call endrun(subname // ':: ERROR finding lai_streams namelist') + end if + close(nu_nml) + endif + call shr_mpi_bcast(stream_year_first_lai , mpicom) + call shr_mpi_bcast(stream_year_last_lai , mpicom) + call shr_mpi_bcast(model_year_align_lai , mpicom) + call shr_mpi_bcast(stream_fldFileName_lai , mpicom) + call shr_mpi_bcast(lai_tintalgo , mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) 'lai_stream settings:' + write(iulog,*) ' stream_year_first_lai = ',stream_year_first_lai + write(iulog,*) ' stream_year_last_lai = ',stream_year_last_lai + write(iulog,*) ' model_year_align_lai = ',model_year_align_lai + write(iulog,*) ' stream_fldFileName_lai = ',trim(stream_fldFileName_lai) + write(iulog,*) ' lai_tintalgo = ',trim(lai_tintalgo) + endif + + call clm_domain_mct (bounds, dom_clm) + + ! create the field list for these lai fields...use in shr_strdata_create + fldList = shr_string_listCreateField( numLaiFields, laiString ) + + call shr_strdata_create(sdat_lai,name="laidyn", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_lai, & + yearLast=stream_year_last_lai, & + yearAlign=model_year_align_lai, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_lai), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/stream_fldFileName_lai/), & + fldListFile=fldList, & + fldListModel=fldList, & + fillalgo='none', & + mapalgo=lai_mapalgo, & + tintalgo=lai_tintalgo, & + calendar=get_calendar(), & + taxmode='cycle' ) + + if (masterproc) then + call shr_strdata_print(sdat_lai,'LAI data') + endif + + end subroutine lai_init + + !============================================================================== + subroutine lai_advance( bounds ) + ! + ! Advance LAI streams + ! + ! !USES: + use clm_time_manager, only : get_curr_date + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: g, ig ! Indices + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + !----------------------------------------------------------------------- + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + + call shr_strdata_advance(sdat_lai, mcdate, sec, mpicom, 'laidyn') + if ( .not. allocated(g_to_ig) )then + allocate (g_to_ig(bounds%begg:bounds%endg) ) + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + g_to_ig(g) = ig + end do + end if + + end subroutine lai_advance + + !============================================================================== + subroutine lai_interp(bounds, canopystate_inst) + ! + ! Interpolate data stream information for Lai. + ! + ! !USES: + use pftconMod , only : noveg + use CanopyStateType , only : canopystate_type + use PatchType , only : patch + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds + type(canopystate_type) , intent(inout) :: canopystate_inst + ! + ! !LOCAL VARIABLES: + integer :: ivt, p, ip, ig + character(len=CL) :: stream_var_name + !----------------------------------------------------------------------- + SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(sdat_lai%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_lai%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) + + do p = bounds%begp, bounds%endp + ivt = patch%itype(p) + ! Set lai for each gridcell/patch combination + if (ivt /= noveg) then + ! vegetated pft + write(stream_var_name,"(i6)") ivt + stream_var_name = 'LAI_'//trim(adjustl(stream_var_name)) + ip = mct_aVect_indexRA(sdat_lai%avs(1),trim(stream_var_name)) + ig = g_to_ig(patch%gridcell(p)) + canopystate_inst%tlai_patch(p) = sdat_lai%avs(1)%rAttr(ip,ig) + else + ! non-vegetated pft + canopystate_inst%tlai_patch(p) = 0._r8 + endif + end do + + end subroutine lai_interp + +end module LaiStreamMod diff --git a/src/cpl/mct/lnd_comp_mct.F90 b/src/cpl/mct/lnd_comp_mct.F90 new file mode 100644 index 0000000000..e50602a378 --- /dev/null +++ b/src/cpl/mct/lnd_comp_mct.F90 @@ -0,0 +1,632 @@ +module lnd_comp_mct + + !--------------------------------------------------------------------------- + ! !DESCRIPTION: + ! Interface of the active land model component of CESM the CLM (Community Land Model) + ! with the main CESM driver. This is a thin interface taking CESM driver information + ! in MCT (Model Coupling Toolkit) format and converting it to use by CLM. + ! + ! !uses: + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_sys_mod , only : shr_sys_flush + use shr_log_mod , only : errMsg => shr_log_errMsg + use mct_mod , only : mct_avect, mct_gsmap, mct_gGrid + use decompmod , only : bounds_type + use lnd_import_export, only : lnd_import, lnd_export + ! + ! !public member functions: + implicit none + private ! by default make data private + ! + ! !public member functions: + public :: lnd_init_mct ! clm initialization + public :: lnd_run_mct ! clm run phase + public :: lnd_final_mct ! clm finalization/cleanup + ! + ! !private member functions: + private :: lnd_domain_mct ! set the land model domain information + private :: lnd_handle_resume ! handle pause/resume signals from the coupler + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +!==================================================================================== +contains +!==================================================================================== + + subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename ) + ! + ! !DESCRIPTION: + ! Initialize land surface model and obtain relevant atmospheric model arrays + ! back from (i.e. albedos, surface temperature and snow cover over land). + ! + ! !USES: + use shr_kind_mod , only : shr_kind_cl + use abortutils , only : endrun + use clm_time_manager , only : get_nstep, set_timemgr_init + use clm_initializeMod, only : initialize1, initialize2 + use clm_instMod , only : water_inst, lnd2atm_inst, lnd2glc_inst + use clm_varctl , only : finidat, single_column, clm_varctl_set, iulog + use clm_varctl , only : inst_index, inst_suffix, inst_name + use clm_varorb , only : eccen, obliqr, lambm0, mvelpp + use controlMod , only : control_setNL + use decompMod , only : get_proc_bounds + use domainMod , only : ldomain + use shr_file_mod , only : shr_file_setLogUnit, shr_file_setLogLevel + use shr_file_mod , only : shr_file_getLogUnit, shr_file_getLogLevel + use shr_file_mod , only : shr_file_getUnit, shr_file_setIO + use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs + use seq_timemgr_mod , only : seq_timemgr_EClockGetData + use seq_infodata_mod , only : seq_infodata_type, seq_infodata_GetData, seq_infodata_PutData, & + seq_infodata_start_type_start, seq_infodata_start_type_cont, & + seq_infodata_start_type_brnch + use seq_comm_mct , only : seq_comm_suffix, seq_comm_inst, seq_comm_name + use seq_flds_mod , only : seq_flds_x2l_fields, seq_flds_l2x_fields + use spmdMod , only : masterproc, spmd_init + use clm_varctl , only : nsrStartup, nsrContinue, nsrBranch + use clm_cpl_indices , only : clm_cpl_indices_set + use mct_mod , only : mct_aVect_init, mct_aVect_zero, mct_gsMap, mct_gsMap_init + use decompMod , only : gindex_global + use lnd_set_decomp_and_domain, only : lnd_set_decomp_and_domain_from_surfrd, gsmap_global + use ESMF + ! + ! !ARGUMENTS: + type(ESMF_Clock), intent(inout) :: EClock ! Input synchronization clock + type(seq_cdata), intent(inout) :: cdata_l ! Input land-model driver data + type(mct_aVect), intent(inout) :: x2l_l, l2x_l ! land model import and export states + character(len=*), optional, intent(in) :: NLFilename ! Namelist filename to read + ! + ! !LOCAL VARIABLES: + integer :: LNDID ! Land identifyer + integer :: mpicom_lnd ! MPI communicator + type(mct_gsMap), pointer :: GSMap_lnd ! Land model MCT GS map + type(mct_gGrid), pointer :: dom_l ! Land model domain + type(seq_infodata_type), pointer :: infodata ! CESM driver level info data + integer :: lsize ! size of attribute vector + integer :: gsize ! global size + integer :: g,i,j ! indices + integer :: dtime_sync ! coupling time-step from the input synchronization clock + logical :: exists ! true if file exists + logical :: atm_aero ! Flag if aerosol data sent from atm model + real(r8) :: scmlat ! single-column latitude + real(r8) :: scmlon ! single-column longitude + character(len=SHR_KIND_CL) :: caseid ! case identifier name + character(len=SHR_KIND_CL) :: ctitle ! case description title + character(len=SHR_KIND_CL) :: starttype ! start-type (startup, continue, branch, hybrid) + character(len=SHR_KIND_CL) :: calendar ! calendar type name + character(len=SHR_KIND_CL) :: hostname ! hostname of machine running on + character(len=SHR_KIND_CL) :: version ! Model version + character(len=SHR_KIND_CL) :: username ! user running the model + integer :: nsrest ! clm restart type + integer :: ref_ymd ! reference date (YYYYMMDD) + integer :: ref_tod ! reference time of day (sec) + integer :: start_ymd ! start date (YYYYMMDD) + integer :: start_tod ! start time of day (sec) + logical :: brnch_retain_casename ! flag if should retain the case name on a branch start type + integer :: lbnum ! input to memory diagnostic + integer :: shrlogunit,shrloglev ! old values for log unit and log level + type(bounds_type) :: bounds ! bounds + logical :: noland + integer :: ni,nj + real(r8) , parameter :: rundef = -9999999._r8 + character(len=32), parameter :: sub = 'lnd_init_mct' + character(len=*), parameter :: format = "('("//trim(sub)//") :',A)" + !----------------------------------------------------------------------- + + ! Set cdata data + call seq_cdata_setptrs(cdata_l, ID=LNDID, mpicom=mpicom_lnd, & + gsMap=GSMap_lnd, dom=dom_l, infodata=infodata) + + ! Determine attriute vector indices + call clm_cpl_indices_set() + + ! Initialize clm MPI communicator + call spmd_init( mpicom_lnd, LNDID ) + +#if (defined _MEMTRACE) + if(masterproc) then + lbnum=1 + call memmon_dump_fort('memmon.out','lnd_init_mct:start::',lbnum) + endif +#endif + + inst_name = seq_comm_name(LNDID) + inst_index = seq_comm_inst(LNDID) + inst_suffix = seq_comm_suffix(LNDID) + ! Initialize io log unit + + call shr_file_getLogUnit (shrlogunit) + if (masterproc) then + inquire(file='lnd_modelio.nml'//trim(inst_suffix),exist=exists) + if (exists) then + iulog = shr_file_getUnit() + call shr_file_setIO('lnd_modelio.nml'//trim(inst_suffix),iulog) + end if + write(iulog,format) "CLM land model initialization" + else + iulog = shrlogunit + end if + + call shr_file_getLogLevel(shrloglev) + call shr_file_setLogUnit (iulog) + + ! Use infodata to set orbital values + call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, & + orb_lambm0=lambm0, orb_obliqr=obliqr ) + + ! Consistency check on namelist filename + call control_setNL("lnd_in"//trim(inst_suffix)) + + ! Initialize clm + ! initialize1 reads namelists + ! decomp and domain are set in lnd_set_decomp_and_domain_from_surfrd + ! initialize2 performs the rest of initialization + call seq_timemgr_EClockGetData(EClock, & + start_ymd=start_ymd, & + start_tod=start_tod, ref_ymd=ref_ymd, & + ref_tod=ref_tod, & + calendar=calendar, & + dtime=dtime_sync) + if (masterproc) then + write(iulog,*)'dtime = ',dtime_sync + end if + call seq_infodata_GetData(infodata, case_name=caseid, & + case_desc=ctitle, single_column=single_column, & + scmlat=scmlat, scmlon=scmlon, & + brnch_retain_casename=brnch_retain_casename, & + start_type=starttype, model_version=version, & + hostname=hostname, username=username ) + + ! Single Column + if ( single_column .and. (scmlat == rundef .or. scmlon == rundef ) ) then + call endrun(msg=' ERROR:: single column mode on -- but scmlat and scmlon are NOT set'//& + errMsg(sourcefile, __LINE__)) + end if + + ! Note that we assume that CTSM's internal dtime matches the coupling time step. + ! i.e., we currently do NOT allow sub-cycling within a coupling time step. + call set_timemgr_init( calendar_in=calendar, start_ymd_in=start_ymd, start_tod_in=start_tod, & + ref_ymd_in=ref_ymd, ref_tod_in=ref_tod, dtime_in=dtime_sync) + + if ( trim(starttype) == trim(seq_infodata_start_type_start)) then + nsrest = nsrStartup + else if (trim(starttype) == trim(seq_infodata_start_type_cont) ) then + nsrest = nsrContinue + else if (trim(starttype) == trim(seq_infodata_start_type_brnch)) then + nsrest = nsrBranch + else + call endrun( sub//' ERROR: unknown starttype' ) + end if + + ! set default values for run control variables + call clm_varctl_set(caseid_in=caseid, ctitle_in=ctitle, & + brnch_retain_casename_in=brnch_retain_casename, & + single_column_in=single_column, scmlat_in=scmlat, & + scmlon_in=scmlon, nsrest_in=nsrest, version_in=version, & + hostname_in=hostname, username_in=username) + + ! Read namelists + call initialize1(dtime=dtime_sync) + + ! Initialize decomposition and domain (ldomain) type + call lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj) + + ! If no land then exit out of initialization + if ( noland ) then + + call seq_infodata_PutData( infodata, lnd_present =.false.) + call seq_infodata_PutData( infodata, lnd_prognostic=.false.) + + else + + ! Determine if aerosol and dust deposition come from atmosphere component + call seq_infodata_GetData(infodata, atm_aero=atm_aero ) + if ( .not. atm_aero )then + call endrun( sub//' ERROR: atmosphere model MUST send aerosols to CLM' ) + end if + + ! Initialize clm gsMap, clm domain and clm attribute vectors + call get_proc_bounds( bounds ) + lsize = bounds%endg - bounds%begg + 1 + gsize = ldomain%ni * ldomain%nj + call mct_gsMap_init( gsMap_lnd, gindex_global, mpicom_lnd, LNDID, lsize, gsize ) + gsmap_global => gsmap_lnd ! module variable in lnd_set_decomp_and_domain + call lnd_domain_mct( bounds, lsize, gsMap_lnd, dom_l ) + call mct_aVect_init(x2l_l, rList=seq_flds_x2l_fields, lsize=lsize) + call mct_aVect_zero(x2l_l) + call mct_aVect_init(l2x_l, rList=seq_flds_l2x_fields, lsize=lsize) + call mct_aVect_zero(l2x_l) + + ! Finish initializing clm + call initialize2(ni,nj) + + ! Create land export state + call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr) + + ! Fill in infodata settings + call seq_infodata_PutData(infodata, lnd_prognostic=.true.) + call seq_infodata_PutData(infodata, lnd_nx=ldomain%ni, lnd_ny=ldomain%nj) + call lnd_handle_resume( cdata_l ) + + ! Reset shr logging to original values + call shr_file_setLogUnit (shrlogunit) + call shr_file_setLogLevel(shrloglev) + +#if (defined _MEMTRACE) + if(masterproc) then + write(iulog,*) TRIM(Sub) // ':end::' + lbnum=1 + call memmon_dump_fort('memmon.out','lnd_int_mct:end::',lbnum) + call memmon_reset_addr() + endif +#endif + end if + + end subroutine lnd_init_mct + + !==================================================================================== + subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l) + ! + ! !DESCRIPTION: + ! Run clm model + ! + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8 + use clm_instMod , only : water_inst, lnd2atm_inst, atm2lnd_inst, lnd2glc_inst, glc2lnd_inst + use clm_driver , only : clm_drv + use clm_time_manager, only : get_curr_date, get_nstep, get_curr_calday, get_step_size + use clm_time_manager, only : advance_timestep, update_rad_dtime + use decompMod , only : get_proc_bounds + use abortutils , only : endrun + use clm_varctl , only : iulog + use clm_varorb , only : eccen, obliqr, lambm0, mvelpp + use shr_file_mod , only : shr_file_setLogUnit, shr_file_setLogLevel + use shr_file_mod , only : shr_file_getLogUnit, shr_file_getLogLevel + use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs + use seq_timemgr_mod , only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn + use seq_timemgr_mod , only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync + use seq_infodata_mod, only : seq_infodata_type, seq_infodata_GetData + use spmdMod , only : masterproc, mpicom + use perf_mod , only : t_startf, t_stopf, t_barrierf + use shr_orb_mod , only : shr_orb_decl + use ESMF + ! + ! !ARGUMENTS: + type(ESMF_Clock) , intent(inout) :: EClock ! Input synchronization clock from driver + type(seq_cdata) , intent(inout) :: cdata_l ! Input driver data for land model + type(mct_aVect) , intent(inout) :: x2l_l ! Import state to land model + type(mct_aVect) , intent(inout) :: l2x_l ! Export state from land model + ! + ! !LOCAL VARIABLES: + integer :: ymd_sync ! Sync date (YYYYMMDD) + integer :: yr_sync ! Sync current year + integer :: mon_sync ! Sync current month + integer :: day_sync ! Sync current day + integer :: tod_sync ! Sync current time of day (sec) + integer :: ymd ! CLM current date (YYYYMMDD) + integer :: yr ! CLM current year + integer :: mon ! CLM current month + integer :: day ! CLM current day + integer :: tod ! CLM current time of day (sec) + integer :: dtime ! time step increment (sec) + integer :: nstep ! time step index + logical :: rstwr_sync ! .true. ==> write restart file before returning + logical :: rstwr ! .true. ==> write restart file before returning + logical :: nlend_sync ! Flag signaling last time-step + logical :: nlend ! .true. ==> last time-step + logical :: dosend ! true => send data back to driver + logical :: doalb ! .true. ==> do albedo calculation on this time step + logical :: rof_prognostic ! .true. => running with a prognostic ROF model + logical :: glc_present ! .true. => running with a non-stub GLC model + real(r8) :: nextsw_cday ! calday from clock of next radiation computation + real(r8) :: caldayp1 ! clm calday plus dtime offset + integer :: shrlogunit,shrloglev ! old values for share log unit and log level + integer :: lbnum ! input to memory diagnostic + integer :: g,i,lsize ! counters + real(r8) :: calday ! calendar day for nstep + real(r8) :: declin ! solar declination angle in radians for nstep + real(r8) :: declinp1 ! solar declination angle in radians for nstep+1 + real(r8) :: eccf ! earth orbit eccentricity factor + real(r8) :: recip ! reciprical + logical,save :: first_call = .true. ! first call work + type(seq_infodata_type),pointer :: infodata ! CESM information from the driver + type(mct_gGrid), pointer :: dom_l ! Land model domain data + type(bounds_type) :: bounds ! bounds + character(len=32) :: rdate ! date char string for restart file names + character(len=32), parameter :: sub = "lnd_run_mct" + !--------------------------------------------------------------------------- + + ! Determine processor bounds + + call get_proc_bounds(bounds) + +#if (defined _MEMTRACE) + if(masterproc) then + lbnum=1 + call memmon_dump_fort('memmon.out','lnd_run_mct:start::',lbnum) + endif +#endif + + ! Reset shr logging to my log file + call shr_file_getLogUnit (shrlogunit) + call shr_file_getLogLevel(shrloglev) + call shr_file_setLogUnit (iulog) + + ! Determine time of next atmospheric shortwave calculation + call seq_cdata_setptrs(cdata_l, infodata=infodata, dom=dom_l) + call seq_timemgr_EClockGetData(EClock, & + curr_ymd=ymd, curr_tod=tod_sync, & + curr_yr=yr_sync, curr_mon=mon_sync, curr_day=day_sync) + call seq_infodata_GetData(infodata, nextsw_cday=nextsw_cday ) + + dtime = get_step_size() + + ! Handle pause/resume signals from coupler + call lnd_handle_resume( cdata_l ) + + write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync,mon_sync,day_sync,tod_sync + nlend_sync = seq_timemgr_StopAlarmIsOn( EClock ) + rstwr_sync = seq_timemgr_RestartAlarmIsOn( EClock ) + + ! Determine if we're running with a prognostic ROF model, and if we're running with a + ! non-stub GLC model. These won't change throughout the run, but we can't count on + ! their being set in initialization, so need to get them in the run method. + + call seq_infodata_GetData( infodata, & + rof_prognostic=rof_prognostic, & + glc_present=glc_present) + + ! Map MCT to land data type + ! Perform downscaling if appropriate + + + ! Map to clm (only when state and/or fluxes need to be updated) + + call t_startf ('lc_lnd_import') + call lnd_import( bounds, & + x2l = x2l_l%rattr, & + glc_present = glc_present, & + atm2lnd_inst = atm2lnd_inst, & + glc2lnd_inst = glc2lnd_inst, & + wateratm2lndbulk_inst = water_inst%wateratm2lndbulk_inst) + call t_stopf ('lc_lnd_import') + + ! Use infodata to set orbital values if updated mid-run + + call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, & + orb_lambm0=lambm0, orb_obliqr=obliqr ) + + ! Loop over time steps in coupling interval + + dosend = .false. + do while(.not. dosend) + + ! Determine if dosend + ! When time is not updated at the beginning of the loop - then return only if + ! are in sync with clock before time is updated + ! + ! NOTE(wjs, 2020-03-09) I think the do while (.not. dosend) loop only is important + ! for the first time step (when we run 2 steps). After that, we now assume that we + ! run one time step per coupling interval (based on setting the model's dtime from + ! the driver). (According to Mariana Vertenstein, sub-cycling (running multiple + ! land model time steps per coupling interval) used to be supported, but hasn't + ! been fully supported for a long time.) We may want to rework this logic to make + ! this more explicit, or - ideally - get rid of this extra time step at the start + ! of the run, at which point I think we could do away with this looping entirely. + + call get_curr_date( yr, mon, day, tod ) + ymd = yr*10000 + mon*100 + day + tod = tod + dosend = (seq_timemgr_EClockDateInSync( EClock, ymd, tod)) + + ! Determine doalb based on nextsw_cday sent from atm model + + nstep = get_nstep() + caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.) + if (nstep == 0) then + doalb = .false. + else if (nstep == 1) then + doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8) + else + doalb = (nextsw_cday >= -0.5_r8) + end if + call update_rad_dtime(doalb) + + ! Determine if time to write restart and stop + + rstwr = .false. + if (rstwr_sync .and. dosend) rstwr = .true. + nlend = .false. + if (nlend_sync .and. dosend) nlend = .true. + + ! Run clm + + call t_barrierf('sync_clm_run1', mpicom) + call t_startf ('clm_run') + call t_startf ('shr_orb_decl') + calday = get_curr_calday(reuse_day_365_for_day_366=.true.) + call shr_orb_decl( calday , eccen, mvelpp, lambm0, obliqr, declin , eccf ) + call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf ) + call t_stopf ('shr_orb_decl') + call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic) + call t_stopf ('clm_run') + + ! Create l2x_l export state - add river runoff input to l2x_l if appropriate + + call t_startf ('lc_lnd_export') + call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr) + call t_stopf ('lc_lnd_export') + + ! Advance clm time step + + call t_startf ('lc_clm2_adv_timestep') + call advance_timestep() + call t_stopf ('lc_clm2_adv_timestep') + + end do + + ! Check that internal clock is in sync with master clock + + call get_curr_date( yr, mon, day, tod, offset=-dtime ) + ymd = yr*10000 + mon*100 + day + tod = tod + if ( .not. seq_timemgr_EClockDateInSync( EClock, ymd, tod ) )then + call seq_timemgr_EclockGetData( EClock, curr_ymd=ymd_sync, curr_tod=tod_sync ) + write(iulog,*)' clm ymd=',ymd ,' clm tod= ',tod + write(iulog,*)'sync ymd=',ymd_sync,' sync tod= ',tod_sync + call endrun( sub//":: CLM clock not in sync with Master Sync clock" ) + end if + + ! Reset shr logging to my original values + + call shr_file_setLogUnit (shrlogunit) + call shr_file_setLogLevel(shrloglev) + +#if (defined _MEMTRACE) + if(masterproc) then + lbnum=1 + call memmon_dump_fort('memmon.out','lnd_run_mct:end::',lbnum) + call memmon_reset_addr() + endif +#endif + + first_call = .false. + + end subroutine lnd_run_mct + + !==================================================================================== + subroutine lnd_final_mct( EClock, cdata_l, x2l_l, l2x_l) + ! + ! !DESCRIPTION: + ! Finalize land surface model + + use seq_cdata_mod ,only : seq_cdata, seq_cdata_setptrs + use seq_timemgr_mod ,only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn + use seq_timemgr_mod ,only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync + use esmf + ! + ! !ARGUMENTS: + type(ESMF_Clock) , intent(inout) :: EClock ! Input synchronization clock from driver + type(seq_cdata) , intent(inout) :: cdata_l ! Input driver data for land model + type(mct_aVect) , intent(inout) :: x2l_l ! Import state to land model + type(mct_aVect) , intent(inout) :: l2x_l ! Export state from land model + !--------------------------------------------------------------------------- + + ! fill this in + end subroutine lnd_final_mct + + !==================================================================================== + subroutine lnd_domain_mct( bounds, lsize, gsMap_l, dom_l ) + ! + ! !DESCRIPTION: + ! Send the land model domain information to the coupler + ! + ! !USES: + use clm_varcon , only: re + use domainMod , only: ldomain + use spmdMod , only: iam + use mct_mod , only: mct_gGrid_importIAttr + use mct_mod , only: mct_gGrid_importRAttr, mct_gGrid_init, mct_gsMap_orderedPoints + use seq_flds_mod, only: seq_flds_dom_coord, seq_flds_dom_other + ! + ! !ARGUMENTS: + type(bounds_type), intent(in) :: bounds ! bounds + integer , intent(in) :: lsize ! land model domain data size + type(mct_gsMap), intent(inout) :: gsMap_l ! Output land model MCT GS map + type(mct_ggrid), intent(out) :: dom_l ! Output domain information for land model + ! + ! Local Variables + integer :: g,i,j ! index + real(r8), pointer :: data(:) ! temporary + integer , pointer :: idata(:) ! temporary + !--------------------------------------------------------------------------- + ! + ! Initialize mct domain type + ! lat/lon in degrees, area in radians^2, mask is 1 (land), 0 (non-land) + ! Note that in addition land carries around landfrac for the purposes of domain checking + ! + call mct_gGrid_init( GGrid=dom_l, CoordChars=trim(seq_flds_dom_coord), & + OtherChars=trim(seq_flds_dom_other), lsize=lsize ) + ! + ! Allocate memory + ! + allocate(data(lsize)) + ! + ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT + ! + call mct_gsMap_orderedPoints(gsMap_l, iam, idata) + call mct_gGrid_importIAttr(dom_l,'GlobGridNum',idata,lsize) + ! + ! Determine domain (numbering scheme is: West to East and South to North to South pole) + ! Initialize attribute vector with special value + ! + data(:) = -9999.0_R8 + call mct_gGrid_importRAttr(dom_l,"lat" ,data,lsize) + call mct_gGrid_importRAttr(dom_l,"lon" ,data,lsize) + call mct_gGrid_importRAttr(dom_l,"area" ,data,lsize) + call mct_gGrid_importRAttr(dom_l,"aream",data,lsize) + data(:) = 0.0_R8 + call mct_gGrid_importRAttr(dom_l,"mask" ,data,lsize) + ! + ! Fill in correct values for domain components + ! Note aream will be filled in in the atm-lnd mapper + ! + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = ldomain%lonc(g) + end do + call mct_gGrid_importRattr(dom_l,"lon",data,lsize) + + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = ldomain%latc(g) + end do + call mct_gGrid_importRattr(dom_l,"lat",data,lsize) + + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = ldomain%area(g)/(re*re) + end do + call mct_gGrid_importRattr(dom_l,"area",data,lsize) + + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = real(ldomain%mask(g), r8) + end do + call mct_gGrid_importRattr(dom_l,"mask",data,lsize) + + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = real(ldomain%frac(g), r8) + end do + call mct_gGrid_importRattr(dom_l,"frac",data,lsize) + + deallocate(data) + deallocate(idata) + + end subroutine lnd_domain_mct + + !==================================================================================== + subroutine lnd_handle_resume( cdata_l ) + ! + ! !DESCRIPTION: + ! Handle resume signals for Data Assimilation (DA) + ! + ! !USES: + use clm_time_manager , only : update_DA_nstep + use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs + implicit none + ! !ARGUMENTS: + type(seq_cdata), intent(inout) :: cdata_l ! Input land-model driver data + ! !LOCAL VARIABLES: + logical :: resume_from_data_assim ! flag if we are resuming after data assimulation was done + !--------------------------------------------------------------------------- + + ! Check to see if restart was modified and we are resuming from data + ! assimilation + call seq_cdata_setptrs(cdata_l, post_assimilation=resume_from_data_assim) + if ( resume_from_data_assim ) call update_DA_nstep() + + end subroutine lnd_handle_resume + +end module lnd_comp_mct diff --git a/src/cpl/mct/lnd_import_export.F90 b/src/cpl/mct/lnd_import_export.F90 new file mode 100644 index 0000000000..537abd49d9 --- /dev/null +++ b/src/cpl/mct/lnd_import_export.F90 @@ -0,0 +1,354 @@ +module lnd_import_export + + use shr_kind_mod , only: r8 => shr_kind_r8, cl=>shr_kind_cl + use abortutils , only: endrun + use decompmod , only: bounds_type, subgrid_level_gridcell + use lnd2atmType , only: lnd2atm_type + use lnd2glcMod , only: lnd2glc_type + use atm2lndType , only: atm2lnd_type + use glc2lndMod , only: glc2lnd_type + use Waterlnd2atmBulkType , only: waterlnd2atmbulk_type + use Wateratm2lndBulkType , only: wateratm2lndbulk_type + use clm_cpl_indices + use GridcellType , only : grc + ! + implicit none + !=============================================================================== + +contains + + !=============================================================================== + subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst, wateratm2lndbulk_inst) + + !--------------------------------------------------------------------------- + ! !DESCRIPTION: + ! Convert the input data from the coupler to the land model + ! + ! !USES: + use seq_flds_mod , only: seq_flds_x2l_fields + use clm_varctl , only: co2_type, co2_ppmv, iulog, use_c13 + use clm_varctl , only: ndep_from_cpl + use clm_varcon , only: c13ratio + use domainMod , only: ldomain + use lnd_import_export_utils, only : derive_quantities, check_for_errors, check_for_nans + ! + ! !ARGUMENTS: + type(bounds_type) , intent(in) :: bounds ! bounds + real(r8) , intent(in) :: x2l(:,:) ! driver import state to land model + logical , intent(in) :: glc_present ! .true. => running with a non-stub GLC model + type(atm2lnd_type) , intent(inout) :: atm2lnd_inst ! clm internal input data type + type(glc2lnd_type) , intent(inout) :: glc2lnd_inst ! clm internal input data type + type(wateratm2lndbulk_type), intent(inout) :: wateratm2lndbulk_inst ! clm internal input data type + ! + ! !LOCAL VARIABLES: + integer :: begg, endg ! bounds + integer :: g,i,k,nstep,ier ! indices, number of steps, and error code + real(r8) :: qsat_kg_kg ! saturation specific humidity (kg/kg) + real(r8) :: forc_pbot ! atmospheric pressure (Pa) + real(r8) :: forc_rainc(bounds%begg:bounds%endg) ! rainxy Atm flux mm/s + real(r8) :: forc_rainl(bounds%begg:bounds%endg) ! rainxy Atm flux mm/s + real(r8) :: forc_snowc(bounds%begg:bounds%endg) ! snowfxy Atm flux mm/s + real(r8) :: forc_snowl(bounds%begg:bounds%endg) ! snowfxl Atm flux mm/s + real(r8) :: co2_ppmv_diag ! temporary + real(r8) :: co2_ppmv_prog ! temporary + real(r8) :: co2_ppmv_val ! temporary + integer :: co2_type_idx ! integer flag for co2_type options + character(len=32) :: fname ! name of field that is NaN + character(len=32), parameter :: sub = 'lnd_import' + + !--------------------------------------------------------------------------- + + ! Set bounds + begg = bounds%begg; endg = bounds%endg + + co2_type_idx = 0 + if (co2_type == 'prognostic') then + co2_type_idx = 1 + else if (co2_type == 'diagnostic') then + co2_type_idx = 2 + end if + if (co2_type == 'prognostic' .and. index_x2l_Sa_co2prog == 0) then + call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2prog for co2_type equal to prognostic' ) + else if (co2_type == 'diagnostic' .and. index_x2l_Sa_co2diag == 0) then + call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2diag for co2_type equal to diagnostic' ) + end if + + ! Note that the precipitation fluxes received from the coupler + ! are in units of kg/s/m^2. To convert these precipitation rates + ! in units of mm/sec, one must divide by 1000 kg/m^3 and multiply + ! by 1000 mm/m resulting in an overall factor of unity. + ! Below the units are therefore given in mm/s. + + do g = begg,endg + i = 1 + (g - begg) + + ! Determine flooding input, sign convention is positive downward and + ! hierarchy is atm/glc/lnd/rof/ice/ocn. so water sent from rof to land is negative, + ! change the sign to indicate addition of water to system. + + wateratm2lndbulk_inst%forc_flood_grc(g) = -x2l(index_x2l_Flrr_flood,i) + + wateratm2lndbulk_inst%volr_grc(g) = x2l(index_x2l_Flrr_volr,i) * (ldomain%area(g) * 1.e6_r8) + wateratm2lndbulk_inst%volrmch_grc(g)= x2l(index_x2l_Flrr_volrmch,i) * (ldomain%area(g) * 1.e6_r8) + + ! Determine required receive fields + + atm2lnd_inst%forc_hgt_grc(g) = x2l(index_x2l_Sa_z,i) ! zgcmxy Atm state m + atm2lnd_inst%forc_topo_grc(g) = x2l(index_x2l_Sa_topo,i) ! Atm surface height (m) + atm2lnd_inst%forc_u_grc(g) = x2l(index_x2l_Sa_u,i) ! forc_uxy Atm state m/s + atm2lnd_inst%forc_v_grc(g) = x2l(index_x2l_Sa_v,i) ! forc_vxy Atm state m/s + atm2lnd_inst%forc_solad_not_downscaled_grc(g,2) = x2l(index_x2l_Faxa_swndr,i) ! forc_sollxy Atm flux W/m^2 + atm2lnd_inst%forc_solad_not_downscaled_grc(g,1) = x2l(index_x2l_Faxa_swvdr,i) ! forc_solsxy Atm flux W/m^2 + atm2lnd_inst%forc_solai_grc(g,2) = x2l(index_x2l_Faxa_swndf,i) ! forc_solldxy Atm flux W/m^2 + atm2lnd_inst%forc_solai_grc(g,1) = x2l(index_x2l_Faxa_swvdf,i) ! forc_solsdxy Atm flux W/m^2 + + atm2lnd_inst%forc_th_not_downscaled_grc(g) = x2l(index_x2l_Sa_ptem,i) ! forc_thxy Atm state K + wateratm2lndbulk_inst%forc_q_not_downscaled_grc(g) = x2l(index_x2l_Sa_shum,i) ! forc_qxy Atm state kg/kg + atm2lnd_inst%forc_pbot_not_downscaled_grc(g) = x2l(index_x2l_Sa_pbot,i) ! ptcmxy Atm state Pa + atm2lnd_inst%forc_t_not_downscaled_grc(g) = x2l(index_x2l_Sa_tbot,i) ! forc_txy Atm state K + atm2lnd_inst%forc_lwrad_not_downscaled_grc(g) = x2l(index_x2l_Faxa_lwdn,i) ! flwdsxy Atm flux W/m^2 + + forc_rainc(g) = x2l(index_x2l_Faxa_rainc,i) ! mm/s + forc_rainl(g) = x2l(index_x2l_Faxa_rainl,i) ! mm/s + forc_snowc(g) = x2l(index_x2l_Faxa_snowc,i) ! mm/s + forc_snowl(g) = x2l(index_x2l_Faxa_snowl,i) ! mm/s + + ! atmosphere coupling, for prognostic/prescribed aerosols + atm2lnd_inst%forc_aer_grc(g,1) = x2l(index_x2l_Faxa_bcphidry,i) + atm2lnd_inst%forc_aer_grc(g,2) = x2l(index_x2l_Faxa_bcphodry,i) + atm2lnd_inst%forc_aer_grc(g,3) = x2l(index_x2l_Faxa_bcphiwet,i) + atm2lnd_inst%forc_aer_grc(g,4) = x2l(index_x2l_Faxa_ocphidry,i) + atm2lnd_inst%forc_aer_grc(g,5) = x2l(index_x2l_Faxa_ocphodry,i) + atm2lnd_inst%forc_aer_grc(g,6) = x2l(index_x2l_Faxa_ocphiwet,i) + atm2lnd_inst%forc_aer_grc(g,7) = x2l(index_x2l_Faxa_dstwet1,i) + atm2lnd_inst%forc_aer_grc(g,8) = x2l(index_x2l_Faxa_dstdry1,i) + atm2lnd_inst%forc_aer_grc(g,9) = x2l(index_x2l_Faxa_dstwet2,i) + atm2lnd_inst%forc_aer_grc(g,10) = x2l(index_x2l_Faxa_dstdry2,i) + atm2lnd_inst%forc_aer_grc(g,11) = x2l(index_x2l_Faxa_dstwet3,i) + atm2lnd_inst%forc_aer_grc(g,12) = x2l(index_x2l_Faxa_dstdry3,i) + atm2lnd_inst%forc_aer_grc(g,13) = x2l(index_x2l_Faxa_dstwet4,i) + atm2lnd_inst%forc_aer_grc(g,14) = x2l(index_x2l_Faxa_dstdry4,i) + + if (index_x2l_Sa_methane /= 0) then + atm2lnd_inst%forc_pch4_grc(g) = x2l(index_x2l_Sa_methane,i) + endif + + !-------------------------- + ! Check for nans from coupler + !-------------------------- + + call check_for_nans(x2l(:,i), fname, begg, "x2l") + + end do + + !-------------------------- + ! Derived quantities for required fields + ! and corresponding error checks + !-------------------------- + + call derive_quantities(bounds, atm2lnd_inst, wateratm2lndbulk_inst, & + forc_rainc, forc_rainl, forc_snowc, forc_snowl) + + call check_for_errors(bounds, atm2lnd_inst, wateratm2lndbulk_inst) + + ! Determine derived quantities for optional fields + ! Note that the following does unit conversions from ppmv to partial pressures (Pa) + ! Note that forc_pbot is in Pa + + do g = begg,endg + i = 1 + (g - begg) + + forc_pbot = atm2lnd_inst%forc_pbot_not_downscaled_grc(g) + + ! Determine optional receive fields + if (index_x2l_Sa_co2prog /= 0) then + co2_ppmv_prog = x2l(index_x2l_Sa_co2prog,i) ! co2 atm state prognostic + else + co2_ppmv_prog = co2_ppmv + end if + if (index_x2l_Sa_co2diag /= 0) then + co2_ppmv_diag = x2l(index_x2l_Sa_co2diag,i) ! co2 atm state diagnostic + else + co2_ppmv_diag = co2_ppmv + end if + + if (co2_type_idx == 1) then + co2_ppmv_val = co2_ppmv_prog + else if (co2_type_idx == 2) then + co2_ppmv_val = co2_ppmv_diag + else + co2_ppmv_val = co2_ppmv + end if + if ( (co2_ppmv_val < 10.0_r8) .or. (co2_ppmv_val > 15000.0_r8) )then + call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, & + msg = sub//' ERROR: CO2 is outside of an expected range' ) + end if + atm2lnd_inst%forc_pco2_grc(g) = co2_ppmv_val * 1.e-6_r8 * forc_pbot + if (use_c13) then + atm2lnd_inst%forc_pc13o2_grc(g) = co2_ppmv_val * c13ratio * 1.e-6_r8 * forc_pbot + end if + + if (ndep_from_cpl) then + ! The coupler is sending ndep in units if kgN/m2/s - and clm uses units of gN/m2/sec - so the + ! following conversion needs to happen + atm2lnd_inst%forc_ndep_grc(g) = (x2l(index_x2l_Faxa_nhx, i) + x2l(index_x2l_faxa_noy, i))*1000._r8 + end if + + end do + + call glc2lnd_inst%set_glc2lnd_fields_mct( & + bounds = bounds, & + glc_present = glc_present, & + ! NOTE(wjs, 2017-12-13) the x2l argument doesn't have the typical bounds + ! subsetting (bounds%begg:bounds%endg). This mirrors the lack of these bounds in + ! the call to lnd_import from lnd_run_mct. This is okay as long as this code is + ! outside a clump loop. + x2l = x2l, & + index_x2l_Sg_ice_covered = index_x2l_Sg_ice_covered, & + index_x2l_Sg_topo = index_x2l_Sg_topo, & + index_x2l_Flgg_hflx = index_x2l_Flgg_hflx, & + index_x2l_Sg_icemask = index_x2l_Sg_icemask, & + index_x2l_Sg_icemask_coupled_fluxes = index_x2l_Sg_icemask_coupled_fluxes) + + end subroutine lnd_import + + !=============================================================================== + + subroutine lnd_export( bounds, waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x) + + !--------------------------------------------------------------------------- + ! !DESCRIPTION: + ! Convert the data to be sent from the clm model to the coupler + ! + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8 + use seq_flds_mod , only : seq_flds_l2x_fields + use clm_varctl , only : iulog + use shr_drydep_mod , only : n_drydep + use shr_megan_mod , only : shr_megan_mechcomps_n + use shr_fire_emis_mod , only : shr_fire_emis_mechcomps_n + use lnd_import_export_utils, only : check_for_nans + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds ! bounds + type(lnd2atm_type), intent(inout) :: lnd2atm_inst ! clm land to atmosphere exchange data type + type(lnd2glc_type), intent(inout) :: lnd2glc_inst ! clm land to atmosphere exchange data type + type(waterlnd2atmbulk_type), intent(in) :: waterlnd2atmbulk_inst + real(r8) , intent(out) :: l2x(:,:)! land to coupler export state on land grid + ! + ! !LOCAL VARIABLES: + integer :: begg, endg ! bounds + integer :: g,i,k ! indices + integer :: ier ! error status + integer :: nstep ! time step index + integer :: dtime ! time step + integer :: num ! counter + character(len=32) :: fname ! name of field that is NaN + character(len=32), parameter :: sub = 'lnd_export' + !--------------------------------------------------------------------------- + + ! Set bounds + begg = bounds%begg; endg = bounds%endg + + ! cesm sign convention is that fluxes are positive downward + + l2x(:,:) = 0.0_r8 + + do g = begg,endg + i = 1 + (g-begg) + l2x(index_l2x_Sl_t,i) = lnd2atm_inst%t_rad_grc(g) + l2x(index_l2x_Sl_snowh,i) = waterlnd2atmbulk_inst%h2osno_grc(g) + l2x(index_l2x_Sl_avsdr,i) = lnd2atm_inst%albd_grc(g,1) + l2x(index_l2x_Sl_anidr,i) = lnd2atm_inst%albd_grc(g,2) + l2x(index_l2x_Sl_avsdf,i) = lnd2atm_inst%albi_grc(g,1) + l2x(index_l2x_Sl_anidf,i) = lnd2atm_inst%albi_grc(g,2) + l2x(index_l2x_Sl_tref,i) = lnd2atm_inst%t_ref2m_grc(g) + l2x(index_l2x_Sl_qref,i) = waterlnd2atmbulk_inst%q_ref2m_grc(g) + l2x(index_l2x_Sl_u10,i) = lnd2atm_inst%u_ref10m_grc(g) + l2x(index_l2x_Fall_taux,i) = -lnd2atm_inst%taux_grc(g) + l2x(index_l2x_Fall_tauy,i) = -lnd2atm_inst%tauy_grc(g) + l2x(index_l2x_Fall_lat,i) = -lnd2atm_inst%eflx_lh_tot_grc(g) + l2x(index_l2x_Fall_sen,i) = -lnd2atm_inst%eflx_sh_tot_grc(g) + l2x(index_l2x_Fall_lwup,i) = -lnd2atm_inst%eflx_lwrad_out_grc(g) + l2x(index_l2x_Fall_evap,i) = -waterlnd2atmbulk_inst%qflx_evap_tot_grc(g) + l2x(index_l2x_Fall_swnet,i) = lnd2atm_inst%fsa_grc(g) + if (index_l2x_Fall_fco2_lnd /= 0) then + l2x(index_l2x_Fall_fco2_lnd,i) = -lnd2atm_inst%net_carbon_exchange_grc(g) + end if + + ! Additional fields for DUST, PROGSSLT, dry-deposition and VOC + ! These are now standard fields, but the check on the index makes sure the driver handles them + if (index_l2x_Sl_ram1 /= 0 ) l2x(index_l2x_Sl_ram1,i) = lnd2atm_inst%ram1_grc(g) + if (index_l2x_Sl_fv /= 0 ) l2x(index_l2x_Sl_fv,i) = lnd2atm_inst%fv_grc(g) + if (index_l2x_Sl_soilw /= 0 ) l2x(index_l2x_Sl_soilw,i) = waterlnd2atmbulk_inst%h2osoi_vol_grc(g,1) + if (index_l2x_Fall_flxdst1 /= 0 ) l2x(index_l2x_Fall_flxdst1,i)= -lnd2atm_inst%flxdst_grc(g,1) + if (index_l2x_Fall_flxdst2 /= 0 ) l2x(index_l2x_Fall_flxdst2,i)= -lnd2atm_inst%flxdst_grc(g,2) + if (index_l2x_Fall_flxdst3 /= 0 ) l2x(index_l2x_Fall_flxdst3,i)= -lnd2atm_inst%flxdst_grc(g,3) + if (index_l2x_Fall_flxdst4 /= 0 ) l2x(index_l2x_Fall_flxdst4,i)= -lnd2atm_inst%flxdst_grc(g,4) + + + ! for dry dep velocities + if (index_l2x_Sl_ddvel /= 0 ) then + l2x(index_l2x_Sl_ddvel:index_l2x_Sl_ddvel+n_drydep-1,i) = & + lnd2atm_inst%ddvel_grc(g,:n_drydep) + end if + + ! for MEGAN VOC emis fluxes + if (index_l2x_Fall_flxvoc /= 0 ) then + l2x(index_l2x_Fall_flxvoc:index_l2x_Fall_flxvoc+shr_megan_mechcomps_n-1,i) = & + -lnd2atm_inst%flxvoc_grc(g,:shr_megan_mechcomps_n) + end if + + + ! for fire emis fluxes + if (index_l2x_Fall_flxfire /= 0 ) then + l2x(index_l2x_Fall_flxfire:index_l2x_Fall_flxfire+shr_fire_emis_mechcomps_n-1,i) = & + -lnd2atm_inst%fireflx_grc(g,:shr_fire_emis_mechcomps_n) + l2x(index_l2x_Sl_ztopfire,i) = lnd2atm_inst%fireztop_grc(g) + end if + + if (index_l2x_Fall_methane /= 0) then + l2x(index_l2x_Fall_methane,i) = -lnd2atm_inst%ch4_surf_flux_tot_grc(g) + endif + + ! sign convention is positive downward with + ! hierarchy of atm/glc/lnd/rof/ice/ocn. + ! I.e. water sent from land to rof is positive + + l2x(index_l2x_Flrl_rofsur,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsur_grc(g) + + ! subsurface runoff is the sum of qflx_drain and qflx_perched_drain + l2x(index_l2x_Flrl_rofsub,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsub_grc(g) & + + waterlnd2atmbulk_inst%qflx_rofliq_drain_perched_grc(g) + + ! qgwl sent individually to coupler + l2x(index_l2x_Flrl_rofgwl,i) = waterlnd2atmbulk_inst%qflx_rofliq_qgwl_grc(g) + + ! ice sent individually to coupler + l2x(index_l2x_Flrl_rofi,i) = waterlnd2atmbulk_inst%qflx_rofice_grc(g) + + ! irrigation flux to be removed from main channel storage (negative) + l2x(index_l2x_Flrl_irrig,i) = - waterlnd2atmbulk_inst%qirrig_grc(g) + + ! glc coupling + ! We could avoid setting these fields if glc_present is .false., if that would + ! help with performance. (The downside would be that we wouldn't have these fields + ! available for diagnostic purposes or to force a later T compset with dlnd.) + do num = 0,glc_nec + l2x(index_l2x_Sl_tsrf(num),i) = lnd2glc_inst%tsrf_grc(g,num) + l2x(index_l2x_Sl_topo(num),i) = lnd2glc_inst%topo_grc(g,num) + l2x(index_l2x_Flgl_qice(num),i) = lnd2glc_inst%qice_grc(g,num) + end do + + !-------------------------- + ! Check for nans to coupler + !-------------------------- + + call check_for_nans(l2x(:,i), fname, begg, "l2x") + + end do + + end subroutine lnd_export + +end module lnd_import_export diff --git a/src/cpl/mct/lnd_set_decomp_and_domain.F90 b/src/cpl/mct/lnd_set_decomp_and_domain.F90 new file mode 100644 index 0000000000..0a37554313 --- /dev/null +++ b/src/cpl/mct/lnd_set_decomp_and_domain.F90 @@ -0,0 +1,352 @@ +module lnd_set_decomp_and_domain + + use shr_kind_mod , only : r8 => shr_kind_r8 + use spmdMod , only : masterproc + use clm_varctl , only : iulog + use mct_mod , only : mct_gsMap + + implicit none + private ! except + + ! public member routines + public :: lnd_set_decomp_and_domain_from_surfrd + + ! private member routines + private :: surfrd_get_globmask ! Reads global land mask (needed for setting domain decomp) + private :: surfrd_get_grid ! Read grid/ladnfrac data into domain (after domain decomp) + + ! translation between local and global indices at gridcell level + type(mct_gsmap), pointer, public :: gsmap_global + + ! translation between local and global indices at gridcell level for multiple levels + ! needed for 3d soil moisture stream + type(mct_gsmap), target , public :: gsMap_lnd2Dsoi_gdc2glo + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +!=============================================================================== +contains +!=============================================================================== + + subroutine lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj) + + ! Initialize ldomain data types + + use clm_varpar , only: nlevsoi + use clm_varctl , only: fatmlndfrc, use_soil_moisture_streams + use decompInitMod , only: decompInit_lnd + use decompMod , only: bounds_type, get_proc_bounds + use domainMod , only: ldomain, domain_check + + ! input/output variables + logical, intent(out) :: noland + integer, intent(out) :: ni, nj ! global grid sizes + + ! local variables + integer ,pointer :: amask(:) ! global land mask + integer :: begg, endg ! processor bounds + type(bounds_type) :: bounds ! bounds + character(len=32) :: subname = 'lnd_set_decomp_and_domain_from_surfrd' + !----------------------------------------------------------------------- + + ! Read in global land grid and land mask (amask)- needed to set decomposition + ! global memory for amask is allocate in surfrd_get_glomask - must be deallocated below + if (masterproc) then + write(iulog,*) 'Attempting to read global land mask from ',trim(fatmlndfrc) + endif + + ! Get global mask, ni and nj + call surfrd_get_globmask(filename=fatmlndfrc, mask=amask, ni=ni, nj=nj) + + ! Exit early if no valid land points + if ( all(amask == 0) )then + if (masterproc) write(iulog,*) trim(subname)//': no valid land points do NOT run clm' + noland = .true. + return + else + noland = .false. + end if + + ! Determine ctsm gridcell decomposition and processor bounds for gridcells + call decompInit_lnd(ni, nj, amask) + deallocate(amask) + if (use_soil_moisture_streams) call decompInit_lnd3D(ni, nj, nlevsoi) + + ! Initialize bounds for just gridcells + ! Remaining bounds (landunits, columns, patches) will be determined + ! after the call to decompInit_glcp - so get_proc_bounds is called + ! twice and the gridcell information is just filled in twice + call get_proc_bounds(bounds) + + ! Get grid cell bounds values + begg = bounds%begg + endg = bounds%endg + + ! Initialize ldomain data type + if (masterproc) then + write(iulog,*) 'Attempting to read ldomain from ',trim(fatmlndfrc) + endif + call surfrd_get_grid(begg, endg, ldomain, fatmlndfrc) + if (masterproc) then + call domain_check(ldomain) + endif + ldomain%mask = 1 !!! TODO - is this needed? + + end subroutine lnd_set_decomp_and_domain_from_surfrd + + !----------------------------------------------------------------------- + subroutine surfrd_get_globmask(filename, mask, ni, nj) + + ! Read the surface dataset grid related information + ! This is used to set the domain decomposition - so global data is read here + + use fileutils , only : getfil + use ncdio_pio , only : ncd_io, ncd_pio_openfile, ncd_pio_closefile, ncd_inqfdims, file_desc_t + use abortutils , only : endrun + use shr_log_mod, only : errMsg => shr_log_errMsg + + ! input/output variables + character(len=*), intent(in) :: filename ! grid filename + integer , pointer :: mask(:) ! grid mask + integer , intent(out) :: ni, nj ! global grid sizes + + ! local variables + logical :: isgrid2d + integer :: dimid,varid ! netCDF id's + integer :: ns ! size of grid on file + integer :: n,i,j ! index + integer :: ier ! error status + type(file_desc_t) :: ncid ! netcdf id + character(len=256) :: locfn ! local file name + logical :: readvar ! read variable in or not + integer , allocatable :: idata2d(:,:) + character(len=32) :: subname = 'surfrd_get_globmask' ! subroutine name + !----------------------------------------------------------------------- + + if (filename == ' ') then + mask(:) = 1 + else + ! Check if file exists + if (masterproc) then + if (filename == ' ') then + write(iulog,*) trim(subname),' ERROR: filename must be specified ' + call endrun(msg=errMsg(sourcefile, __LINE__)) + endif + end if + + ! Open file + call getfil( filename, locfn, 0 ) + call ncd_pio_openfile (ncid, trim(locfn), 0) + + ! Determine dimensions and if grid file is 2d or 1d + call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns) + if (masterproc) then + write(iulog,*)'lat/lon grid flag (isgrid2d) is ',isgrid2d + end if + allocate(mask(ns)) + mask(:) = 1 + if (isgrid2d) then + ! Grid is 2d + allocate(idata2d(ni,nj)) + idata2d(:,:) = 1 + call ncd_io(ncid=ncid, varname='LANDMASK', data=idata2d, flag='read', readvar=readvar) + if (.not. readvar) then + call ncd_io(ncid=ncid, varname='mask', data=idata2d, flag='read', readvar=readvar) + end if + if (readvar) then + do j = 1,nj + do i = 1,ni + n = (j-1)*ni + i + mask(n) = idata2d(i,j) + enddo + enddo + end if + deallocate(idata2d) + else + ! Grid is not 2d + call ncd_io(ncid=ncid, varname='LANDMASK', data=mask, flag='read', readvar=readvar) + if (.not. readvar) then + call ncd_io(ncid=ncid, varname='mask', data=mask, flag='read', readvar=readvar) + end if + end if + if (.not. readvar) call endrun( msg=' ERROR: landmask not on fatmlndfrc file'//errMsg(sourcefile, __LINE__)) + + ! Close file + call ncd_pio_closefile(ncid) + end if + + end subroutine surfrd_get_globmask + + !----------------------------------------------------------------------- + subroutine surfrd_get_grid(begg, endg, ldomain, filename) + + ! Read the surface dataset grid related information: + ! This is called after the domain decomposition has been created + ! - real latitude of grid cell (degrees) + ! - real longitude of grid cell (degrees) + + use clm_varcon , only : spval, re, grlnd + use domainMod , only : domain_type, lon1d, lat1d, domain_init + use fileutils , only : getfil + use abortutils , only : endrun + use shr_log_mod , only : errMsg => shr_log_errMsg + use ncdio_pio , only : file_desc_t, ncd_pio_openfile, ncd_pio_closefile + use ncdio_pio , only : ncd_io, check_var, ncd_inqfdims, check_dim_size + use pio + + ! input/output variables + integer , intent(in) :: begg, endg + type(domain_type) , intent(inout) :: ldomain ! domain to init + character(len=*) , intent(in) :: filename ! grid filename + + ! local variables + type(file_desc_t) :: ncid ! netcdf id + integer :: beg ! local beg index + integer :: end ! local end index + integer :: ni,nj,ns ! size of grid on file + logical :: readvar ! true => variable is on input file + logical :: isgrid2d ! true => file is 2d lat/lon + logical :: istype_domain ! true => input file is of type domain + real(r8), allocatable :: rdata2d(:,:) ! temporary + character(len=16) :: vname ! temporary + character(len=256) :: locfn ! local file name + integer :: n ! indices + character(len=32) :: subname = 'surfrd_get_grid' ! subroutine name + !----------------------------------------------------------------------- + + if (masterproc) then + if (filename == ' ') then + write(iulog,*) trim(subname),' ERROR: filename must be specified ' + call endrun(msg=errMsg(sourcefile, __LINE__)) + endif + end if + + call getfil( filename, locfn, 0 ) + call ncd_pio_openfile (ncid, trim(locfn), 0) + + ! Determine dimensions + call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns) + + ! Determine isgrid2d flag for domain + call domain_init(ldomain, isgrid2d=isgrid2d, ni=ni, nj=nj, nbeg=begg, nend=endg) + + ! Determine type of file - old style grid file or new style domain file + call check_var(ncid=ncid, varname='xc', readvar=readvar) + if (readvar)then + istype_domain = .true. + else + istype_domain = .false. + end if + + ! Read in area, lon, lat + if (istype_domain) then + call ncd_io(ncid=ncid, varname= 'area', flag='read', data=ldomain%area, & + dim1name=grlnd, readvar=readvar) + ! convert from radians**2 to km**2 + ldomain%area = ldomain%area * (re**2) + if (.not. readvar) call endrun( msg=' ERROR: area NOT on file'//errMsg(sourcefile, __LINE__)) + call ncd_io(ncid=ncid, varname= 'xc', flag='read', data=ldomain%lonc, & + dim1name=grlnd, readvar=readvar) + if (.not. readvar) call endrun( msg=' ERROR: xc NOT on file'//errMsg(sourcefile, __LINE__)) + call ncd_io(ncid=ncid, varname= 'yc', flag='read', data=ldomain%latc, & + dim1name=grlnd, readvar=readvar) + if (.not. readvar) call endrun( msg=' ERROR: yc NOT on file'//errMsg(sourcefile, __LINE__)) + else + call endrun( msg=" ERROR: can no longer read non domain files" ) + end if + + if (isgrid2d) then + allocate(rdata2d(ni,nj), lon1d(ni), lat1d(nj)) + if (istype_domain) vname = 'xc' + call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar) + lon1d(:) = rdata2d(:,1) + if (istype_domain) vname = 'yc' + call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar) + lat1d(:) = rdata2d(1,:) + deallocate(rdata2d) + end if + + ! Check lat limited to -90,90 + if (minval(ldomain%latc) < -90.0_r8 .or. & + maxval(ldomain%latc) > 90.0_r8) then + write(iulog,*) trim(subname),' WARNING: lat/lon min/max is ', & + minval(ldomain%latc),maxval(ldomain%latc) + endif + if ( any(ldomain%lonc < 0.0_r8) )then + call endrun( msg=' ERROR: lonc is negative (see https://github.com/ESCOMP/ctsm/issues/507)' & + //errMsg(sourcefile, __LINE__)) + endif + call ncd_io(ncid=ncid, varname='mask', flag='read', data=ldomain%mask, & + dim1name=grlnd, readvar=readvar) + if (.not. readvar) then + call endrun( msg=' ERROR: LANDMASK NOT on fracdata file'//errMsg(sourcefile, __LINE__)) + end if + call ncd_io(ncid=ncid, varname='frac', flag='read', data=ldomain%frac, & + dim1name=grlnd, readvar=readvar) + if (.not. readvar) then + call endrun( msg=' ERROR: LANDFRAC NOT on fracdata file'//errMsg(sourcefile, __LINE__)) + end if + + call ncd_pio_closefile(ncid) + + end subroutine surfrd_get_grid + + !------------------------------------------------------------------------------ + subroutine decompInit_lnd3D(lni,lnj,lnk) + ! + ! !DESCRIPTION: + ! Create a 3D decomposition gsmap for the global 2D grid with soil levels + ! as the 3rd dimesnion. + ! + ! !USES: + use decompMod, only : gindex_global, bounds_type, get_proc_bounds + use spmdMod , only : comp_id, mpicom + use mct_mod , only : mct_gsmap_init + ! + ! !ARGUMENTS: + integer , intent(in) :: lni,lnj,lnk ! domain global size + ! + ! !LOCAL VARIABLES: + integer :: m,n,k ! indices + integer :: begg,endg,lsize,gsize ! used for gsmap init + integer :: begg3d,endg3d + integer, pointer :: gindex(:) ! global index for gsmap init + type(bounds_type) :: bounds + !------------------------------------------------------------------------------ + + ! Initialize gsmap_lnd2dsoi_gdc2glo + call get_proc_bounds(bounds) + begg = bounds%begg; endg=bounds%endg + + begg3d = (begg-1)*lnk + 1 + endg3d = endg*lnk + lsize = (endg3d - begg3d + 1 ) + allocate(gindex(begg3d:endg3d)) + do k = 1, lnk + do n = begg,endg + m = (begg-1)*lnk + (k-1)*(endg-begg+1) + (n-begg+1) + gindex(m) = gindex_global(n-begg+1) + (k-1)*(lni*lnj) + enddo + enddo + gsize = lni * lnj * lnk + call mct_gsMap_init(gsMap_lnd2Dsoi_gdc2glo, gindex, mpicom, comp_id, lsize, gsize) + + ! Diagnostic output + + if (masterproc) then + write(iulog,*)' 3D GSMap' + write(iulog,*)' longitude points = ',lni + write(iulog,*)' latitude points = ',lnj + write(iulog,*)' soil levels = ',lnk + write(iulog,*)' gsize = ',gsize + write(iulog,*)' lsize = ',lsize + write(iulog,*)' bounds(gindex) = ',size(gindex) + write(iulog,*) + end if + + deallocate(gindex) + + end subroutine decompInit_lnd3D + +end module lnd_set_decomp_and_domain diff --git a/src/cpl/mct/ndepStreamMod.F90 b/src/cpl/mct/ndepStreamMod.F90 new file mode 100644 index 0000000000..d26ff7c95e --- /dev/null +++ b/src/cpl/mct/ndepStreamMod.F90 @@ -0,0 +1,376 @@ +module ndepStreamMod + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Contains methods for reading in nitrogen deposition data file + ! Also includes functions for dynamic ndep file handling and + ! interpolation. + ! + ! !USES + use shr_kind_mod, only: r8 => shr_kind_r8, CL => shr_kind_cl + use shr_strdata_mod, only: shr_strdata_type, shr_strdata_create + use shr_strdata_mod, only: shr_strdata_print, shr_strdata_advance + use mct_mod , only: mct_ggrid + use spmdMod , only: mpicom, masterproc, comp_id, iam + use clm_varctl , only: iulog, inst_name + use abortutils , only: endrun + use decompMod , only: bounds_type + use domainMod , only: ldomain + + ! !PUBLIC TYPES: + implicit none + private + + ! !PUBLIC MEMBER FUNCTIONS: + public :: ndep_init ! position datasets for dynamic ndep + public :: ndep_interp ! interpolates between two years of ndep file data + public :: clm_domain_mct ! Sets up MCT domain for this resolution + + ! !PRIVATE MEMBER FUNCTIONS: + private :: check_units ! Check the units and make sure they can be used + + ! ! PRIVATE TYPES + type(shr_strdata_type) :: sdat ! input data stream + integer :: stream_year_first_ndep ! first year in stream to use + integer :: stream_year_last_ndep ! last year in stream to use + integer :: model_year_align_ndep ! align stream_year_firstndep with + logical :: divide_by_secs_per_yr = .true. ! divide by the number of seconds per year + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + !============================================================================== + +contains + + !============================================================================== + + subroutine ndep_init(bounds, NLFilename) + ! + ! Initialize data stream information. + ! + ! Uses: + use shr_kind_mod , only : CS => shr_kind_cs + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use shr_nl_mod , only : shr_nl_find_group_name + use shr_log_mod , only : errMsg => shr_log_errMsg + use shr_mpi_mod , only : shr_mpi_bcast + use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global + ! + ! arguments + implicit none + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! local variables + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + type(mct_ggrid) :: dom_clm ! domain information + character(len=CL) :: stream_fldFileName_ndep + character(len=CL) :: ndepmapalgo = 'bilinear' + character(len=CL) :: ndep_tintalgo = 'linear' + character(len=CS) :: ndep_taxmode = 'extend' + character(len=CL) :: ndep_varlist = 'NDEP_year' + character(*), parameter :: shr_strdata_unset = 'NOT_SET' + character(*), parameter :: subName = "('ndepdyn_init')" + character(*), parameter :: F00 = "('(ndepdyn_init) ',4a)" + !----------------------------------------------------------------------- + + namelist /ndepdyn_nml/ & + stream_year_first_ndep, & + stream_year_last_ndep, & + model_year_align_ndep, & + ndepmapalgo, ndep_taxmode, & + ndep_varlist, & + stream_fldFileName_ndep, & + ndep_tintalgo + + ! Default values for namelist + stream_year_first_ndep = 1 ! first year in stream to use + stream_year_last_ndep = 1 ! last year in stream to use + model_year_align_ndep = 1 ! align stream_year_first_ndep with this model year + stream_fldFileName_ndep = ' ' + + ! Read ndepdyn_nml namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call shr_nl_find_group_name(nu_nml, 'ndepdyn_nml', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=ndepdyn_nml,iostat=nml_error) + if (nml_error /= 0) then + call endrun(msg=' ERROR reading ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__)) + end if + else + call endrun(msg=' ERROR finding ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__)) + end if + close(nu_nml) + endif + + call shr_mpi_bcast(stream_year_first_ndep , mpicom) + call shr_mpi_bcast(stream_year_last_ndep , mpicom) + call shr_mpi_bcast(model_year_align_ndep , mpicom) + call shr_mpi_bcast(stream_fldFileName_ndep, mpicom) + call shr_mpi_bcast(ndep_varlist , mpicom) + call shr_mpi_bcast(ndep_taxmode , mpicom) + call shr_mpi_bcast(ndep_tintalgo , mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) 'ndepdyn stream settings:' + write(iulog,*) ' stream_year_first_ndep = ',stream_year_first_ndep + write(iulog,*) ' stream_year_last_ndep = ',stream_year_last_ndep + write(iulog,*) ' model_year_align_ndep = ',model_year_align_ndep + write(iulog,*) ' stream_fldFileName_ndep = ',stream_fldFileName_ndep + write(iulog,*) ' ndep_varList = ',ndep_varList + write(iulog,*) ' ndep_taxmode = ',ndep_taxmode + write(iulog,*) ' ndep_tintalgo = ',ndep_tintalgo + write(iulog,*) ' ' + endif + ! Read in units + call check_units( stream_fldFileName_ndep, ndep_varList ) + + ! Set domain and create streams + call clm_domain_mct (bounds, dom_clm) + + call shr_strdata_create(sdat,name="clmndep", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_ndep, & + yearLast=stream_year_last_ndep, & + yearAlign=model_year_align_ndep, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_ndep), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/trim(stream_fldFileName_ndep)/),& + fldListFile=ndep_varlist, & + fldListModel=ndep_varlist, & + fillalgo='none', & + mapalgo=ndepmapalgo, & + tintalgo=ndep_tintalgo, & + calendar=get_calendar(), & + taxmode=ndep_taxmode ) + + + if (masterproc) then + call shr_strdata_print(sdat,'CLMNDEP data') + endif + + end subroutine ndep_init + !================================================================ + + subroutine check_units( stream_fldFileName_ndep, ndep_varList ) + !------------------------------------------------------------------- + ! Check that units are correct on the file and if need any conversion + use ncdio_pio , only : ncd_pio_openfile, ncd_inqvid, ncd_getatt, ncd_pio_closefile, ncd_nowrite + use ncdio_pio , only : file_desc_t, var_desc_t + use shr_kind_mod , only : CS => shr_kind_cs + use shr_log_mod , only : errMsg => shr_log_errMsg + use shr_string_mod, only : shr_string_listGetName + implicit none + + !----------------------------------------------------------------------- + ! + ! Arguments + character(len=*), intent(IN) :: stream_fldFileName_ndep ! ndep filename + character(len=*), intent(IN) :: ndep_varList ! ndep variable list to examine + ! + ! Local variables + type(file_desc_t) :: ncid ! NetCDF filehandle for ndep file + type(var_desc_t) :: vardesc ! variable descriptor + integer :: varid ! variable index + logical :: readvar ! If variable was read + character(len=CS) :: ndepunits! ndep units + character(len=CS) :: fname ! ndep field name + !----------------------------------------------------------------------- + call ncd_pio_openfile( ncid, trim(stream_fldFileName_ndep), ncd_nowrite ) + call shr_string_listGetName( ndep_varList, 1, fname ) + call ncd_inqvid( ncid, fname, varid, vardesc, readvar=readvar ) + if ( readvar ) then + call ncd_getatt( ncid, varid, "units", ndepunits ) + else + call endrun(msg=' ERROR finding variable: '//trim(fname)//" in file: "// & + trim(stream_fldFileName_ndep)//errMsg(sourcefile, __LINE__)) + end if + call ncd_pio_closefile( ncid ) + + ! Now check to make sure they are correct + if ( trim(ndepunits) == "g(N)/m2/s" )then + divide_by_secs_per_yr = .false. + else if ( trim(ndepunits) == "g(N)/m2/yr" )then + divide_by_secs_per_yr = .true. + else + call endrun(msg=' ERROR in units for nitrogen deposition equal to: '//trim(ndepunits)//" not units expected"// & + errMsg(sourcefile, __LINE__)) + end if + + end subroutine check_units + + !================================================================ + subroutine ndep_interp(bounds, atm2lnd_inst) + + !----------------------------------------------------------------------- + use clm_time_manager, only : get_curr_date, get_curr_days_per_year + use clm_varcon , only : secspday + use atm2lndType , only : atm2lnd_type + ! + ! Arguments + type(bounds_type) , intent(in) :: bounds + type(atm2lnd_type), intent(inout) :: atm2lnd_inst + ! + ! Local variables + integer :: g, ig + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + integer :: dayspyr ! days per year + !----------------------------------------------------------------------- + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + + call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ndepdyn') + + if ( divide_by_secs_per_yr )then + ig = 0 + dayspyr = get_curr_days_per_year( ) + do g = bounds%begg,bounds%endg + ig = ig+1 + atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) / (secspday * dayspyr) + end do + else + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) + end do + end if + + end subroutine ndep_interp + + !============================================================================== + subroutine clm_domain_mct(bounds, dom_clm, nlevels) + + !------------------------------------------------------------------- + ! Set domain data type for internal clm grid + use clm_varcon , only : re + use domainMod , only : ldomain + use mct_mod , only : mct_ggrid, mct_gsMap_lsize, mct_gGrid_init + use mct_mod , only : mct_gsMap_orderedPoints, mct_gGrid_importIAttr + use mct_mod , only : mct_gGrid_importRAttr, mct_gsMap + use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global + implicit none + ! + ! arguments + type(bounds_type), intent(in) :: bounds + type(mct_ggrid), intent(out) :: dom_clm ! Output domain information for land model + integer, intent(in), optional :: nlevels ! Number of levels if this is a 3D field + ! + ! local variables + integer :: g,i,j,k ! index + integer :: lsize ! land model domain data size + real(r8), pointer :: data(:) ! temporary + integer , pointer :: idata(:) ! temporary + integer :: nlevs ! Number of vertical levels + type(mct_gsMap), pointer :: gsmap => null() ! MCT GS map + !------------------------------------------------------------------- + ! SEt number of levels, and get the GS map for either the 2D or 3D grid + nlevs = 1 + if ( present(nlevels) ) nlevs = nlevels + if ( nlevs == 1 ) then + gsmap => gsmap_global + else + gsmap => gsMap_lnd2Dsoi_gdc2glo + end if + ! + ! Initialize mct domain type + ! lat/lon in degrees, area in radians^2, mask is 1 (land), 0 (non-land) + ! Note that in addition land carries around landfrac for the purposes of domain checking + ! + lsize = mct_gsMap_lsize(gsmap, mpicom) + call mct_gGrid_init( GGrid=dom_clm, & + CoordChars='lat:lon:hgt', OtherChars='area:aream:mask:frac', lsize=lsize ) + ! + ! Allocate memory + ! + allocate(data(lsize)) + ! + ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT + ! + call mct_gsMap_orderedPoints(gsmap, iam, idata) + gsmap => null() + call mct_gGrid_importIAttr(dom_clm,'GlobGridNum',idata,lsize) + ! + ! Determine domain (numbering scheme is: West to East and South to North to South pole) + ! Initialize attribute vector with special value + ! + data(:) = -9999.0_R8 + call mct_gGrid_importRAttr(dom_clm,"lat" ,data,lsize) + call mct_gGrid_importRAttr(dom_clm,"lon" ,data,lsize) + call mct_gGrid_importRAttr(dom_clm,"area" ,data,lsize) + call mct_gGrid_importRAttr(dom_clm,"aream",data,lsize) + data(:) = 0.0_R8 + call mct_gGrid_importRAttr(dom_clm,"mask" ,data,lsize) + ! + ! Determine bounds + ! + ! Fill in correct values for domain components + ! Note aream will be filled in in the atm-lnd mapper + ! + do k = 1, nlevs + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = ldomain%lonc(g) + end do + end do + call mct_gGrid_importRattr(dom_clm,"lon",data,lsize) + + do k = 1, nlevs + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = ldomain%latc(g) + end do + end do + call mct_gGrid_importRattr(dom_clm,"lat",data,lsize) + + do k = 1, nlevs + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = ldomain%area(g)/(re*re) + end do + end do + call mct_gGrid_importRattr(dom_clm,"area",data,lsize) + + do k = 1, nlevs + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = real(ldomain%mask(g), r8) + end do + end do + call mct_gGrid_importRattr(dom_clm,"mask",data,lsize) + + do k = 1, nlevs + do g = bounds%begg,bounds%endg + i = 1 + (g - bounds%begg) + data(i) = real(ldomain%frac(g), r8) + end do + end do + call mct_gGrid_importRattr(dom_clm,"frac",data,lsize) + + deallocate(data) + deallocate(idata) + + end subroutine clm_domain_mct + +end module ndepStreamMod From 7c295b84189ae3e2e62d369cc8e65fbac80406b5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 16 May 2024 14:47:23 -0600 Subject: [PATCH 132/408] Remove test/tools/test_driver.sh, unrelated to this PR, good to clean up --- test/tools/test_driver.sh | 721 -------------------------------------- 1 file changed, 721 deletions(-) delete mode 100755 test/tools/test_driver.sh diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh deleted file mode 100755 index 307d1accf8..0000000000 --- a/test/tools/test_driver.sh +++ /dev/null @@ -1,721 +0,0 @@ -#!/bin/sh -# -# test_driver.sh: driver script for the offline testing of CLM of tools -# -# interactive usage on all machines: -# -# env ./test_driver.sh -i -# -# valid arguments: -# -i interactive usage -# -d debug usage -- display tests that will run -- but do NOT actually execute them -# -f force batch submission (avoids user prompt) -# -h displays this help message -# -# -# **pass environment variables by preceding above commands -# with 'env var1=setting var2=setting ' -# **more details in the CLM testing user's guide, accessible -# from the CLM developers web page - - -#will attach timestamp onto end of script name to prevent overwriting -cur_time=`date '+%H:%M:%S'` - -hostname=`hostname` -echo $hostname -case $hostname in - - ##Derecho - derecho* | dec*) - submit_script="test_driver_derecho${cur_time}.sh" - -##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv -cat > ./${submit_script} << EOF -#!/bin/sh -# - -interactive="YES" -input_file="tests_pretag_derecho_nompi" -c_threads=128 - -export INITMODULES="/glade/u/apps/derecho/23.06/spack/opt/spack/lmod/8.7.20/gcc/7.5.0/pdxb/lmod/lmod/init/sh" -. \$INITMODULES - -module --force purge -module load ncarenv -module load craype -module load intel -module load mkl -module load ncarcompilers -module load netcdf -module load nco -module load ncl - -#omp threads -if [ -z "\$CLM_THREADS" ]; then #threads NOT set on command line - export CLM_THREADS=\$c_threads -fi - -# Stop on first failed test -if [ -z "\$CLM_SOFF" ]; then #CLM_SOFF NOT set - export CLM_SOFF=FALSE -fi - -export CESM_MACH="derecho" -export CESM_COMP="intel" - -export NETCDF_DIR=\$NETCDF -export INC_NETCDF=\$NETCDF/include -export LIB_NETCDF=\$NETCDF/lib -export MAKE_CMD="gmake -j " -export CFG_STRING="" -export TOOLS_MAKE_STRING="USER_FC=ifort USER_LINKER=ifort USER_CPPDEFS=-DLINUX" -export MACH_WORKSPACE=\$SCRATCH -export CPRNC_EXE="$CESMDATAROOT/cprnc/cprnc" -dataroot="$CESMDATAROOT/inputdata" -export TOOLSLIBS="" -export REGRID_PROC=1 -export TOOLS_CONF_STRING="--mpilib mpi-serial" - - -echo_arg="" - -EOF -#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^ - ;; - - ##cheyenne - cheyenne* | r*i*n*) - submit_script="test_driver_cheyenne${cur_time}.sh" - -#vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv -at > ./${submit_script} << EOF -!/bin/sh - - -interactive="YES" -input_file="tests_pretag_cheyenne_nompi" -c_threads=36 - - -export INITMODULES="/glade/u/apps/ch/opt/lmod/8.1.7/lmod/lmod/init/sh" -. \$INITMODULES - -module purge -module load ncarenv -module load intel -module load mkl -module load ncarcompilers -module load netcdf - -module load nco -module load ncl - -module load conda - - -##omp threads -if [ -z "\$CLM_THREADS" ]; then #threads NOT set on command line - export CLM_THREADS=\$c_threads -fi - -# Stop on first failed test -if [ -z "\$CLM_SOFF" ]; then #CLM_SOFF NOT set - export CLM_SOFF=FALSE -fi - -export CESM_MACH="cheyenne" -export CESM_COMP="intel" - -export NETCDF_DIR=\$NETCDF -export INC_NETCDF=\$NETCDF/include -export LIB_NETCDF=\$NETCDF/lib -export MAKE_CMD="gmake -j " -export CFG_STRING="" -export TOOLS_MAKE_STRING="USER_FC=ifort USER_LINKER=ifort USER_CPPDEFS=-DLINUX" -export MACH_WORKSPACE="/glade/scratch" -export CPRNC_EXE="$CESMDATAROOT/tools/cime/tools/cprnc/cprnc.cheyenne" -dataroot="$CESMDATAROOT" -export TOOLSLIBS="" -export REGRID_PROC=1 -export TOOLS_CONF_STRING="--mpilib mpi-serial" - - -echo_arg="" - -EOF -##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^ - ;; - - ## DAV cluster - casper* | pronghorn*) - submit_script="test_driver_dav${cur_time}.sh" - -##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv -cat > ./${submit_script} << EOF -#!/bin/sh -# - -interactive="YES" -input_file="tests_posttag_dav_mpi" -c_threads=36 - - -export INITMODULES="/glade/u/apps/ch/opt/lmod/8.1.7/lmod/lmod/init/sh" -. \$INITMODULES - -module purge -module load ncarenv -module load intel -module load mkl -module load ncarcompilers -module load netcdf -module load openmpi - -module load nco -module load conda -module load ncl - - -##omp threads -if [ -z "\$CLM_THREADS" ]; then #threads NOT set on command line - export CLM_THREADS=\$c_threads -fi - -# Stop on first failed test -if [ -z "\$CLM_SOFF" ]; then #CLM_SOFF NOT set - export CLM_SOFF=FALSE -fi - -export CESM_MACH="cheyenne" -export CESM_COMP="intel" - -export NETCDF_DIR=\$NETCDF -export INC_NETCDF=\$NETCDF/include -export LIB_NETCDF=\$NETCDF/lib -export MAKE_CMD="gmake -j " -export CFG_STRING="" -export TOOLS_MAKE_STRING="USER_FC=ifort USER_LINKER=ifort USER_CPPDEFS=-DLINUX" -export MACH_WORKSPACE="/glade/scratch" -export CPRNC_EXE="$CESMDATAROOT/tools/cime/tools/cprnc/cprnc.cheyenne" -dataroot="$CESMDATAROOT" -export TOOLSLIBS="" -export TOOLS_CONF_STRING="--mpilib mpich" - - -echo_arg="" - -EOF -##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^ - ;; - - ## hobart - hobart* | h*.cgd.ucar.edu) - submit_script="test_driver_hobart_${cur_time}.sh" - export PATH=/cluster/torque/bin:${PATH} - -##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv -cat > ./${submit_script} << EOF -#!/bin/sh -# - -# Name of the queue (CHANGE THIS if needed) -#PBS -q long -# Number of nodes (CHANGE THIS if needed) -#PBS -l nodes=1:ppn=24 -# output file base name -#PBS -N test_dr -# Put standard error and standard out in same file -#PBS -j oe -# Export all Environment variables -#PBS -V -# End of options - -if [ -n "\$PBS_JOBID" ]; then #batch job - export JOBID=\`echo \${PBS_JOBID} | cut -f1 -d'.'\` - initdir=\${PBS_O_WORKDIR} -fi - -if [ "\$PBS_ENVIRONMENT" = "PBS_BATCH" ]; then - interactive="NO" - input_file="tests_posttag_hobart" -else - interactive="YES" - input_file="tests_posttag_hobart_nompi" -fi - -##omp threads -if [ -z "\$CLM_THREADS" ]; then #threads NOT set on command line - export CLM_THREADS=2 -fi -export CLM_RESTART_THREADS=1 - -##mpi tasks -export CLM_TASKS=24 -export CLM_RESTART_TASKS=20 - -export P4_GLOBMEMSIZE=500000000 - - -export CESM_MACH="hobart" - -ulimit -s unlimited -ulimit -c unlimited - -export CESM_COMP="intel" -export TOOLS_MAKE_STRING="USER_FC=ifort USER_CC=icc " -export TOOLS_CONF_STRING=" -mpilib mpi-serial" -export CFG_STRING="" -export INITMODULES="/usr/share/Modules/init/sh" - -. \$INITMODULES -module purge -module load compiler/intel -module load tool/nco -module load tool/netcdf -module load lang/python - -export NETCDF_DIR=\$NETCDF_PATH -export INC_NETCDF=\${NETCDF_PATH}/include -export LIB_NETCDF=\${NETCDF_PATH}/lib -export MAKE_CMD="gmake -j 5" ##using hyper-threading on hobart -export MACH_WORKSPACE="/scratch/cluster" -export CPRNC_EXE=/fs/cgd/csm/tools/cprnc/cprnc -export DATM_QIAN_DATA_DIR="/project/tss/atm_forcing.datm7.Qian.T62.c080727" -dataroot="/fs/cgd/csm" -export TOOLSSLIBS="" -echo_arg="-e" - -EOF -##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^ - ;; - - ## izumi - izumi* | i*.unified.ucar.edu) - submit_script="test_driver_izumi_${cur_time}.sh" - export PATH=/cluster/torque/bin:${PATH} - -##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv -cat > ./${submit_script} << EOF -#!/bin/sh -# - -# Name of the queue (CHANGE THIS if needed) -#PBS -q long -# Number of nodes (CHANGE THIS if needed) -#PBS -l nodes=1:ppn=24 -# output file base name -#PBS -N test_dr -# Put standard error and standard out in same file -#PBS -j oe -# Export all Environment variables -#PBS -V -# End of options - -if [ -n "\$PBS_JOBID" ]; then #batch job - export JOBID=\`echo \${PBS_JOBID} | cut -f1 -d'.'\` - initdir=\${PBS_O_WORKDIR} -fi - -if [ "\$PBS_ENVIRONMENT" = "PBS_BATCH" ]; then - interactive="NO" - input_file="tests_posttag_izumi" -else - interactive="YES" - input_file="tests_posttag_izumi_nompi" -fi - -##omp threads -if [ -z "\$CLM_THREADS" ]; then #threads NOT set on command line - export CLM_THREADS=2 -fi -export CLM_RESTART_THREADS=1 - -##mpi tasks -export CLM_TASKS=24 -export CLM_RESTART_TASKS=20 - -export P4_GLOBMEMSIZE=500000000 - - -export CESM_MACH="izumi" - -ulimit -s unlimited -ulimit -c unlimited - -export CESM_COMP="intel" -export TOOLS_MAKE_STRING="USER_FC=ifort USER_CC=icc " -export TOOLS_CONF_STRING=" -mpilib mpi-serial" -export CFG_STRING="" -export INITMODULES="/usr/share/Modules/init/sh" - -. \$INITMODULES -module purge -module load compiler/intel -module load tool/nco -module load tool/netcdf -module load lang/python - -export NETCDF_DIR=\$NETCDF_PATH -export INC_NETCDF=\${NETCDF_PATH}/include -export LIB_NETCDF=\${NETCDF_PATH}/lib -export MAKE_CMD="gmake -j 5" ##using hyper-threading on izumi -export MACH_WORKSPACE="/scratch/cluster" -export CPRNC_EXE=/fs/cgd/csm/tools/cprnc/cprnc.izumi -export DATM_QIAN_DATA_DIR="/project/tss/atm_forcing.datm7.Qian.T62.c080727" -dataroot="/fs/cgd/csm" -export TOOLSSLIBS="" -echo_arg="-e" - -EOF -##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^ - ;; - - * ) - echo "Only setup to work on: derecho, cheyenne, hobart and izumi" - exit - - -esac - -##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv -cat >> ./${submit_script} << EOF - -export CPRNC_OPT="" -if [ -n "\${CLM_JOBID}" ]; then - export JOBID=\${CLM_JOBID} -fi -##check if interactive job - -if [ "\$interactive" = "YES" ]; then - - if [ -z "\${JOBID}" ]; then - export JOBID=\$\$ - fi - echo "test_driver.sh: interactive run - setting JOBID to \$JOBID" - if [ \$0 = "test_driver.sh" ]; then - initdir="." - else - initdir=\${0%/*} - fi -else - echo "ERROR: you *always* need to use the interactive option (-i)" - echo " currently doesn't work without it" - exit 3 -fi - -##establish script dir and clm_root -if [ -f \${initdir}/test_driver.sh ]; then - export CLM_SCRIPTDIR=\`cd \${initdir}; pwd \` - export CLM_ROOT=\`cd \${CLM_SCRIPTDIR}/../..; pwd \` - export CTSM_ROOT=\${CLM_ROOT} - if [ -d \${CLM_ROOT}/cime ]; then - export CIME_ROOT=\${CLM_ROOT}/cime - else - export CIME_ROOT=\${CLM_ROOT}/../../cime - fi - if [ ! -d \${CIME_ROOT} ]; then - echo "ERROR: trouble finding the CIME_ROOT directory: \$CIME_ROOT" - exit 3 - fi -else - if [ -n "\${CLM_ROOT}" ] && [ -f \${CLM_ROOT}/test/tools/test_driver.sh ]; then - export CLM_SCRIPTDIR=\`cd \${CLM_ROOT}/test/tools; pwd \` - else - echo "ERROR: unable to determine script directory " - echo " if initiating batch job from directory other than the one containing test_driver.sh, " - echo " you must set the environment variable CLM_ROOT to the full path of directory containing " - echo " . " - exit 3 - fi -fi - -# Setup conda environment -conda activate ctsm_pylib -if [ \$? -ne 0 ]; then - echo "ERROR: Trouble activating the ctsm_pylib conda environment, be sure it's setup with \$CLM_ROOT/py_env_create, then rerun" - exit 4 -fi - -##output files -clm_log=\${initdir}/td.\${JOBID}.log -if [ -f \$clm_log ]; then - rm \$clm_log -fi -clm_status=\${initdir}/td.\${JOBID}.status -if [ -f \$clm_status ]; then - rm \$clm_status -fi - -##setup test work directory -if [ -z "\$CLM_TESTDIR" ]; then - export CLM_TESTDIR=\${MACH_WORKSPACE}/\$LOGNAME/clmTests/test-driver.\${JOBID} - if [ -d \$CLM_TESTDIR ] && [ \$CLM_RETAIN_FILES != "TRUE" ]; then - rm -r \$CLM_TESTDIR - fi -fi -if [ ! -d \$CLM_TESTDIR ]; then - mkdir -p \$CLM_TESTDIR - if [ \$? -ne 0 ]; then - echo "ERROR: unable to create work directory \$CLM_TESTDIR" - exit 4 - fi -fi - -## PIO build directory -export PIO_LIBDIR=\$CLM_TESTDIR/pio - -##set our own environment vars -export CSMDATA=\${dataroot}/inputdata -export DIN_LOC_ROOT=\${CSMDATA} -export MPI_TYPE_MAX=100000 - -##process other env vars possibly coming in -if [ -z "\$CLM_RETAIN_FILES" ]; then - export CLM_RETAIN_FILES=FALSE -fi -if [ -n "\${CLM_INPUT_TESTS}" ]; then - input_file=\$CLM_INPUT_TESTS -else - input_file=\${CLM_SCRIPTDIR}/\${input_file} -fi -if [ ! -f \${input_file} ]; then - echo "ERROR: unable to locate input file \${input_file}" - exit 5 -fi - -if [ \$interactive = "YES" ]; then - echo "reading tests from \${input_file}" -else - echo "reading tests from \${input_file}" >> \${clm_log} -fi - -num_tests=\`wc -w < \${input_file}\` -echo "STATUS OF CLM TESTING UNDER JOB \${JOBID}; scheduled to run \$num_tests tests from:" >> \${clm_status} -echo "\$input_file" >> \${clm_status} -echo "" >> \${clm_status} -echo " on machine: $hostname" >> \${clm_status} -if [ -n "${BL_ROOT}" ]; then - echo "tests of baseline will use source code from:" >> \${clm_status} - echo "\$BL_ROOT" >> \${clm_status} -fi -if [ \$interactive = "NO" ]; then - echo "see \${clm_log} for more detailed output" >> \${clm_status} -fi -echo "" >> \${clm_status} - -test_list="" -while read input_line; do - test_list="\${test_list}\${input_line} " -done < \${input_file} - - -##initialize flags, counter -skipped_tests="NO" -pending_tests="NO" -count=0 - -##loop through the tests of input file -for test_id in \${test_list}; do - count=\`expr \$count + 1\` - while [ \${#count} -lt 3 ]; do - count="0\${count}" - done - - master_line=\`grep \$test_id \${CLM_SCRIPTDIR}/input_tests_master\` - status_out="" - for arg in \${master_line}; do - status_out="\${status_out}\${arg} " - done - - if [ -z "\$status_out" ]; then - echo "No test matches \$test_id in \${CLM_SCRIPTDIR}/input_tests_master" - exit 3 - fi - - test_cmd=\${status_out#* } - - status_out="\${count} \${status_out}" - - if [ \$interactive = "YES" ]; then - echo "" - echo "***********************************************************************************" - echo "\${status_out}" - echo "***********************************************************************************" - else - echo "" >> \${clm_log} - echo "***********************************************************************************"\ - >> \${clm_log} - echo "\$status_out" >> \${clm_log} - echo "***********************************************************************************"\ - >> \${clm_log} - fi - - if [ \${#status_out} -gt 94 ]; then - status_out=\`echo "\${status_out}" | cut -c1-100\` - fi - while [ \${#status_out} -lt 97 ]; do - status_out="\${status_out}." - done - - echo \$echo_arg "\$status_out\c" >> \${clm_status} - - if [ \$interactive = "YES" ]; then - \${CLM_SCRIPTDIR}/\${test_cmd} - rc=\$? - else - \${CLM_SCRIPTDIR}/\${test_cmd} >> \${clm_log} 2>&1 - rc=\$? - fi - if [ \$rc -eq 0 ]; then - echo "PASS" >> \${clm_status} - elif [ \$rc -eq 255 ]; then - echo "SKIPPED*" >> \${clm_status} - skipped_tests="YES" - elif [ \$rc -eq 254 ]; then - echo "PENDING**" >> \${clm_status} - pending_tests="YES" - else - echo " rc=\$rc FAIL" >> \${clm_status} - if [ "\$CLM_SOFF" = "TRUE" ]; then - echo "stopping on first failure" >> \${clm_status} - echo "stopping on first failure" >> \${clm_log} - exit 6 - fi - fi -done - -echo "end of input" >> \${clm_status} -if [ \$interactive = "YES" ]; then - echo "end of input" -else - echo "end of input" >> \${clm_log} -fi - -if [ \$skipped_tests = "YES" ]; then - echo "* please verify that any skipped tests are not required of your clm commit" >> \${clm_status} -fi -if [ \$pending_tests = "YES" ]; then - echo "** tests that are pending must be checked manually for a successful completion" >> \${clm_status} - if [ \$interactive = "NO" ]; then - echo " see the test's output in \${clm_log} " >> \${clm_status} - echo " for the location of test results" >> \${clm_status} - fi -fi - -if [ "\$interactive" = "YES" ]; then - passInt="test_driver.sh-i" -else - passInt="test_driver.sh" -fi - -../../bld/unit_testers/xFail/wrapClmTests.pl -statusFile "\${clm_status}" -numberOfTests "\${num_tests}" -callingScript "\${passInt}" - -exit 0 - -EOF -##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^ - - -chmod a+x $submit_script -if [ ! -z "$CLM_RETAIN_FILES" ]; then - export CLM_RETAIN_FILES="FALSE" -fi -arg1=${1##*-} -case $arg1 in - [iI]* ) - debug="NO" - interactive="YES" - compile_only="NO" - export debug - export interactive - export compile_only - ./${submit_script} - exit 0 - ;; - - [cC]* ) - debug="NO" - interactive="YES" - compile_only="YES" - export debug - export CLM_RETAIN_FILES="TRUE" - export interactive - export compile_only - export CLM_RETAIN_FILES="TRUE" - ./${submit_script} - exit 0 - ;; - - [dD]* ) - debug="YES" - interactive="YES" - compile_only="NO" - export debug - export interactive - export compile_only - ./${submit_script} - exit 0 - ;; - - [fF]* ) - debug="NO" - interactive="NO" - compile_only="NO" - export debug - export interactive - export compile_only - ;; - - "" ) - echo "" - echo "**********************" - echo "$submit_script has been created and will be submitted to the batch queue..." - echo "(ret) to continue, (a) to abort" - read ans - case $ans in - [aA]* ) - echo "aborting...type ./test_driver.sh -h for help message" - exit 0 - ;; - esac - debug="NO" - interactive="NO" - compile_only="NO" - export debug - export interactive - export compile_only - ;; - - * ) - echo "" - echo "**********************" - echo "usage on derecho, cheyenne, hobart, and izumi: " - echo "./test_driver.sh -i" - echo "" - echo "valid arguments: " - echo "-i interactive usage" - echo "-c compile-only usage (run configure and compile do not run clm)" - echo "-d debug-only usage (run configure and build-namelist do NOT compile or run clm)" - echo "-f force batch submission (avoids user prompt)" - echo "-h displays this help message" - echo "" - echo "**pass environment variables by preceding above commands " - echo " with 'env var1=setting var2=setting '" - echo "" - echo "**********************" - exit 0 - ;; -esac - -echo "submitting..." -case $hostname in - #default - * ) - echo "no submission capability on this machine use the interactive option: -i" - exit 0 - ;; - -esac -exit 0 From 7c5c632f02b54f2285bdfb3902834d78715077f7 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 16 May 2024 15:03:31 -0600 Subject: [PATCH 133/408] fix namelist definition --- bld/namelist_files/namelist_definition_ctsm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 03b1e9e64d..58e0aca3a6 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -734,8 +734,8 @@ Toggle to turn on no competition mode (only relevant if FATES is being used). Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used). - + Set FATES harvesting mode by setting fates_harvest_mode to a valid string option. Allowed values are: no_harvest: no fates harvesting of any kind From 5e9bc2e9a40987ff5477d0b3cdc742c3fbcf5f23 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 16 May 2024 15:04:39 -0600 Subject: [PATCH 134/408] Update finidat that previously failing test now picks up by default --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index c62df7d77b..90e397d544 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1097,7 +1097,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false." ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true." lnd_tuning_mode="clm6_0_GSWP3v1" ->lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc +>lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm52BgcCrop.2000-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240515.nc From 0266a70e98142750e6c34494740a8dd3e600a93c Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 16 May 2024 15:22:10 -0600 Subject: [PATCH 135/408] update landuse parameters from ints to chars --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index d9bd0352ca..f330ee2b78 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -35,11 +35,11 @@ module dynFATESLandUseChangeMod integer, public, parameter :: num_landuse_harvest_vars = 5 ! Define the fates landuse namelist mode switch values - integer, public, parameter :: fates_harvest_no_logging = 0 - integer, public, parameter :: fates_harvest_logging_only = 1 - integer, public, parameter :: fates_harvest_clmlanduse = 2 - integer, public, parameter :: fates_harvest_luh_area = 3 - integer, public, parameter :: fates_harvest_luh_mass = 4 + character(len=13), public, parameter :: fates_harvest_no_logging = 'no_harvest' + character(len=13), public, parameter :: fates_harvest_logging_only = 'event_code' + character(len=13), public, parameter :: fates_harvest_clmlanduse = 'surfdata_file' + character(len=13), public, parameter :: fates_harvest_luh_area = 'luhdata_area' + character(len=13), public, parameter :: fates_harvest_luh_mass = 'luhdata_mass' ! Define landuse harvest unit integer representation integer, public, parameter :: landuse_harvest_area_units = 1 From 0a08723cfe7365a7fb639513232bbeb1c12716c9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 16 May 2024 16:38:06 -0600 Subject: [PATCH 136/408] Fix for issue #2546 --- cime_config/config_component.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index be6916ae0c..d69bdbc302 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -78,7 +78,7 @@ UNSET - clm5_0_cam6.0,clm5_0_cam7.0,clm5.0_cam5.0,clm5.0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm5_1_CRUv7,clm5_1_GSWP3v1,clm5_1_cam6.0,clm5_1_QIAN,clm5_1_1PT,clm5_1_NLDAS2,clm5_1_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5 + clm5_0_cam6.0,clm5_0_cam7.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm5_0_QIAN,clm5_0_1PT,clm5_0_NLDAS2,clm5_0_ERA5,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_QIAN,clm4_5_cam6.0,clm4_5_cam7.0,clm4_5_cam5.0,clm4_5_cam4.0,clm4_5_1PT,clm4_5_NLDAS2,clm4_5_ERA5,clm5_1_CRUv7,clm5_1_GSWP3v1,clm5_1_cam6.0,clm5_1_QIAN,clm5_1_1PT,clm5_1_NLDAS2,clm5_1_ERA5,clm6_0_CRUv7,clm6_0_GSWP3v1,clm6_0_cam6.0,clm6_0_cam7.0,clm6_0_cam5.0,clm6_0_cam4.0,clm6_0_QIAN,clm6_0_1PT,clm6_0_NLDAS2,clm6_0_ERA5 From 438d85a58b120a1329db4c47520ff473a40bcc5b Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 17 May 2024 09:27:55 -0600 Subject: [PATCH 137/408] Added a missing bracket --- bld/CLMBuildNamelist.pm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index ad378ffc6d..3658f681af 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -785,7 +785,7 @@ sub setup_cmdl_fates_mode { "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode", "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries", - "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel"); + "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel" ); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { @@ -4517,7 +4517,7 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","fates_seeddisp_cadence","fates_history_dimlevel", - "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage"); + "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" ); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, @@ -4564,12 +4564,12 @@ sub setup_logic_fates { # fates landuse can't be on with FATES SP mode is active if ( &value_is_true($nl->get_value('use_fates_luh')) ) { - $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true'); + $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true'); + } # hydro isn't currently supported to work when FATES SP mode is active if (&value_is_true( $nl->get_value('use_fates_planthydro') )) { $log->fatal_error('fates sp mode is currently not supported to work with fates hydro'); - } } } From 21f38b4701491c98281f2accdcb6d878c3d1fa67 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 17 May 2024 11:43:26 -0600 Subject: [PATCH 138/408] Add an empty unit tester for DUSTMod --- .../test/DustEmis_test/CMakeLists.txt | 6 ++ .../test/DustEmis_test/test_DustEmis.pf | 34 +++++++ .../share_esmf/ZenderSoilErodStreamType.F90 | 88 +++++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 src/biogeochem/test/DustEmis_test/CMakeLists.txt create mode 100644 src/biogeochem/test/DustEmis_test/test_DustEmis.pf create mode 100644 src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90 diff --git a/src/biogeochem/test/DustEmis_test/CMakeLists.txt b/src/biogeochem/test/DustEmis_test/CMakeLists.txt new file mode 100644 index 0000000000..a618489386 --- /dev/null +++ b/src/biogeochem/test/DustEmis_test/CMakeLists.txt @@ -0,0 +1,6 @@ +set (pfunit_sources + test_DustEmis.pf) + +add_pfunit_ctest(DustEmis + TEST_SOURCES "${pfunit_sources}" + LINK_LIBRARIES clm csm_share esmf_wrf_timemgr) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf new file mode 100644 index 0000000000..e0e668ea67 --- /dev/null +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -0,0 +1,34 @@ +module test_DustEmis + + ! Tests of DustEmis + + use funit + use DUSTMod + use shr_kind_mod , only : r8 => shr_kind_r8 + + implicit none + + @TestCase + type, extends(TestCase) :: TestDustEmis + contains + procedure :: setUp + procedure :: tearDown + end type TestDustEmis + +contains + + subroutine setUp(this) + class(TestDustEmis), intent(inout) :: this + end subroutine setUp + + subroutine tearDown(this) + class(TestDustEmis), intent(inout) :: this + end subroutine tearDown + + @Test + subroutine check_dust_emis(this) + class(TestDustEmis), intent(inout) :: this + + end subroutine check_dust_emis + +end module test_DustEmis \ No newline at end of file diff --git a/src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90 b/src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90 new file mode 100644 index 0000000000..570fcec05f --- /dev/null +++ b/src/unit_test_stubs/share_esmf/ZenderSoilErodStreamType.F90 @@ -0,0 +1,88 @@ +module ZenderSoilErodStreamType + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! UNIT-TEST STUB for ZenderSoilErodStreamType + ! + ! !USES + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_cl + use shr_log_mod , only : errMsg => shr_log_errMsg + use abortutils , only : endrun + use decompMod , only : bounds_type + + ! !PUBLIC TYPES: + implicit none + private + + type, public :: soil_erod_stream_type + contains + + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Init ! Initialize and read data in + procedure, public :: CalcDustSource ! Calculate dust source spatial filter (basically truncating stream data value smaller than 0.1 following CAM's practice) based on input streams + procedure, public :: UseStreams ! If streams will be used + + end type soil_erod_stream_type + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine Init(this, bounds, NLFilename) + ! + ! Initialize the Zender soil eroditability stream object + ! + ! Uses: + ! + ! arguments + implicit none + class(soil_erod_stream_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! local variables + !----------------------------------------------------------------------- + + end subroutine Init + + !============================================================================== + logical function UseStreams(this) + ! + ! !DESCRIPTION: + ! Return true if the Zender method is being used and the soil erodability + ! file is being used with it + ! + ! !USES: + ! + ! !ARGUMENTS: + implicit none + class(soil_erod_stream_type) :: this + ! + ! !LOCAL VARIABLES: + UseStreams = .false. + end function UseStreams + + !============================================================================== + subroutine CalcDustSource(this, bounds, soil_erod) + ! + ! !DESCRIPTION: + ! Calculate the soil eroditability for the Zender dust method. + ! + ! !USES: + !USES + ! + ! !ARGUMENTS: + implicit none + class(soil_erod_stream_type) :: this + type(bounds_type) , intent(in) :: bounds + real(r8) , intent(inout) :: soil_erod(bounds%begc:) ! [fraction] rock drag partition factor (roughness effect) + ! + ! !LOCAL VARIABLES: + !--------------------------------------------------------------------- + + end subroutine CalcDustSource + +end module ZenderSoilErodStreamType From 7d8213bc814be0b9274feea0c4d0472b8f96bf07 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 17 May 2024 11:43:37 -0600 Subject: [PATCH 139/408] Add an empty unit tester for DUSTMod --- src/biogeochem/CMakeLists.txt | 1 + src/biogeochem/test/CMakeLists.txt | 1 + src/biogeophys/CMakeLists.txt | 1 + src/unit_test_stubs/share_esmf/CMakeLists.txt | 1 + 4 files changed, 4 insertions(+) diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt index e31bbc80f8..0f46dc665d 100644 --- a/src/biogeochem/CMakeLists.txt +++ b/src/biogeochem/CMakeLists.txt @@ -6,6 +6,7 @@ list(APPEND clm_sources CNPhenologyMod.F90 CNSpeciesMod.F90 CNDVType.F90 + DUSTMod.F90 CropReprPoolsMod.F90 CropType.F90 CNVegStateType.F90 diff --git a/src/biogeochem/test/CMakeLists.txt b/src/biogeochem/test/CMakeLists.txt index 81fe9bbaf0..e22a720523 100644 --- a/src/biogeochem/test/CMakeLists.txt +++ b/src/biogeochem/test/CMakeLists.txt @@ -2,3 +2,4 @@ add_subdirectory(Species_test) add_subdirectory(CNVegComputeSeed_test) add_subdirectory(CNPhenology_test) add_subdirectory(Latbaset_test) +add_subdirectory(DustEmis_test) diff --git a/src/biogeophys/CMakeLists.txt b/src/biogeophys/CMakeLists.txt index 2ffc346670..86edcca9f9 100644 --- a/src/biogeophys/CMakeLists.txt +++ b/src/biogeophys/CMakeLists.txt @@ -7,6 +7,7 @@ list(APPEND clm_sources BalanceCheckMod.F90 CanopyStateType.F90 EnergyFluxType.F90 + FrictionVelocityMod.F90 GlacierSurfaceMassBalanceMod.F90 HillslopeHydrologyUtilsMod.F90 HumanIndexMod.F90 diff --git a/src/unit_test_stubs/share_esmf/CMakeLists.txt b/src/unit_test_stubs/share_esmf/CMakeLists.txt index 5eb2d42415..5ffce0ba94 100644 --- a/src/unit_test_stubs/share_esmf/CMakeLists.txt +++ b/src/unit_test_stubs/share_esmf/CMakeLists.txt @@ -1,5 +1,6 @@ list(APPEND clm_sources ExcessIceStreamType.F90 + ZenderSoilErodStreamType.F90 ) sourcelist_to_parent(clm_sources) From 3254949e133f5fd42411a896690b256529ea150c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 17 May 2024 13:09:31 -0600 Subject: [PATCH 140/408] Add objects needed and a failing unit test that just runs the two main subroutines, needs to add initialization of the input objects --- .../test/DustEmis_test/test_DustEmis.pf | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index e0e668ea67..ff4b69ab72 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -3,13 +3,31 @@ module test_DustEmis ! Tests of DustEmis use funit + use unittestSubgridMod + use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch use DUSTMod use shr_kind_mod , only : r8 => shr_kind_r8 + use unittestFilterBuilderMod, only : filter_from_range + use atm2lndType, only : atm2lnd_type + use SoilStateType, only : soilstate_type + use CanopyStateType, only : canopystate_type + use WaterStateBulkType, only : waterstatebulk_type + use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type + use FrictionVelocityMod, only : frictionvel_type implicit none @TestCase type, extends(TestCase) :: TestDustEmis + type(dust_type) :: dust_emis + integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) + integer :: num_nolakep ! number of patches in non-lake filter + type(atm2lnd_type) :: atm2lnd_inst + type(soilstate_type) :: soilstate_inst + type(canopystate_type) :: canopystate_inst + type(WaterStateBulk_Type) :: waterstatebulk_inst + type(waterdiagnosticbulk_type) :: waterdiagnosticbulk_inst + type(frictionvel_type) :: frictionvel_inst contains procedure :: setUp procedure :: tearDown @@ -19,16 +37,30 @@ contains subroutine setUp(this) class(TestDustEmis), intent(inout) :: this + + character(len=5) :: NLFilename = 'none' + + call setup_single_veg_patch( pft_type=0 ) + call this%dust_emis%Init( bounds, NLFilename ) + call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) end subroutine setUp subroutine tearDown(this) class(TestDustEmis), intent(inout) :: this + + call unittest_subgrid_teardown() + deallocate( this%filter_nolakep ) end subroutine tearDown @Test subroutine check_dust_emis(this) class(TestDustEmis), intent(inout) :: this + call DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%waterstatebulk_inst, & + this%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis) + call DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst, this%dust_emis) + end subroutine check_dust_emis end module test_DustEmis \ No newline at end of file From e4544510e23abf8a9a68e8dd143840742eb8b2fc Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 17 May 2024 13:55:46 -0600 Subject: [PATCH 141/408] Add izumi nag debug tests to ExpectedTestFails as per ESCOMP/CMEPS#460 --- cime_config/testdefs/ExpectedTestFails.xml | 85 ++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index f600444547..09a425ed9e 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,6 +44,91 @@ + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + + + FAIL + https://github.com/ESCOMP/CMEPS/pull/460 + + + FAIL From e6f62c431b05460f62c6549e464797df7a7ebf58 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 17 May 2024 15:56:00 -0600 Subject: [PATCH 142/408] fix reading of fates_harvest_modes during namelist build checks --- bld/CLMBuildNamelist.pm | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 01f7918d62..c1ec60fb33 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4487,8 +4487,9 @@ sub setup_logic_fates { if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { $log->fatal_error("use_fates_luh must be true when $var is true" ); } - if ( $nl->get_value('fates_harvest_mode') ne 'no_harvest') { - $log->fatal_error("fates_harvest_mode must be off (i.e. set to zero) when $var is true" ); + my $var = remove_leading_and_trailing_quotes($nl->get_value('fates_harvest_mode')); + if ( $var ne 'no_harvest') { + $log->fatal_error("fates_harvest_mode set to $var. It must set to no_harvest when use_potential_veg is true." ); } my $var = "fluh_timeseries"; if ( defined($nl->get_value($var)) ) { @@ -4500,10 +4501,22 @@ sub setup_logic_fates { my $var = "fates_harvest_mode"; if ( defined($nl->get_value($var)) ) { # using fates_harvest mode with raw luh2 harvest data - if ( $nl->get_value($var) eq 'luhdata_area' || $nl->get_value($var) eq 'luhdata_mass' ) { + my $mode = remove_leading_and_trailing_quotes($nl->get_value($var)); + if ( $mode eq 'luhdata_area' || $mode eq 'luhdata_mass' ) { # Make sure that use_fates_luh is true when using raw fates luh2 harvest data if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { - $log->fatal_error("use_fates_luh is required to be true when $var is greater than 2" ); + $log->fatal_error("use_fates_luh is required to be true when $var is luhdata_mass or luhdata_area" ); + } + } elsif ( $mode eq 'surfdata_file' ) { + # Check to make sure that the user set the flanduse_timeseries file + # Since the flanduse_timeseries logic checking is upstream of the fates logic, + # don't try and add the default here + my $var = "flanduse_timeseries"; + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + if ( ! defined($nl->get_value($var)) ) { + $log->fatal_error("$var is required when fates_harvest_mode is surfdata_file" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$var does NOT point to a valid filename" ); } } } From 093f0666b9b1d78701240a2036e1efca8e073133 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 17 May 2024 16:18:20 -0600 Subject: [PATCH 143/408] minor comment update --- bld/CLMBuildNamelist.pm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c1ec60fb33..e563bdffa8 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4510,7 +4510,8 @@ sub setup_logic_fates { } elsif ( $mode eq 'surfdata_file' ) { # Check to make sure that the user set the flanduse_timeseries file # Since the flanduse_timeseries logic checking is upstream of the fates logic, - # don't try and add the default here + # don't add the default here. The onus is on the user to match the correct timeseries + # data to the correct surface dataset resolution my $var = "flanduse_timeseries"; my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { From 9397431486d17cfdda6267c6eca77d2f65a888ae Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 17 May 2024 16:46:18 -0600 Subject: [PATCH 144/408] First draft ChangeLog/ChangeSum --- doc/ChangeLog | 106 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 107 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index de37d4934c..e4af944b8f 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,110 @@ =============================================================== +Tag name: ctsm5.2.006 +Originator(s): slevis (Samuel Levis) +Date: Fri May 17 16:17:54 MDT 2024 +One-line Summary: Update externals to cesm2_3_beta17 + +Purpose and description of changes +---------------------------------- + +#2493 update externals to beta17 +#2294 remove references to mct but do not remove /src/mct + +Changes unrelated to the tag's title: +#2546 fix error in cam4/cam5 test +Remove /test/tools/test_driver.sh + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: +Fixes #2493 update externals to beta17 +Fixes #2546 fix error in cam4/cam5 test (unrelated) + +Notes of particular relevance for users +--------------------------------------- +Changes to documentation: Remove references to mct and cpl7 + +Substantial timing or memory changes: Not considered + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +I added a long list of izumi nag debug tests to ExpectedFailures as per +https://github.com/ESCOMP/CMEPS/pull/460 + +Testing summary: +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- + izumi ------- IN PROGRESS + + any other testing (give details below): + + ctsm_sci + derecho ---- + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] + + Summarize any changes to answers, i.e., + - what code configurations: + - what platforms/compilers: + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + If bitwise differences were observed, how did you show they were no worse + than roundoff? Roundoff differences means one or more lines of code change results + only by roundoff level (because order of operation changes for example). Roundoff + changes to state fields usually grow to greater than roundoff as the simulation progresses. + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +cism, ccs_config, cime, cmeps, cdeps + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2539 + +=============================================================== +=============================================================== Tag name: ctsm5.2.005 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Mon 13 May 2024 04:46:10 PM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index 0edccb3a18..c73cb19309 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.006 slevis 05/17/2024 Update externals to cesm2_3_beta17 ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev From 6b460a21afc98134f330a37f9a6cda837f364aee Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 17 May 2024 18:40:30 -0600 Subject: [PATCH 145/408] Update ntests in build-namelist_test.pl --- bld/unit_testers/build-namelist_test.pl | 2 +- doc/ChangeLog | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index aa579cf908..53c71ae0e9 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 3313; +my $ntests = 3254; if ( defined($opts{'compare'}) ) { $ntests += 2001; diff --git a/doc/ChangeLog b/doc/ChangeLog index e4af944b8f..5644ed295d 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -11,7 +11,7 @@ Purpose and description of changes #2294 remove references to mct but do not remove /src/mct Changes unrelated to the tag's title: -#2546 fix error in cam4/cam5 test +#2546 fix error in cam4/cam5 test (ekluzek) Remove /test/tools/test_driver.sh Significant changes to scientifically-supported configurations From 5244813b54835ba58582afcc17b5b02d80ad442e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 18 May 2024 16:25:32 -0600 Subject: [PATCH 146/408] Initialize input fields needed for unit-testing of dust emissions and get the unit tester to PASS! --- .../test/DustEmis_test/test_DustEmis.pf | 205 +++++++++++++++++- src/biogeophys/CanopyStateType.F90 | 17 ++ src/biogeophys/FrictionVelocityMod.F90 | 18 ++ src/main/clm_instMod.F90 | 10 +- 4 files changed, 235 insertions(+), 15 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index ff4b69ab72..b7ea76df9c 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -5,15 +5,20 @@ module test_DustEmis use funit use unittestSubgridMod use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch + use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init + use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit + use clm_varcon, only : clm_varcon_init, clm_varcon_clean + use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting use DUSTMod use shr_kind_mod , only : r8 => shr_kind_r8 use unittestFilterBuilderMod, only : filter_from_range - use atm2lndType, only : atm2lnd_type + use atm2lndType, only : atm2lnd_type, atm2lnd_params_type use SoilStateType, only : soilstate_type use CanopyStateType, only : canopystate_type - use WaterStateBulkType, only : waterstatebulk_type - use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type + use TemperatureType, only : temperature_type + use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type + use unittestWaterTypeFactory, only : unittest_water_type_factory_type implicit none @@ -25,42 +30,222 @@ module test_DustEmis type(atm2lnd_type) :: atm2lnd_inst type(soilstate_type) :: soilstate_inst type(canopystate_type) :: canopystate_inst - type(WaterStateBulk_Type) :: waterstatebulk_inst - type(waterdiagnosticbulk_type) :: waterdiagnosticbulk_inst + type(temperature_type) :: temperature_inst + type(unittest_water_type_factory_type) :: water_factory + type(water_type) :: water_inst type(frictionvel_type) :: frictionvel_inst contains procedure :: setUp procedure :: tearDown + procedure :: setupEnvironment + procedure :: create_atm2lnd + procedure :: create_fv end type TestDustEmis contains + !----------------------------------------------------------------------- + subroutine setUp(this) + use ColumnType, only : col class(TestDustEmis), intent(inout) :: this character(len=5) :: NLFilename = 'none' + real(r8), allocatable :: snow_depth_col(:) + real(r8), allocatable :: urb_em(:) + integer :: begl, endl, begc, endc + integer :: c + type(atm2lnd_params_type) :: atm2lnd_params + + soil_layerstruct_predefined = '20SL_8.5m' + create_crop_landunit = .true. + use_crop = .false. + call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) + call clm_varcon_init( is_simple_buildtemp=.true.) + call this%water_factory%init() + call this%water_factory%setup_before_subgrid( & + my_nlevsoi = nlevsoi, & + nlevgrnd_additional = nlevgrnd - nlevsoi, & + my_nlevsno = 3) + call setup_single_veg_patch( pft_type=0 ) + begl = bounds%begl + endl = bounds%endl + begc = bounds%begc + endc = bounds%endc + allocate( urb_em(begl:endl) ) - call setup_single_veg_patch( pft_type=0 ) - call this%dust_emis%Init( bounds, NLFilename ) - call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) + call this%dust_emis%Init( bounds, NLFilename ) + call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) + atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & + glcmec_downscale_longwave = .false., & + lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) + ) + allocate (snow_depth_col(begc:endc)) + snow_depth_col(begc:endc) = 0.0_r8 + call SnowHydrologySetControlForTesting() + call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc)) + call this%water_factory%setup_after_subgrid(snl = 3) + call this%soilstate_inst%Init(bounds) + do c = begc, endc + this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1) + end do + call this%setupEnvironment( ) + call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) + call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) + call this%canopystate_inst%SetNMLForTesting() + call this%canopystate_inst%Init(bounds) + call this%frictionvel_inst%InitForTesting(bounds) + urb_em(begl:endl) = 0.99_r8 + call this%temperature_inst%Init(bounds, & + em_roof_lun=urb_em(begl:endl), & + em_wall_lun=urb_em(begl:endl), & + em_improad_lun=urb_em(begl:endl), & + em_perroad_lun=urb_em(begl:endl), & + is_simple_buildtemp=.true., is_prog_buildtemp=.false.) + deallocate (snow_depth_col ) + deallocate( urb_em ) end subroutine setUp + !----------------------------------------------------------------------- + subroutine tearDown(this) class(TestDustEmis), intent(inout) :: this + call this%water_factory%teardown(this%water_inst) call unittest_subgrid_teardown() + call this%atm2lnd_inst%Clean() + call clm_varcon_clean() deallocate( this%filter_nolakep ) end subroutine tearDown + !----------------------------------------------------------------------- + + subroutine setupEnvironment(this) + ! + ! !DESCRIPTION: + ! Sets up the external environment used by Dust emissions - i.e., things accessed via + ! 'use' statements. + ! + ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has + ! been completed. + ! + use ColumnType, only : col + use GridcellType, only : grc + class(TestDustEmis), intent(in) :: this + ! + integer :: c,j + real(r8), parameter :: clay = 10.0_r8 + + !----------------------------------------------------------------------- + col%dz(:,1:nlevgrnd) = 1.0_r8 + do j = 1, nlevgrnd + do c = bounds%begc, bounds%endc + col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j) + end do + end do + + do c = bounds%begc, bounds%endc + ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are + ! considered bedrock + col%nbedrock(c) = nlevsoi + + this%soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 + this%soilstate_inst%mss_frc_cly_vld_col(c) = 0.17_r8 + end do + + + ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager) + grc%londeg(:) = 0.0_r8 + + grc%area(:) = 10.0_r8 + + end subroutine setupEnvironment + + !----------------------------------------------------------------------- + + subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho ) + ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets + ! forcing fields based on inputs. Excluded inputs are given a default value + class(TestDustEmis), intent(inout) :: this + real(r8), intent(in), optional :: forc_t(:) + real(r8), intent(in), optional :: forc_pbot(:) + real(r8), intent(in), optional :: forc_rho(:) + + real(r8), parameter :: forc_t_default = 301._r8 + real(r8), parameter :: forc_pbot_default = 100000._r8 + real(r8), parameter :: forc_rho_default = 1.1_r8 + ! ------------------------------------------------------------------------ + + if (present(forc_t)) then + this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:) + else + this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default + end if + + if (present(forc_pbot)) then + this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:) + else + this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default + end if + + if (present(forc_rho)) then + this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:) + else + this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default + end if + + end subroutine create_atm2lnd + + !----------------------------------------------------------------------- + + subroutine create_fv(this, fv, u10, ram1) + ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets + ! fields based on inputs. Excluded inputs are given a default value + class(TestDustEmis), intent(inout) :: this + real(r8), intent(in), optional :: fv(:) + real(r8), intent(in), optional :: u10(:) + real(r8), intent(in), optional :: ram1(:) + + real(r8), parameter :: fv_default = 0.2_r8 + real(r8), parameter :: u10_default = 4._r8 + real(r8), parameter :: ram1_default = 200._r8 + ! ------------------------------------------------------------------------ + + if (present(fv)) then + this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv(:) + else + this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default + end if + + if (present(u10)) then + this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10(:) + else + this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default + end if + + if (present(ram1)) then + this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1(:) + else + this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default + end if + + end subroutine create_fv + + !----------------------------------------------------------------------- + @Test subroutine check_dust_emis(this) class(TestDustEmis), intent(inout) :: this + call this%create_atm2lnd() + call this%create_fv() call DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%waterstatebulk_inst, & - this%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis) + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis) call DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst, this%dust_emis) + !----------------------------------------------------------------------- + end subroutine check_dust_emis end module test_DustEmis \ No newline at end of file diff --git a/src/biogeophys/CanopyStateType.F90 b/src/biogeophys/CanopyStateType.F90 index 313f7a83f3..4bfc08fc80 100644 --- a/src/biogeophys/CanopyStateType.F90 +++ b/src/biogeophys/CanopyStateType.F90 @@ -72,6 +72,8 @@ module CanopyStateType procedure, public :: UpdateAccVars procedure, public :: Restart + procedure, public :: SetNMLForTesting ! Set namelist for unit-testing + end type CanopyState_type character(len=*), parameter, private :: sourcefile = & @@ -442,6 +444,21 @@ subroutine ReadNML( this, NLFilename ) end subroutine ReadNML + !----------------------------------------------------------------------- + + subroutine SetNMLForTesting( this ) + ! + ! Set canopy parameter namelist control settings for unit-testing + ! + class(canopystate_type) :: this + ! LOCAL VARIABLES: + !----------------------------------------------------------------------- + + + this%leaf_mr_vcm = 0.015_r8 + + end subroutine SetNMLForTesting + !----------------------------------------------------------------------- subroutine UpdateAccVars (this, bounds) ! diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 7cea2a22f9..042415f545 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -89,6 +89,8 @@ module FrictionVelocityMod procedure, public :: FrictionVelocity ! Calculate friction velocity procedure, public :: MoninObukIni ! Initialization of the Monin-Obukhov length + procedure, public :: InitForTesting ! version of Init meant for unit testing + ! Private procedures procedure, private :: InitAllocate procedure, private :: InitHistory @@ -122,6 +124,22 @@ subroutine Init(this, bounds, NLFilename, params_ncid) end subroutine Init + !------------------------------------------------------------------------ + subroutine InitForTesting(this, bounds) + ! Initialization for unit testing, hardcodes namelist and parameter file settings + class(frictionvel_type) :: this + type(bounds_type), intent(in) :: bounds + + call this%InitAllocate(bounds) + call this%InitHistory(bounds) + call this%InitCold(bounds) + this%zetamaxstable = 0.5_r8 + this%zsno = 0.00085_r8 + this%zlnd = 0.000775_r8 + this%zglc = 0.00230000005_r8 + + end subroutine InitForTesting + !------------------------------------------------------------------------ subroutine InitAllocate(this, bounds) ! diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index b9d74c418a..a24e05b27c 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -296,11 +296,11 @@ subroutine clm_instInit(bounds) ! Initialization of public data types call temperature_inst%Init(bounds, & - urbanparams_inst%em_roof(begl:endl), & - urbanparams_inst%em_wall(begl:endl), & - urbanparams_inst%em_improad(begl:endl), & - urbanparams_inst%em_perroad(begl:endl), & - IsSimpleBuildTemp(), IsProgBuildTemp() ) + em_roof_lun=urbanparams_inst%em_roof(begl:endl), & + em_wall_lun=urbanparams_inst%em_wall(begl:endl), & + em_improad_lun=urbanparams_inst%em_improad(begl:endl), & + em_perroad_lun=urbanparams_inst%em_perroad(begl:endl), & + is_simple_buildtemp=IsSimpleBuildTemp(), is_prog_buildtemp=IsProgBuildTemp() ) call active_layer_inst%Init(bounds) From 9bf2ad13acdca56437392b0e80e715320c3a7eb5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 18 May 2024 22:17:39 -0600 Subject: [PATCH 147/408] Put DustEmission and DustDryDep as methods inside of the dust_type --- src/biogeochem/DUSTMod.F90 | 39 +++++++++---------- .../test/DustEmis_test/test_DustEmis.pf | 10 ++--- 2 files changed, 23 insertions(+), 26 deletions(-) diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90 index ffa2bfe6f0..e0e4e469a1 100644 --- a/src/biogeochem/DUSTMod.F90 +++ b/src/biogeochem/DUSTMod.F90 @@ -37,11 +37,6 @@ module DUSTMod implicit none private ! - ! !PUBLIC MEMBER FUNCTIONS: - ! - public DustEmission ! Dust mobilization - public DustDryDep ! Turbulent dry deposition for dust - ! ! !PUBLIC DATA: ! real(r8) , allocatable :: ovr_src_snk_mss(:,:) @@ -61,16 +56,18 @@ module DUSTMod real(r8), pointer, private :: vlc_trb_2_patch (:) ! turbulent deposition velocity 2(m/s) real(r8), pointer, private :: vlc_trb_3_patch (:) ! turbulent deposition velocity 3(m/s) real(r8), pointer, private :: vlc_trb_4_patch (:) ! turbulent deposition velocity 4(m/s) - type(soil_erod_stream_type), private :: soil_erod_stream ! Zender soil erodibility stream data + type(soil_erod_stream_type), private :: soil_erod_stream ! Zender soil erodibility stream data real(r8), pointer, private :: mbl_bsn_fct_col (:) ! [dimensionless] basin factor, or soil erodibility, time-constant contains procedure , public :: Init + procedure , public :: DustEmission ! Dust mobilization + procedure , public :: DustDryDep ! Turbulent dry deposition for dust procedure , private :: InitAllocate procedure , private :: InitHistory procedure , private :: InitCold - procedure , private :: InitDustVars ! Initialize variables used in subroutine Dust + procedure , private :: InitDustVars ! Initialize variables used in DustEmission method end type dust_type !------------------------------------------------------------------------ @@ -213,10 +210,10 @@ subroutine InitCold(this, bounds) end subroutine InitCold !------------------------------------------------------------------------ - subroutine DustEmission (bounds, & + subroutine DustEmission (this, bounds, & num_nolakep, filter_nolakep, & atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, & - frictionvel_inst, dust_inst) + frictionvel_inst) ! ! !DESCRIPTION: ! Dust mobilization. This code simulates dust mobilization due to wind @@ -230,6 +227,7 @@ subroutine DustEmission (bounds, & use subgridaveMod, only : p2g ! ! !ARGUMENTS: + class (dust_type) :: this type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter integer , intent(in) :: filter_nolakep(num_nolakep) ! patch filter for non-lake points @@ -239,7 +237,6 @@ subroutine DustEmission (bounds, & type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst type(frictionvel_type) , intent(in) :: frictionvel_inst - type(dust_type) , intent(inout) :: dust_inst ! ! !LOCAL VARIABLES @@ -291,9 +288,9 @@ subroutine DustEmission (bounds, & fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) (for dust model) u10 => frictionvel_inst%u10_patch , & ! Input: [real(r8) (:) ] 10-m wind (m/s) (created for dust model) - mbl_bsn_fct => dust_inst%mbl_bsn_fct_col , & ! Input: [real(r8) (:) ] basin factor - flx_mss_vrt_dst => dust_inst%flx_mss_vrt_dst_patch , & ! Output: [real(r8) (:,:) ] surface dust emission (kg/m**2/s) - flx_mss_vrt_dst_tot => dust_inst%flx_mss_vrt_dst_tot_patch & ! Output: [real(r8) (:) ] total dust flux back to atmosphere (pft) + mbl_bsn_fct => this%mbl_bsn_fct_col , & ! Input: [real(r8) (:) ] basin factor + flx_mss_vrt_dst => this%flx_mss_vrt_dst_patch , & ! Output: [real(r8) (:,:) ] surface dust emission (kg/m**2/s) + flx_mss_vrt_dst_tot => this%flx_mss_vrt_dst_tot_patch & ! Output: [real(r8) (:) ] total dust flux back to atmosphere (pft) ) ttlai(bounds%begp : bounds%endp) = 0._r8 @@ -498,8 +495,8 @@ subroutine DustEmission (bounds, & end subroutine DustEmission !------------------------------------------------------------------------ - subroutine DustDryDep (bounds, & - atm2lnd_inst, frictionvel_inst, dust_inst) + subroutine DustDryDep (this, bounds, & + atm2lnd_inst, frictionvel_inst) ! ! !DESCRIPTION: ! @@ -520,10 +517,10 @@ subroutine DustDryDep (bounds, & use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ ! ! !ARGUMENTS: + class (dust_type) :: this type(bounds_type) , intent(in) :: bounds type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(frictionvel_type) , intent(in) :: frictionvel_inst - type(dust_type) , intent(inout) :: dust_inst ! ! !LOCAL VARIABLES integer :: p,c,g,m,n ! indices @@ -550,11 +547,11 @@ subroutine DustDryDep (bounds, & ram1 => frictionvel_inst%ram1_patch , & ! Input: [real(r8) (:) ] aerodynamical resistance (s/m) fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) - vlc_trb => dust_inst%vlc_trb_patch , & ! Output: [real(r8) (:,:) ] Turbulent deposn velocity (m/s) - vlc_trb_1 => dust_inst%vlc_trb_1_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 1 - vlc_trb_2 => dust_inst%vlc_trb_2_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 2 - vlc_trb_3 => dust_inst%vlc_trb_3_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 3 - vlc_trb_4 => dust_inst%vlc_trb_4_patch & ! Output: [real(r8) (:) ] Turbulent deposition velocity 4 + vlc_trb => this%vlc_trb_patch , & ! Output: [real(r8) (:,:) ] Turbulent deposn velocity (m/s) + vlc_trb_1 => this%vlc_trb_1_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 1 + vlc_trb_2 => this%vlc_trb_2_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 2 + vlc_trb_3 => this%vlc_trb_3_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 3 + vlc_trb_4 => this%vlc_trb_4_patch & ! Output: [real(r8) (:) ] Turbulent deposition velocity 4 ) do p = bounds%begp,bounds%endp diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index b7ea76df9c..9be97453b0 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -239,13 +239,13 @@ contains call this%create_atm2lnd() call this%create_fv() - call DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst, this%dust_emis) - call DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst, this%dust_emis) - - !----------------------------------------------------------------------- + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) end subroutine check_dust_emis + !----------------------------------------------------------------------- + end module test_DustEmis \ No newline at end of file From 7072f7aa8e1e44a5af15b5c82c4634268b5dc50b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 20 May 2024 11:29:08 -0600 Subject: [PATCH 148/408] Resolve the mizuRoute issue --- Externals.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index a8a77a40f1..cb2622dedf 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -27,10 +27,10 @@ tag = mosart1_0_49 required = True [mizuRoute] -local_path = components/mizuRoute +tag = cesm-coupling.n02_v2.1.2 protocol = git +local_path = components/mizuroute repo_url = https://github.com/ESCOMP/mizuRoute -hash = 81c720c required = True [ccs_config] From ff4d35f2607bb637e37baaca0109d4d189efe0fd Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 10:30:14 -0600 Subject: [PATCH 149/408] Remove set_glc2lnd_fields_mct (not tested, yet) --- src/main/glc2lndMod.F90 | 56 ----------------------------------------- 1 file changed, 56 deletions(-) diff --git a/src/main/glc2lndMod.F90 b/src/main/glc2lndMod.F90 index ecd6818210..2d0dbb5791 100644 --- a/src/main/glc2lndMod.F90 +++ b/src/main/glc2lndMod.F90 @@ -78,7 +78,6 @@ module glc2lndMod ! - set_glc2lnd_fields ! - update_glc2lnd_fracs ! - update_glc2lnd_topo - procedure, public :: set_glc2lnd_fields_mct ! set coupling fields sent from glc to lnd procedure, public :: set_glc2lnd_fields_nuopc ! set coupling fields sent from glc to lnd procedure, public :: update_glc2lnd_fracs ! update subgrid fractions based on input from GLC procedure, public :: update_glc2lnd_topo ! update topographic heights @@ -242,61 +241,6 @@ subroutine Clean(this) end subroutine Clean - !----------------------------------------------------------------------- - subroutine set_glc2lnd_fields_mct(this, bounds, glc_present, x2l, & - index_x2l_Sg_ice_covered, index_x2l_Sg_topo, index_x2l_Flgg_hflx, & - index_x2l_Sg_icemask, index_x2l_Sg_icemask_coupled_fluxes) - ! - ! !DESCRIPTION: - ! Set coupling fields sent from glc to lnd - ! - ! If glc_present is true, then the given fields are all assumed to be valid; if - ! glc_present is false, then these fields are ignored. - ! - ! !ARGUMENTS: - class(glc2lnd_type), intent(inout) :: this - type(bounds_type) , intent(in) :: bounds - logical , intent(in) :: glc_present ! true if running with a non-stub glc model - real(r8) , intent(in) :: x2l(:, bounds%begg: ) ! driver import state to land model [field, gridcell] - integer , intent(in) :: index_x2l_Sg_ice_covered( 0: ) ! indices of ice-covered field in x2l, for each elevation class - integer , intent(in) :: index_x2l_Sg_topo( 0: ) ! indices of topo field in x2l, for each elevation class - integer , intent(in) :: index_x2l_Flgg_hflx( 0: ) ! indices of heat flux field in x2l, for each elevation class - integer , intent(in) :: index_x2l_Sg_icemask ! index of icemask field in x2l - integer , intent(in) :: index_x2l_Sg_icemask_coupled_fluxes ! index of icemask_coupled_fluxes field in x2l - ! - ! !LOCAL VARIABLES: - integer :: g - integer :: ice_class - - character(len=*), parameter :: subname = 'set_glc2lnd_fields_mct' - !----------------------------------------------------------------------- - - SHR_ASSERT_FL((ubound(x2l, 2) == bounds%endg), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(index_x2l_Sg_ice_covered) == (/maxpatch_glc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(index_x2l_Sg_topo) == (/maxpatch_glc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(index_x2l_Flgg_hflx) == (/maxpatch_glc/)), sourcefile, __LINE__) - - if (glc_present) then - do g = bounds%begg, bounds%endg - do ice_class = 0, maxpatch_glc - this%frac_grc(g,ice_class) = x2l(index_x2l_Sg_ice_covered(ice_class),g) - this%topo_grc(g,ice_class) = x2l(index_x2l_Sg_topo(ice_class),g) - this%hflx_grc(g,ice_class) = x2l(index_x2l_Flgg_hflx(ice_class),g) - end do - this%icemask_grc(g) = x2l(index_x2l_Sg_icemask,g) - this%icemask_coupled_fluxes_grc(g) = x2l(index_x2l_Sg_icemask_coupled_fluxes,g) - end do - - call this%set_glc2lnd_fields_wrapup(bounds) - else - if (glc_do_dynglacier) then - call endrun(' ERROR: With glc_present false (e.g., a stub glc model), glc_do_dynglacier must be false '// & - errMsg(sourcefile, __LINE__)) - end if - end if - - end subroutine set_glc2lnd_fields_mct - !----------------------------------------------------------------------- subroutine set_glc2lnd_fields_nuopc(this, bounds, glc_present, & frac_grc, topo_grc, hflx_grc, icemask_grc, icemask_coupled_fluxes_grc) From 4d62578a920eae09f482776576a30e9750e1e8e1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 10:47:56 -0600 Subject: [PATCH 150/408] Remove /src/cpl/mct again; I was right the first time --- src/cpl/mct/ExcessIceStreamType.F90 | 144 ----- src/cpl/mct/FireDataBaseType.F90 | 561 ------------------- src/cpl/mct/SoilMoistureStreamMod.F90 | 418 -------------- src/cpl/mct/UrbanTimeVarType.F90 | 314 ----------- src/cpl/mct/ch4FInundatedStreamType.F90 | 389 ------------- src/cpl/mct/clm_cpl_indices.F90 | 330 ----------- src/cpl/mct/laiStreamMod.F90 | 241 --------- src/cpl/mct/lnd_comp_mct.F90 | 632 ---------------------- src/cpl/mct/lnd_import_export.F90 | 354 ------------ src/cpl/mct/lnd_set_decomp_and_domain.F90 | 352 ------------ src/cpl/mct/ndepStreamMod.F90 | 376 ------------- 11 files changed, 4111 deletions(-) delete mode 100644 src/cpl/mct/ExcessIceStreamType.F90 delete mode 100644 src/cpl/mct/FireDataBaseType.F90 delete mode 100644 src/cpl/mct/SoilMoistureStreamMod.F90 delete mode 100644 src/cpl/mct/UrbanTimeVarType.F90 delete mode 100644 src/cpl/mct/ch4FInundatedStreamType.F90 delete mode 100644 src/cpl/mct/clm_cpl_indices.F90 delete mode 100644 src/cpl/mct/laiStreamMod.F90 delete mode 100644 src/cpl/mct/lnd_comp_mct.F90 delete mode 100644 src/cpl/mct/lnd_import_export.F90 delete mode 100644 src/cpl/mct/lnd_set_decomp_and_domain.F90 delete mode 100644 src/cpl/mct/ndepStreamMod.F90 diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90 deleted file mode 100644 index 5c5394233c..0000000000 --- a/src/cpl/mct/ExcessIceStreamType.F90 +++ /dev/null @@ -1,144 +0,0 @@ -module ExcessIceStreamType - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Stub for ExcessIceStreams for the MCT driver. So that MCT can be used - ! without excess ice streams. - ! - ! !USES - use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL - use shr_log_mod , only : errMsg => shr_log_errMsg - use spmdMod , only : mpicom, masterproc - use clm_varctl , only : iulog - use abortutils , only : endrun - use decompMod , only : bounds_type - - ! !PUBLIC TYPES: - implicit none - private - - public :: UseExcessIceStreams ! If streams will be used - - type, public :: excessicestream_type - contains - - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: Init ! Initialize and read data in - procedure, public :: CalcExcessIce ! Calculate excess ice ammount - - ! !PRIVATE MEMBER FUNCTIONS: - procedure, private :: ReadNML ! Read in namelist - - end type excessicestream_type - ! ! PRIVATE DATA: - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -!============================================================================== -contains -!============================================================================== - - subroutine Init(this, bounds, NLFilename) - ! - ! - ! arguments - implicit none - class(excessicestream_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - - ! - ! local variables - - call this%ReadNML( bounds, NLFileName ) - end subroutine Init - - subroutine CalcExcessIce(this,bounds,exice_bulk_init) - - ! only transfers grid values to columns - implicit none - class(excessicestream_type) :: this - type(bounds_type), intent(in) :: bounds - real(r8) , intent(inout) :: exice_bulk_init(bounds%begc:bounds%endc) - ! - ! !LOCAL VARIABLES: - - end subroutine CalcExcessIce - - logical function UseExcessIceStreams() - ! - ! !DESCRIPTION: - ! Return true if - ! - ! !USES: - ! - ! !ARGUMENTS: - implicit none - ! - ! !LOCAL VARIABLES: - UseExcessIceStreams = .false. -end function UseExcessIceStreams - -subroutine ReadNML(this, bounds, NLFilename) - ! - ! Read the namelist data stream information. - ! - ! Uses: - use shr_nl_mod , only : shr_nl_find_group_name - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_mpi_mod , only : shr_mpi_bcast - ! - ! arguments - implicit none - class(excessicestream_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - logical :: use_excess_ice_streams = .false. ! logical to turn on use of excess ice streams - character(len=CL) :: stream_fldFileName_exice = ' ' - character(len=CL) :: stream_mapalgo_exice = 'none' - character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read - character(len=*), parameter :: subName = "('exice_streams::ReadNML')" - !----------------------------------------------------------------------- - - namelist /exice_streams/ & ! MUST agree with namelist_name above - stream_mapalgo_exice, stream_fldFileName_exice, use_excess_ice_streams - !----------------------------------------------------------------------- - ! Default values for namelist - - ! Read excess ice namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=exice_streams,iostat=nml_error) ! MUST agree with namelist_name above - if (nml_error /= 0) then - call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - else - call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - close(nu_nml) - endif - - call shr_mpi_bcast(use_excess_ice_streams , mpicom) - - if (masterproc) then - if ( use_excess_ice_streams ) then - call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__)) - end if - if ( trim(stream_fldFileName_exice) /= '' ) then - call endrun(msg=' ERROR stream_fldFileName_exice can NOT be set for the MCT driver'//errMsg(sourcefile, __LINE__)) - end if - if ( trim(stream_mapalgo_exice) /= 'none' ) then - call endrun(msg=' ERROR stream_mapalgo_exice can only be none for the MCT driver'//errMsg(sourcefile, __LINE__)) - end if - endif - -end subroutine ReadNML - -end module ExcessIceStreamType diff --git a/src/cpl/mct/FireDataBaseType.F90 b/src/cpl/mct/FireDataBaseType.F90 deleted file mode 100644 index 0ee635b2fa..0000000000 --- a/src/cpl/mct/FireDataBaseType.F90 +++ /dev/null @@ -1,561 +0,0 @@ -module FireDataBaseType - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! module for handling of fire data - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create, shr_strdata_print - use shr_strdata_mod , only : shr_strdata_advance - use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog, inst_name - use spmdMod , only : masterproc, mpicom, comp_id - use fileutils , only : getavu, relavu - use domainMod , only : ldomain - use abortutils , only : endrun - use decompMod , only : bounds_type - use FireMethodType , only : fire_method_type - use lnd_set_decomp_and_domain, only : gsmap_global - use mct_mod - ! - implicit none - private - ! - ! !PUBLIC TYPES: - public :: fire_base_type - - ! - type, abstract, extends(fire_method_type) :: fire_base_type - private - ! !PRIVATE MEMBER DATA: - - real(r8), public, pointer :: forc_lnfm(:) ! Lightning frequency - real(r8), public, pointer :: forc_hdm(:) ! Human population density - - real(r8), public, pointer :: gdp_lf_col(:) ! col global real gdp data (k US$/capita) - real(r8), public, pointer :: peatf_lf_col(:) ! col global peatland fraction data (0-1) - integer , public, pointer :: abm_lf_col(:) ! col global peak month of crop fire emissions - - type(shr_strdata_type) :: sdat_hdm ! Human population density input data stream - type(shr_strdata_type) :: sdat_lnfm ! Lightning input data stream - - contains - ! - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: FireInit => BaseFireInit ! Initialization of Fire - procedure, public :: BaseFireInit ! Initialization of Fire - procedure(FireReadNML_interface), public, deferred :: FireReadNML ! Read in namelist for Fire - procedure, public :: FireInterp ! Interpolate fire data - procedure(need_lightning_and_popdens_interface), public, deferred :: & - need_lightning_and_popdens ! Returns true if need lightning & popdens - ! - ! !PRIVATE MEMBER FUNCTIONS: - procedure, private :: hdm_init ! position datasets for dynamic human population density - procedure, private :: hdm_interp ! interpolates between two years of human pop. density file data - procedure, private :: lnfm_init ! position datasets for Lightning - procedure, private :: lnfm_interp ! interpolates between two years of Lightning file data - procedure, private :: surfdataread ! read fire related data from surface data set - end type fire_base_type - !----------------------------------------------------------------------- - - abstract interface - !----------------------------------------------------------------------- - function need_lightning_and_popdens_interface(this) result(need_lightning_and_popdens) - ! - ! !DESCRIPTION: - ! Returns true if need lightning and popdens, false otherwise - ! - ! USES - import :: fire_base_type - ! - ! !ARGUMENTS: - class(fire_base_type), intent(in) :: this - logical :: need_lightning_and_popdens ! function result - !----------------------------------------------------------------------- - end function need_lightning_and_popdens_interface - end interface - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -contains - - !----------------------------------------------------------------------- - subroutine FireReadNML_interface( this, NLFilename ) - ! - ! !DESCRIPTION: - ! Read the namelist for Fire - ! - ! !USES: - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - character(len=*), intent(in) :: NLFilename ! Namelist filename - end subroutine FireReadNML_interface - - !----------------------------------------------------------------------- - subroutine BaseFireInit( this, bounds, NLFilename ) - ! - ! !DESCRIPTION: - ! Initialize CN Fire module - ! !USES: - use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename - !----------------------------------------------------------------------- - - if ( this%need_lightning_and_popdens() ) then - ! Allocate lightning forcing data - allocate( this%forc_lnfm(bounds%begg:bounds%endg) ) - this%forc_lnfm(bounds%begg:) = nan - ! Allocate pop dens forcing data - allocate( this%forc_hdm(bounds%begg:bounds%endg) ) - this%forc_hdm(bounds%begg:) = nan - - ! Allocate real gdp data - allocate(this%gdp_lf_col(bounds%begc:bounds%endc)) - ! Allocate peatland fraction data - allocate(this%peatf_lf_col(bounds%begc:bounds%endc)) - ! Allocates peak month of crop fire emissions - allocate(this%abm_lf_col(bounds%begc:bounds%endc)) - - - call this%hdm_init(bounds, NLFilename) - call this%hdm_interp(bounds) - call this%lnfm_init(bounds, NLFilename) - call this%lnfm_interp(bounds) - call this%surfdataread(bounds) - end if - - end subroutine BaseFireInit - - !----------------------------------------------------------------------- - subroutine FireInterp(this,bounds) - ! - ! !DESCRIPTION: - ! Interpolate CN Fire datasets - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - !----------------------------------------------------------------------- - - if ( this%need_lightning_and_popdens() ) then - call this%hdm_interp(bounds) - call this%lnfm_interp(bounds) - end if - - end subroutine FireInterp - - !----------------------------------------------------------------------- - subroutine hdm_init( this, bounds, NLFilename ) - ! - ! !DESCRIPTION: - ! Initialize data stream information for population density. - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use histFileMod , only : hist_addfld1d - ! - ! !ARGUMENTS: - implicit none - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! !LOCAL VARIABLES: - integer :: stream_year_first_popdens ! first year in pop. dens. stream to use - integer :: stream_year_last_popdens ! last year in pop. dens. stream to use - integer :: model_year_align_popdens ! align stream_year_first_hdm with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_popdens ! population density streams filename - character(len=CL) :: popdensmapalgo = 'bilinear' ! mapping alogrithm for population density - character(len=CL) :: popdens_tintalgo = 'nearest'! time interpolation alogrithm for population density - character(len=CL) :: stream_meshfile_popdens ! not used - character(*), parameter :: subName = "('hdmdyn_init')" - character(*), parameter :: F00 = "('(hdmdyn_init) ',4a)" - !----------------------------------------------------------------------- - - namelist /popd_streams/ & - stream_year_first_popdens, & - stream_year_last_popdens, & - model_year_align_popdens, & - popdensmapalgo, & - stream_fldFileName_popdens, & - stream_meshfile_popdens , & - popdens_tintalgo - - ! Default values for namelist - stream_year_first_popdens = 1 ! first year in stream to use - stream_year_last_popdens = 1 ! last year in stream to use - model_year_align_popdens = 1 ! align stream_year_first_popdens with this model year - stream_fldFileName_popdens = ' ' - - ! Read popd_streams namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'popd_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=popd_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg='ERROR reading popd_streams namelist'//errMsg(sourcefile, __LINE__)) - end if - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_year_first_popdens, mpicom) - call shr_mpi_bcast(stream_year_last_popdens, mpicom) - call shr_mpi_bcast(model_year_align_popdens, mpicom) - call shr_mpi_bcast(stream_fldFileName_popdens, mpicom) - call shr_mpi_bcast(popdens_tintalgo, mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'popdens_streams settings:' - write(iulog,*) ' stream_year_first_popdens = ',stream_year_first_popdens - write(iulog,*) ' stream_year_last_popdens = ',stream_year_last_popdens - write(iulog,*) ' model_year_align_popdens = ',model_year_align_popdens - write(iulog,*) ' stream_fldFileName_popdens = ',stream_fldFileName_popdens - write(iulog,*) ' popdens_tintalgo = ',popdens_tintalgo - write(iulog,*) ' ' - endif - - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(this%sdat_hdm,name="clmhdm", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_popdens, & - yearLast=stream_year_last_popdens, & - yearAlign=model_year_align_popdens, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_popdens), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/trim(stream_fldFileName_popdens)/) , & - fldListFile='hdm', & - fldListModel='hdm', & - fillalgo='none', & - mapalgo=popdensmapalgo, & - calendar=get_calendar(), & - tintalgo=popdens_tintalgo, & - taxmode='extend' ) - - if (masterproc) then - call shr_strdata_print(this%sdat_hdm,'population density data') - endif - - ! Add history fields - call hist_addfld1d (fname='HDM', units='counts/km^2', & - avgflag='A', long_name='human population density', & - ptr_lnd=this%forc_hdm, default='inactive') - - end subroutine hdm_init - - !----------------------------------------------------------------------- - subroutine hdm_interp( this, bounds) - ! - ! !DESCRIPTION: - ! Interpolate data stream information for population density. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g, ig - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(this%sdat_hdm, mcdate, sec, mpicom, 'hdmdyn') - - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - this%forc_hdm(g) = this%sdat_hdm%avs(1)%rAttr(1,ig) - end do - - end subroutine hdm_interp - - !----------------------------------------------------------------------- - subroutine lnfm_init( this, bounds, NLFilename ) - ! - ! !DESCRIPTION: - ! - ! Initialize data stream information for Lightning. - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use histFileMod , only : hist_addfld1d - ! - ! !ARGUMENTS: - implicit none - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename - ! - ! !LOCAL VARIABLES: - integer :: stream_year_first_lightng ! first year in Lightning stream to use - integer :: stream_year_last_lightng ! last year in Lightning stream to use - integer :: model_year_align_lightng ! align stream_year_first_lnfm with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_lightng ! lightning stream filename to read - character(len=CL) :: lightng_tintalgo = 'linear'! time interpolation alogrithm - character(len=CL) :: lightngmapalgo = 'bilinear'! Mapping alogrithm - character(*), parameter :: subName = "('lnfmdyn_init')" - character(*), parameter :: F00 = "('(lnfmdyn_init) ',4a)" - !----------------------------------------------------------------------- - - namelist /light_streams/ & - stream_year_first_lightng, & - stream_year_last_lightng, & - model_year_align_lightng, & - lightngmapalgo, & - stream_fldFileName_lightng, & - lightng_tintalgo - - ! Default values for namelist - stream_year_first_lightng = 1 ! first year in stream to use - stream_year_last_lightng = 1 ! last year in stream to use - model_year_align_lightng = 1 ! align stream_year_first_lnfm with this model year - stream_fldFileName_lightng = ' ' - - ! Read light_streams namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'light_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=light_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg='ERROR reading light_streams namelist'//errMsg(sourcefile, __LINE__)) - end if - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_year_first_lightng, mpicom) - call shr_mpi_bcast(stream_year_last_lightng, mpicom) - call shr_mpi_bcast(model_year_align_lightng, mpicom) - call shr_mpi_bcast(stream_fldFileName_lightng, mpicom) - call shr_mpi_bcast(lightng_tintalgo, mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'light_stream settings:' - write(iulog,*) ' stream_year_first_lightng = ',stream_year_first_lightng - write(iulog,*) ' stream_year_last_lightng = ',stream_year_last_lightng - write(iulog,*) ' model_year_align_lightng = ',model_year_align_lightng - write(iulog,*) ' stream_fldFileName_lightng = ',stream_fldFileName_lightng - write(iulog,*) ' lightng_tintalgo = ',lightng_tintalgo - write(iulog,*) ' ' - endif - - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(this%sdat_lnfm,name="clmlnfm", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_lightng, & - yearLast=stream_year_last_lightng, & - yearAlign=model_year_align_lightng, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_lightng), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/trim(stream_fldFileName_lightng)/), & - fldListFile='lnfm', & - fldListModel='lnfm', & - fillalgo='none', & - tintalgo=lightng_tintalgo, & - mapalgo=lightngmapalgo, & - calendar=get_calendar(), & - taxmode='cycle' ) - - if (masterproc) then - call shr_strdata_print(this%sdat_lnfm,'Lightning data') - endif - - ! Add history fields - call hist_addfld1d (fname='LNFM', units='counts/km^2/hr', & - avgflag='A', long_name='Lightning frequency', & - ptr_lnd=this%forc_lnfm, default='inactive') - - end subroutine lnfm_init - - !----------------------------------------------------------------------- - subroutine lnfm_interp(this, bounds ) - ! - ! !DESCRIPTION: - ! Interpolate data stream information for Lightning. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g, ig - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(this%sdat_lnfm, mcdate, sec, mpicom, 'lnfmdyn') - - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - this%forc_lnfm(g) = this%sdat_lnfm%avs(1)%rAttr(1,ig) - end do - - end subroutine lnfm_interp - - !----------------------------------------------------------------------- - subroutine surfdataread(this, bounds) - ! - ! !DESCRIPTION: - ! Read surface data set to populate relevant fire-related variables - ! - ! !USES: - use spmdMod , only : masterproc - use clm_varctl , only : nsrest, nsrStartup, fsurdat - use clm_varcon , only : grlnd - use ColumnType , only : col - use fileutils , only : getfil - use ncdio_pio - ! - ! !ARGUMENTS: - class(fire_base_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g,c ! indices - type(file_desc_t) :: ncid ! netcdf id - logical :: readvar ! true => variable is on initial dataset - character(len=256) :: locfn ! local filename - real(r8), pointer :: gdp(:) ! global gdp data (needs to be a pointer for use in ncdio) - real(r8), pointer :: peatf(:) ! global peatf data (needs to be a pointer for use in ncdio) - integer, pointer :: abm(:) ! global abm data (needs to be a pointer for use in ncdio) - !----------------------------------------------------------------------- - - ! -------------------------------------------------------------------- - ! Open surface dataset - ! -------------------------------------------------------------------- - - call getfil (fsurdat, locfn, 0) - call ncd_pio_openfile (ncid, locfn, 0) - - ! -------------------------------------------------------------------- - ! Read in GDP data - ! -------------------------------------------------------------------- - - allocate(gdp(bounds%begg:bounds%endg)) - call ncd_io(ncid=ncid, varname='gdp', flag='read', data=gdp, dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun(msg=' ERROR: gdp NOT on surfdata file'//errMsg(sourcefile, __LINE__)) - end if - do c = bounds%begc, bounds%endc - g = col%gridcell(c) - this%gdp_lf_col(c) = gdp(g) - end do - deallocate(gdp) - - ! -------------------------------------------------------------------- - ! Read in peatf data - ! -------------------------------------------------------------------- - - allocate(peatf(bounds%begg:bounds%endg)) - call ncd_io(ncid=ncid, varname='peatf', flag='read', data=peatf, dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun(msg=' ERROR: peatf NOT on surfdata file'//errMsg(sourcefile, __LINE__)) - end if - do c = bounds%begc, bounds%endc - g = col%gridcell(c) - this%peatf_lf_col(c) = peatf(g) - end do - deallocate(peatf) - - ! -------------------------------------------------------------------- - ! Read in ABM data - ! -------------------------------------------------------------------- - - allocate(abm(bounds%begg:bounds%endg)) - call ncd_io(ncid=ncid, varname='abm', flag='read', data=abm, dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun(msg=' ERROR: abm NOT on surfdata file'//errMsg(sourcefile, __LINE__)) - end if - do c = bounds%begc, bounds%endc - g = col%gridcell(c) - this%abm_lf_col(c) = abm(g) - end do - deallocate(abm) - - ! Close file - - call ncd_pio_closefile(ncid) - - if (masterproc) then - write(iulog,*) 'Successfully read fmax, soil color, sand and clay boundary data' - write(iulog,*) - endif - - end subroutine surfdataread - - -end module FireDataBaseType diff --git a/src/cpl/mct/SoilMoistureStreamMod.F90 b/src/cpl/mct/SoilMoistureStreamMod.F90 deleted file mode 100644 index 8b366d6c8e..0000000000 --- a/src/cpl/mct/SoilMoistureStreamMod.F90 +++ /dev/null @@ -1,418 +0,0 @@ -module SoilMoistureStreamMod - - ! ********************************************************************** - ! --------------------------- IMPORTANT NOTE --------------------------- - ! - ! In cases using the NUOPC driver/mediator, we use a different version of this module, - ! based on CDEPS, which resides in src/cpl/nuopc/. Changes to the science here should - ! also be made in the similar file in src/cpl/nuopc. Once we start using CDEPS by - ! default, we can remove this version and move the CDEPS-based version into its place. - ! ********************************************************************** - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Read in soil moisture from data stream - ! - ! !USES: - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create - use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance - use shr_kind_mod , only : r8 => shr_kind_r8 - use shr_kind_mod , only : CL => shr_kind_CL, CXX => shr_kind_CXX - use shr_log_mod , only : errMsg => shr_log_errMsg - use decompMod , only : bounds_type, subgrid_level_column - use abortutils , only : endrun - use clm_varctl , only : iulog, use_soil_moisture_streams, inst_name - use clm_varcon , only : grlnd - use controlMod , only : NLFilename - use domainMod , only : ldomain - use LandunitType , only : lun - use ColumnType , only : col - use SoilStateType , only : soilstate_type - use WaterStateBulkType , only : waterstatebulk_type - use perf_mod , only : t_startf, t_stopf - use spmdMod , only : masterproc, mpicom, comp_id - use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo - use mct_mod - use ncdio_pio - ! - ! !PUBLIC TYPES: - implicit none - private - ! - ! !PUBLIC MEMBER FUNCTIONS: - public :: PrescribedSoilMoistureInit ! position datasets for soil moisture - public :: PrescribedSoilMoistureAdvance ! Advance the soil moisture stream (outside of Open-MP loops) - public :: PrescribedSoilMoistureInterp ! interpolates between two periods of soil moisture data - - ! !PRIVATE MEMBER DATA: - type(shr_strdata_type) :: sdat_soilm ! soil moisture input data stream - integer :: ism ! Soil moisture steram index - integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - logical :: soilm_ignore_data_if_missing ! If should ignore overridding a point with soil moisture data - ! from the streams file, if the streams file shows that point - ! as missing (namelist item) - ! - ! !PRIVATE TYPES: - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - !----------------------------------------------------------------------- - -contains - - !----------------------------------------------------------------------- - ! - ! soil_moisture_init - ! - !----------------------------------------------------------------------- - subroutine PrescribedSoilMoistureInit(bounds) - ! - ! Initialize data stream information for soil moisture. - ! - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use shr_stream_mod , only : shr_stream_file_null - use shr_string_mod , only : shr_string_listCreateField - use clm_varpar , only : nlevsoi - ! - ! !ARGUMENTS: - implicit none - type(bounds_type), intent(in) :: bounds ! bounds - ! - ! !LOCAL VARIABLES: - integer :: i ! index - integer :: stream_year_first_soilm ! first year in Ustar stream to use - integer :: stream_year_last_soilm ! last year in Ustar stream to use - integer :: model_year_align_soilm ! align stream_year_first_soilm with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - integer :: soilm_offset ! Offset in time for dataset (sec) - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldfilename_soilm ! ustar stream filename to read - character(len=CL) :: soilm_tintalgo = 'linear' ! Time interpolation alogrithm - - character(*), parameter :: subName = "('PrescribedSoilMoistureInit')" - character(*), parameter :: F00 = "('(PrescribedSoilMoistureInit) ',4a)" - character(*), parameter :: soilmString = "H2OSOI" ! base string for field string - character(CXX) :: fldList ! field string - !----------------------------------------------------------------------- - ! - ! deal with namelist variables here in init - ! - namelist /soil_moisture_streams/ & - stream_year_first_soilm, & - stream_year_last_soilm, & - model_year_align_soilm, & - soilm_tintalgo, & - soilm_offset, & - soilm_ignore_data_if_missing, & - stream_fldfilename_soilm - - ! Default values for namelist - stream_year_first_soilm = 1 ! first year in stream to use - stream_year_last_soilm = 1 ! last year in stream to use - model_year_align_soilm = 1 ! align stream_year_first_soilm with this model year - stream_fldfilename_soilm = shr_stream_file_null - soilm_offset = 0 - soilm_ignore_data_if_missing = .false. - - ! Read soilm_streams namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'soil_moisture_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=soil_moisture_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(subname // ':: ERROR reading soil_moisture_streams namelist') - end if - else - call endrun(subname // ':: ERROR finding soilm_streams namelist') - end if - close(nu_nml) - endif - - call shr_mpi_bcast(stream_year_first_soilm, mpicom) - call shr_mpi_bcast(stream_year_last_soilm, mpicom) - call shr_mpi_bcast(model_year_align_soilm, mpicom) - call shr_mpi_bcast(stream_fldfilename_soilm, mpicom) - call shr_mpi_bcast(soilm_tintalgo, mpicom) - call shr_mpi_bcast(soilm_offset, mpicom) - call shr_mpi_bcast(soilm_ignore_data_if_missing, mpicom) - - if (masterproc) then - - write(iulog,*) ' ' - write(iulog,*) 'soil_moisture_stream settings:' - write(iulog,*) ' stream_year_first_soilm = ',stream_year_first_soilm - write(iulog,*) ' stream_year_last_soilm = ',stream_year_last_soilm - write(iulog,*) ' model_year_align_soilm = ',model_year_align_soilm - write(iulog,*) ' stream_fldfilename_soilm = ',trim(stream_fldfilename_soilm) - write(iulog,*) ' soilm_tintalgo = ',trim(soilm_tintalgo) - write(iulog,*) ' soilm_offset = ',soilm_offset - if ( soilm_ignore_data_if_missing )then - write(iulog,*) ' Do NOT override a point with streams data if the streams data is missing' - else - write(iulog,*) ' Abort, if you find a model point where the input streams data is set to missing value' - end if - - endif - - call clm_domain_mct (bounds, dom_clm, nlevels=nlevsoi) - - ! create the field list for these fields...use in shr_strdata_create - fldList = trim(soilmString) - if (masterproc) write(iulog,*) 'fieldlist: ', trim(fldList) - - call shr_strdata_create(sdat_soilm,name="soil_moisture", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsMap_lnd2Dsoi_gdc2glo, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - nzg=nlevsoi, & - yearFirst=stream_year_first_soilm, & - yearLast=stream_year_last_soilm, & - yearAlign=model_year_align_soilm, & - offset=soilm_offset, & - domFilePath='', & - domFileName=trim(stream_fldFileName_soilm), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domZvarName='levsoi' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/stream_fldFileName_soilm/), & - fldListFile=fldList, & - fldListModel=fldList, & - fillalgo='none', & - mapalgo='none', & - tintalgo=soilm_tintalgo, & - calendar=get_calendar(), & - dtlimit = 15._r8, & - taxmode='cycle' ) - - if (masterproc) then - call shr_strdata_print(sdat_soilm,'soil moisture data') - endif - - end subroutine PrescribedSoilMoistureInit - - - !----------------------------------------------------------------------- - ! - ! PrescribedSoilMoistureAdvance - ! - !----------------------------------------------------------------------- - subroutine PrescribedSoilMoistureAdvance( bounds ) - ! - ! Advanace the prescribed soil moisture stream - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - type(bounds_type) , intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - character(len=CL) :: stream_var_name - integer :: g, ig - integer :: ier ! error code - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - stream_var_name = 'H2OSOI' - - ! Determine variable index - ism = mct_aVect_indexRA(sdat_soilm%avs(1),trim(stream_var_name)) - - call shr_strdata_advance(sdat_soilm, mcdate, sec, mpicom, trim(stream_var_name)) - - ! Map gridcell to AV index - ier = 0 - if ( .not. allocated(g_to_ig) )then - allocate (g_to_ig(bounds%begg:bounds%endg), stat=ier) - if (ier /= 0) then - write(iulog,*) 'Prescribed soil moisture allocation error' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - g_to_ig(g) = ig - end do - end if - - end subroutine PrescribedSoilMoistureAdvance - - !----------------------------------------------------------------------- - ! - ! PrescribedSoilMoistureInterp - ! - !----------------------------------------------------------------------- - subroutine PrescribedSoilMoistureInterp(bounds, soilstate_inst, & - waterstatebulk_inst) - ! - ! Assign data stream information for prescribed soil moisture. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - use clm_varpar , only : nlevsoi - use clm_varcon , only : denh2o, denice, watmin, spval - use landunit_varcon , only : istsoil, istcrop - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - type(soilstate_type) , intent(in) :: soilstate_inst - type(waterstatebulk_type) , intent(inout) :: waterstatebulk_inst - ! - ! !LOCAL VARIABLES: - integer :: c, g, j, ig, n - real(r8) :: soilm_liq_frac ! liquid fraction of soil moisture - real(r8) :: soilm_ice_frac ! ice fraction of soil moisture - real(r8) :: moisture_increment ! soil moisture adjustment increment - real(r8) :: h2osoi_vol_initial ! initial vwc value - character(*), parameter :: subName = "('PrescribedSoilMoistureInterp')" - - !----------------------------------------------------------------------- - - SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,1) == ism ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(sdat_soilm%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_soilm%avs(1)%rAttr,2) >= g_to_ig(bounds%endg)+(nlevsoi-1)*size(g_to_ig) ), sourcefile, __LINE__) - associate( & - dz => col%dz , & ! Input: [real(r8) (:,:) ] layer depth (m) - watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] volumetric soil water at saturation (porosity) - h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input/Output: [real(r8) (:,:) ] liquid water (kg/m2) - h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input/Output: [real(r8) (:,:) ] ice water (kg/m2) - h2osoi_vol => waterstatebulk_inst%h2osoi_vol_col , & ! Output: volumetric soil water (m3/m3) - h2osoi_vol_prs => waterstatebulk_inst%h2osoi_vol_prs_grc & ! Output: prescribed volumetric soil water (m3/m3) - ) - SHR_ASSERT_FL( (lbound(h2osoi_vol,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_vol,2) == 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(dz,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(dz,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(dz,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(dz,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(watsat,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(watsat,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(watsat,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(watsat,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_liq,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_liq,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_liq,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_liq,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_ice,1) <= bounds%begc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_ice,1) >= bounds%endc ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_ice,2) <= 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_ice,2) >= nlevsoi ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,1) >= bounds%endg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(h2osoi_vol_prs,2) == 1 ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(h2osoi_vol_prs,2) >= nlevsoi ), sourcefile, __LINE__) - ! - ! Set the prescribed soil moisture read from the file everywhere - ! - do g = bounds%begg, bounds%endg - ig = g_to_ig(g) - do j = 1, nlevsoi - - !n = ig + (j-1)*size(g_to_ig) - n = ig + (j-1)*size(g_to_ig) - - h2osoi_vol_prs(g,j) = sdat_soilm%avs(1)%rAttr(ism,n) - - ! If soil moiture is being interpolated in time and the result is - ! large that probably means one of the two data points is missing (set to spval) - if ( h2osoi_vol_prs(g,j) > 10.0_r8 .and. (h2osoi_vol_prs(g,j) /= spval) )then - h2osoi_vol_prs(g,j) = spval - end if - - end do - end do - - do c = bounds%begc, bounds%endc - ! - ! Set variable for each gridcell/column combination - ! - g = col%gridcell(c) - ig = g_to_ig(g) - - ! EBK Jan/2020, also check weights on gridcell (See https://github.com/ESCOMP/CTSM/issues/847) - if ( (lun%itype(col%landunit(c)) == istsoil) .or. (lun%itype(col%landunit(c)) == istcrop) .and. & - (col%wtgcell(c) /= 0._r8) ) then - ! this is a 2d field (gridcell/nlevsoi) ! - do j = 1, nlevsoi - - n = ig + (j-1)*size(g_to_ig) - - ! if soil water is zero, liq/ice fractions cannot be calculated - if((h2osoi_liq(c, j) + h2osoi_ice(c, j)) > 0._r8) then - - ! save original soil moisture value - h2osoi_vol_initial = h2osoi_vol(c,j) - - ! Check if the vegetated land mask from the dataset on the - ! file is different - if ( (h2osoi_vol_prs(g,j) == spval) .and. (h2osoi_vol_initial /= spval) )then - if ( soilm_ignore_data_if_missing )then - cycle - else - write(iulog,*) 'Input soil moisture dataset is not vegetated as expected: gridcell=', & - g, ' active = ', col%active(c) - call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, & - msg = subname // & - ' ERROR:: The input soil moisture stream is NOT vegetated for one of the land points' ) - end if - end if - - ! update volumetric soil moisture from data prescribed from the file - h2osoi_vol(c,j) = h2osoi_vol_prs(g,j) - - - ! calculate liq/ice mass fractions - soilm_liq_frac = h2osoi_liq(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j)) - soilm_ice_frac = h2osoi_ice(c, j) /(h2osoi_liq(c, j) + h2osoi_ice(c, j)) - - ! calculate moisture increment - moisture_increment = h2osoi_vol(c,j) - h2osoi_vol_initial - ! add limitation check - moisture_increment = min((watsat(c,j) - h2osoi_vol_initial),max(-(h2osoi_vol_initial-watmin),moisture_increment)) - - ! update liq/ice water mass due to (volumetric) moisture increment - h2osoi_liq(c,j) = h2osoi_liq(c,j) + (soilm_liq_frac * moisture_increment * dz(c, j) * denh2o) - h2osoi_ice(c,j) = h2osoi_ice(c,j) + (soilm_ice_frac * moisture_increment * dz(c, j) * denice) - - else - call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, & - msg = subname // ':: ERROR h2osoil liquid plus ice is zero') - endif - enddo - endif - end do - - end associate - - end subroutine PrescribedSoilMoistureInterp - -end module SoilMoistureStreamMod diff --git a/src/cpl/mct/UrbanTimeVarType.F90 b/src/cpl/mct/UrbanTimeVarType.F90 deleted file mode 100644 index 805ac47fbf..0000000000 --- a/src/cpl/mct/UrbanTimeVarType.F90 +++ /dev/null @@ -1,314 +0,0 @@ -module UrbanTimeVarType - - !------------------------------------------------------------------------------ - ! !DESCRIPTION: - ! Urban Time Varying Data - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL - use shr_log_mod , only : errMsg => shr_log_errMsg - use abortutils , only : endrun - use decompMod , only : bounds_type, subgrid_level_landunit - use clm_varctl , only : iulog, inst_name - use landunit_varcon , only : isturb_MIN, isturb_MAX - use clm_varcon , only : spval - use LandunitType , only : lun - use GridcellType , only : grc - use mct_mod - use shr_strdata_mod , only : shr_strdata_type - ! - implicit none - save - private - ! - ! - - ! !PUBLIC TYPE - type, public :: urbantv_type - - real(r8), public, pointer :: t_building_max(:) ! lun maximum internal building air temperature (K) - type(shr_strdata_type) :: sdat_urbantv ! urban time varying input data stream - contains - - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: Init ! Allocate and initialize urbantv - procedure, public :: urbantv_init ! Initialize urban time varying stream - procedure, public :: urbantv_interp ! Interpolate urban time varying stream - - end type urbantv_type - - !----------------------------------------------------------------------- - character(15), private :: stream_var_name(isturb_MIN:isturb_MAX) - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -contains - - !----------------------------------------------------------------------- - subroutine Init(this, bounds, NLFilename) - ! - ! Allocate module variables and data structures - ! - ! !USES: - use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) - use histFileMod , only : hist_addfld1d - ! - ! !ARGUMENTS: - class(urbantv_type) :: this - type(bounds_type) , intent(in) :: bounds - character(len=*) , intent(in) :: NLFilename ! Namelist filename - ! - ! !LOCAL VARIABLES: - integer :: begl, endl - !--------------------------------------------------------------------- - - begl = bounds%begl; endl = bounds%endl - - ! Allocate urbantv data structure - - allocate(this%t_building_max (begl:endl)) ; this%t_building_max (:) = nan - - call this%urbantv_init(bounds, NLFilename) - call this%urbantv_interp(bounds) - - ! Add history fields - call hist_addfld1d (fname='TBUILD_MAX', units='K', & - avgflag='A', long_name='prescribed maximum interior building temperature', & - ptr_lunit=this%t_building_max, default='inactive', set_nourb=spval, & - l2g_scale_type='unity') - - - end subroutine Init - - !----------------------------------------------------------------------- - - !----------------------------------------------------------------------- - subroutine urbantv_init(this, bounds, NLFilename) - ! - ! !DESCRIPTION: - ! Initialize data stream information for urban time varying data - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use spmdMod , only : masterproc, mpicom, comp_id - use fileutils , only : getavu, relavu - use shr_mpi_mod , only : shr_mpi_bcast - use shr_string_mod , only : shr_string_listAppend - use shr_strdata_mod , only : shr_strdata_create, shr_strdata_print - use domainMod , only : ldomain - use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) - use landunit_varcon , only : isturb_TBD, isturb_HD, isturb_MD - use lnd_set_decomp_and_domain , only : gsmap_global - ! - ! !ARGUMENTS: - implicit none - class(urbantv_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! !LOCAL VARIABLES: - integer :: begl, endl ! landunits - integer :: ifield ! field index - integer :: stream_year_first_urbantv ! first year in urban tv stream to use - integer :: stream_year_last_urbantv ! last year in urban tv stream to use - integer :: model_year_align_urbantv ! align stream_year_first_urbantv - ! with this model year - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_urbantv ! urban tv streams filename - character(len=CL) :: urbantvmapalgo = 'nn' ! mapping alogrithm for urban ac - character(len=CL) :: urbantv_tintalgo = 'linear' ! time interpolation alogrithm - character(len=CL) :: fldList ! field string - character(*), parameter :: urbantvString = "tbuildmax_" ! base string for field string - character(*), parameter :: subName = "('urbantv_init')" - character(*), parameter :: F00 = "('(urbantv_init) ',4a)" - !----------------------------------------------------------------------- - namelist /urbantv_streams/ & - stream_year_first_urbantv, & - stream_year_last_urbantv, & - model_year_align_urbantv, & - urbantvmapalgo, & - stream_fldFileName_urbantv, & - urbantv_tintalgo - !----------------------------------------------------------------------- - - begl = bounds%begl; endl = bounds%endl - - ! Default values for namelist - stream_year_first_urbantv = 1 ! first year in stream to use - stream_year_last_urbantv = 1 ! last year in stream to use - model_year_align_urbantv = 1 ! align stream_year_first_urbantv with this model year - stream_fldFileName_urbantv = ' ' - - ! Read urbantv_streams namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'urbantv_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=urbantv_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg='ERROR reading urbantv_streams namelist'//errMsg(sourcefile, __LINE__)) - end if - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_year_first_urbantv, mpicom) - call shr_mpi_bcast(stream_year_last_urbantv, mpicom) - call shr_mpi_bcast(model_year_align_urbantv, mpicom) - call shr_mpi_bcast(stream_fldFileName_urbantv, mpicom) - call shr_mpi_bcast(urbantv_tintalgo, mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'urbantv_streams settings:' - write(iulog,*) ' stream_year_first_urbantv = ',stream_year_first_urbantv - write(iulog,*) ' stream_year_last_urbantv = ',stream_year_last_urbantv - write(iulog,*) ' model_year_align_urbantv = ',model_year_align_urbantv - write(iulog,*) ' stream_fldFileName_urbantv = ',stream_fldFileName_urbantv - write(iulog,*) ' urbantv_tintalgo = ',urbantv_tintalgo - write(iulog,*) ' ' - endif - - call clm_domain_mct (bounds, dom_clm) - - ! create the field list for these urbantv fields...use in shr_strdata_create - stream_var_name(:) = "NOT_SET" - stream_var_name(isturb_TBD) = urbantvString//"TBD" - stream_var_name(isturb_HD) = urbantvString//"HD" - stream_var_name(isturb_MD) = urbantvString//"MD" - fldList = "" - do ifield = isturb_MIN, isturb_MAX - call shr_string_listAppend( fldList, stream_var_name(ifield) ) - end do - - call shr_strdata_create(this%sdat_urbantv,name="clmurbantv", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_urbantv, & - yearLast=stream_year_last_urbantv, & - yearAlign=model_year_align_urbantv, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_urbantv), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='LANDMASK', & - filePath='', & - filename=(/trim(stream_fldFileName_urbantv)/) , & - fldListFile=fldList, & - fldListModel=fldList, & - fillalgo='none', & - mapalgo=urbantvmapalgo, & - calendar=get_calendar(), & - tintalgo=urbantv_tintalgo, & - taxmode='extend' ) - - if (masterproc) then - call shr_strdata_print(this%sdat_urbantv,'urban time varying data') - endif - - - end subroutine urbantv_init - - !----------------------------------------------------------------------- - subroutine urbantv_interp(this, bounds) - ! - ! !DESCRIPTION: - ! Interpolate data stream information for urban time varying data. - ! - ! !USES: - use clm_time_manager, only : get_curr_date - use spmdMod , only : mpicom - use shr_strdata_mod , only : shr_strdata_advance - use clm_instur , only : urban_valid - ! - ! !ARGUMENTS: - class(urbantv_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - logical :: found - integer :: l, glun, ig, g, ip - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - integer :: lindx ! landunit index - integer :: gindx ! gridcell index - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(this%sdat_urbantv, mcdate, sec, mpicom, 'urbantvdyn') - - do l = bounds%begl,bounds%endl - if (lun%urbpoi(l)) then - glun = lun%gridcell(l) - ip = mct_aVect_indexRA(this%sdat_urbantv%avs(1),trim(stream_var_name(lun%itype(l)))) - ! - ! Determine vector index corresponding to glun - ! - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - if (g == glun) exit - end do - - this%t_building_max(l) = this%sdat_urbantv%avs(1)%rAttr(ip,ig) - else - this%t_building_max(l) = spval - end if - end do - - found = .false. - do l = bounds%begl,bounds%endl - if (lun%urbpoi(l)) then - glun = lun%gridcell(l) - ! - ! Determine vector index corresponding to glun - ! - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - if (g == glun) exit - end do - - if ( .not. urban_valid(g) .or. (this%t_building_max(l) <= 0._r8)) then - found = .true. - gindx = g - lindx = l - exit - end if - end if - end do - if ( found ) then - write(iulog,*)'ERROR: no valid urban data for g= ',gindx - write(iulog,*)'landunit type: ',lun%itype(lindx) - write(iulog,*)'urban_valid: ',urban_valid(gindx) - write(iulog,*)'t_building_max: ',this%t_building_max(lindx) - call endrun(subgrid_index=lindx, subgrid_level=subgrid_level_landunit, & - msg=errmsg(sourcefile, __LINE__)) - end if - - - end subroutine urbantv_interp - - !----------------------------------------------------------------------- - -end module UrbanTimeVarType diff --git a/src/cpl/mct/ch4FInundatedStreamType.F90 b/src/cpl/mct/ch4FInundatedStreamType.F90 deleted file mode 100644 index 3c26f4d109..0000000000 --- a/src/cpl/mct/ch4FInundatedStreamType.F90 +++ /dev/null @@ -1,389 +0,0 @@ -module ch4FInundatedStreamType - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Contains methods for reading in finundated streams file for methane code. - ! - ! !USES - use shr_kind_mod , only: r8 => shr_kind_r8, CL => shr_kind_cl - use spmdMod , only: mpicom, masterproc - use clm_varctl , only: iulog, inst_name - use abortutils , only: endrun - use decompMod , only: bounds_type - use ch4varcon , only: finundation_mtd - - ! !PUBLIC TYPES: - implicit none - private - save - - type, public :: ch4finundatedstream_type - real(r8), pointer, private :: zwt0_gdc (:) ! col coefficient for determining finundated (m) - real(r8), pointer, private :: f0_gdc (:) ! col maximum inundated fraction for a gridcell (for methane code) - real(r8), pointer, private :: p3_gdc (:) ! col coefficient for determining finundated (m) - real(r8), pointer, private :: fws_slope_gdc (:) ! col slope in fws = slope * tws + intercept (A coefficient) - real(r8), pointer, private :: fws_intercept_gdc (:) ! col slope in fws = slope * tws + intercept (B coefficient) - contains - - ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: Init ! Initialize and read data in - procedure, public :: CalcFinundated ! Calculate finundated based on input streams - procedure, public :: UseStreams ! If streams will be used - - ! !PRIVATE MEMBER FUNCTIONS: - procedure, private :: InitAllocate ! Allocate data - - end type ch4finundatedstream_type - - - ! ! PRIVATE DATA: - - type, private :: streamcontrol_type - character(len=CL) :: stream_fldFileName_ch4finundated ! Filename - character(len=CL) :: ch4finundatedmapalgo ! map algo - character(len=CL) :: fldList ! List of fields to read - contains - procedure, private :: ReadNML ! Read in namelist - end type streamcontrol_type - - type(streamcontrol_type), private :: control ! Stream control data - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - !============================================================================== - -contains - - !============================================================================== - - subroutine Init(this, bounds, NLFilename) - ! - ! Initialize the ch4 finundated stream object - ! - ! Uses: - use clm_time_manager , only : get_calendar, get_curr_date - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_nl_mod , only : shr_nl_find_group_name - use shr_mpi_mod , only : shr_mpi_bcast - use ndepStreamMod , only : clm_domain_mct - use domainMod , only : ldomain - use decompMod , only : bounds_type - use mct_mod , only : mct_ggrid, mct_avect_indexra - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create - use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance - use spmdMod , only : comp_id, iam - use ch4varcon , only : finundation_mtd_h2osfc - use ch4varcon , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion - use lnd_set_decomp_and_domain , only : gsmap_global - ! - ! arguments - implicit none - class(ch4finundatedstream_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: ig, g ! Indices - type(mct_ggrid) :: dom_clm ! domain information - type(shr_strdata_type) :: sdat ! input data stream - integer :: index_ZWT0 = 0 ! Index of ZWT0 field - integer :: index_F0 = 0 ! Index of F0 field - integer :: index_P3 = 0 ! Index of P3 field - integer :: index_FWS_TWS_A = 0 ! Index of FWS_TWS_A field - integer :: index_FWS_TWS_B = 0 ! Index of FWS_TWS_B field - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - character(len=*), parameter :: stream_name = 'ch4finundated' - character(*), parameter :: subName = "('ch4finundatedstream::Init')" - !----------------------------------------------------------------------- - if ( finundation_mtd /= finundation_mtd_h2osfc )then - call this%InitAllocate( bounds ) - call control%ReadNML( bounds, NLFileName ) - - if ( this%useStreams() )then - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(sdat,name=stream_name, & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=1996, & - yearLast=1996, & - yearAlign=1, & - offset=0, & - domFilePath='', & - domFileName=trim(control%stream_fldFileName_ch4finundated), & - domTvarName='time', & - domXvarName='LONGXY' , & - domYvarName='LATIXY' , & - domAreaName='AREA', & - domMaskName='LANDMASK', & - filePath='', & - filename=(/trim(control%stream_fldFileName_ch4finundated)/), & - fldListFile=control%fldList, & - fldListModel=control%fldList, & - fillalgo='none', & - mapalgo=control%ch4finundatedmapalgo, & - calendar=get_calendar(), & - taxmode='extend' ) - - if (masterproc) then - call shr_strdata_print(sdat,'CLM '//stream_name//' data') - endif - - if( finundation_mtd == finundation_mtd_ZWT_inversion )then - index_ZWT0 = mct_avect_indexra(sdat%avs(1),'ZWT0') - index_F0 = mct_avect_indexra(sdat%avs(1),'F0' ) - index_P3 = mct_avect_indexra(sdat%avs(1),'P3' ) - else if( finundation_mtd == finundation_mtd_TWS_inversion )then - index_FWS_TWS_A = mct_avect_indexra(sdat%avs(1),'FWS_TWS_A') - index_FWS_TWS_B = mct_avect_indexra(sdat%avs(1),'FWS_TWS_B') - end if - - - ! Explicitly set current date to a hardcoded constant value. Otherwise - ! using the real date can cause roundoff differences that are - ! detrected as issues with exact restart. EBK M05/20/2017 - !call get_curr_date(year, mon, day, sec) - year = 1996 - mon = 12 - day = 31 - sec = 0 - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ch4finundated') - - ! Get the data - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - if ( index_ZWT0 > 0 )then - this%zwt0_gdc(g) = sdat%avs(1)%rAttr(index_ZWT0,ig) - end if - if ( index_F0 > 0 )then - this%f0_gdc(g) = sdat%avs(1)%rAttr(index_F0,ig) - end if - if ( index_P3 > 0 )then - this%p3_gdc(g) = sdat%avs(1)%rAttr(index_P3,ig) - end if - if ( index_FWS_TWS_A > 0 )then - this%fws_slope_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_A,ig) - end if - if ( index_FWS_TWS_B > 0 )then - this%fws_intercept_gdc(g) = sdat%avs(1)%rAttr(index_FWS_TWS_B,ig) - end if - end do - end if - end if - - end subroutine Init - - !----------------------------------------------------------------------- - logical function UseStreams(this) - ! - ! !DESCRIPTION: - ! Return true if - ! - ! !USES: - ! - ! !ARGUMENTS: - implicit none - class(ch4finundatedstream_type) :: this - ! - ! !LOCAL VARIABLES: - if ( trim(control%stream_fldFileName_ch4finundated) == '' )then - UseStreams = .false. - else - UseStreams = .true. - end if - end function UseStreams - - !----------------------------------------------------------------------- - subroutine InitAllocate(this, bounds) - ! - ! !DESCRIPTION: - ! Allocate module variables and data structures - ! - ! !USES: - use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=) - use ch4varcon , only: finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion - ! - ! !ARGUMENTS: - implicit none - class(ch4finundatedstream_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: begc, endc - integer :: begg, endg - !--------------------------------------------------------------------- - - begc = bounds%begc; endc = bounds%endc - begg = bounds%begg; endg = bounds%endg - - if( finundation_mtd == finundation_mtd_ZWT_inversion )then - allocate(this%zwt0_gdc (begg:endg)) ; this%zwt0_gdc (:) = nan - allocate(this%f0_gdc (begg:endg)) ; this%f0_gdc (:) = nan - allocate(this%p3_gdc (begg:endg)) ; this%p3_gdc (:) = nan - else if( finundation_mtd == finundation_mtd_TWS_inversion )then - allocate(this%fws_slope_gdc (begg:endg)) ; this%fws_slope_gdc (:) = nan - allocate(this%fws_intercept_gdc(begg:endg)) ; this%fws_intercept_gdc(:) = nan - end if - - end subroutine InitAllocate - - !----------------------------------------------------------------------- - subroutine CalcFinundated(this, bounds, num_soilc, filter_soilc, soilhydrology_inst, & - waterdiagnosticbulk_inst, qflx_surf_lag_col, finundated ) - ! - ! !DESCRIPTION: - ! - ! Calculate finundated according to the appropriate methodology - ! - ! !USES: - use ColumnType , only : col - use ch4varcon , only : finundation_mtd_h2osfc, finundation_mtd_ZWT_inversion - use ch4varcon , only : finundation_mtd_TWS_inversion - use clm_varpar , only : nlevsoi - use SoilHydrologyType, only : soilhydrology_type - use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type - ! - ! !ARGUMENTS: - implicit none - class(ch4finundatedstream_type) :: this - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of column soil points in column filter - integer , intent(in) :: filter_soilc(:) ! column filter for soil points - type(soilhydrology_type) , intent(in) :: soilhydrology_inst - type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst - real(r8) , intent(in) :: qflx_surf_lag_col(bounds%begc:) !time-lagged surface runoff (mm H2O /s) - real(r8) , intent(inout) :: finundated(bounds%begc:) ! fractional inundated area in soil column (excluding dedicated wetland columns) - ! - ! !LOCAL VARIABLES: - integer :: g, c, fc ! Indices - real(r8) :: zwt_actual ! Total water storage (ZWT) to use either perched or total depending on conditions - - SHR_ASSERT_ALL_FL((ubound(qflx_surf_lag_col) == (/bounds%endc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(finundated) == (/bounds%endc/)), sourcefile, __LINE__) - - associate( & - z => col%z , & ! Input: [real(r8) (:,:) ] layer depth (m) (-nlevsno+1:nlevsoi) - zwt => soilhydrology_inst%zwt_col , & ! Input: [real(r8) (:) ] water table depth (m) - zwt_perched => soilhydrology_inst%zwt_perched_col , & ! Input: [real(r8) (:) ] perched water table depth (m) - tws => waterdiagnosticbulk_inst%tws_grc , & ! Input: [real(r8) (:) ] total water storage (kg m-2) - frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) - ) - - ! Calculate finundated - do fc = 1, num_soilc - c = filter_soilc(fc) - g = col%gridcell(c) - select case( finundation_mtd ) - case ( finundation_mtd_h2osfc ) - finundated(c) = frac_h2osfc(c) - case ( finundation_mtd_ZWT_inversion ) - if (this%zwt0_gdc(g) > 0._r8) then - if (zwt_perched(c) < z(c,nlevsoi)-1.e-5_r8 .and. zwt_perched(c) < zwt(c)) then - zwt_actual = zwt_perched(c) - else - zwt_actual = zwt(c) - end if - finundated(c) = this%f0_gdc(g) * exp(-zwt_actual/this%zwt0_gdc(g)) + this%p3_gdc(g)*qflx_surf_lag_col(c) - else - finundated(c) = this%p3_gdc(g)*qflx_surf_lag_col(c) - end if - case ( finundation_mtd_TWS_inversion ) - finundated(c) = this%fws_slope_gdc(g) * tws(g) + this%fws_intercept_gdc(g) - end select - finundated(c) = min( 1.0_r8, max( 0.0_r8, finundated(c) ) ) - end do - end associate - - end subroutine CalcFinundated - !============================================================================== - - subroutine ReadNML(this, bounds, NLFilename) - ! - ! Read the namelist data stream information. - ! - ! Uses: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_nl_mod , only : shr_nl_find_group_name - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_mpi_mod , only : shr_mpi_bcast - use fileutils , only : getavu, relavu - use ch4varcon , only : finundation_mtd_ZWT_inversion, finundation_mtd_TWS_inversion - ! - ! arguments - implicit none - class(streamcontrol_type) :: this - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - character(len=CL) :: stream_fldFileName_ch4finundated = ' ' - character(len=CL) :: ch4finundatedmapalgo = 'bilinear' - character(len=*), parameter :: namelist_name = 'ch4finundated' ! MUST agree with name in namelist and read - character(len=*), parameter :: shr_strdata_unset = 'NOT_SET' - character(len=*), parameter :: subName = "('ch4finundated::ReadNML')" - character(len=*), parameter :: F00 = "('(ch4finundated_readnml) ',4a)" - !----------------------------------------------------------------------- - - namelist /ch4finundated/ & ! MUST agree with namelist_name above - ch4finundatedmapalgo, stream_fldFileName_ch4finundated - - ! Default values for namelist - - ! Read ch4finundated namelist - if (masterproc) then - nu_nml = getavu() - open( nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=ch4finundated,iostat=nml_error) ! MUST agree with namelist_name above - if (nml_error /= 0) then - call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - else - call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) - end if - close(nu_nml) - call relavu( nu_nml ) - endif - - call shr_mpi_bcast(stream_fldFileName_ch4finundated, mpicom) - call shr_mpi_bcast(ch4finundatedmapalgo , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) namelist_name, ' stream settings:' - write(iulog,*) ' stream_fldFileName_ch4finundated = ',stream_fldFileName_ch4finundated - write(iulog,*) ' ch4finundatedmapalgo = ',ch4finundatedmapalgo - write(iulog,*) ' ' - endif - this%stream_fldFileName_ch4finundated = stream_fldFileName_ch4finundated - this%ch4finundatedmapalgo = ch4finundatedmapalgo - if ( finundation_mtd == finundation_mtd_ZWT_inversion )then - this%fldList = "ZWT0:F0:P3" - else if ( finundation_mtd == finundation_mtd_TWS_inversion )then - this%fldList = "FWS_TWS_A:FWS_TWS_B" - else - call endrun(msg=' ERROR do NOT know what list of variables to read for this finundation_mtd type'// & - errMsg(sourcefile, __LINE__)) - end if - - end subroutine ReadNML - -end module ch4FInundatedStreamType diff --git a/src/cpl/mct/clm_cpl_indices.F90 b/src/cpl/mct/clm_cpl_indices.F90 deleted file mode 100644 index 09ed89e92d..0000000000 --- a/src/cpl/mct/clm_cpl_indices.F90 +++ /dev/null @@ -1,330 +0,0 @@ -module clm_cpl_indices - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Module containing the indices for the fields passed between CLM and - ! the driver. Includes the River Transport Model fields (RTM) and the - ! fields needed by the land-ice component (sno). - ! - ! !USES: - - use shr_sys_mod, only : shr_sys_abort - implicit none - - SAVE - private ! By default make data private - ! - ! !PUBLIC MEMBER FUNCTIONS: - public :: clm_cpl_indices_set ! Set the coupler indices - ! - ! !PUBLIC DATA MEMBERS: - ! - integer , public :: glc_nec ! number of elevation classes for glacier_mec landunits - ! (from coupler) - must equal maxpatch_glc from namelist - - ! lnd -> drv (required) - - integer, public ::index_l2x_Flrl_rofsur ! lnd->rtm input liquid surface fluxes - integer, public ::index_l2x_Flrl_rofgwl ! lnd->rtm input liquid gwl fluxes - integer, public ::index_l2x_Flrl_rofsub ! lnd->rtm input liquid subsurface fluxes - integer, public ::index_l2x_Flrl_rofi ! lnd->rtm input frozen fluxes - integer, public ::index_l2x_Flrl_irrig ! irrigation withdrawal - - integer, public ::index_l2x_Sl_t ! temperature - integer, public ::index_l2x_Sl_tref ! 2m reference temperature - integer, public ::index_l2x_Sl_qref ! 2m reference specific humidity - integer, public ::index_l2x_Sl_avsdr ! albedo: direct , visible - integer, public ::index_l2x_Sl_anidr ! albedo: direct , near-ir - integer, public ::index_l2x_Sl_avsdf ! albedo: diffuse, visible - integer, public ::index_l2x_Sl_anidf ! albedo: diffuse, near-ir - integer, public ::index_l2x_Sl_snowh ! snow height - integer, public ::index_l2x_Sl_u10 ! 10m wind - integer, public ::index_l2x_Sl_ddvel ! dry deposition velocities (optional) - integer, public ::index_l2x_Sl_fv ! friction velocity - integer, public ::index_l2x_Sl_ram1 ! aerodynamical resistance - integer, public ::index_l2x_Sl_soilw ! volumetric soil water - integer, public ::index_l2x_Fall_taux ! wind stress, zonal - integer, public ::index_l2x_Fall_tauy ! wind stress, meridional - integer, public ::index_l2x_Fall_lat ! latent heat flux - integer, public ::index_l2x_Fall_sen ! sensible heat flux - integer, public ::index_l2x_Fall_lwup ! upward longwave heat flux - integer, public ::index_l2x_Fall_evap ! evaporation water flux - integer, public ::index_l2x_Fall_swnet ! heat flux shortwave net - integer, public ::index_l2x_Fall_fco2_lnd ! co2 flux **For testing set to 0 - integer, public ::index_l2x_Fall_flxdst1 ! dust flux size bin 1 - integer, public ::index_l2x_Fall_flxdst2 ! dust flux size bin 2 - integer, public ::index_l2x_Fall_flxdst3 ! dust flux size bin 3 - integer, public ::index_l2x_Fall_flxdst4 ! dust flux size bin 4 - integer, public ::index_l2x_Fall_flxvoc ! MEGAN fluxes - integer, public ::index_l2x_Fall_flxfire ! Fire fluxes - integer, public ::index_l2x_Sl_ztopfire ! Top of fire emissions (m) - - ! In the following, index 0 is bare land, other indices are glc elevation classes - integer, allocatable, public ::index_l2x_Sl_tsrf(:) ! glc MEC temperature - integer, allocatable, public ::index_l2x_Sl_topo(:) ! glc MEC topo height - integer, allocatable, public ::index_l2x_Flgl_qice(:) ! glc MEC ice flux - - integer, public ::index_x2l_Sa_methane - integer, public ::index_l2x_Fall_methane - - integer, public :: nflds_l2x = 0 - - ! drv -> lnd (required) - - integer, public ::index_x2l_Sa_z ! bottom atm level height - integer, public ::index_x2l_Sa_topo ! atm surface height (m) - integer, public ::index_x2l_Sa_u ! bottom atm level zon wind - integer, public ::index_x2l_Sa_v ! bottom atm level mer wind - integer, public ::index_x2l_Sa_ptem ! bottom atm level pot temp - integer, public ::index_x2l_Sa_shum ! bottom atm level spec hum - integer, public ::index_x2l_Sa_pbot ! bottom atm level pressure - integer, public ::index_x2l_Sa_tbot ! bottom atm level temp - integer, public ::index_x2l_Faxa_lwdn ! downward lw heat flux - integer, public ::index_x2l_Faxa_rainc ! prec: liquid "convective" - integer, public ::index_x2l_Faxa_rainl ! prec: liquid "large scale" - integer, public ::index_x2l_Faxa_snowc ! prec: frozen "convective" - integer, public ::index_x2l_Faxa_snowl ! prec: frozen "large scale" - integer, public ::index_x2l_Faxa_swndr ! sw: nir direct downward - integer, public ::index_x2l_Faxa_swvdr ! sw: vis direct downward - integer, public ::index_x2l_Faxa_swndf ! sw: nir diffuse downward - integer, public ::index_x2l_Faxa_swvdf ! sw: vis diffuse downward - integer, public ::index_x2l_Sa_co2prog ! bottom atm level prognostic co2 - integer, public ::index_x2l_Sa_co2diag ! bottom atm level diagnostic co2 - integer, public ::index_x2l_Faxa_bcphidry ! flux: Black Carbon hydrophilic dry deposition - integer, public ::index_x2l_Faxa_bcphodry ! flux: Black Carbon hydrophobic dry deposition - integer, public ::index_x2l_Faxa_bcphiwet ! flux: Black Carbon hydrophilic wet deposition - integer, public ::index_x2l_Faxa_ocphidry ! flux: Organic Carbon hydrophilic dry deposition - integer, public ::index_x2l_Faxa_ocphodry ! flux: Organic Carbon hydrophobic dry deposition - integer, public ::index_x2l_Faxa_ocphiwet ! flux: Organic Carbon hydrophilic dry deposition - integer, public ::index_x2l_Faxa_dstwet1 ! flux: Size 1 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstwet2 ! flux: Size 2 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstwet3 ! flux: Size 3 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstwet4 ! flux: Size 4 dust -- wet deposition - integer, public ::index_x2l_Faxa_dstdry1 ! flux: Size 1 dust -- dry deposition - integer, public ::index_x2l_Faxa_dstdry2 ! flux: Size 2 dust -- dry deposition - integer, public ::index_x2l_Faxa_dstdry3 ! flux: Size 3 dust -- dry deposition - integer, public ::index_x2l_Faxa_dstdry4 ! flux: Size 4 dust -- dry deposition - - integer, public ::index_x2l_Faxa_nhx ! flux nhx from atm - integer, public ::index_x2l_Faxa_noy ! flux noy from atm - - integer, public ::index_x2l_Flrr_flood ! rtm->lnd rof flood flux - integer, public ::index_x2l_Flrr_volr ! rtm->lnd rof volr total volume - integer, public ::index_x2l_Flrr_volrmch ! rtm->lnd rof volr main channel volume - - ! In the following, index 0 is bare land, other indices are glc elevation classes - integer, allocatable, public ::index_x2l_Sg_ice_covered(:) ! Fraction of glacier from glc model - integer, allocatable, public ::index_x2l_Sg_topo(:) ! Topo height from glc model - integer, allocatable, public ::index_x2l_Flgg_hflx(:) ! Heat flux from glc model - - integer, public ::index_x2l_Sg_icemask - integer, public ::index_x2l_Sg_icemask_coupled_fluxes - - integer, public :: nflds_x2l = 0 - - !----------------------------------------------------------------------- - -contains - - !----------------------------------------------------------------------- - subroutine clm_cpl_indices_set( ) - ! - ! !DESCRIPTION: - ! Set the coupler indices needed by the land model coupler - ! interface. - ! - ! !USES: - use seq_flds_mod , only: seq_flds_x2l_fields, seq_flds_l2x_fields - use mct_mod , only: mct_aVect, mct_aVect_init, mct_avect_indexra - use mct_mod , only: mct_aVect_clean, mct_avect_nRattr - use shr_drydep_mod , only: drydep_fields_token, n_drydep - use shr_megan_mod , only: shr_megan_fields_token, shr_megan_mechcomps_n - use shr_fire_emis_mod,only: shr_fire_emis_fields_token, shr_fire_emis_ztop_token, shr_fire_emis_mechcomps_n - use clm_varctl , only: ndep_from_cpl - use glc_elevclass_mod, only: glc_get_num_elevation_classes, glc_elevclass_as_string - ! - ! !ARGUMENTS: - implicit none - ! - ! !REVISION HISTORY: - ! Author: Mariana Vertenstein - ! 01/2011, Erik Kluzek: Added protex headers - ! - ! !LOCAL VARIABLES: - type(mct_aVect) :: l2x ! temporary, land to coupler - type(mct_aVect) :: x2l ! temporary, coupler to land - integer :: num - character(len=:), allocatable :: nec_str ! string version of glc elev. class number - character(len=64) :: name - character(len=32) :: subname = 'clm_cpl_indices_set' ! subroutine name - !----------------------------------------------------------------------- - - ! Determine attribute vector indices - - ! create temporary attribute vectors - call mct_aVect_init(x2l, rList=seq_flds_x2l_fields, lsize=1) - nflds_x2l = mct_avect_nRattr(x2l) - - call mct_aVect_init(l2x, rList=seq_flds_l2x_fields, lsize=1) - nflds_l2x = mct_avect_nRattr(l2x) - - !------------------------------------------------------------- - ! clm -> drv - !------------------------------------------------------------- - - index_l2x_Flrl_rofsur = mct_avect_indexra(l2x,'Flrl_rofsur') - index_l2x_Flrl_rofgwl = mct_avect_indexra(l2x,'Flrl_rofgwl') - index_l2x_Flrl_rofsub = mct_avect_indexra(l2x,'Flrl_rofsub') - index_l2x_Flrl_rofi = mct_avect_indexra(l2x,'Flrl_rofi') - index_l2x_Flrl_irrig = mct_avect_indexra(l2x,'Flrl_irrig') - - index_l2x_Sl_t = mct_avect_indexra(l2x,'Sl_t') - index_l2x_Sl_snowh = mct_avect_indexra(l2x,'Sl_snowh') - index_l2x_Sl_avsdr = mct_avect_indexra(l2x,'Sl_avsdr') - index_l2x_Sl_anidr = mct_avect_indexra(l2x,'Sl_anidr') - index_l2x_Sl_avsdf = mct_avect_indexra(l2x,'Sl_avsdf') - index_l2x_Sl_anidf = mct_avect_indexra(l2x,'Sl_anidf') - index_l2x_Sl_tref = mct_avect_indexra(l2x,'Sl_tref') - index_l2x_Sl_qref = mct_avect_indexra(l2x,'Sl_qref') - index_l2x_Sl_u10 = mct_avect_indexra(l2x,'Sl_u10') - index_l2x_Sl_ram1 = mct_avect_indexra(l2x,'Sl_ram1') - index_l2x_Sl_fv = mct_avect_indexra(l2x,'Sl_fv') - index_l2x_Sl_soilw = mct_avect_indexra(l2x,'Sl_soilw',perrwith='quiet') - - if ( n_drydep>0 )then - index_l2x_Sl_ddvel = mct_avect_indexra(l2x, trim(drydep_fields_token)) - else - index_l2x_Sl_ddvel = 0 - end if - - index_l2x_Fall_taux = mct_avect_indexra(l2x,'Fall_taux') - index_l2x_Fall_tauy = mct_avect_indexra(l2x,'Fall_tauy') - index_l2x_Fall_lat = mct_avect_indexra(l2x,'Fall_lat') - index_l2x_Fall_sen = mct_avect_indexra(l2x,'Fall_sen') - index_l2x_Fall_lwup = mct_avect_indexra(l2x,'Fall_lwup') - index_l2x_Fall_evap = mct_avect_indexra(l2x,'Fall_evap') - index_l2x_Fall_swnet = mct_avect_indexra(l2x,'Fall_swnet') - index_l2x_Fall_flxdst1 = mct_avect_indexra(l2x,'Fall_flxdst1') - index_l2x_Fall_flxdst2 = mct_avect_indexra(l2x,'Fall_flxdst2') - index_l2x_Fall_flxdst3 = mct_avect_indexra(l2x,'Fall_flxdst3') - index_l2x_Fall_flxdst4 = mct_avect_indexra(l2x,'Fall_flxdst4') - - index_l2x_Fall_fco2_lnd = mct_avect_indexra(l2x,'Fall_fco2_lnd',perrwith='quiet') - - index_l2x_Fall_methane = mct_avect_indexra(l2x,'Fall_methane',perrWith='quiet') - - ! MEGAN fluxes - if (shr_megan_mechcomps_n>0) then - index_l2x_Fall_flxvoc = mct_avect_indexra(l2x,trim(shr_megan_fields_token)) - else - index_l2x_Fall_flxvoc = 0 - endif - - ! Fire fluxes - if (shr_fire_emis_mechcomps_n>0) then - index_l2x_Fall_flxfire = mct_avect_indexra(l2x,trim(shr_fire_emis_fields_token)) - index_l2x_Sl_ztopfire = mct_avect_indexra(l2x,trim(shr_fire_emis_ztop_token)) - else - index_l2x_Fall_flxfire = 0 - index_l2x_Sl_ztopfire = 0 - endif - - !------------------------------------------------------------- - ! drv -> clm - !------------------------------------------------------------- - - index_x2l_Sa_z = mct_avect_indexra(x2l,'Sa_z') - index_x2l_Sa_topo = mct_avect_indexra(x2l,'Sa_topo') - index_x2l_Sa_u = mct_avect_indexra(x2l,'Sa_u') - index_x2l_Sa_v = mct_avect_indexra(x2l,'Sa_v') - index_x2l_Sa_ptem = mct_avect_indexra(x2l,'Sa_ptem') - index_x2l_Sa_pbot = mct_avect_indexra(x2l,'Sa_pbot') - index_x2l_Sa_tbot = mct_avect_indexra(x2l,'Sa_tbot') - index_x2l_Sa_shum = mct_avect_indexra(x2l,'Sa_shum') - index_x2l_Sa_co2prog = mct_avect_indexra(x2l,'Sa_co2prog',perrwith='quiet') - index_x2l_Sa_co2diag = mct_avect_indexra(x2l,'Sa_co2diag',perrwith='quiet') - - index_x2l_Sa_methane = mct_avect_indexra(x2l,'Sa_methane',perrWith='quiet') - - index_x2l_Flrr_volr = mct_avect_indexra(x2l,'Flrr_volr') - index_x2l_Flrr_volrmch = mct_avect_indexra(x2l,'Flrr_volrmch') - - index_x2l_Faxa_lwdn = mct_avect_indexra(x2l,'Faxa_lwdn') - index_x2l_Faxa_rainc = mct_avect_indexra(x2l,'Faxa_rainc') - index_x2l_Faxa_rainl = mct_avect_indexra(x2l,'Faxa_rainl') - index_x2l_Faxa_snowc = mct_avect_indexra(x2l,'Faxa_snowc') - index_x2l_Faxa_snowl = mct_avect_indexra(x2l,'Faxa_snowl') - index_x2l_Faxa_swndr = mct_avect_indexra(x2l,'Faxa_swndr') - index_x2l_Faxa_swvdr = mct_avect_indexra(x2l,'Faxa_swvdr') - index_x2l_Faxa_swndf = mct_avect_indexra(x2l,'Faxa_swndf') - index_x2l_Faxa_swvdf = mct_avect_indexra(x2l,'Faxa_swvdf') - index_x2l_Faxa_bcphidry = mct_avect_indexra(x2l,'Faxa_bcphidry') - index_x2l_Faxa_bcphodry = mct_avect_indexra(x2l,'Faxa_bcphodry') - index_x2l_Faxa_bcphiwet = mct_avect_indexra(x2l,'Faxa_bcphiwet') - index_x2l_Faxa_ocphidry = mct_avect_indexra(x2l,'Faxa_ocphidry') - index_x2l_Faxa_ocphodry = mct_avect_indexra(x2l,'Faxa_ocphodry') - index_x2l_Faxa_ocphiwet = mct_avect_indexra(x2l,'Faxa_ocphiwet') - index_x2l_Faxa_dstdry1 = mct_avect_indexra(x2l,'Faxa_dstdry1') - index_x2l_Faxa_dstdry2 = mct_avect_indexra(x2l,'Faxa_dstdry2') - index_x2l_Faxa_dstdry3 = mct_avect_indexra(x2l,'Faxa_dstdry3') - index_x2l_Faxa_dstdry4 = mct_avect_indexra(x2l,'Faxa_dstdry4') - index_x2l_Faxa_dstwet1 = mct_avect_indexra(x2l,'Faxa_dstwet1') - index_x2l_Faxa_dstwet2 = mct_avect_indexra(x2l,'Faxa_dstwet2') - index_x2l_Faxa_dstwet3 = mct_avect_indexra(x2l,'Faxa_dstwet3') - index_x2l_Faxa_dstwet4 = mct_avect_indexra(x2l,'Faxa_dstwet4') - - index_x2l_Faxa_nhx = mct_avect_indexra(x2l,'Faxa_nhx', perrWith='quiet') - index_x2l_Faxa_noy = mct_avect_indexra(x2l,'Faxa_noy', perrWith='quiet') - - if (index_x2l_Faxa_nhx > 0 .and. index_x2l_Faxa_noy > 0) then - ndep_from_cpl = .true. - end if - - index_x2l_Flrr_flood = mct_avect_indexra(x2l,'Flrr_flood') - - !------------------------------------------------------------- - ! glc coupling - !------------------------------------------------------------- - - index_x2l_Sg_icemask = mct_avect_indexra(x2l,'Sg_icemask') - index_x2l_Sg_icemask_coupled_fluxes = mct_avect_indexra(x2l,'Sg_icemask_coupled_fluxes') - - glc_nec = glc_get_num_elevation_classes() - if (glc_nec < 1) then - call shr_sys_abort('ERROR: In CLM4.5 and later, glc_nec must be at least 1.') - end if - - ! Create coupling fields for all glc elevation classes (1:glc_nec) plus bare land - ! (index 0). - allocate(index_l2x_Sl_tsrf(0:glc_nec)) - allocate(index_l2x_Sl_topo(0:glc_nec)) - allocate(index_l2x_Flgl_qice(0:glc_nec)) - allocate(index_x2l_Sg_ice_covered(0:glc_nec)) - allocate(index_x2l_Sg_topo(0:glc_nec)) - allocate(index_x2l_Flgg_hflx(0:glc_nec)) - - do num = 0,glc_nec - nec_str = glc_elevclass_as_string(num) - - name = 'Sg_ice_covered' // nec_str - index_x2l_Sg_ice_covered(num) = mct_avect_indexra(x2l,trim(name)) - name = 'Sg_topo' // nec_str - index_x2l_Sg_topo(num) = mct_avect_indexra(x2l,trim(name)) - name = 'Flgg_hflx' // nec_str - index_x2l_Flgg_hflx(num) = mct_avect_indexra(x2l,trim(name)) - - name = 'Sl_tsrf' // nec_str - index_l2x_Sl_tsrf(num) = mct_avect_indexra(l2x,trim(name)) - name = 'Sl_topo' // nec_str - index_l2x_Sl_topo(num) = mct_avect_indexra(l2x,trim(name)) - name = 'Flgl_qice' // nec_str - index_l2x_Flgl_qice(num) = mct_avect_indexra(l2x,trim(name)) - end do - - call mct_aVect_clean(x2l) - call mct_aVect_clean(l2x) - - end subroutine clm_cpl_indices_set - -!======================================================================= - -end module clm_cpl_indices diff --git a/src/cpl/mct/laiStreamMod.F90 b/src/cpl/mct/laiStreamMod.F90 deleted file mode 100644 index 47d25287b7..0000000000 --- a/src/cpl/mct/laiStreamMod.F90 +++ /dev/null @@ -1,241 +0,0 @@ -module laiStreamMod - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Read LAI from stream - ! - ! !USES: - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create - use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance - use shr_kind_mod , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX - use shr_log_mod , only : errMsg => shr_log_errMsg - use decompMod , only : bounds_type - use abortutils , only : endrun - use clm_varctl , only : iulog, inst_name - use perf_mod , only : t_startf, t_stopf - use spmdMod , only : masterproc, mpicom, comp_id - use ncdio_pio - use mct_mod - ! - ! !PUBLIC TYPES: - implicit none - private - - ! !PUBLIC MEMBER FUNCTIONS: - public :: lai_init ! position datasets for LAI - public :: lai_advance ! Advance the LAI streams (outside of a Open-MP threading loop) - public :: lai_interp ! interpolates between two years of LAI data (when LAI streams - - ! !PRIVATE MEMBER DATA: - integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - type(shr_strdata_type) :: sdat_lai ! LAI input data stream - - character(len=*), parameter :: sourcefile = & - __FILE__ - -!============================================================================== -contains -!============================================================================== - - subroutine lai_init(bounds) - ! - ! Initialize data stream information for LAI. - ! - ! !USES: - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_stream_mod , only : shr_stream_file_null - use shr_string_mod , only : shr_string_listCreateField - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use histFileMod , only : hist_addfld1d - use domainMod , only : ldomain - use controlMod , only : NLFilename - use lnd_set_decomp_and_domain , only : gsmap_global - ! - ! !ARGUMENTS: - implicit none - type(bounds_type), intent(in) :: bounds ! bounds - ! - ! !LOCAL VARIABLES: - integer :: stream_year_first_lai ! first year in Lai stream to use - integer :: stream_year_last_lai ! last year in Lai stream to use - integer :: model_year_align_lai ! align stream_year_first_lai with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_lai ! lai stream filename to read - character(len=CL) :: lai_mapalgo = 'bilinear' ! Mapping alogrithm - character(len=CL) :: lai_tintalgo = 'linear' ! Time interpolation alogrithm - character(len=CXX) :: fldList ! field string - character(*), parameter :: laiString = "LAI" ! base string for field string - integer , parameter :: numLaiFields = 16 ! number of fields to build field string - character(*), parameter :: subName = "('laidyn_init')" - !----------------------------------------------------------------------- - ! - ! deal with namelist variables here in init - ! - namelist /lai_streams/ & - stream_year_first_lai, & - stream_year_last_lai, & - model_year_align_lai, & - lai_mapalgo, & - stream_fldFileName_lai, & - lai_tintalgo - - ! Default values for namelist - stream_year_first_lai = 1 ! first year in stream to use - stream_year_last_lai = 1 ! last year in stream to use - model_year_align_lai = 1 ! align stream_year_first_lai with this model year - stream_fldFileName_lai = shr_stream_file_null - - ! Read lai_streams namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'lai_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=lai_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(subname // ':: ERROR reading lai_streams namelist') - end if - else - call endrun(subname // ':: ERROR finding lai_streams namelist') - end if - close(nu_nml) - endif - call shr_mpi_bcast(stream_year_first_lai , mpicom) - call shr_mpi_bcast(stream_year_last_lai , mpicom) - call shr_mpi_bcast(model_year_align_lai , mpicom) - call shr_mpi_bcast(stream_fldFileName_lai , mpicom) - call shr_mpi_bcast(lai_tintalgo , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'lai_stream settings:' - write(iulog,*) ' stream_year_first_lai = ',stream_year_first_lai - write(iulog,*) ' stream_year_last_lai = ',stream_year_last_lai - write(iulog,*) ' model_year_align_lai = ',model_year_align_lai - write(iulog,*) ' stream_fldFileName_lai = ',trim(stream_fldFileName_lai) - write(iulog,*) ' lai_tintalgo = ',trim(lai_tintalgo) - endif - - call clm_domain_mct (bounds, dom_clm) - - ! create the field list for these lai fields...use in shr_strdata_create - fldList = shr_string_listCreateField( numLaiFields, laiString ) - - call shr_strdata_create(sdat_lai,name="laidyn", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_lai, & - yearLast=stream_year_last_lai, & - yearAlign=model_year_align_lai, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_lai), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/stream_fldFileName_lai/), & - fldListFile=fldList, & - fldListModel=fldList, & - fillalgo='none', & - mapalgo=lai_mapalgo, & - tintalgo=lai_tintalgo, & - calendar=get_calendar(), & - taxmode='cycle' ) - - if (masterproc) then - call shr_strdata_print(sdat_lai,'LAI data') - endif - - end subroutine lai_init - - !============================================================================== - subroutine lai_advance( bounds ) - ! - ! Advance LAI streams - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g, ig ! Indices - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(sdat_lai, mcdate, sec, mpicom, 'laidyn') - if ( .not. allocated(g_to_ig) )then - allocate (g_to_ig(bounds%begg:bounds%endg) ) - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - g_to_ig(g) = ig - end do - end if - - end subroutine lai_advance - - !============================================================================== - subroutine lai_interp(bounds, canopystate_inst) - ! - ! Interpolate data stream information for Lai. - ! - ! !USES: - use pftconMod , only : noveg - use CanopyStateType , only : canopystate_type - use PatchType , only : patch - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - type(canopystate_type) , intent(inout) :: canopystate_inst - ! - ! !LOCAL VARIABLES: - integer :: ivt, p, ip, ig - character(len=CL) :: stream_var_name - !----------------------------------------------------------------------- - SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(sdat_lai%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_lai%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - - do p = bounds%begp, bounds%endp - ivt = patch%itype(p) - ! Set lai for each gridcell/patch combination - if (ivt /= noveg) then - ! vegetated pft - write(stream_var_name,"(i6)") ivt - stream_var_name = 'LAI_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_lai%avs(1),trim(stream_var_name)) - ig = g_to_ig(patch%gridcell(p)) - canopystate_inst%tlai_patch(p) = sdat_lai%avs(1)%rAttr(ip,ig) - else - ! non-vegetated pft - canopystate_inst%tlai_patch(p) = 0._r8 - endif - end do - - end subroutine lai_interp - -end module LaiStreamMod diff --git a/src/cpl/mct/lnd_comp_mct.F90 b/src/cpl/mct/lnd_comp_mct.F90 deleted file mode 100644 index e50602a378..0000000000 --- a/src/cpl/mct/lnd_comp_mct.F90 +++ /dev/null @@ -1,632 +0,0 @@ -module lnd_comp_mct - - !--------------------------------------------------------------------------- - ! !DESCRIPTION: - ! Interface of the active land model component of CESM the CLM (Community Land Model) - ! with the main CESM driver. This is a thin interface taking CESM driver information - ! in MCT (Model Coupling Toolkit) format and converting it to use by CLM. - ! - ! !uses: - use shr_kind_mod , only : r8 => shr_kind_r8 - use shr_sys_mod , only : shr_sys_flush - use shr_log_mod , only : errMsg => shr_log_errMsg - use mct_mod , only : mct_avect, mct_gsmap, mct_gGrid - use decompmod , only : bounds_type - use lnd_import_export, only : lnd_import, lnd_export - ! - ! !public member functions: - implicit none - private ! by default make data private - ! - ! !public member functions: - public :: lnd_init_mct ! clm initialization - public :: lnd_run_mct ! clm run phase - public :: lnd_final_mct ! clm finalization/cleanup - ! - ! !private member functions: - private :: lnd_domain_mct ! set the land model domain information - private :: lnd_handle_resume ! handle pause/resume signals from the coupler - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -!==================================================================================== -contains -!==================================================================================== - - subroutine lnd_init_mct( EClock, cdata_l, x2l_l, l2x_l, NLFilename ) - ! - ! !DESCRIPTION: - ! Initialize land surface model and obtain relevant atmospheric model arrays - ! back from (i.e. albedos, surface temperature and snow cover over land). - ! - ! !USES: - use shr_kind_mod , only : shr_kind_cl - use abortutils , only : endrun - use clm_time_manager , only : get_nstep, set_timemgr_init - use clm_initializeMod, only : initialize1, initialize2 - use clm_instMod , only : water_inst, lnd2atm_inst, lnd2glc_inst - use clm_varctl , only : finidat, single_column, clm_varctl_set, iulog - use clm_varctl , only : inst_index, inst_suffix, inst_name - use clm_varorb , only : eccen, obliqr, lambm0, mvelpp - use controlMod , only : control_setNL - use decompMod , only : get_proc_bounds - use domainMod , only : ldomain - use shr_file_mod , only : shr_file_setLogUnit, shr_file_setLogLevel - use shr_file_mod , only : shr_file_getLogUnit, shr_file_getLogLevel - use shr_file_mod , only : shr_file_getUnit, shr_file_setIO - use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs - use seq_timemgr_mod , only : seq_timemgr_EClockGetData - use seq_infodata_mod , only : seq_infodata_type, seq_infodata_GetData, seq_infodata_PutData, & - seq_infodata_start_type_start, seq_infodata_start_type_cont, & - seq_infodata_start_type_brnch - use seq_comm_mct , only : seq_comm_suffix, seq_comm_inst, seq_comm_name - use seq_flds_mod , only : seq_flds_x2l_fields, seq_flds_l2x_fields - use spmdMod , only : masterproc, spmd_init - use clm_varctl , only : nsrStartup, nsrContinue, nsrBranch - use clm_cpl_indices , only : clm_cpl_indices_set - use mct_mod , only : mct_aVect_init, mct_aVect_zero, mct_gsMap, mct_gsMap_init - use decompMod , only : gindex_global - use lnd_set_decomp_and_domain, only : lnd_set_decomp_and_domain_from_surfrd, gsmap_global - use ESMF - ! - ! !ARGUMENTS: - type(ESMF_Clock), intent(inout) :: EClock ! Input synchronization clock - type(seq_cdata), intent(inout) :: cdata_l ! Input land-model driver data - type(mct_aVect), intent(inout) :: x2l_l, l2x_l ! land model import and export states - character(len=*), optional, intent(in) :: NLFilename ! Namelist filename to read - ! - ! !LOCAL VARIABLES: - integer :: LNDID ! Land identifyer - integer :: mpicom_lnd ! MPI communicator - type(mct_gsMap), pointer :: GSMap_lnd ! Land model MCT GS map - type(mct_gGrid), pointer :: dom_l ! Land model domain - type(seq_infodata_type), pointer :: infodata ! CESM driver level info data - integer :: lsize ! size of attribute vector - integer :: gsize ! global size - integer :: g,i,j ! indices - integer :: dtime_sync ! coupling time-step from the input synchronization clock - logical :: exists ! true if file exists - logical :: atm_aero ! Flag if aerosol data sent from atm model - real(r8) :: scmlat ! single-column latitude - real(r8) :: scmlon ! single-column longitude - character(len=SHR_KIND_CL) :: caseid ! case identifier name - character(len=SHR_KIND_CL) :: ctitle ! case description title - character(len=SHR_KIND_CL) :: starttype ! start-type (startup, continue, branch, hybrid) - character(len=SHR_KIND_CL) :: calendar ! calendar type name - character(len=SHR_KIND_CL) :: hostname ! hostname of machine running on - character(len=SHR_KIND_CL) :: version ! Model version - character(len=SHR_KIND_CL) :: username ! user running the model - integer :: nsrest ! clm restart type - integer :: ref_ymd ! reference date (YYYYMMDD) - integer :: ref_tod ! reference time of day (sec) - integer :: start_ymd ! start date (YYYYMMDD) - integer :: start_tod ! start time of day (sec) - logical :: brnch_retain_casename ! flag if should retain the case name on a branch start type - integer :: lbnum ! input to memory diagnostic - integer :: shrlogunit,shrloglev ! old values for log unit and log level - type(bounds_type) :: bounds ! bounds - logical :: noland - integer :: ni,nj - real(r8) , parameter :: rundef = -9999999._r8 - character(len=32), parameter :: sub = 'lnd_init_mct' - character(len=*), parameter :: format = "('("//trim(sub)//") :',A)" - !----------------------------------------------------------------------- - - ! Set cdata data - call seq_cdata_setptrs(cdata_l, ID=LNDID, mpicom=mpicom_lnd, & - gsMap=GSMap_lnd, dom=dom_l, infodata=infodata) - - ! Determine attriute vector indices - call clm_cpl_indices_set() - - ! Initialize clm MPI communicator - call spmd_init( mpicom_lnd, LNDID ) - -#if (defined _MEMTRACE) - if(masterproc) then - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_init_mct:start::',lbnum) - endif -#endif - - inst_name = seq_comm_name(LNDID) - inst_index = seq_comm_inst(LNDID) - inst_suffix = seq_comm_suffix(LNDID) - ! Initialize io log unit - - call shr_file_getLogUnit (shrlogunit) - if (masterproc) then - inquire(file='lnd_modelio.nml'//trim(inst_suffix),exist=exists) - if (exists) then - iulog = shr_file_getUnit() - call shr_file_setIO('lnd_modelio.nml'//trim(inst_suffix),iulog) - end if - write(iulog,format) "CLM land model initialization" - else - iulog = shrlogunit - end if - - call shr_file_getLogLevel(shrloglev) - call shr_file_setLogUnit (iulog) - - ! Use infodata to set orbital values - call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, & - orb_lambm0=lambm0, orb_obliqr=obliqr ) - - ! Consistency check on namelist filename - call control_setNL("lnd_in"//trim(inst_suffix)) - - ! Initialize clm - ! initialize1 reads namelists - ! decomp and domain are set in lnd_set_decomp_and_domain_from_surfrd - ! initialize2 performs the rest of initialization - call seq_timemgr_EClockGetData(EClock, & - start_ymd=start_ymd, & - start_tod=start_tod, ref_ymd=ref_ymd, & - ref_tod=ref_tod, & - calendar=calendar, & - dtime=dtime_sync) - if (masterproc) then - write(iulog,*)'dtime = ',dtime_sync - end if - call seq_infodata_GetData(infodata, case_name=caseid, & - case_desc=ctitle, single_column=single_column, & - scmlat=scmlat, scmlon=scmlon, & - brnch_retain_casename=brnch_retain_casename, & - start_type=starttype, model_version=version, & - hostname=hostname, username=username ) - - ! Single Column - if ( single_column .and. (scmlat == rundef .or. scmlon == rundef ) ) then - call endrun(msg=' ERROR:: single column mode on -- but scmlat and scmlon are NOT set'//& - errMsg(sourcefile, __LINE__)) - end if - - ! Note that we assume that CTSM's internal dtime matches the coupling time step. - ! i.e., we currently do NOT allow sub-cycling within a coupling time step. - call set_timemgr_init( calendar_in=calendar, start_ymd_in=start_ymd, start_tod_in=start_tod, & - ref_ymd_in=ref_ymd, ref_tod_in=ref_tod, dtime_in=dtime_sync) - - if ( trim(starttype) == trim(seq_infodata_start_type_start)) then - nsrest = nsrStartup - else if (trim(starttype) == trim(seq_infodata_start_type_cont) ) then - nsrest = nsrContinue - else if (trim(starttype) == trim(seq_infodata_start_type_brnch)) then - nsrest = nsrBranch - else - call endrun( sub//' ERROR: unknown starttype' ) - end if - - ! set default values for run control variables - call clm_varctl_set(caseid_in=caseid, ctitle_in=ctitle, & - brnch_retain_casename_in=brnch_retain_casename, & - single_column_in=single_column, scmlat_in=scmlat, & - scmlon_in=scmlon, nsrest_in=nsrest, version_in=version, & - hostname_in=hostname, username_in=username) - - ! Read namelists - call initialize1(dtime=dtime_sync) - - ! Initialize decomposition and domain (ldomain) type - call lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj) - - ! If no land then exit out of initialization - if ( noland ) then - - call seq_infodata_PutData( infodata, lnd_present =.false.) - call seq_infodata_PutData( infodata, lnd_prognostic=.false.) - - else - - ! Determine if aerosol and dust deposition come from atmosphere component - call seq_infodata_GetData(infodata, atm_aero=atm_aero ) - if ( .not. atm_aero )then - call endrun( sub//' ERROR: atmosphere model MUST send aerosols to CLM' ) - end if - - ! Initialize clm gsMap, clm domain and clm attribute vectors - call get_proc_bounds( bounds ) - lsize = bounds%endg - bounds%begg + 1 - gsize = ldomain%ni * ldomain%nj - call mct_gsMap_init( gsMap_lnd, gindex_global, mpicom_lnd, LNDID, lsize, gsize ) - gsmap_global => gsmap_lnd ! module variable in lnd_set_decomp_and_domain - call lnd_domain_mct( bounds, lsize, gsMap_lnd, dom_l ) - call mct_aVect_init(x2l_l, rList=seq_flds_x2l_fields, lsize=lsize) - call mct_aVect_zero(x2l_l) - call mct_aVect_init(l2x_l, rList=seq_flds_l2x_fields, lsize=lsize) - call mct_aVect_zero(l2x_l) - - ! Finish initializing clm - call initialize2(ni,nj) - - ! Create land export state - call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr) - - ! Fill in infodata settings - call seq_infodata_PutData(infodata, lnd_prognostic=.true.) - call seq_infodata_PutData(infodata, lnd_nx=ldomain%ni, lnd_ny=ldomain%nj) - call lnd_handle_resume( cdata_l ) - - ! Reset shr logging to original values - call shr_file_setLogUnit (shrlogunit) - call shr_file_setLogLevel(shrloglev) - -#if (defined _MEMTRACE) - if(masterproc) then - write(iulog,*) TRIM(Sub) // ':end::' - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_int_mct:end::',lbnum) - call memmon_reset_addr() - endif -#endif - end if - - end subroutine lnd_init_mct - - !==================================================================================== - subroutine lnd_run_mct(EClock, cdata_l, x2l_l, l2x_l) - ! - ! !DESCRIPTION: - ! Run clm model - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_instMod , only : water_inst, lnd2atm_inst, atm2lnd_inst, lnd2glc_inst, glc2lnd_inst - use clm_driver , only : clm_drv - use clm_time_manager, only : get_curr_date, get_nstep, get_curr_calday, get_step_size - use clm_time_manager, only : advance_timestep, update_rad_dtime - use decompMod , only : get_proc_bounds - use abortutils , only : endrun - use clm_varctl , only : iulog - use clm_varorb , only : eccen, obliqr, lambm0, mvelpp - use shr_file_mod , only : shr_file_setLogUnit, shr_file_setLogLevel - use shr_file_mod , only : shr_file_getLogUnit, shr_file_getLogLevel - use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs - use seq_timemgr_mod , only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn - use seq_timemgr_mod , only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync - use seq_infodata_mod, only : seq_infodata_type, seq_infodata_GetData - use spmdMod , only : masterproc, mpicom - use perf_mod , only : t_startf, t_stopf, t_barrierf - use shr_orb_mod , only : shr_orb_decl - use ESMF - ! - ! !ARGUMENTS: - type(ESMF_Clock) , intent(inout) :: EClock ! Input synchronization clock from driver - type(seq_cdata) , intent(inout) :: cdata_l ! Input driver data for land model - type(mct_aVect) , intent(inout) :: x2l_l ! Import state to land model - type(mct_aVect) , intent(inout) :: l2x_l ! Export state from land model - ! - ! !LOCAL VARIABLES: - integer :: ymd_sync ! Sync date (YYYYMMDD) - integer :: yr_sync ! Sync current year - integer :: mon_sync ! Sync current month - integer :: day_sync ! Sync current day - integer :: tod_sync ! Sync current time of day (sec) - integer :: ymd ! CLM current date (YYYYMMDD) - integer :: yr ! CLM current year - integer :: mon ! CLM current month - integer :: day ! CLM current day - integer :: tod ! CLM current time of day (sec) - integer :: dtime ! time step increment (sec) - integer :: nstep ! time step index - logical :: rstwr_sync ! .true. ==> write restart file before returning - logical :: rstwr ! .true. ==> write restart file before returning - logical :: nlend_sync ! Flag signaling last time-step - logical :: nlend ! .true. ==> last time-step - logical :: dosend ! true => send data back to driver - logical :: doalb ! .true. ==> do albedo calculation on this time step - logical :: rof_prognostic ! .true. => running with a prognostic ROF model - logical :: glc_present ! .true. => running with a non-stub GLC model - real(r8) :: nextsw_cday ! calday from clock of next radiation computation - real(r8) :: caldayp1 ! clm calday plus dtime offset - integer :: shrlogunit,shrloglev ! old values for share log unit and log level - integer :: lbnum ! input to memory diagnostic - integer :: g,i,lsize ! counters - real(r8) :: calday ! calendar day for nstep - real(r8) :: declin ! solar declination angle in radians for nstep - real(r8) :: declinp1 ! solar declination angle in radians for nstep+1 - real(r8) :: eccf ! earth orbit eccentricity factor - real(r8) :: recip ! reciprical - logical,save :: first_call = .true. ! first call work - type(seq_infodata_type),pointer :: infodata ! CESM information from the driver - type(mct_gGrid), pointer :: dom_l ! Land model domain data - type(bounds_type) :: bounds ! bounds - character(len=32) :: rdate ! date char string for restart file names - character(len=32), parameter :: sub = "lnd_run_mct" - !--------------------------------------------------------------------------- - - ! Determine processor bounds - - call get_proc_bounds(bounds) - -#if (defined _MEMTRACE) - if(masterproc) then - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_run_mct:start::',lbnum) - endif -#endif - - ! Reset shr logging to my log file - call shr_file_getLogUnit (shrlogunit) - call shr_file_getLogLevel(shrloglev) - call shr_file_setLogUnit (iulog) - - ! Determine time of next atmospheric shortwave calculation - call seq_cdata_setptrs(cdata_l, infodata=infodata, dom=dom_l) - call seq_timemgr_EClockGetData(EClock, & - curr_ymd=ymd, curr_tod=tod_sync, & - curr_yr=yr_sync, curr_mon=mon_sync, curr_day=day_sync) - call seq_infodata_GetData(infodata, nextsw_cday=nextsw_cday ) - - dtime = get_step_size() - - ! Handle pause/resume signals from coupler - call lnd_handle_resume( cdata_l ) - - write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync,mon_sync,day_sync,tod_sync - nlend_sync = seq_timemgr_StopAlarmIsOn( EClock ) - rstwr_sync = seq_timemgr_RestartAlarmIsOn( EClock ) - - ! Determine if we're running with a prognostic ROF model, and if we're running with a - ! non-stub GLC model. These won't change throughout the run, but we can't count on - ! their being set in initialization, so need to get them in the run method. - - call seq_infodata_GetData( infodata, & - rof_prognostic=rof_prognostic, & - glc_present=glc_present) - - ! Map MCT to land data type - ! Perform downscaling if appropriate - - - ! Map to clm (only when state and/or fluxes need to be updated) - - call t_startf ('lc_lnd_import') - call lnd_import( bounds, & - x2l = x2l_l%rattr, & - glc_present = glc_present, & - atm2lnd_inst = atm2lnd_inst, & - glc2lnd_inst = glc2lnd_inst, & - wateratm2lndbulk_inst = water_inst%wateratm2lndbulk_inst) - call t_stopf ('lc_lnd_import') - - ! Use infodata to set orbital values if updated mid-run - - call seq_infodata_GetData( infodata, orb_eccen=eccen, orb_mvelpp=mvelpp, & - orb_lambm0=lambm0, orb_obliqr=obliqr ) - - ! Loop over time steps in coupling interval - - dosend = .false. - do while(.not. dosend) - - ! Determine if dosend - ! When time is not updated at the beginning of the loop - then return only if - ! are in sync with clock before time is updated - ! - ! NOTE(wjs, 2020-03-09) I think the do while (.not. dosend) loop only is important - ! for the first time step (when we run 2 steps). After that, we now assume that we - ! run one time step per coupling interval (based on setting the model's dtime from - ! the driver). (According to Mariana Vertenstein, sub-cycling (running multiple - ! land model time steps per coupling interval) used to be supported, but hasn't - ! been fully supported for a long time.) We may want to rework this logic to make - ! this more explicit, or - ideally - get rid of this extra time step at the start - ! of the run, at which point I think we could do away with this looping entirely. - - call get_curr_date( yr, mon, day, tod ) - ymd = yr*10000 + mon*100 + day - tod = tod - dosend = (seq_timemgr_EClockDateInSync( EClock, ymd, tod)) - - ! Determine doalb based on nextsw_cday sent from atm model - - nstep = get_nstep() - caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.) - if (nstep == 0) then - doalb = .false. - else if (nstep == 1) then - doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8) - else - doalb = (nextsw_cday >= -0.5_r8) - end if - call update_rad_dtime(doalb) - - ! Determine if time to write restart and stop - - rstwr = .false. - if (rstwr_sync .and. dosend) rstwr = .true. - nlend = .false. - if (nlend_sync .and. dosend) nlend = .true. - - ! Run clm - - call t_barrierf('sync_clm_run1', mpicom) - call t_startf ('clm_run') - call t_startf ('shr_orb_decl') - calday = get_curr_calday(reuse_day_365_for_day_366=.true.) - call shr_orb_decl( calday , eccen, mvelpp, lambm0, obliqr, declin , eccf ) - call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf ) - call t_stopf ('shr_orb_decl') - call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic) - call t_stopf ('clm_run') - - ! Create l2x_l export state - add river runoff input to l2x_l if appropriate - - call t_startf ('lc_lnd_export') - call lnd_export(bounds, water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x_l%rattr) - call t_stopf ('lc_lnd_export') - - ! Advance clm time step - - call t_startf ('lc_clm2_adv_timestep') - call advance_timestep() - call t_stopf ('lc_clm2_adv_timestep') - - end do - - ! Check that internal clock is in sync with master clock - - call get_curr_date( yr, mon, day, tod, offset=-dtime ) - ymd = yr*10000 + mon*100 + day - tod = tod - if ( .not. seq_timemgr_EClockDateInSync( EClock, ymd, tod ) )then - call seq_timemgr_EclockGetData( EClock, curr_ymd=ymd_sync, curr_tod=tod_sync ) - write(iulog,*)' clm ymd=',ymd ,' clm tod= ',tod - write(iulog,*)'sync ymd=',ymd_sync,' sync tod= ',tod_sync - call endrun( sub//":: CLM clock not in sync with Master Sync clock" ) - end if - - ! Reset shr logging to my original values - - call shr_file_setLogUnit (shrlogunit) - call shr_file_setLogLevel(shrloglev) - -#if (defined _MEMTRACE) - if(masterproc) then - lbnum=1 - call memmon_dump_fort('memmon.out','lnd_run_mct:end::',lbnum) - call memmon_reset_addr() - endif -#endif - - first_call = .false. - - end subroutine lnd_run_mct - - !==================================================================================== - subroutine lnd_final_mct( EClock, cdata_l, x2l_l, l2x_l) - ! - ! !DESCRIPTION: - ! Finalize land surface model - - use seq_cdata_mod ,only : seq_cdata, seq_cdata_setptrs - use seq_timemgr_mod ,only : seq_timemgr_EClockGetData, seq_timemgr_StopAlarmIsOn - use seq_timemgr_mod ,only : seq_timemgr_RestartAlarmIsOn, seq_timemgr_EClockDateInSync - use esmf - ! - ! !ARGUMENTS: - type(ESMF_Clock) , intent(inout) :: EClock ! Input synchronization clock from driver - type(seq_cdata) , intent(inout) :: cdata_l ! Input driver data for land model - type(mct_aVect) , intent(inout) :: x2l_l ! Import state to land model - type(mct_aVect) , intent(inout) :: l2x_l ! Export state from land model - !--------------------------------------------------------------------------- - - ! fill this in - end subroutine lnd_final_mct - - !==================================================================================== - subroutine lnd_domain_mct( bounds, lsize, gsMap_l, dom_l ) - ! - ! !DESCRIPTION: - ! Send the land model domain information to the coupler - ! - ! !USES: - use clm_varcon , only: re - use domainMod , only: ldomain - use spmdMod , only: iam - use mct_mod , only: mct_gGrid_importIAttr - use mct_mod , only: mct_gGrid_importRAttr, mct_gGrid_init, mct_gsMap_orderedPoints - use seq_flds_mod, only: seq_flds_dom_coord, seq_flds_dom_other - ! - ! !ARGUMENTS: - type(bounds_type), intent(in) :: bounds ! bounds - integer , intent(in) :: lsize ! land model domain data size - type(mct_gsMap), intent(inout) :: gsMap_l ! Output land model MCT GS map - type(mct_ggrid), intent(out) :: dom_l ! Output domain information for land model - ! - ! Local Variables - integer :: g,i,j ! index - real(r8), pointer :: data(:) ! temporary - integer , pointer :: idata(:) ! temporary - !--------------------------------------------------------------------------- - ! - ! Initialize mct domain type - ! lat/lon in degrees, area in radians^2, mask is 1 (land), 0 (non-land) - ! Note that in addition land carries around landfrac for the purposes of domain checking - ! - call mct_gGrid_init( GGrid=dom_l, CoordChars=trim(seq_flds_dom_coord), & - OtherChars=trim(seq_flds_dom_other), lsize=lsize ) - ! - ! Allocate memory - ! - allocate(data(lsize)) - ! - ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT - ! - call mct_gsMap_orderedPoints(gsMap_l, iam, idata) - call mct_gGrid_importIAttr(dom_l,'GlobGridNum',idata,lsize) - ! - ! Determine domain (numbering scheme is: West to East and South to North to South pole) - ! Initialize attribute vector with special value - ! - data(:) = -9999.0_R8 - call mct_gGrid_importRAttr(dom_l,"lat" ,data,lsize) - call mct_gGrid_importRAttr(dom_l,"lon" ,data,lsize) - call mct_gGrid_importRAttr(dom_l,"area" ,data,lsize) - call mct_gGrid_importRAttr(dom_l,"aream",data,lsize) - data(:) = 0.0_R8 - call mct_gGrid_importRAttr(dom_l,"mask" ,data,lsize) - ! - ! Fill in correct values for domain components - ! Note aream will be filled in in the atm-lnd mapper - ! - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%lonc(g) - end do - call mct_gGrid_importRattr(dom_l,"lon",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%latc(g) - end do - call mct_gGrid_importRattr(dom_l,"lat",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%area(g)/(re*re) - end do - call mct_gGrid_importRattr(dom_l,"area",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%mask(g), r8) - end do - call mct_gGrid_importRattr(dom_l,"mask",data,lsize) - - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%frac(g), r8) - end do - call mct_gGrid_importRattr(dom_l,"frac",data,lsize) - - deallocate(data) - deallocate(idata) - - end subroutine lnd_domain_mct - - !==================================================================================== - subroutine lnd_handle_resume( cdata_l ) - ! - ! !DESCRIPTION: - ! Handle resume signals for Data Assimilation (DA) - ! - ! !USES: - use clm_time_manager , only : update_DA_nstep - use seq_cdata_mod , only : seq_cdata, seq_cdata_setptrs - implicit none - ! !ARGUMENTS: - type(seq_cdata), intent(inout) :: cdata_l ! Input land-model driver data - ! !LOCAL VARIABLES: - logical :: resume_from_data_assim ! flag if we are resuming after data assimulation was done - !--------------------------------------------------------------------------- - - ! Check to see if restart was modified and we are resuming from data - ! assimilation - call seq_cdata_setptrs(cdata_l, post_assimilation=resume_from_data_assim) - if ( resume_from_data_assim ) call update_DA_nstep() - - end subroutine lnd_handle_resume - -end module lnd_comp_mct diff --git a/src/cpl/mct/lnd_import_export.F90 b/src/cpl/mct/lnd_import_export.F90 deleted file mode 100644 index 537abd49d9..0000000000 --- a/src/cpl/mct/lnd_import_export.F90 +++ /dev/null @@ -1,354 +0,0 @@ -module lnd_import_export - - use shr_kind_mod , only: r8 => shr_kind_r8, cl=>shr_kind_cl - use abortutils , only: endrun - use decompmod , only: bounds_type, subgrid_level_gridcell - use lnd2atmType , only: lnd2atm_type - use lnd2glcMod , only: lnd2glc_type - use atm2lndType , only: atm2lnd_type - use glc2lndMod , only: glc2lnd_type - use Waterlnd2atmBulkType , only: waterlnd2atmbulk_type - use Wateratm2lndBulkType , only: wateratm2lndbulk_type - use clm_cpl_indices - use GridcellType , only : grc - ! - implicit none - !=============================================================================== - -contains - - !=============================================================================== - subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst, wateratm2lndbulk_inst) - - !--------------------------------------------------------------------------- - ! !DESCRIPTION: - ! Convert the input data from the coupler to the land model - ! - ! !USES: - use seq_flds_mod , only: seq_flds_x2l_fields - use clm_varctl , only: co2_type, co2_ppmv, iulog, use_c13 - use clm_varctl , only: ndep_from_cpl - use clm_varcon , only: c13ratio - use domainMod , only: ldomain - use lnd_import_export_utils, only : derive_quantities, check_for_errors, check_for_nans - ! - ! !ARGUMENTS: - type(bounds_type) , intent(in) :: bounds ! bounds - real(r8) , intent(in) :: x2l(:,:) ! driver import state to land model - logical , intent(in) :: glc_present ! .true. => running with a non-stub GLC model - type(atm2lnd_type) , intent(inout) :: atm2lnd_inst ! clm internal input data type - type(glc2lnd_type) , intent(inout) :: glc2lnd_inst ! clm internal input data type - type(wateratm2lndbulk_type), intent(inout) :: wateratm2lndbulk_inst ! clm internal input data type - ! - ! !LOCAL VARIABLES: - integer :: begg, endg ! bounds - integer :: g,i,k,nstep,ier ! indices, number of steps, and error code - real(r8) :: qsat_kg_kg ! saturation specific humidity (kg/kg) - real(r8) :: forc_pbot ! atmospheric pressure (Pa) - real(r8) :: forc_rainc(bounds%begg:bounds%endg) ! rainxy Atm flux mm/s - real(r8) :: forc_rainl(bounds%begg:bounds%endg) ! rainxy Atm flux mm/s - real(r8) :: forc_snowc(bounds%begg:bounds%endg) ! snowfxy Atm flux mm/s - real(r8) :: forc_snowl(bounds%begg:bounds%endg) ! snowfxl Atm flux mm/s - real(r8) :: co2_ppmv_diag ! temporary - real(r8) :: co2_ppmv_prog ! temporary - real(r8) :: co2_ppmv_val ! temporary - integer :: co2_type_idx ! integer flag for co2_type options - character(len=32) :: fname ! name of field that is NaN - character(len=32), parameter :: sub = 'lnd_import' - - !--------------------------------------------------------------------------- - - ! Set bounds - begg = bounds%begg; endg = bounds%endg - - co2_type_idx = 0 - if (co2_type == 'prognostic') then - co2_type_idx = 1 - else if (co2_type == 'diagnostic') then - co2_type_idx = 2 - end if - if (co2_type == 'prognostic' .and. index_x2l_Sa_co2prog == 0) then - call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2prog for co2_type equal to prognostic' ) - else if (co2_type == 'diagnostic' .and. index_x2l_Sa_co2diag == 0) then - call endrun( sub//' ERROR: must have nonzero index_x2l_Sa_co2diag for co2_type equal to diagnostic' ) - end if - - ! Note that the precipitation fluxes received from the coupler - ! are in units of kg/s/m^2. To convert these precipitation rates - ! in units of mm/sec, one must divide by 1000 kg/m^3 and multiply - ! by 1000 mm/m resulting in an overall factor of unity. - ! Below the units are therefore given in mm/s. - - do g = begg,endg - i = 1 + (g - begg) - - ! Determine flooding input, sign convention is positive downward and - ! hierarchy is atm/glc/lnd/rof/ice/ocn. so water sent from rof to land is negative, - ! change the sign to indicate addition of water to system. - - wateratm2lndbulk_inst%forc_flood_grc(g) = -x2l(index_x2l_Flrr_flood,i) - - wateratm2lndbulk_inst%volr_grc(g) = x2l(index_x2l_Flrr_volr,i) * (ldomain%area(g) * 1.e6_r8) - wateratm2lndbulk_inst%volrmch_grc(g)= x2l(index_x2l_Flrr_volrmch,i) * (ldomain%area(g) * 1.e6_r8) - - ! Determine required receive fields - - atm2lnd_inst%forc_hgt_grc(g) = x2l(index_x2l_Sa_z,i) ! zgcmxy Atm state m - atm2lnd_inst%forc_topo_grc(g) = x2l(index_x2l_Sa_topo,i) ! Atm surface height (m) - atm2lnd_inst%forc_u_grc(g) = x2l(index_x2l_Sa_u,i) ! forc_uxy Atm state m/s - atm2lnd_inst%forc_v_grc(g) = x2l(index_x2l_Sa_v,i) ! forc_vxy Atm state m/s - atm2lnd_inst%forc_solad_not_downscaled_grc(g,2) = x2l(index_x2l_Faxa_swndr,i) ! forc_sollxy Atm flux W/m^2 - atm2lnd_inst%forc_solad_not_downscaled_grc(g,1) = x2l(index_x2l_Faxa_swvdr,i) ! forc_solsxy Atm flux W/m^2 - atm2lnd_inst%forc_solai_grc(g,2) = x2l(index_x2l_Faxa_swndf,i) ! forc_solldxy Atm flux W/m^2 - atm2lnd_inst%forc_solai_grc(g,1) = x2l(index_x2l_Faxa_swvdf,i) ! forc_solsdxy Atm flux W/m^2 - - atm2lnd_inst%forc_th_not_downscaled_grc(g) = x2l(index_x2l_Sa_ptem,i) ! forc_thxy Atm state K - wateratm2lndbulk_inst%forc_q_not_downscaled_grc(g) = x2l(index_x2l_Sa_shum,i) ! forc_qxy Atm state kg/kg - atm2lnd_inst%forc_pbot_not_downscaled_grc(g) = x2l(index_x2l_Sa_pbot,i) ! ptcmxy Atm state Pa - atm2lnd_inst%forc_t_not_downscaled_grc(g) = x2l(index_x2l_Sa_tbot,i) ! forc_txy Atm state K - atm2lnd_inst%forc_lwrad_not_downscaled_grc(g) = x2l(index_x2l_Faxa_lwdn,i) ! flwdsxy Atm flux W/m^2 - - forc_rainc(g) = x2l(index_x2l_Faxa_rainc,i) ! mm/s - forc_rainl(g) = x2l(index_x2l_Faxa_rainl,i) ! mm/s - forc_snowc(g) = x2l(index_x2l_Faxa_snowc,i) ! mm/s - forc_snowl(g) = x2l(index_x2l_Faxa_snowl,i) ! mm/s - - ! atmosphere coupling, for prognostic/prescribed aerosols - atm2lnd_inst%forc_aer_grc(g,1) = x2l(index_x2l_Faxa_bcphidry,i) - atm2lnd_inst%forc_aer_grc(g,2) = x2l(index_x2l_Faxa_bcphodry,i) - atm2lnd_inst%forc_aer_grc(g,3) = x2l(index_x2l_Faxa_bcphiwet,i) - atm2lnd_inst%forc_aer_grc(g,4) = x2l(index_x2l_Faxa_ocphidry,i) - atm2lnd_inst%forc_aer_grc(g,5) = x2l(index_x2l_Faxa_ocphodry,i) - atm2lnd_inst%forc_aer_grc(g,6) = x2l(index_x2l_Faxa_ocphiwet,i) - atm2lnd_inst%forc_aer_grc(g,7) = x2l(index_x2l_Faxa_dstwet1,i) - atm2lnd_inst%forc_aer_grc(g,8) = x2l(index_x2l_Faxa_dstdry1,i) - atm2lnd_inst%forc_aer_grc(g,9) = x2l(index_x2l_Faxa_dstwet2,i) - atm2lnd_inst%forc_aer_grc(g,10) = x2l(index_x2l_Faxa_dstdry2,i) - atm2lnd_inst%forc_aer_grc(g,11) = x2l(index_x2l_Faxa_dstwet3,i) - atm2lnd_inst%forc_aer_grc(g,12) = x2l(index_x2l_Faxa_dstdry3,i) - atm2lnd_inst%forc_aer_grc(g,13) = x2l(index_x2l_Faxa_dstwet4,i) - atm2lnd_inst%forc_aer_grc(g,14) = x2l(index_x2l_Faxa_dstdry4,i) - - if (index_x2l_Sa_methane /= 0) then - atm2lnd_inst%forc_pch4_grc(g) = x2l(index_x2l_Sa_methane,i) - endif - - !-------------------------- - ! Check for nans from coupler - !-------------------------- - - call check_for_nans(x2l(:,i), fname, begg, "x2l") - - end do - - !-------------------------- - ! Derived quantities for required fields - ! and corresponding error checks - !-------------------------- - - call derive_quantities(bounds, atm2lnd_inst, wateratm2lndbulk_inst, & - forc_rainc, forc_rainl, forc_snowc, forc_snowl) - - call check_for_errors(bounds, atm2lnd_inst, wateratm2lndbulk_inst) - - ! Determine derived quantities for optional fields - ! Note that the following does unit conversions from ppmv to partial pressures (Pa) - ! Note that forc_pbot is in Pa - - do g = begg,endg - i = 1 + (g - begg) - - forc_pbot = atm2lnd_inst%forc_pbot_not_downscaled_grc(g) - - ! Determine optional receive fields - if (index_x2l_Sa_co2prog /= 0) then - co2_ppmv_prog = x2l(index_x2l_Sa_co2prog,i) ! co2 atm state prognostic - else - co2_ppmv_prog = co2_ppmv - end if - if (index_x2l_Sa_co2diag /= 0) then - co2_ppmv_diag = x2l(index_x2l_Sa_co2diag,i) ! co2 atm state diagnostic - else - co2_ppmv_diag = co2_ppmv - end if - - if (co2_type_idx == 1) then - co2_ppmv_val = co2_ppmv_prog - else if (co2_type_idx == 2) then - co2_ppmv_val = co2_ppmv_diag - else - co2_ppmv_val = co2_ppmv - end if - if ( (co2_ppmv_val < 10.0_r8) .or. (co2_ppmv_val > 15000.0_r8) )then - call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, & - msg = sub//' ERROR: CO2 is outside of an expected range' ) - end if - atm2lnd_inst%forc_pco2_grc(g) = co2_ppmv_val * 1.e-6_r8 * forc_pbot - if (use_c13) then - atm2lnd_inst%forc_pc13o2_grc(g) = co2_ppmv_val * c13ratio * 1.e-6_r8 * forc_pbot - end if - - if (ndep_from_cpl) then - ! The coupler is sending ndep in units if kgN/m2/s - and clm uses units of gN/m2/sec - so the - ! following conversion needs to happen - atm2lnd_inst%forc_ndep_grc(g) = (x2l(index_x2l_Faxa_nhx, i) + x2l(index_x2l_faxa_noy, i))*1000._r8 - end if - - end do - - call glc2lnd_inst%set_glc2lnd_fields_mct( & - bounds = bounds, & - glc_present = glc_present, & - ! NOTE(wjs, 2017-12-13) the x2l argument doesn't have the typical bounds - ! subsetting (bounds%begg:bounds%endg). This mirrors the lack of these bounds in - ! the call to lnd_import from lnd_run_mct. This is okay as long as this code is - ! outside a clump loop. - x2l = x2l, & - index_x2l_Sg_ice_covered = index_x2l_Sg_ice_covered, & - index_x2l_Sg_topo = index_x2l_Sg_topo, & - index_x2l_Flgg_hflx = index_x2l_Flgg_hflx, & - index_x2l_Sg_icemask = index_x2l_Sg_icemask, & - index_x2l_Sg_icemask_coupled_fluxes = index_x2l_Sg_icemask_coupled_fluxes) - - end subroutine lnd_import - - !=============================================================================== - - subroutine lnd_export( bounds, waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, l2x) - - !--------------------------------------------------------------------------- - ! !DESCRIPTION: - ! Convert the data to be sent from the clm model to the coupler - ! - ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 - use seq_flds_mod , only : seq_flds_l2x_fields - use clm_varctl , only : iulog - use shr_drydep_mod , only : n_drydep - use shr_megan_mod , only : shr_megan_mechcomps_n - use shr_fire_emis_mod , only : shr_fire_emis_mechcomps_n - use lnd_import_export_utils, only : check_for_nans - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds ! bounds - type(lnd2atm_type), intent(inout) :: lnd2atm_inst ! clm land to atmosphere exchange data type - type(lnd2glc_type), intent(inout) :: lnd2glc_inst ! clm land to atmosphere exchange data type - type(waterlnd2atmbulk_type), intent(in) :: waterlnd2atmbulk_inst - real(r8) , intent(out) :: l2x(:,:)! land to coupler export state on land grid - ! - ! !LOCAL VARIABLES: - integer :: begg, endg ! bounds - integer :: g,i,k ! indices - integer :: ier ! error status - integer :: nstep ! time step index - integer :: dtime ! time step - integer :: num ! counter - character(len=32) :: fname ! name of field that is NaN - character(len=32), parameter :: sub = 'lnd_export' - !--------------------------------------------------------------------------- - - ! Set bounds - begg = bounds%begg; endg = bounds%endg - - ! cesm sign convention is that fluxes are positive downward - - l2x(:,:) = 0.0_r8 - - do g = begg,endg - i = 1 + (g-begg) - l2x(index_l2x_Sl_t,i) = lnd2atm_inst%t_rad_grc(g) - l2x(index_l2x_Sl_snowh,i) = waterlnd2atmbulk_inst%h2osno_grc(g) - l2x(index_l2x_Sl_avsdr,i) = lnd2atm_inst%albd_grc(g,1) - l2x(index_l2x_Sl_anidr,i) = lnd2atm_inst%albd_grc(g,2) - l2x(index_l2x_Sl_avsdf,i) = lnd2atm_inst%albi_grc(g,1) - l2x(index_l2x_Sl_anidf,i) = lnd2atm_inst%albi_grc(g,2) - l2x(index_l2x_Sl_tref,i) = lnd2atm_inst%t_ref2m_grc(g) - l2x(index_l2x_Sl_qref,i) = waterlnd2atmbulk_inst%q_ref2m_grc(g) - l2x(index_l2x_Sl_u10,i) = lnd2atm_inst%u_ref10m_grc(g) - l2x(index_l2x_Fall_taux,i) = -lnd2atm_inst%taux_grc(g) - l2x(index_l2x_Fall_tauy,i) = -lnd2atm_inst%tauy_grc(g) - l2x(index_l2x_Fall_lat,i) = -lnd2atm_inst%eflx_lh_tot_grc(g) - l2x(index_l2x_Fall_sen,i) = -lnd2atm_inst%eflx_sh_tot_grc(g) - l2x(index_l2x_Fall_lwup,i) = -lnd2atm_inst%eflx_lwrad_out_grc(g) - l2x(index_l2x_Fall_evap,i) = -waterlnd2atmbulk_inst%qflx_evap_tot_grc(g) - l2x(index_l2x_Fall_swnet,i) = lnd2atm_inst%fsa_grc(g) - if (index_l2x_Fall_fco2_lnd /= 0) then - l2x(index_l2x_Fall_fco2_lnd,i) = -lnd2atm_inst%net_carbon_exchange_grc(g) - end if - - ! Additional fields for DUST, PROGSSLT, dry-deposition and VOC - ! These are now standard fields, but the check on the index makes sure the driver handles them - if (index_l2x_Sl_ram1 /= 0 ) l2x(index_l2x_Sl_ram1,i) = lnd2atm_inst%ram1_grc(g) - if (index_l2x_Sl_fv /= 0 ) l2x(index_l2x_Sl_fv,i) = lnd2atm_inst%fv_grc(g) - if (index_l2x_Sl_soilw /= 0 ) l2x(index_l2x_Sl_soilw,i) = waterlnd2atmbulk_inst%h2osoi_vol_grc(g,1) - if (index_l2x_Fall_flxdst1 /= 0 ) l2x(index_l2x_Fall_flxdst1,i)= -lnd2atm_inst%flxdst_grc(g,1) - if (index_l2x_Fall_flxdst2 /= 0 ) l2x(index_l2x_Fall_flxdst2,i)= -lnd2atm_inst%flxdst_grc(g,2) - if (index_l2x_Fall_flxdst3 /= 0 ) l2x(index_l2x_Fall_flxdst3,i)= -lnd2atm_inst%flxdst_grc(g,3) - if (index_l2x_Fall_flxdst4 /= 0 ) l2x(index_l2x_Fall_flxdst4,i)= -lnd2atm_inst%flxdst_grc(g,4) - - - ! for dry dep velocities - if (index_l2x_Sl_ddvel /= 0 ) then - l2x(index_l2x_Sl_ddvel:index_l2x_Sl_ddvel+n_drydep-1,i) = & - lnd2atm_inst%ddvel_grc(g,:n_drydep) - end if - - ! for MEGAN VOC emis fluxes - if (index_l2x_Fall_flxvoc /= 0 ) then - l2x(index_l2x_Fall_flxvoc:index_l2x_Fall_flxvoc+shr_megan_mechcomps_n-1,i) = & - -lnd2atm_inst%flxvoc_grc(g,:shr_megan_mechcomps_n) - end if - - - ! for fire emis fluxes - if (index_l2x_Fall_flxfire /= 0 ) then - l2x(index_l2x_Fall_flxfire:index_l2x_Fall_flxfire+shr_fire_emis_mechcomps_n-1,i) = & - -lnd2atm_inst%fireflx_grc(g,:shr_fire_emis_mechcomps_n) - l2x(index_l2x_Sl_ztopfire,i) = lnd2atm_inst%fireztop_grc(g) - end if - - if (index_l2x_Fall_methane /= 0) then - l2x(index_l2x_Fall_methane,i) = -lnd2atm_inst%ch4_surf_flux_tot_grc(g) - endif - - ! sign convention is positive downward with - ! hierarchy of atm/glc/lnd/rof/ice/ocn. - ! I.e. water sent from land to rof is positive - - l2x(index_l2x_Flrl_rofsur,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsur_grc(g) - - ! subsurface runoff is the sum of qflx_drain and qflx_perched_drain - l2x(index_l2x_Flrl_rofsub,i) = waterlnd2atmbulk_inst%qflx_rofliq_qsub_grc(g) & - + waterlnd2atmbulk_inst%qflx_rofliq_drain_perched_grc(g) - - ! qgwl sent individually to coupler - l2x(index_l2x_Flrl_rofgwl,i) = waterlnd2atmbulk_inst%qflx_rofliq_qgwl_grc(g) - - ! ice sent individually to coupler - l2x(index_l2x_Flrl_rofi,i) = waterlnd2atmbulk_inst%qflx_rofice_grc(g) - - ! irrigation flux to be removed from main channel storage (negative) - l2x(index_l2x_Flrl_irrig,i) = - waterlnd2atmbulk_inst%qirrig_grc(g) - - ! glc coupling - ! We could avoid setting these fields if glc_present is .false., if that would - ! help with performance. (The downside would be that we wouldn't have these fields - ! available for diagnostic purposes or to force a later T compset with dlnd.) - do num = 0,glc_nec - l2x(index_l2x_Sl_tsrf(num),i) = lnd2glc_inst%tsrf_grc(g,num) - l2x(index_l2x_Sl_topo(num),i) = lnd2glc_inst%topo_grc(g,num) - l2x(index_l2x_Flgl_qice(num),i) = lnd2glc_inst%qice_grc(g,num) - end do - - !-------------------------- - ! Check for nans to coupler - !-------------------------- - - call check_for_nans(l2x(:,i), fname, begg, "l2x") - - end do - - end subroutine lnd_export - -end module lnd_import_export diff --git a/src/cpl/mct/lnd_set_decomp_and_domain.F90 b/src/cpl/mct/lnd_set_decomp_and_domain.F90 deleted file mode 100644 index 0a37554313..0000000000 --- a/src/cpl/mct/lnd_set_decomp_and_domain.F90 +++ /dev/null @@ -1,352 +0,0 @@ -module lnd_set_decomp_and_domain - - use shr_kind_mod , only : r8 => shr_kind_r8 - use spmdMod , only : masterproc - use clm_varctl , only : iulog - use mct_mod , only : mct_gsMap - - implicit none - private ! except - - ! public member routines - public :: lnd_set_decomp_and_domain_from_surfrd - - ! private member routines - private :: surfrd_get_globmask ! Reads global land mask (needed for setting domain decomp) - private :: surfrd_get_grid ! Read grid/ladnfrac data into domain (after domain decomp) - - ! translation between local and global indices at gridcell level - type(mct_gsmap), pointer, public :: gsmap_global - - ! translation between local and global indices at gridcell level for multiple levels - ! needed for 3d soil moisture stream - type(mct_gsmap), target , public :: gsMap_lnd2Dsoi_gdc2glo - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -!=============================================================================== -contains -!=============================================================================== - - subroutine lnd_set_decomp_and_domain_from_surfrd(noland, ni, nj) - - ! Initialize ldomain data types - - use clm_varpar , only: nlevsoi - use clm_varctl , only: fatmlndfrc, use_soil_moisture_streams - use decompInitMod , only: decompInit_lnd - use decompMod , only: bounds_type, get_proc_bounds - use domainMod , only: ldomain, domain_check - - ! input/output variables - logical, intent(out) :: noland - integer, intent(out) :: ni, nj ! global grid sizes - - ! local variables - integer ,pointer :: amask(:) ! global land mask - integer :: begg, endg ! processor bounds - type(bounds_type) :: bounds ! bounds - character(len=32) :: subname = 'lnd_set_decomp_and_domain_from_surfrd' - !----------------------------------------------------------------------- - - ! Read in global land grid and land mask (amask)- needed to set decomposition - ! global memory for amask is allocate in surfrd_get_glomask - must be deallocated below - if (masterproc) then - write(iulog,*) 'Attempting to read global land mask from ',trim(fatmlndfrc) - endif - - ! Get global mask, ni and nj - call surfrd_get_globmask(filename=fatmlndfrc, mask=amask, ni=ni, nj=nj) - - ! Exit early if no valid land points - if ( all(amask == 0) )then - if (masterproc) write(iulog,*) trim(subname)//': no valid land points do NOT run clm' - noland = .true. - return - else - noland = .false. - end if - - ! Determine ctsm gridcell decomposition and processor bounds for gridcells - call decompInit_lnd(ni, nj, amask) - deallocate(amask) - if (use_soil_moisture_streams) call decompInit_lnd3D(ni, nj, nlevsoi) - - ! Initialize bounds for just gridcells - ! Remaining bounds (landunits, columns, patches) will be determined - ! after the call to decompInit_glcp - so get_proc_bounds is called - ! twice and the gridcell information is just filled in twice - call get_proc_bounds(bounds) - - ! Get grid cell bounds values - begg = bounds%begg - endg = bounds%endg - - ! Initialize ldomain data type - if (masterproc) then - write(iulog,*) 'Attempting to read ldomain from ',trim(fatmlndfrc) - endif - call surfrd_get_grid(begg, endg, ldomain, fatmlndfrc) - if (masterproc) then - call domain_check(ldomain) - endif - ldomain%mask = 1 !!! TODO - is this needed? - - end subroutine lnd_set_decomp_and_domain_from_surfrd - - !----------------------------------------------------------------------- - subroutine surfrd_get_globmask(filename, mask, ni, nj) - - ! Read the surface dataset grid related information - ! This is used to set the domain decomposition - so global data is read here - - use fileutils , only : getfil - use ncdio_pio , only : ncd_io, ncd_pio_openfile, ncd_pio_closefile, ncd_inqfdims, file_desc_t - use abortutils , only : endrun - use shr_log_mod, only : errMsg => shr_log_errMsg - - ! input/output variables - character(len=*), intent(in) :: filename ! grid filename - integer , pointer :: mask(:) ! grid mask - integer , intent(out) :: ni, nj ! global grid sizes - - ! local variables - logical :: isgrid2d - integer :: dimid,varid ! netCDF id's - integer :: ns ! size of grid on file - integer :: n,i,j ! index - integer :: ier ! error status - type(file_desc_t) :: ncid ! netcdf id - character(len=256) :: locfn ! local file name - logical :: readvar ! read variable in or not - integer , allocatable :: idata2d(:,:) - character(len=32) :: subname = 'surfrd_get_globmask' ! subroutine name - !----------------------------------------------------------------------- - - if (filename == ' ') then - mask(:) = 1 - else - ! Check if file exists - if (masterproc) then - if (filename == ' ') then - write(iulog,*) trim(subname),' ERROR: filename must be specified ' - call endrun(msg=errMsg(sourcefile, __LINE__)) - endif - end if - - ! Open file - call getfil( filename, locfn, 0 ) - call ncd_pio_openfile (ncid, trim(locfn), 0) - - ! Determine dimensions and if grid file is 2d or 1d - call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns) - if (masterproc) then - write(iulog,*)'lat/lon grid flag (isgrid2d) is ',isgrid2d - end if - allocate(mask(ns)) - mask(:) = 1 - if (isgrid2d) then - ! Grid is 2d - allocate(idata2d(ni,nj)) - idata2d(:,:) = 1 - call ncd_io(ncid=ncid, varname='LANDMASK', data=idata2d, flag='read', readvar=readvar) - if (.not. readvar) then - call ncd_io(ncid=ncid, varname='mask', data=idata2d, flag='read', readvar=readvar) - end if - if (readvar) then - do j = 1,nj - do i = 1,ni - n = (j-1)*ni + i - mask(n) = idata2d(i,j) - enddo - enddo - end if - deallocate(idata2d) - else - ! Grid is not 2d - call ncd_io(ncid=ncid, varname='LANDMASK', data=mask, flag='read', readvar=readvar) - if (.not. readvar) then - call ncd_io(ncid=ncid, varname='mask', data=mask, flag='read', readvar=readvar) - end if - end if - if (.not. readvar) call endrun( msg=' ERROR: landmask not on fatmlndfrc file'//errMsg(sourcefile, __LINE__)) - - ! Close file - call ncd_pio_closefile(ncid) - end if - - end subroutine surfrd_get_globmask - - !----------------------------------------------------------------------- - subroutine surfrd_get_grid(begg, endg, ldomain, filename) - - ! Read the surface dataset grid related information: - ! This is called after the domain decomposition has been created - ! - real latitude of grid cell (degrees) - ! - real longitude of grid cell (degrees) - - use clm_varcon , only : spval, re, grlnd - use domainMod , only : domain_type, lon1d, lat1d, domain_init - use fileutils , only : getfil - use abortutils , only : endrun - use shr_log_mod , only : errMsg => shr_log_errMsg - use ncdio_pio , only : file_desc_t, ncd_pio_openfile, ncd_pio_closefile - use ncdio_pio , only : ncd_io, check_var, ncd_inqfdims, check_dim_size - use pio - - ! input/output variables - integer , intent(in) :: begg, endg - type(domain_type) , intent(inout) :: ldomain ! domain to init - character(len=*) , intent(in) :: filename ! grid filename - - ! local variables - type(file_desc_t) :: ncid ! netcdf id - integer :: beg ! local beg index - integer :: end ! local end index - integer :: ni,nj,ns ! size of grid on file - logical :: readvar ! true => variable is on input file - logical :: isgrid2d ! true => file is 2d lat/lon - logical :: istype_domain ! true => input file is of type domain - real(r8), allocatable :: rdata2d(:,:) ! temporary - character(len=16) :: vname ! temporary - character(len=256) :: locfn ! local file name - integer :: n ! indices - character(len=32) :: subname = 'surfrd_get_grid' ! subroutine name - !----------------------------------------------------------------------- - - if (masterproc) then - if (filename == ' ') then - write(iulog,*) trim(subname),' ERROR: filename must be specified ' - call endrun(msg=errMsg(sourcefile, __LINE__)) - endif - end if - - call getfil( filename, locfn, 0 ) - call ncd_pio_openfile (ncid, trim(locfn), 0) - - ! Determine dimensions - call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns) - - ! Determine isgrid2d flag for domain - call domain_init(ldomain, isgrid2d=isgrid2d, ni=ni, nj=nj, nbeg=begg, nend=endg) - - ! Determine type of file - old style grid file or new style domain file - call check_var(ncid=ncid, varname='xc', readvar=readvar) - if (readvar)then - istype_domain = .true. - else - istype_domain = .false. - end if - - ! Read in area, lon, lat - if (istype_domain) then - call ncd_io(ncid=ncid, varname= 'area', flag='read', data=ldomain%area, & - dim1name=grlnd, readvar=readvar) - ! convert from radians**2 to km**2 - ldomain%area = ldomain%area * (re**2) - if (.not. readvar) call endrun( msg=' ERROR: area NOT on file'//errMsg(sourcefile, __LINE__)) - call ncd_io(ncid=ncid, varname= 'xc', flag='read', data=ldomain%lonc, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) call endrun( msg=' ERROR: xc NOT on file'//errMsg(sourcefile, __LINE__)) - call ncd_io(ncid=ncid, varname= 'yc', flag='read', data=ldomain%latc, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) call endrun( msg=' ERROR: yc NOT on file'//errMsg(sourcefile, __LINE__)) - else - call endrun( msg=" ERROR: can no longer read non domain files" ) - end if - - if (isgrid2d) then - allocate(rdata2d(ni,nj), lon1d(ni), lat1d(nj)) - if (istype_domain) vname = 'xc' - call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar) - lon1d(:) = rdata2d(:,1) - if (istype_domain) vname = 'yc' - call ncd_io(ncid=ncid, varname=trim(vname), data=rdata2d, flag='read', readvar=readvar) - lat1d(:) = rdata2d(1,:) - deallocate(rdata2d) - end if - - ! Check lat limited to -90,90 - if (minval(ldomain%latc) < -90.0_r8 .or. & - maxval(ldomain%latc) > 90.0_r8) then - write(iulog,*) trim(subname),' WARNING: lat/lon min/max is ', & - minval(ldomain%latc),maxval(ldomain%latc) - endif - if ( any(ldomain%lonc < 0.0_r8) )then - call endrun( msg=' ERROR: lonc is negative (see https://github.com/ESCOMP/ctsm/issues/507)' & - //errMsg(sourcefile, __LINE__)) - endif - call ncd_io(ncid=ncid, varname='mask', flag='read', data=ldomain%mask, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun( msg=' ERROR: LANDMASK NOT on fracdata file'//errMsg(sourcefile, __LINE__)) - end if - call ncd_io(ncid=ncid, varname='frac', flag='read', data=ldomain%frac, & - dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun( msg=' ERROR: LANDFRAC NOT on fracdata file'//errMsg(sourcefile, __LINE__)) - end if - - call ncd_pio_closefile(ncid) - - end subroutine surfrd_get_grid - - !------------------------------------------------------------------------------ - subroutine decompInit_lnd3D(lni,lnj,lnk) - ! - ! !DESCRIPTION: - ! Create a 3D decomposition gsmap for the global 2D grid with soil levels - ! as the 3rd dimesnion. - ! - ! !USES: - use decompMod, only : gindex_global, bounds_type, get_proc_bounds - use spmdMod , only : comp_id, mpicom - use mct_mod , only : mct_gsmap_init - ! - ! !ARGUMENTS: - integer , intent(in) :: lni,lnj,lnk ! domain global size - ! - ! !LOCAL VARIABLES: - integer :: m,n,k ! indices - integer :: begg,endg,lsize,gsize ! used for gsmap init - integer :: begg3d,endg3d - integer, pointer :: gindex(:) ! global index for gsmap init - type(bounds_type) :: bounds - !------------------------------------------------------------------------------ - - ! Initialize gsmap_lnd2dsoi_gdc2glo - call get_proc_bounds(bounds) - begg = bounds%begg; endg=bounds%endg - - begg3d = (begg-1)*lnk + 1 - endg3d = endg*lnk - lsize = (endg3d - begg3d + 1 ) - allocate(gindex(begg3d:endg3d)) - do k = 1, lnk - do n = begg,endg - m = (begg-1)*lnk + (k-1)*(endg-begg+1) + (n-begg+1) - gindex(m) = gindex_global(n-begg+1) + (k-1)*(lni*lnj) - enddo - enddo - gsize = lni * lnj * lnk - call mct_gsMap_init(gsMap_lnd2Dsoi_gdc2glo, gindex, mpicom, comp_id, lsize, gsize) - - ! Diagnostic output - - if (masterproc) then - write(iulog,*)' 3D GSMap' - write(iulog,*)' longitude points = ',lni - write(iulog,*)' latitude points = ',lnj - write(iulog,*)' soil levels = ',lnk - write(iulog,*)' gsize = ',gsize - write(iulog,*)' lsize = ',lsize - write(iulog,*)' bounds(gindex) = ',size(gindex) - write(iulog,*) - end if - - deallocate(gindex) - - end subroutine decompInit_lnd3D - -end module lnd_set_decomp_and_domain diff --git a/src/cpl/mct/ndepStreamMod.F90 b/src/cpl/mct/ndepStreamMod.F90 deleted file mode 100644 index d26ff7c95e..0000000000 --- a/src/cpl/mct/ndepStreamMod.F90 +++ /dev/null @@ -1,376 +0,0 @@ -module ndepStreamMod - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Contains methods for reading in nitrogen deposition data file - ! Also includes functions for dynamic ndep file handling and - ! interpolation. - ! - ! !USES - use shr_kind_mod, only: r8 => shr_kind_r8, CL => shr_kind_cl - use shr_strdata_mod, only: shr_strdata_type, shr_strdata_create - use shr_strdata_mod, only: shr_strdata_print, shr_strdata_advance - use mct_mod , only: mct_ggrid - use spmdMod , only: mpicom, masterproc, comp_id, iam - use clm_varctl , only: iulog, inst_name - use abortutils , only: endrun - use decompMod , only: bounds_type - use domainMod , only: ldomain - - ! !PUBLIC TYPES: - implicit none - private - - ! !PUBLIC MEMBER FUNCTIONS: - public :: ndep_init ! position datasets for dynamic ndep - public :: ndep_interp ! interpolates between two years of ndep file data - public :: clm_domain_mct ! Sets up MCT domain for this resolution - - ! !PRIVATE MEMBER FUNCTIONS: - private :: check_units ! Check the units and make sure they can be used - - ! ! PRIVATE TYPES - type(shr_strdata_type) :: sdat ! input data stream - integer :: stream_year_first_ndep ! first year in stream to use - integer :: stream_year_last_ndep ! last year in stream to use - integer :: model_year_align_ndep ! align stream_year_firstndep with - logical :: divide_by_secs_per_yr = .true. ! divide by the number of seconds per year - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - !============================================================================== - -contains - - !============================================================================== - - subroutine ndep_init(bounds, NLFilename) - ! - ! Initialize data stream information. - ! - ! Uses: - use shr_kind_mod , only : CS => shr_kind_cs - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_nl_mod , only : shr_nl_find_group_name - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_mpi_mod , only : shr_mpi_bcast - use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global - ! - ! arguments - implicit none - type(bounds_type), intent(in) :: bounds - character(len=*), intent(in) :: NLFilename ! Namelist filename - ! - ! local variables - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_ndep - character(len=CL) :: ndepmapalgo = 'bilinear' - character(len=CL) :: ndep_tintalgo = 'linear' - character(len=CS) :: ndep_taxmode = 'extend' - character(len=CL) :: ndep_varlist = 'NDEP_year' - character(*), parameter :: shr_strdata_unset = 'NOT_SET' - character(*), parameter :: subName = "('ndepdyn_init')" - character(*), parameter :: F00 = "('(ndepdyn_init) ',4a)" - !----------------------------------------------------------------------- - - namelist /ndepdyn_nml/ & - stream_year_first_ndep, & - stream_year_last_ndep, & - model_year_align_ndep, & - ndepmapalgo, ndep_taxmode, & - ndep_varlist, & - stream_fldFileName_ndep, & - ndep_tintalgo - - ! Default values for namelist - stream_year_first_ndep = 1 ! first year in stream to use - stream_year_last_ndep = 1 ! last year in stream to use - model_year_align_ndep = 1 ! align stream_year_first_ndep with this model year - stream_fldFileName_ndep = ' ' - - ! Read ndepdyn_nml namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call shr_nl_find_group_name(nu_nml, 'ndepdyn_nml', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=ndepdyn_nml,iostat=nml_error) - if (nml_error /= 0) then - call endrun(msg=' ERROR reading ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__)) - end if - else - call endrun(msg=' ERROR finding ndepdyn_nml namelist'//errMsg(sourcefile, __LINE__)) - end if - close(nu_nml) - endif - - call shr_mpi_bcast(stream_year_first_ndep , mpicom) - call shr_mpi_bcast(stream_year_last_ndep , mpicom) - call shr_mpi_bcast(model_year_align_ndep , mpicom) - call shr_mpi_bcast(stream_fldFileName_ndep, mpicom) - call shr_mpi_bcast(ndep_varlist , mpicom) - call shr_mpi_bcast(ndep_taxmode , mpicom) - call shr_mpi_bcast(ndep_tintalgo , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'ndepdyn stream settings:' - write(iulog,*) ' stream_year_first_ndep = ',stream_year_first_ndep - write(iulog,*) ' stream_year_last_ndep = ',stream_year_last_ndep - write(iulog,*) ' model_year_align_ndep = ',model_year_align_ndep - write(iulog,*) ' stream_fldFileName_ndep = ',stream_fldFileName_ndep - write(iulog,*) ' ndep_varList = ',ndep_varList - write(iulog,*) ' ndep_taxmode = ',ndep_taxmode - write(iulog,*) ' ndep_tintalgo = ',ndep_tintalgo - write(iulog,*) ' ' - endif - ! Read in units - call check_units( stream_fldFileName_ndep, ndep_varList ) - - ! Set domain and create streams - call clm_domain_mct (bounds, dom_clm) - - call shr_strdata_create(sdat,name="clmndep", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_ndep, & - yearLast=stream_year_last_ndep, & - yearAlign=model_year_align_ndep, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_ndep), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/trim(stream_fldFileName_ndep)/),& - fldListFile=ndep_varlist, & - fldListModel=ndep_varlist, & - fillalgo='none', & - mapalgo=ndepmapalgo, & - tintalgo=ndep_tintalgo, & - calendar=get_calendar(), & - taxmode=ndep_taxmode ) - - - if (masterproc) then - call shr_strdata_print(sdat,'CLMNDEP data') - endif - - end subroutine ndep_init - !================================================================ - - subroutine check_units( stream_fldFileName_ndep, ndep_varList ) - !------------------------------------------------------------------- - ! Check that units are correct on the file and if need any conversion - use ncdio_pio , only : ncd_pio_openfile, ncd_inqvid, ncd_getatt, ncd_pio_closefile, ncd_nowrite - use ncdio_pio , only : file_desc_t, var_desc_t - use shr_kind_mod , only : CS => shr_kind_cs - use shr_log_mod , only : errMsg => shr_log_errMsg - use shr_string_mod, only : shr_string_listGetName - implicit none - - !----------------------------------------------------------------------- - ! - ! Arguments - character(len=*), intent(IN) :: stream_fldFileName_ndep ! ndep filename - character(len=*), intent(IN) :: ndep_varList ! ndep variable list to examine - ! - ! Local variables - type(file_desc_t) :: ncid ! NetCDF filehandle for ndep file - type(var_desc_t) :: vardesc ! variable descriptor - integer :: varid ! variable index - logical :: readvar ! If variable was read - character(len=CS) :: ndepunits! ndep units - character(len=CS) :: fname ! ndep field name - !----------------------------------------------------------------------- - call ncd_pio_openfile( ncid, trim(stream_fldFileName_ndep), ncd_nowrite ) - call shr_string_listGetName( ndep_varList, 1, fname ) - call ncd_inqvid( ncid, fname, varid, vardesc, readvar=readvar ) - if ( readvar ) then - call ncd_getatt( ncid, varid, "units", ndepunits ) - else - call endrun(msg=' ERROR finding variable: '//trim(fname)//" in file: "// & - trim(stream_fldFileName_ndep)//errMsg(sourcefile, __LINE__)) - end if - call ncd_pio_closefile( ncid ) - - ! Now check to make sure they are correct - if ( trim(ndepunits) == "g(N)/m2/s" )then - divide_by_secs_per_yr = .false. - else if ( trim(ndepunits) == "g(N)/m2/yr" )then - divide_by_secs_per_yr = .true. - else - call endrun(msg=' ERROR in units for nitrogen deposition equal to: '//trim(ndepunits)//" not units expected"// & - errMsg(sourcefile, __LINE__)) - end if - - end subroutine check_units - - !================================================================ - subroutine ndep_interp(bounds, atm2lnd_inst) - - !----------------------------------------------------------------------- - use clm_time_manager, only : get_curr_date, get_curr_days_per_year - use clm_varcon , only : secspday - use atm2lndType , only : atm2lnd_type - ! - ! Arguments - type(bounds_type) , intent(in) :: bounds - type(atm2lnd_type), intent(inout) :: atm2lnd_inst - ! - ! Local variables - integer :: g, ig - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - integer :: dayspyr ! days per year - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - call shr_strdata_advance(sdat, mcdate, sec, mpicom, 'ndepdyn') - - if ( divide_by_secs_per_yr )then - ig = 0 - dayspyr = get_curr_days_per_year( ) - do g = bounds%begg,bounds%endg - ig = ig+1 - atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) / (secspday * dayspyr) - end do - else - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - atm2lnd_inst%forc_ndep_grc(g) = sdat%avs(1)%rAttr(1,ig) - end do - end if - - end subroutine ndep_interp - - !============================================================================== - subroutine clm_domain_mct(bounds, dom_clm, nlevels) - - !------------------------------------------------------------------- - ! Set domain data type for internal clm grid - use clm_varcon , only : re - use domainMod , only : ldomain - use mct_mod , only : mct_ggrid, mct_gsMap_lsize, mct_gGrid_init - use mct_mod , only : mct_gsMap_orderedPoints, mct_gGrid_importIAttr - use mct_mod , only : mct_gGrid_importRAttr, mct_gsMap - use lnd_set_decomp_and_domain , only : gsMap_lnd2Dsoi_gdc2glo, gsmap_global - implicit none - ! - ! arguments - type(bounds_type), intent(in) :: bounds - type(mct_ggrid), intent(out) :: dom_clm ! Output domain information for land model - integer, intent(in), optional :: nlevels ! Number of levels if this is a 3D field - ! - ! local variables - integer :: g,i,j,k ! index - integer :: lsize ! land model domain data size - real(r8), pointer :: data(:) ! temporary - integer , pointer :: idata(:) ! temporary - integer :: nlevs ! Number of vertical levels - type(mct_gsMap), pointer :: gsmap => null() ! MCT GS map - !------------------------------------------------------------------- - ! SEt number of levels, and get the GS map for either the 2D or 3D grid - nlevs = 1 - if ( present(nlevels) ) nlevs = nlevels - if ( nlevs == 1 ) then - gsmap => gsmap_global - else - gsmap => gsMap_lnd2Dsoi_gdc2glo - end if - ! - ! Initialize mct domain type - ! lat/lon in degrees, area in radians^2, mask is 1 (land), 0 (non-land) - ! Note that in addition land carries around landfrac for the purposes of domain checking - ! - lsize = mct_gsMap_lsize(gsmap, mpicom) - call mct_gGrid_init( GGrid=dom_clm, & - CoordChars='lat:lon:hgt', OtherChars='area:aream:mask:frac', lsize=lsize ) - ! - ! Allocate memory - ! - allocate(data(lsize)) - ! - ! Determine global gridpoint number attribute, GlobGridNum, which is set automatically by MCT - ! - call mct_gsMap_orderedPoints(gsmap, iam, idata) - gsmap => null() - call mct_gGrid_importIAttr(dom_clm,'GlobGridNum',idata,lsize) - ! - ! Determine domain (numbering scheme is: West to East and South to North to South pole) - ! Initialize attribute vector with special value - ! - data(:) = -9999.0_R8 - call mct_gGrid_importRAttr(dom_clm,"lat" ,data,lsize) - call mct_gGrid_importRAttr(dom_clm,"lon" ,data,lsize) - call mct_gGrid_importRAttr(dom_clm,"area" ,data,lsize) - call mct_gGrid_importRAttr(dom_clm,"aream",data,lsize) - data(:) = 0.0_R8 - call mct_gGrid_importRAttr(dom_clm,"mask" ,data,lsize) - ! - ! Determine bounds - ! - ! Fill in correct values for domain components - ! Note aream will be filled in in the atm-lnd mapper - ! - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%lonc(g) - end do - end do - call mct_gGrid_importRattr(dom_clm,"lon",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%latc(g) - end do - end do - call mct_gGrid_importRattr(dom_clm,"lat",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = ldomain%area(g)/(re*re) - end do - end do - call mct_gGrid_importRattr(dom_clm,"area",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%mask(g), r8) - end do - end do - call mct_gGrid_importRattr(dom_clm,"mask",data,lsize) - - do k = 1, nlevs - do g = bounds%begg,bounds%endg - i = 1 + (g - bounds%begg) - data(i) = real(ldomain%frac(g), r8) - end do - end do - call mct_gGrid_importRattr(dom_clm,"frac",data,lsize) - - deallocate(data) - deallocate(idata) - - end subroutine clm_domain_mct - -end module ndepStreamMod From 4cbc00d42ba54b07fd1992e7d574b94c29ae939b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 10:48:35 -0600 Subject: [PATCH 151/408] Remove another mct comment --- src/cpl/nuopc/lnd_import_export.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/cpl/nuopc/lnd_import_export.F90 b/src/cpl/nuopc/lnd_import_export.F90 index 11cc807640..b9966f81e9 100644 --- a/src/cpl/nuopc/lnd_import_export.F90 +++ b/src/cpl/nuopc/lnd_import_export.F90 @@ -248,7 +248,6 @@ subroutine advertise_fields(gcomp, flds_scalar_name, glc_present, cism_evolve, r if (shr_megan_mechcomps_n .ne. megan_nflds) call shr_sys_abort('ERROR: megan field count mismatch') ! CARMA volumetric soil water from land - ! TODO: is the following correct - the CARMA field exchange is very confusing in mct call shr_carma_readnl('drv_flds_in', carma_fields) ! export to atm From 854ff9d438aa24edb644459f31c89494ed4ee983 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 10:50:43 -0600 Subject: [PATCH 152/408] Remove cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb directory --- .../testdefs/testmods_dirs/clm/nuopc_cap_bfb/README | 10 ---------- .../testmods_dirs/clm/nuopc_cap_bfb/include_user_mods | 1 - .../testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl | 4 ---- 3 files changed, 15 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README delete mode 100644 cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README deleted file mode 100644 index aefd8adee7..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/README +++ /dev/null @@ -1,10 +0,0 @@ -This testmod directory currently isn't used in any tests, but is useful -for the following reason: - -According to Mariana Vertenstein: At least at one point, you could get -bit-for-bit answers when comparing the mct and nuopc versions of CTSM in -an I compset with SROF and SGLC, if using the changes in this testmod in -both the mct and nuopc runs. - -So we are keeping this around in case someone wants to reproduce that -comparison. diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods deleted file mode 100644 index fe0e18cf88..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../default diff --git a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl b/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl deleted file mode 100644 index 6bfefec90b..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/nuopc_cap_bfb/user_nl_cpl +++ /dev/null @@ -1,4 +0,0 @@ -orb_eccen = 0. -orb_mvelp = 0. -orb_obliq = 0. -orb_mode = "fixed_parameters" From 6b6ea52f5271866c525cef19c480c2c7bbc35031 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 10:55:30 -0600 Subject: [PATCH 153/408] Remove mention of mct in README.NUOPC_driver.md --- README.NUOPC_driver.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/README.NUOPC_driver.md b/README.NUOPC_driver.md index 9eb5d5b2cb..6caf63a9bd 100644 --- a/README.NUOPC_driver.md +++ b/README.NUOPC_driver.md @@ -40,9 +40,3 @@ ESMF_PROFILING_LEVEL --- Verbosity level for ESMF profiling nuopc.runseq is a text file that determines how the driver operates. You can change the operation by having an updated copy in your case directory. - -## What if I want to use the MCT driver? - -The MCT driver is now removed. For more notes see: - -https://docs.google.com/presentation/d/1yjiKSEV53JDAJbYxhpY2T9GTxlWFzQAn From 40367c56210797ae6fe27991be8cb82f9708894d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 10:56:28 -0600 Subject: [PATCH 154/408] Remove an expected failure the mentions mct in ExpectedTestFails.xml --- cime_config/testdefs/ExpectedTestFails.xml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index dc850d51ab..a29e55cc9e 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -143,13 +143,6 @@ - - - FAIL - #1887 - - - FAIL From e99eaeaba4a502277e4b2f99096b0e130cff46d8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 11:00:11 -0600 Subject: [PATCH 155/408] Add back mct to Externals.cfg --- Externals.cfg | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/Externals.cfg b/Externals.cfg index cb2622dedf..8ef524bf24 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -69,6 +69,13 @@ repo_url = https://github.com/ESCOMP/CESM_share local_path = share required = True +[mct] +tag = MCT_2.11.0 +protocol = git +repo_url = https://github.com/MCSclimate/MCT +local_path = libraries/mct +required = True + [parallelio] tag = pio2_6_2 protocol = git From fed6805e85ca0c2ccb6eada9946f4c4f634f5e54 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 11:05:10 -0600 Subject: [PATCH 156/408] Remove /test subdirectory --- test/tools/CLM_compare.sh | 39 ----- test/tools/Makefile | 12 -- test/tools/README | 73 ---------- test/tools/README.testnames | 69 --------- test/tools/TBLCFGtools.sh | 120 ---------------- test/tools/TBLscript_tools.sh | 122 ---------------- test/tools/TBLtools.sh | 119 --------------- test/tools/TCBCFGtools.sh | 135 ------------------ test/tools/TCBtools.sh | 121 ---------------- test/tools/TSMCFGtools.sh | 113 --------------- test/tools/TSMscript_tools.sh | 98 ------------- test/tools/TSMtools.sh | 117 --------------- test/tools/config_files/CFGtools__ds | 0 test/tools/config_files/README | 9 -- test/tools/config_files/tools__do | 1 - test/tools/config_files/tools__ds | 1 - test/tools/config_files/tools__o | 1 - test/tools/config_files/tools__s | 1 - test/tools/gen_test_table.sh | 80 ----------- test/tools/get_cprnc_diffs.sh | 56 -------- test/tools/input_tests_master | 32 ----- test/tools/nl_files/mesh_maker_fv09 | 1 - test/tools/nl_files/mkmapdata_if10 | 1 - test/tools/nl_files/mkmapdata_ne30np4 | 1 - .../nl_files/mkprocdata_ne30_to_f19_I2000 | 1 - test/tools/nl_files/modify_data_YELL | 1 - test/tools/nl_files/run_neon_OSBS | 1 - test/tools/nl_files/run_neon_YELL_PRISM | 1 - test/tools/nl_files/subset_data_KONA | 1 - test/tools/nl_files/subset_data_US-UMB | 1 - test/tools/nl_files/subset_data_YELL | 1 - .../nl_files/subset_data_f09_1x1pt_townshipSD | 1 - .../subset_data_f09_37x288pt_PanBoreal | 1 - .../subset_data_f09_4x9pt_AlaskaTananaValley | 1 - .../subset_data_f09_58x45pt_SouthAmerica | 1 - .../subset_data_f09_90x288pt_1850PanTropics | 1 - test/tools/show_var_diffs.sh | 79 ---------- test/tools/tests_posttag_hobart_nompi | 1 - test/tools/tests_posttag_nompi_regression | 1 - test/tools/tests_pretag_cheyenne_nompi | 3 - test/tools/tests_pretag_derecho_nompi | 9 -- test/tools/tests_pretag_nompi_neon | 8 -- 42 files changed, 1435 deletions(-) delete mode 100755 test/tools/CLM_compare.sh delete mode 100644 test/tools/Makefile delete mode 100644 test/tools/README delete mode 100644 test/tools/README.testnames delete mode 100755 test/tools/TBLCFGtools.sh delete mode 100755 test/tools/TBLscript_tools.sh delete mode 100755 test/tools/TBLtools.sh delete mode 100755 test/tools/TCBCFGtools.sh delete mode 100755 test/tools/TCBtools.sh delete mode 100755 test/tools/TSMCFGtools.sh delete mode 100755 test/tools/TSMscript_tools.sh delete mode 100755 test/tools/TSMtools.sh delete mode 100644 test/tools/config_files/CFGtools__ds delete mode 100644 test/tools/config_files/README delete mode 100644 test/tools/config_files/tools__do delete mode 100644 test/tools/config_files/tools__ds delete mode 100644 test/tools/config_files/tools__o delete mode 100644 test/tools/config_files/tools__s delete mode 100755 test/tools/gen_test_table.sh delete mode 100755 test/tools/get_cprnc_diffs.sh delete mode 100644 test/tools/input_tests_master delete mode 100644 test/tools/nl_files/mesh_maker_fv09 delete mode 100644 test/tools/nl_files/mkmapdata_if10 delete mode 100644 test/tools/nl_files/mkmapdata_ne30np4 delete mode 100644 test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 delete mode 100644 test/tools/nl_files/modify_data_YELL delete mode 100644 test/tools/nl_files/run_neon_OSBS delete mode 100644 test/tools/nl_files/run_neon_YELL_PRISM delete mode 100644 test/tools/nl_files/subset_data_KONA delete mode 100644 test/tools/nl_files/subset_data_US-UMB delete mode 100644 test/tools/nl_files/subset_data_YELL delete mode 100644 test/tools/nl_files/subset_data_f09_1x1pt_townshipSD delete mode 100644 test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal delete mode 100644 test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley delete mode 100644 test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica delete mode 100644 test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics delete mode 100755 test/tools/show_var_diffs.sh delete mode 100644 test/tools/tests_posttag_hobart_nompi delete mode 100644 test/tools/tests_posttag_nompi_regression delete mode 100644 test/tools/tests_pretag_cheyenne_nompi delete mode 100644 test/tools/tests_pretag_derecho_nompi delete mode 100644 test/tools/tests_pretag_nompi_neon diff --git a/test/tools/CLM_compare.sh b/test/tools/CLM_compare.sh deleted file mode 100755 index 38f547c3ab..0000000000 --- a/test/tools/CLM_compare.sh +++ /dev/null @@ -1,39 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 2 ]; then - echo "CLM_compare.sh: incorrect number of input arguments" - exit 1 -fi - -echo "CLM_compare.sh: comparing $1 " -echo " with $2" - -##note syntax here as stderr and stdout from cprnc command go -##to separate places! -${CPRNC_EXE} ${CPRNC_OPT} $1 $2 2>&1 > cprnc.out -rc=$? -if [ $rc -ne 0 ]; then - echo "CLM_compare.sh: error doing comparison, cprnc error= $rc" - exit 2 -fi - -result_old=`perl -e 'while (my $ll = <>) \ - { if ($ll =~ /(\d+)[^0-9]+compared[^0-9]+(\d+)/) \ - { print "PASS" if $1>0 && $2==0 }}' cprnc.out` -if grep -c "the two files seem to be IDENTICAL" cprnc.out > /dev/null; then - result=PASS -elif grep -c "the two files seem to be DIFFERENT" cprnc.out > /dev/null; then - result=FAIL -else - result=$result_old -fi - -if [ "$result" = "PASS" ]; then - echo "CLM_compare.sh: files are b4b" -else - echo "CLM_compare.sh: files are NOT b4b" - exit 3 -fi - -exit 0 diff --git a/test/tools/Makefile b/test/tools/Makefile deleted file mode 100644 index b5031abdba..0000000000 --- a/test/tools/Makefile +++ /dev/null @@ -1,12 +0,0 @@ -# -# Makefile to build clm testing documentation -# - -# Get list of tests_ files -SOURCES = $(wildcard tests_*) - -all: test_table.html - -test_table.html: $(SOURCES) - gen_test_table.sh - diff --git a/test/tools/README b/test/tools/README deleted file mode 100644 index c545f625b8..0000000000 --- a/test/tools/README +++ /dev/null @@ -1,73 +0,0 @@ -$CTSMROOT/clm/test/tools/README 06/08/2018 - -Scripts for testing the CLM support tools with many different -configurations and run-time options. - -I. MAIN SCRIPTS: - -test_driver.sh - Test the CLM offline tools - -To use... - -./test_driver.sh -i - -on Derecho - -qcmd -l walltime=08:00:00 -- ./test_driver.sh -i >& run.out & - -And to for example to compare to another baseline code (in this case ctsm5.1.dev066, which would need to be cloned at the given -path) ... - -qcmd -l walltime=08:00:00 -- env BL_ROOT=/glade/scratch/erik/ctsm5.1.dev066 ./test_driver.sh -i >& run.out & - -on izumi - -nohup ./test_driver.sh -i >& run.out & - -release tests - -qcmd -l walltime=10:00:00 -- env CLM_INPUT_TESTS=`pwd`/tests_posttag_nompi_regression \ -./test_driver.sh -i >& run_regress.out & - -To run neon-specific tests, please use login nodes: -env CLM_INPUT_TESTS=`pwd`/tests_pretag_nompi_neon ./test_driver.sh -i > & run_neon.out & - - -Intended for use on NCAR machines Derecho, Casper (DAV) and izumi. - -II. RUNNING test_driver.sh TOOLS TESTING: - -Basic use: - -./test_driver.sh -i -./test_driver.sh -h # to get help on options - -Important environment variables (just used by test_driver.sh) - -BL_ROOT ---------------- Root directory of CLM baseline code to compare to - (if not set BL test will not be performed) -BL_TESTDIR ------------- Root directory of where to put baseline tests -CLM_INPUT_TESTS -------- Filename of file with list of tests to perform -CLM_TESTDIR ------------ Root directory of where to put most tests -CLM_RETAIN_FILES ------- If set to TRUE -- don't cleanup files after testing -CLM_FC ----------------- Use given compiler -CLM_JOBID -------------- Job identification number to use (rather than process ID) -CLM_THREADS ------------ Number of open-MP threads to use - (by default this is set differently by machine) -CLM_SOFF --------------- If set to TRUE -- stop on first failed test (default FALSE) - -Important files for test_driver tools testing: - -test_driver.sh ------- Main test script for tools -nl_files ------------- Directory with various namelists to test -config_files --------- Directory with various configurations to test -input_tests_master --- Master list of tests -tests_pretag_* ------- Tests for specific machines to do by default before a tag is done -tests_posttag_* ------ Tests for specific machines to do for more extensive testing - after a tag is done -CLM_compare.sh ------- Compares output history files between two cases -T*.sh ---------------- Basic test script to do a specific type of test -gen_test_table.sh ---- Creates HTML table of tests -Makefile ------------- Will build the HTML table of tests - -../../tools/README.testing - Information on how the testing works for the CLM tools diff --git a/test/tools/README.testnames b/test/tools/README.testnames deleted file mode 100644 index 74dbe8e5f3..0000000000 --- a/test/tools/README.testnames +++ /dev/null @@ -1,69 +0,0 @@ -Tests for test_driver are for the CLM tools only. - -Test naming conventions for the test_driver.sh script: - -Test names are: - -xxnmi - -Where: xx is the two-letter test type - sm=smoke, br=branch, er=exact restart, bl=base-line comparision, - cb=configure-build, rp=reproducibility, op=OpenMP threading for tools - -n is the configuration type: - -1 -- unused -2 -- unused -3 -- unused -4 -- unused -5 -- unused -6 -- unused -7 -- unused -8 -- unused -9 -- mesh_maker -0 -- run_neon -a -- modify_data -b -- subset_data -c -- mkprocdata_map -d -- mkmapgrids -e -- unused -f -- unused -g -- unused -h -- unused -i -- tools scripts - -m is the resolution - -0 -- 0.9x1.25 -1 -- 48x96 -5 -- 10x15 -6 -- 5x5_amazon -7 -- 1x1 brazil -8 -- US-UMB -9 -- 4x5 -a -- NEON YELL -b -- NEON KONA -c -- NEON OSBS -d -- SouthAmerica -e -- 1850PanTropics -f -- PanBoreal -g -- AlaskaTananaValley -h -- single point from the 0.9x1.25 grid (Township SD) -y -- 1.9x2.5 with transient 1850-2100 for rcp=2.6 and glacier-MEC on -T -- 1x1_numaIA -Z -- 10x15 with crop on -@ -- ne120np4 -# -- ne30np4 - -i is the specific test (usually this implies...) - -1 -- Serial script -2 -- Serial -3 -- OpenMP only -4 -- serial, DEBUG -7 -- OpenMP only second test, DEBUG -8 -- OpenMP only third test, DEBUG -9 -- Serial Script -0 -- Serial Script - - diff --git a/test/tools/TBLCFGtools.sh b/test/tools/TBLCFGtools.sh deleted file mode 100755 index 6276c885e2..0000000000 --- a/test/tools/TBLCFGtools.sh +++ /dev/null @@ -1,120 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 3 ]; then - echo "TBLCFGtools.sh: incorrect number of input arguments" - exit 1 -fi - -if [ -z "$BL_ROOT" ] && [ -z "$BL_TESTDIR" ]; then - echo "TBL.sh: no environment variables set for baseline test - will skip" - exit 255 -fi - -tool=$(basename $1) -test_name=TBLCFGtools.$tool.$2.$3 - -if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TBLCFGtools.sh: smoke test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TBLCFGtools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TBLCFGtools.sh: smoke test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TBLCFGtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -rundir=${CLM_TESTDIR}/${test_name} -if [ -d ${rundir} ]; then - rm -r ${rundir} -fi -mkdir -p ${rundir} -if [ $? -ne 0 ]; then - echo "TBLCFGtools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${rundir} - -echo "TBLCFGtools.sh: calling TSMCFGtools.sh to run $tool executable" -${CLM_SCRIPTDIR}/TSMCFGtools.sh $1 $2 $3 -rc=$? -if [ $rc -ne 0 ]; then - echo "TBLCFGtools.sh: error from TSMCFGtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 -fi - -if [ -n "${BL_ROOT}" ]; then - if [ -z "$BL_TESTDIR" ]; then - BL_TESTDIR=${CLM_TESTDIR}.bl - fi - echo "TBLCFGtools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR" - - echo "TBLCFGtools.sh: calling ****baseline**** TSMCFGtools.sh for smoke test" - bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools` - env CLM_TESTDIR=${BL_TESTDIR} \ - CLM_ROOT=${BL_ROOT} \ - CLM_SCRIPTDIR=$bl_dir \ - $bl_dir/TSMCFGtools.sh $1 $2 $3 - rc=$? - if [ $rc -ne 0 ]; then - echo "TBLCFGtools.sh: error from *baseline* TSMCFGtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 5 - fi -fi - -echo "TBLCFGtools.sh: starting b4b comparisons " -files_to_compare=`cd ${CLM_TESTDIR}/TSMCFGtools.$tool.$2.$3; ls *.nc` -if [ -z "${files_to_compare}" ] && [ "$debug" != "YES" ]; then - echo "TBLCFGtools.sh: error locating files to compare" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 -fi - -all_comparisons_good="TRUE" -for compare_file in ${files_to_compare}; do - - env CPRNC_OPT="-m" \ - ${CLM_SCRIPTDIR}/CLM_compare.sh \ - ${BL_TESTDIR}/TSMCFGtools.$tool.$2.$3/${compare_file} \ - ${CLM_TESTDIR}/TSMCFGtools.$tool.$2.$3/${compare_file} - rc=$? - mv cprnc.out cprnc.${compare_file}.out - if [ $rc -eq 0 ]; then - echo "TBLCFGtools.sh: comparison successful; output in ${rundir}/cprnc.${compare_file}.out" - else - echo "TBLCFGtools.sh: error from CLM_compare.sh= $rc; see ${rundir}/cprnc.${compare_file}.out for details -" - all_comparisons_good="FALSE" - fi -done - -if [ ${all_comparisons_good} = "TRUE" ]; then - echo "TBLCFGtools.sh: baseline test passed" - echo "PASS" > TestStatus - if [ $CLM_RETAIN_FILES != "TRUE" ]; then - echo "TBLCFGtools.sh: removing some unneeded files to save disc space" - rm *.nc - rm *.r* - fi -else - echo "TBLCFGtools.sh: at least one file comparison did not pass" - echo "FAIL.job${JOBID}" > TestStatus - exit 7 -fi - -exit 0 diff --git a/test/tools/TBLscript_tools.sh b/test/tools/TBLscript_tools.sh deleted file mode 100755 index d05492c687..0000000000 --- a/test/tools/TBLscript_tools.sh +++ /dev/null @@ -1,122 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 3 ]; then - echo "TBLscript_tools.sh: incorrect number of input arguments" - exit 1 -fi - -if [ -z "$BL_ROOT" ] && [ -z "$BL_TESTDIR" ]; then - echo "TBLscript_tools.sh: no environment variables set for baseline test - will skip" - exit 255 -fi - -test_name=TBLscript_tools.$1.$2.$3 - -if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TBLscript_tools.sh: smoke test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TBLscript_tools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TBLscript_tools.sh: smoke test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TBLscript_tools.sh: this smoke test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -rundir=${CLM_TESTDIR}/${test_name} -if [ -d ${rundir} ]; then - rm -r ${rundir} -fi -mkdir -p ${rundir} -if [ $? -ne 0 ]; then - echo "TBLscript_tools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${rundir} - -echo "TBLscript_tools.sh: calling TSMscript_tools.sh to run $1 executable" -${CLM_SCRIPTDIR}/TSMscript_tools.sh $1 $2 $3 -rc=$? -if [ $rc -ne 0 ]; then - echo "TBLscript_tools.sh: error from TSMtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 -fi - -if [ -n "${BL_ROOT}" ]; then - if [ -z "$BL_TESTDIR" ]; then - BL_TESTDIR=${CLM_TESTDIR}.bl - fi - echo "TBLscript_tools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR" - - echo "TBLscript_tools.sh: calling ****baseline**** TSMtools.sh for smoke test" - bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools` - env CLM_TESTDIR=${BL_TESTDIR} \ - CLM_SCRIPTDIR=$bl_dir \ - CLM_ROOT=$BL_ROOT \ - CTSM_ROOT=$BL_ROOT \ - CIME_ROOT=$BL_ROOT/cime \ - $bl_dir/TSMscript_tools.sh $1 $2 $3 - rc=$? - if [ $rc -ne 0 ]; then - echo "TBLscript_tools.sh: error from *baseline* TSMscript_tools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 5 - fi -fi - -echo "TBLscript_tools.sh: starting b4b comparisons " -files_to_compare=`cd ${CLM_TESTDIR}/TSMscript_tools.$1.$2.$3; ls *.nc` -if [ -z "${files_to_compare}" ] && [ "$debug" != "YES" ]; then - echo "TBLscript_tools.sh: error locating files to compare" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 -fi - -all_comparisons_good="TRUE" -for compare_file in ${files_to_compare}; do - - env CPRNC_OPT="-m" \ - ${CLM_SCRIPTDIR}/CLM_compare.sh \ - ${BL_TESTDIR}/TSMscript_tools.$1.$2.$3/${compare_file} \ - ${CLM_TESTDIR}/TSMscript_tools.$1.$2.$3/${compare_file} - rc=$? - mv cprnc.out cprnc.${compare_file}.out - if [ $rc -eq 0 ]; then - echo "TBLscript_tools.sh: comparison successful; output in ${rundir}/cprnc.${compare_file}.out" - else - echo "TBLscript_tools.sh: error from CLM_compare.sh= $rc; see ${rundir}/cprnc.${compare_file}.out for details" - all_comparisons_good="FALSE" - fi -done - -if [ ${all_comparisons_good} = "TRUE" ]; then - echo "TBLscript_tools.sh: baseline test passed" - echo "PASS" > TestStatus - if [ $CLM_RETAIN_FILES != "TRUE" ]; then - echo "TBLscript_tools.sh: removing some unneeded files to save disc space" - rm *.nc - rm *.r* - fi -else - echo "TBLscript_tools.sh: at least one file comparison did not pass" - echo "FAIL.job${JOBID}" > TestStatus - exit 7 -fi - - - -exit 0 diff --git a/test/tools/TBLtools.sh b/test/tools/TBLtools.sh deleted file mode 100755 index 555ea7d1be..0000000000 --- a/test/tools/TBLtools.sh +++ /dev/null @@ -1,119 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 3 ]; then - echo "TBLtools.sh: incorrect number of input arguments" - exit 1 -fi - -if [ -z "$BL_ROOT" ] && [ -z "$BL_TESTDIR" ]; then - echo "TBL.sh: no environment variables set for baseline test - will skip" - exit 255 -fi - -test_name=TBLtools.$1.$2.$3 - -if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TBLtools.sh: smoke test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TBLtools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TBLtools.sh: smoke test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TBLtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -rundir=${CLM_TESTDIR}/${test_name} -if [ -d ${rundir} ]; then - rm -r ${rundir} -fi -mkdir -p ${rundir} -if [ $? -ne 0 ]; then - echo "TBLtools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${rundir} - -echo "TBLtools.sh: calling TSMtools.sh to run $1 executable" -${CLM_SCRIPTDIR}/TSMtools.sh $1 $2 $3 -rc=$? -if [ $rc -ne 0 ]; then - echo "TBLtools.sh: error from TSMtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 -fi - -if [ -n "${BL_ROOT}" ]; then - if [ -z "$BL_TESTDIR" ]; then - BL_TESTDIR=${CLM_TESTDIR}.bl - fi - echo "TBLtools.sh: generating baseline data from root $BL_ROOT - results in $BL_TESTDIR" - - echo "TBLtools.sh: calling ****baseline**** TSMtools.sh for smoke test" - bl_dir=`/bin/ls -1d ${BL_ROOT}/test/tools` - env CLM_TESTDIR=${BL_TESTDIR} \ - CLM_ROOT=${BL_ROOT} \ - CLM_SCRIPTDIR=$bl_dir \ - $bl_dir/TSMtools.sh $1 $2 $3 - rc=$? - if [ $rc -ne 0 ]; then - echo "TBLtools.sh: error from *baseline* TSMtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 5 - fi -fi - -echo "TBLtools.sh: starting b4b comparisons " -files_to_compare=`cd ${CLM_TESTDIR}/TSMtools.$1.$2.$3; ls *.nc` -if [ -z "${files_to_compare}" ] && [ "$debug" != "YES" ]; then - echo "TBLtools.sh: error locating files to compare" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 -fi - -all_comparisons_good="TRUE" -for compare_file in ${files_to_compare}; do - - env CPRNC_OPT="-m" \ - ${CLM_SCRIPTDIR}/CLM_compare.sh \ - ${BL_TESTDIR}/TSMtools.$1.$2.$3/${compare_file} \ - ${CLM_TESTDIR}/TSMtools.$1.$2.$3/${compare_file} - rc=$? - mv cprnc.out cprnc.${compare_file}.out - if [ $rc -eq 0 ]; then - echo "TBLtools.sh: comparison successful; output in ${rundir}/cprnc.${compare_file}.out" - else - echo "TBLtools.sh: error from CLM_compare.sh= $rc; see ${rundir}/cprnc.${compare_file}.out for details -" - all_comparisons_good="FALSE" - fi -done - -if [ ${all_comparisons_good} = "TRUE" ]; then - echo "TBLtools.sh: baseline test passed" - echo "PASS" > TestStatus - if [ $CLM_RETAIN_FILES != "TRUE" ]; then - echo "TBLtools.sh: removing some unneeded files to save disc space" - rm *.nc - rm *.r* - fi -else - echo "TBLtools.sh: at least one file comparison did not pass" - echo "FAIL.job${JOBID}" > TestStatus - exit 7 -fi - -exit 0 diff --git a/test/tools/TCBCFGtools.sh b/test/tools/TCBCFGtools.sh deleted file mode 100755 index 5c0b015123..0000000000 --- a/test/tools/TCBCFGtools.sh +++ /dev/null @@ -1,135 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 2 ]; then - echo "TCBCFGtools.sh: incorrect number of input arguments" - exit 1 -fi - -tool=$(basename $1) -test_name=TCBCFGtools.$tool.$2 - -if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TCBCFGtools.sh: build test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TCBCFGtools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TCBCFGtools.sh: build test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TCBCFGtools.sh: this build test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -cfgdir=`ls -1d ${CLM_ROOT}/tools/${1}` -if [ $? -ne 0 ];then - cfgdir=`ls -1d ${CIME_ROOT}/tools/mapping/${1}*` - echo "use: $cfgdir" -fi -blddir=${CLM_TESTDIR}/${test_name}/src -if [ -d ${blddir} ]; then - rm -r ${blddir} -fi -mkdir -p ${blddir} -if [ $? -ne 0 ]; then - echo "TCBCFGtools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${blddir} - -echo "TCBCFGtools.sh: building $tool executable; output in ${blddir}/test.log" -# -# Copy build files over -# -cp $cfgdir/src/Makefile . -cp $cfgdir/src/Filepath . -# -# Add cfgdir path to beginning of each path in Filepath -# -touch Filepath -while read filepath_arg; do - echo "${cfgdir}/src/${filepath_arg}" >> Filepath -done < ${cfgdir}/src/Filepath - -# -# Figure out configuration -# -if [ ! -f ${CLM_SCRIPTDIR}/config_files/$tool ]; then - echo "TCB.sh: configure options file ${CLM_SCRIPTDIR}/config_files/$tool not found" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 -fi - -##construct string of args to configure -config_string=" " -while read config_arg; do - config_string="${config_string}${config_arg} " -done < ${CLM_SCRIPTDIR}/config_files/$tool - -if [ "$TOOLSLIBS" != "" ]; then - export SLIBS=$TOOLSLIBS -fi -echo "env CIMEROOT=$CLM_ROOT/cime COMPILER=$CESM_COMP $config_string $CLM_ROOT/cime/tools/configure --macros-format Makefile --machine $CESM_MACH $TOOLS_CONF_STRING" -env CIMEROOT=$CLM_ROOT/cime COMPILER=$CESM_COMP $config_string $CLM_ROOT/cime/tools/configure --macros-format Makefile --machine $CESM_MACH $TOOLS_CONF_STRING >> test.log 2>&1 -rc=$? -if [ $rc -ne 0 ]; then - echo "TCBCFGtools.sh: configure failed, error from configure= $rc" - echo "TCBCFGtools.sh: see ${blddir}/test.log for details" - echo "FAIL.job${JOBID}" > TestStatus - exit 5 -fi - -. $INITMODULES -. ./.env_mach_specific.sh - -attempt=1 -still_compiling="TRUE" -while [ $still_compiling = "TRUE" ]; do - - echo "TCBCFGtools.sh: call to make:" - echo " ${MAKE_CMD} USER_CPPDEFS=-DLINUX" - if [ "$debug" != "YES" ]; then - ${MAKE_CMD} USER_CPPDEFS=-DLINUX >> test.log 2>&1 - status="PASS" - rc=$? - else - status="GEN" - rc=0 - fi - if [ $rc -eq 0 ]; then - echo "TCBCFGtools.sh: make was successful" - echo "TCBCFGtools.sh: configure and build test passed" - echo "$status" > TestStatus - if [ $CLM_RETAIN_FILES != "TRUE" ]; then - echo "TCBCFGtools.sh: removing some unneeded files to save disc space" - rm *.o - rm *.mod - fi - still_compiling="FALSE" - elif [ $attempt -lt 10 ] && \ - grep -c "LICENSE MANAGER PROBLEM" test.log > /dev/null; then - attempt=`expr $attempt + 1` - echo "TCBCFGtools.sh: encountered License Manager Problem; launching attempt #$attempt" - else - echo "TCBCFGtools.sh: clm build failed, error from make= $rc" - echo "TCBCFGtools.sh: see ${blddir}/test.log for details" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 - fi -done -if [ "$TOOLSLIBS" != "" ]; then - export -n SLIBS -fi - -exit 0 diff --git a/test/tools/TCBtools.sh b/test/tools/TCBtools.sh deleted file mode 100755 index 205b2e9da0..0000000000 --- a/test/tools/TCBtools.sh +++ /dev/null @@ -1,121 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 2 ]; then - echo "TCBtools.sh: incorrect number of input arguments" - exit 1 -fi - -test_name=TCBtools.$1.$2 - -if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TCBtools.sh: build test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TCBtools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TCBtools.sh: build test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TCBtools.sh: this build test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -cfgdir=`ls -1d ${CLM_ROOT}/tools/$1` -blddir=${CLM_TESTDIR}/${test_name}/src -if [ -d ${blddir} ]; then - rm -r ${blddir} -fi -mkdir -p ${blddir} -if [ $? -ne 0 ]; then - echo "TCBtools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${blddir} - -echo "TCBtools.sh: building $1 executable; output in ${blddir}/test.log" -# -# Copy build files over -# -cp $cfgdir/src/Makefile . -cp $cfgdir/src/Srcfiles . -cp $cfgdir/src/Mkdepends . -cp $cfgdir/src/Makefile.common . -# -# Add cfgdir path to beginning of each path in Filepath -# -touch Filepath -while read filepath_arg; do - echo "${cfgdir}/src/${filepath_arg}" >> Filepath -done < ${cfgdir}/src/Filepath - -# -# Figure out configuration -# -if [ ! -f ${CLM_SCRIPTDIR}/config_files/$2 ]; then - echo "TCB.sh: configure options file ${CLM_SCRIPTDIR}/config_files/$2 not found" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 -fi - -##construct string of args to configure -config_string="$TOOLS_MAKE_STRING TOOLROOT=$cfgdir " -while read config_arg; do - config_string="${config_string}${config_arg} " -done < ${CLM_SCRIPTDIR}/config_files/$2 - -attempt=1 -still_compiling="TRUE" -if [ "$TOOLSLIBS" != "" ]; then - export SLIBS=$TOOLSLIBS -fi -while [ $still_compiling = "TRUE" ]; do - - ln -s Macros.make Macros - - echo "TCBtools.sh: call to make:" - echo " ${MAKE_CMD} ${config_string} " - if [ "$debug" != "YES" ]; then - ${MAKE_CMD} ${config_string} >> test.log 2>&1 - status="PASS" - rc=$(( $rc + $? )) - else - status="GEN" - rc=0 - fi - if [ $rc -eq 0 ]; then - echo "TCBtools.sh: make was successful" - echo "TCBtools.sh: configure and build test passed" - echo "$status" > TestStatus - if [ $CLM_RETAIN_FILES != "TRUE" ]; then - echo "TCBtools.sh: removing some unneeded files to save disc space" - rm *.o - rm *.mod - fi - still_compiling="FALSE" - elif [ $attempt -lt 10 ] && \ - grep -c "LICENSE MANAGER PROBLEM" test.log > /dev/null; then - attempt=`expr $attempt + 1` - echo "TCBtools.sh: encountered License Manager Problem; launching attempt #$attempt" - else - echo "TCBtools.sh: clm build failed, error from make= $rc" - echo "TCBtools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 - fi -done -if [ "$TOOLSLIBS" != "" ]; then - export -n SLIBS -fi - -exit 0 diff --git a/test/tools/TSMCFGtools.sh b/test/tools/TSMCFGtools.sh deleted file mode 100755 index b667a4c6ec..0000000000 --- a/test/tools/TSMCFGtools.sh +++ /dev/null @@ -1,113 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 3 ]; then - echo "TSMCFGtools.sh: incorrect number of input arguments" - exit 1 -fi - -tool=$(basename $1) -test_name=TSMCFGtools.$tool.$2.$3 - - -if [ -z "$CLM_RERUN" ]; then - CLM_RERUN="no" -fi - -if [ "$CLM_RERUN" != "yes" ] && [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TSMCFGtools.sh: smoke test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TSMCFGtools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TSMCFGtools.sh: smoke test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TSMCFGtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -cfgdir=`ls -1d ${CLM_ROOT}/tools/${1}*` -rundir=${CLM_TESTDIR}/${test_name} -if [ -d ${rundir} ]; then - rm -r ${rundir} -fi -mkdir -p ${rundir} -if [ $? -ne 0 ]; then - echo "TSMCFGtools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${rundir} - -echo "TSMCFGtools.sh: calling TCBCFGtools.sh to prepare $tool executable" -${CLM_SCRIPTDIR}/TCBCFGtools.sh $1 $2 -rc=$? -if [ $rc -ne 0 ]; then - echo "TSMCFGtools.sh: error from TCBtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 -fi - -echo "TSMCFGtools.sh: running $tool output in ${rundir}/test.log" - -if [ "$2" = "CFGtools__o" ] || [ "$2" = "CFGtools__do" ]; then - toolrun="env OMP_NUM_THREADS=${CLM_THREADS} ${CLM_TESTDIR}/TCBCFGtools.$tool.$2/${tool}*" -else - toolrun="${CLM_TESTDIR}/TCBCFGtools.$tool.$2/${tool}*" -fi - -runfile="${CLM_SCRIPTDIR}/nl_files/$tool.$3" -if [ ! -f "${runfile}" ]; then - echo "TSMCFGtools.sh: error ${runfile} input run file not found" - echo "FAIL.job${JOBID}" > TestStatus - exit 5 -fi - -echo "Run file type = ${3#*.}" -if [ ${3#*.} == "runoptions" ]; then - runopts=`cat ${runfile} | sed -e "s|CSMDATA|$CSMDATA|g"` - echo "$toolrun $runopts" - cp $cfgdir/*.nc . - if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then - $toolrun $runopts >> test.log 2>&1 - rc=$? - status="PASS" - else - echo "Successfully created file" > test.log - status="GEN" - rc=0 - fi -else - echo "$toolrun < ${runfile}" - if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then - $toolrun < ${runfile} >> test.log 2>&1 - rc=$? - status="PASS" - else - echo "Successfully created file" > test.log - status="GEN" - rc=0 - fi -fi - -if [ $rc -eq 0 ] && grep -ci "Successfully created " test.log > /dev/null; then - echo "TSMCFGtools.sh: smoke test passed" - echo "$status" > TestStatus -else - echo "TSMCFGtools.sh: error running $tool, error= $rc" - echo "TSMCFGtools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 -fi - -exit 0 diff --git a/test/tools/TSMscript_tools.sh b/test/tools/TSMscript_tools.sh deleted file mode 100755 index 943fec97f2..0000000000 --- a/test/tools/TSMscript_tools.sh +++ /dev/null @@ -1,98 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 3 ]; then - echo "TSMscript_tools.sh: incorrect number of input arguments" - exit 1 -fi - -test_name=TSMscript_tools.$1.$2.$3 - -if [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TSMscript_tools.sh: smoke test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TSMscript_tools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TSMscript_tools.sh: smoke test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TSMscript_tools.sh: this smoke test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -cfgdir=`ls -1d ${CLM_ROOT}/tools/$1` -rundir=${CLM_TESTDIR}/${test_name} -if [ -d ${rundir} ]; then - rm -r ${rundir} -fi -mkdir -p ${rundir} -if [ $? -ne 0 ]; then - echo "TSMscript_tools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${rundir} - -optfile=${3%^*} -cfgfile=${3#*^} - -if [ "$optfile" != "$3" ]; then - echo "TSMscript_tools.sh: calling TCBtools.sh to prepare $1 executable" - ${CLM_SCRIPTDIR}/TCBtools.sh $1 $cfgfile - rc=$? - if [ $rc -ne 0 ]; then - echo "TSMscript_tools.sh: error from TCBtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 - fi - tcbtools=${CLM_TESTDIR}/TCBtools.$1.$cfgfile -else - tcbtools="$rundir" -fi - -scopts=`cat ${CLM_SCRIPTDIR}/nl_files/$optfile | sed -e "s|CSMDATA|$CSMDATA|g" | sed -e "s|EXEDIR|$tcbtools|g" | sed -e "s|CFGDIR|$cfgdir|g"` -scopts=`echo $scopts | sed -e "s|CTSM_ROOT|$CTSM_ROOT|g" | sed -e "s|CIME_ROOT|$CIME_ROOT|g"` - -echo "TSMscript_tools.sh: running ${cfgdir}/$2 with $scopts; output in ${rundir}/test.log" - -if [ ! -f "${cfgdir}/$2" ]; then - echo "TSMscript_tools.sh: error ${cfgdir}/$2 input script not found" - echo "FAIL.job${JOBID}" > TestStatus - exit 5 -fi - -if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then - ${cfgdir}/$2 $scopts >> test.log 2>&1 - rc=$? - status="PASS" -else - echo "success" > test.log - status="GEN" - rc=0 -fi - -if [ $rc -eq 0 ] && grep -ci "Successfully " test.log > /dev/null; then - echo "TSMscript_tools.sh: smoke test passed" - echo "$status" > TestStatus - # Copy files from subdirectories up... - # (use hard links rather than symbolic links because 'ln -s' does funny - # things when there are no matching files) - ln */*.nc */*/*.nc . -else - echo "TSMscript_tools.sh: error running $2, error= $rc" - echo "TSMscript_tools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 -fi - -exit 0 diff --git a/test/tools/TSMtools.sh b/test/tools/TSMtools.sh deleted file mode 100755 index 33a2316973..0000000000 --- a/test/tools/TSMtools.sh +++ /dev/null @@ -1,117 +0,0 @@ -#!/bin/sh -# - -if [ $# -ne 3 ]; then - echo "TSMtools.sh: incorrect number of input arguments" - exit 1 -fi - -test_name=TSMtools.$1.$2.$3 - -if [ -z "$CLM_RERUN" ]; then - CLM_RERUN="no" -fi - -if [ "$CLM_RERUN" != "yes" ] && [ -f ${CLM_TESTDIR}/${test_name}/TestStatus ]; then - if grep -c PASS ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TSMtools.sh: smoke test has already passed; results are in " - echo " ${CLM_TESTDIR}/${test_name}" - exit 0 - elif grep -c GEN ${CLM_TESTDIR}/${test_name}/TestStatus > /dev/null; then - echo "TSMtools.sh: test already generated" - else - read fail_msg < ${CLM_TESTDIR}/${test_name}/TestStatus - prev_jobid=${fail_msg#*job} - - if [ $JOBID = $prev_jobid ]; then - echo "TSMtools.sh: smoke test has already failed for this job - will not reattempt; " - echo " results are in: ${CLM_TESTDIR}/${test_name}" - exit 2 - else - echo "TSMtools.sh: this smoke test failed under job ${prev_jobid} - moving those results to " - echo " ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid and trying again" - cp -rp ${CLM_TESTDIR}/${test_name} ${CLM_TESTDIR}/${test_name}_FAIL.job$prev_jobid - fi - fi -fi - -cfgdir=`ls -1d ${CLM_ROOT}/tools/$1` -rundir=${CLM_TESTDIR}/${test_name} -if [ -d ${rundir} ]; then - rm -r ${rundir} -fi -mkdir -p ${rundir} -if [ $? -ne 0 ]; then - echo "TSMtools.sh: error, unable to create work subdirectory" - exit 3 -fi -cd ${rundir} - -echo "Copy any text files over" -cp $cfgdir/*.txt $rundir - -echo "TSMtools.sh: calling TCBtools.sh to prepare $1 executable" -${CLM_SCRIPTDIR}/TCBtools.sh $1 $2 -rc=$? -if [ $rc -ne 0 ]; then - echo "TSMtools.sh: error from TCBtools.sh= $rc" - echo "FAIL.job${JOBID}" > TestStatus - exit 4 -fi - -echo "TSMtools.sh: running $1; output in ${rundir}/test.log" - -if [ "$3" = "tools__o" ] || [ "$3" = "tools__do" ]; then - toolrun="env OMP_NUM_THREADS=${CLM_THREADS} ${CLM_TESTDIR}/TCBtools.$1.$2/$1" -else - toolrun="${CLM_TESTDIR}/TCBtools.$1.$2/$1" -fi - -runfile="${cfgdir}/$1.$3" - -if [ ! -f "${runfile}" ]; then - runfile="${CLM_SCRIPTDIR}/nl_files/$1.$3" - if [ ! -f "${runfile}" ]; then - echo "TSMtools.sh: error ${runfile} input run file not found" - echo "FAIL.job${JOBID}" > TestStatus - exit 5 - fi -fi - -echo "Run file type = ${3#*.}" -if [ ${3#*.} == "runoptions" ]; then - echo "$toolrun "`cat ${runfile}` - cp $cfgdir/*.nc . - if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then - $toolrun `cat ${runfile}` >> test.log 2>&1 - rc=$? - status="PASS" - else - echo "Successfully created file" > test.log - status="GEN" - rc=0 - fi -else - echo "$toolrun < ${runfile}" - if [ "$debug" != "YES" ] && [ "$compile_only" != "YES" ]; then - $toolrun < ${runfile} >> test.log 2>&1 - rc=$? - status="PASS" - else - echo "Successfully created file" > test.log - status="GEN" - rc=0 - fi -fi - -if [ $rc -eq 0 ] && grep -ci "Successfully created " test.log > /dev/null; then - echo "TSMtools.sh: smoke test passed" - echo "$status" > TestStatus -else - echo "TSMtools.sh: error running $1, error= $rc" - echo "TSMtools.sh: see ${CLM_TESTDIR}/${test_name}/test.log for details" - echo "FAIL.job${JOBID}" > TestStatus - exit 6 -fi - -exit 0 diff --git a/test/tools/config_files/CFGtools__ds b/test/tools/config_files/CFGtools__ds deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/test/tools/config_files/README b/test/tools/config_files/README deleted file mode 100644 index bdfe5e0dd0..0000000000 --- a/test/tools/config_files/README +++ /dev/null @@ -1,9 +0,0 @@ -_do => debug on, omp only on -_ds => debug on, serial mode (neither mpi nor omp) - -_o => debug off, omp only on -_s => debug off, serial mode (neither mpi nor omp) - -tools__ds => options for tools, debug on, serial mode -tools__do => options for tools, debug on, omp only on -tools__o => options for tools, debug off, omp only on diff --git a/test/tools/config_files/tools__do b/test/tools/config_files/tools__do deleted file mode 100644 index 7f061ed65d..0000000000 --- a/test/tools/config_files/tools__do +++ /dev/null @@ -1 +0,0 @@ -SMP=TRUE OPT=FALSE diff --git a/test/tools/config_files/tools__ds b/test/tools/config_files/tools__ds deleted file mode 100644 index cf2d414b28..0000000000 --- a/test/tools/config_files/tools__ds +++ /dev/null @@ -1 +0,0 @@ -OPT=FALSE diff --git a/test/tools/config_files/tools__o b/test/tools/config_files/tools__o deleted file mode 100644 index 8821e0bc5a..0000000000 --- a/test/tools/config_files/tools__o +++ /dev/null @@ -1 +0,0 @@ -SMP=TRUE OPT=TRUE diff --git a/test/tools/config_files/tools__s b/test/tools/config_files/tools__s deleted file mode 100644 index 507973f8be..0000000000 --- a/test/tools/config_files/tools__s +++ /dev/null @@ -1 +0,0 @@ -OPT=TRUE diff --git a/test/tools/gen_test_table.sh b/test/tools/gen_test_table.sh deleted file mode 100755 index 0791ad0447..0000000000 --- a/test/tools/gen_test_table.sh +++ /dev/null @@ -1,80 +0,0 @@ -#!/bin/sh -# - -# this script, when executed in the directory containing the test-driver -# scripts (~/test/system) will loop through the default test -# lists for pre and post tag testing of clm and create an html file -# (test_table.html) with the specifics of each test detailed - -outfile="./test_table.html" - -echo '' > $outfile -echo '' >> $outfile -echo '' >> $outfile -echo '' >> $outfile -echo 'CLM Testing Information Page' >> $outfile -echo '' >> $outfile -echo '' >> $outfile - -######################################################################################### -for input_file in `ls tests_*` ; do - echo '' >> $outfile - echo "" >> $outfile - echo "" >> $outfile - echo "" >> $outfile - echo "" >> $outfile - echo "" >> $outfile - echo "" >> $outfile - echo "" >> $outfile - echo "" >> $outfile - echo "" >> $outfile - - test_list="" - while read input_line; do - test_list="${test_list}${input_line} " - done < ./${input_file} - - count=0 - ##loop through the tests of input file - for test_id in ${test_list}; do - echo "" >> $outfile - count=`expr $count + 1` - while [ ${#count} -lt 3 ]; do - count="0${count}" - done - echo "" >> $outfile - - master_line=`grep $test_id ./input_tests_master` - dir="" - for arg in ${master_line}; do - arg1=${arg%^*} - arg2=${arg#*^} - if [ -d ../../tools/$arg ]; then - dir=$arg - elif [ -f ./nl_files/$arg ]; then - echo "" >> $outfile - elif [ -f ./config_files/$arg ]; then - echo "" >> $outfile - elif [ -f ./nl_files/$arg1 ] && [ -f ./nl_files/$arg2 ]; then - echo "" >> $outfile - elif [ -f ./nl_files/$arg1 ] && [ -f ./config_files/$arg2 ]; then - echo "" >> $outfile - elif [ -f ../../tools/$dir/$dir.$arg ]; then - echo "" >> $outfile - else - echo "" >> $outfile - fi - done - echo '' >> $outfile - done - echo '
$input_file
test# testid test script arg1 arg2 arg3
$count $arg $arg $arg1^" \ - "$arg2$arg1^" \ - "$arg2$arg $arg
' >> $outfile - echo '
' >> $outfile
-    echo ' ' >> $outfile
-    echo '
' >> $outfile -done -echo '' >> $outfile -echo '' >> $outfile - -exit 0 diff --git a/test/tools/get_cprnc_diffs.sh b/test/tools/get_cprnc_diffs.sh deleted file mode 100755 index 360220cb71..0000000000 --- a/test/tools/get_cprnc_diffs.sh +++ /dev/null @@ -1,56 +0,0 @@ -#!/bin/bash - -# This script extracts lines from the output of cprnc that tell us -# which variables differ between two files -# -# Usage: get_cprnc_diffs filename - -# ---------------------------------------------------------------------- -# SET PARAMETERS HERE -# ---------------------------------------------------------------------- - -# maximum number of differences to extract from the cprnc output -maxdiffs=200 - -# ---------------------------------------------------------------------- -# LOCAL FUNCTIONS DEFINED HERE -# ---------------------------------------------------------------------- - -# This function gets differences for one prefix (e.g., "RMS") -# Usage: get_diffs prefix -# (also uses $infile and $maxdiffs from the parent script) -function get_diffs { - prefix=$1 - outfile=${infile}.${prefix}.$$ - grep "$prefix" $infile > $outfile - numlines=`wc -l $outfile | awk '{print $1}'` - if [ $numlines -gt $maxdiffs ]; then - echo "WARNING: Too many instances of $prefix - only printing last $maxdiffs" - tail -$maxdiffs $outfile - else - cat $outfile - fi - rm $outfile -} - -# ---------------------------------------------------------------------- -# BEGIN MAIN SCRIPT -# ---------------------------------------------------------------------- - -# ---------------------------------------------------------------------- -# Handle command-line arguments -# ---------------------------------------------------------------------- - -if [[ $# -ne 1 ]]; then - echo "Usage: get_cprnc_diffs filename" - exit 1 -fi - -infile=$1 - -# ---------------------------------------------------------------------- -# Do the processing -# ---------------------------------------------------------------------- - -get_diffs RMS -get_diffs FILLDIFF diff --git a/test/tools/input_tests_master b/test/tools/input_tests_master deleted file mode 100644 index 7da8c19803..0000000000 --- a/test/tools/input_tests_master +++ /dev/null @@ -1,32 +0,0 @@ - - -smc#4 TSMscript_tools.sh mkprocdata_map mkprocdata_map_wrap mkprocdata_ne30_to_f19_I2000^tools__ds -blc#4 TBLscript_tools.sh mkprocdata_map mkprocdata_map_wrap mkprocdata_ne30_to_f19_I2000^tools__ds - -sm0c1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_OSBS -bl0c1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_OSBS -sm0a1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_YELL_PRISM -bl0a1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_YELL_PRISM - -smba1 TSMscript_tools.sh site_and_regional subset_data subset_data_YELL -blba1 TBLscript_tools.sh site_and_regional subset_data subset_data_YELL -smbb1 TSMscript_tools.sh site_and_regional subset_data subset_data_KONA -blbb1 TBLscript_tools.sh site_and_regional subset_data subset_data_KONA -smb81 TSMscript_tools.sh site_and_regional subset_data subset_data_US-UMB -blb81 TBLscript_tools.sh site_and_regional subset_data subset_data_US-UMB -smbh1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_1x1pt_townshipSD -blbh1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_1x1pt_townshipSD -smbd1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_58x45pt_SouthAmerica -blbd1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_58x45pt_SouthAmerica -smbe1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_90x288pt_1850PanTropics -blbe1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_90x288pt_1850PanTropics -smbf1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_37x288pt_PanBoreal -blbf1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_37x288pt_PanBoreal -smbg1 TSMscript_tools.sh site_and_regional subset_data subset_data_f09_4x9pt_AlaskaTananaValley -blbg1 TBLscript_tools.sh site_and_regional subset_data subset_data_f09_4x9pt_AlaskaTananaValley - -sm901 TSMscript_tools.sh site_and_regional mesh_maker mesh_maker_fv09 -bl901 TBLscript_tools.sh site_and_regional mesh_maker mesh_maker_fv09 - -smaa2 TSMscript_tools.sh site_and_regional modify_singlept_site_neon.py modify_data_YELL -blaa2 TBLscript_tools.sh site_and_regional modify_singlept_site_neon.py modify_data_YELL diff --git a/test/tools/nl_files/mesh_maker_fv09 b/test/tools/nl_files/mesh_maker_fv09 deleted file mode 100644 index 7de951fee1..0000000000 --- a/test/tools/nl_files/mesh_maker_fv09 +++ /dev/null @@ -1 +0,0 @@ - --input CSMDATA/atm/datm7/domain.lnd.fv0.9x1.25_gx1v6.090309.nc --lat yc --lon xc --overwrite --mask mask --area area --verbose diff --git a/test/tools/nl_files/mkmapdata_if10 b/test/tools/nl_files/mkmapdata_if10 deleted file mode 100644 index f726ea34e7..0000000000 --- a/test/tools/nl_files/mkmapdata_if10 +++ /dev/null @@ -1 +0,0 @@ --r 10x15 --fast --batch diff --git a/test/tools/nl_files/mkmapdata_ne30np4 b/test/tools/nl_files/mkmapdata_ne30np4 deleted file mode 100644 index ae435ac2bc..0000000000 --- a/test/tools/nl_files/mkmapdata_ne30np4 +++ /dev/null @@ -1 +0,0 @@ --r ne30np4 --fast --batch diff --git a/test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 b/test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 deleted file mode 100644 index af85dcf226..0000000000 --- a/test/tools/nl_files/mkprocdata_ne30_to_f19_I2000 +++ /dev/null @@ -1 +0,0 @@ --i CSMDATA/lnd/clm2/test_mkprocdata_map/clm4054_ne30g16_I2000.clm2.h0.2000-01_c170430.nc -o ne30output_onf19grid.nc -m CSMDATA/lnd/clm2/test_mkprocdata_map/map_ne30np4_nomask_to_fv1.9x2.5_nomask_aave_da_c121107.nc -t CSMDATA/lnd/clm2/test_mkprocdata_map/clm4054_f19g16_I2000.clm2.h0.2000-01_c170430.nc -e EXEDIR diff --git a/test/tools/nl_files/modify_data_YELL b/test/tools/nl_files/modify_data_YELL deleted file mode 100644 index 0d180e8bf6..0000000000 --- a/test/tools/nl_files/modify_data_YELL +++ /dev/null @@ -1 +0,0 @@ ---neon_site YELL --surf_dir CSMDATA/lnd/clm2/surfdata_esmf/NEON --out_dir EXEDIR --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/run_neon_OSBS b/test/tools/nl_files/run_neon_OSBS deleted file mode 100644 index 0c274b13ad..0000000000 --- a/test/tools/nl_files/run_neon_OSBS +++ /dev/null @@ -1 +0,0 @@ ---verbose --run-type ad --setup-only --neon-site OSBS diff --git a/test/tools/nl_files/run_neon_YELL_PRISM b/test/tools/nl_files/run_neon_YELL_PRISM deleted file mode 100644 index f5ebdf9fdf..0000000000 --- a/test/tools/nl_files/run_neon_YELL_PRISM +++ /dev/null @@ -1 +0,0 @@ ---verbose --run-type transient --setup-only --neon-site YELL --prism --neon-version v2 --experiment toolstest diff --git a/test/tools/nl_files/subset_data_KONA b/test/tools/nl_files/subset_data_KONA deleted file mode 100644 index 0df59b1b17..0000000000 --- a/test/tools/nl_files/subset_data_KONA +++ /dev/null @@ -1 +0,0 @@ -point --lon 263.38956 --lat 39.1082 --site KONA --dompft 17 19 23 45 --pctpft 28 12 32 28 --crop --create-surface --outdir EXEDIR/KONA_user-mod_and_data --user-mods-dir EXEDIR/KONA_user-mod_and_data --verbose --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_US-UMB b/test/tools/nl_files/subset_data_US-UMB deleted file mode 100644 index 935b0dc99d..0000000000 --- a/test/tools/nl_files/subset_data_US-UMB +++ /dev/null @@ -1 +0,0 @@ -point --lon 275.28626 --lat 45.5598 --site 1x1_US-UMB --dompft 7 --cap-saturation --uniform-snowpack --create-surface --outdir EXEDIR/US-UMB_user-mod_and_data --user-mods-dir EXEDIR/US-UMB_user-mod_and_data --verbose --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_YELL b/test/tools/nl_files/subset_data_YELL deleted file mode 100644 index 0d6960e7f5..0000000000 --- a/test/tools/nl_files/subset_data_YELL +++ /dev/null @@ -1 +0,0 @@ -point --lon 250.45804 --lat 44.95597 --site YELL --dompft 1 --crop --uniform-snowpack --cap-saturation --create-surface --outdir EXEDIR/YELL_user-mod_and_data --user-mods-dir EXEDIR/YELL_user-mod_and_data --silent --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_f09_1x1pt_townshipSD b/test/tools/nl_files/subset_data_f09_1x1pt_townshipSD deleted file mode 100644 index aa25c07d1e..0000000000 --- a/test/tools/nl_files/subset_data_f09_1x1pt_townshipSD +++ /dev/null @@ -1 +0,0 @@ -point --lon 257.5 --lat 43.822 --site f09_1x1pt_townshipSD --include-nonveg --crop --create-datm --create-user-mods --datm-syr 2000 --datm-eyr 2000 --create-surface --outdir EXEDIR/f09_US_pt_user-mod_and_data --user-mods-dir EXEDIR/f09_US_pt_user-mod_and_data --verbose --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal b/test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal deleted file mode 100644 index 448b5052d6..0000000000 --- a/test/tools/nl_files/subset_data_f09_37x288pt_PanBoreal +++ /dev/null @@ -1 +0,0 @@ -region --lat1 55 --lat2 89.1 --lon1 0 --lon2 360 --create-mesh --create-surface --create-domain --create-user-mods --verbose --overwrite --reg f09_37x288pt_PanBoreal --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley b/test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley deleted file mode 100644 index 9928d78429..0000000000 --- a/test/tools/nl_files/subset_data_f09_4x9pt_AlaskaTananaValley +++ /dev/null @@ -1 +0,0 @@ -region --lat1 62 --lat2 66 --lon1 -152 --lon2 -141 --create-mesh --create-domain --create-surface --create-user-mods --verbose --overwrite --reg f09_4x9pt_AlaskaTananaValley --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica b/test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica deleted file mode 100644 index 201dd2c76c..0000000000 --- a/test/tools/nl_files/subset_data_f09_58x45pt_SouthAmerica +++ /dev/null @@ -1 +0,0 @@ -region --lat1 -40 --lat2 15 --lon1 275 --lon2 330 --create-mesh --create-surface --create-user-mods --create-domain --create-landuse --verbose --overwrite --reg f09_58x45_SouthAmerica --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics b/test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics deleted file mode 100644 index 1c9d5eace9..0000000000 --- a/test/tools/nl_files/subset_data_f09_90x288pt_1850PanTropics +++ /dev/null @@ -1 +0,0 @@ -region --lat1 -55 --lat2 30 --lon1 0 --lon2 360 --crop --create-surface --create-domain --create-mesh --overwrite --reg f09_90x288pt_1850PanTropics --inputdata-dir CSMDATA --cfg-file CTSM_ROOT/tools/mksurfdata_map/default_data_1850.cfg --verbose diff --git a/test/tools/show_var_diffs.sh b/test/tools/show_var_diffs.sh deleted file mode 100755 index f462d4ad0c..0000000000 --- a/test/tools/show_var_diffs.sh +++ /dev/null @@ -1,79 +0,0 @@ -#!/bin/bash - -# This script processes a log file that was output by test_driver, -# giving lists of all variables with differences in values (those with -# RMS errors), and all variables with differences in fill patterns. -# -# This assumes that the log file contains output like: -# RMS foo -# RMS bar -# FILLDIFF foo -# FILLDIFF bar -# Some characteristics of these output lines are: -# - they begin with a leading space, followed by RMS or FILLDIFF -# - the variable name is in the second column of the line -# -# Note that (as of 4-5-12) the log file only contains output from the -# last file that didn't match, so this could potentially miss -# something -- especially if there are both h0 and h1 files in the -# comparison. - -# Usage: show_var_diffs logfile - -# ---------------------------------------------------------------------- -# LOCAL FUNCTIONS DEFINED HERE -# ---------------------------------------------------------------------- - -# This function shows the differences for one prefix (e.g., "RMS") -# Usage: show_diffs prefix -# (also uses $logfile from the parent script) -# -# Matches lines that start with the regular expression "^ ${prefix}" -# (note that one leading space is expected before the prefix) -# -# Assumes that the variable name is in the second column of matching lines -function show_diffs { - prefix=$1 - - # first determine if there were warnings relating to this prefix - grep "WARNING: Too many instances of ${prefix}" $logfile > /dev/null - if [ $? -eq 0 ]; then # found a warning - echo "WARNING: Some output was truncated; this may not be a complete list" - fi - - # now make a list of all variables matching this prefix - grep "^ ${prefix}" $logfile > $logfile.tmp.$$ - if [ $? -eq 0 ]; then - awk '{print $2}' $logfile.tmp.$$ | sort | uniq - else - echo "(no differences)" - fi - - rm $logfile.tmp.$$ -} - -# ---------------------------------------------------------------------- -# BEGIN MAIN SCRIPT -# ---------------------------------------------------------------------- - -# ---------------------------------------------------------------------- -# Handle command-line arguments -# ---------------------------------------------------------------------- - -if [[ $# -ne 1 ]]; then - echo "Usage: show_var_diffs logfile" - exit 1 -fi - -logfile=$1 - -# ---------------------------------------------------------------------- -# Do the processing -# ---------------------------------------------------------------------- - -echo "Variables with differences in values:" -show_diffs "RMS" - -echo "" -echo "Variables with differences in fill patterns:" -show_diffs "FILLDIFF" \ No newline at end of file diff --git a/test/tools/tests_posttag_hobart_nompi b/test/tools/tests_posttag_hobart_nompi deleted file mode 100644 index c185428868..0000000000 --- a/test/tools/tests_posttag_hobart_nompi +++ /dev/null @@ -1 +0,0 @@ -smc#4 blc#4 diff --git a/test/tools/tests_posttag_nompi_regression b/test/tools/tests_posttag_nompi_regression deleted file mode 100644 index c185428868..0000000000 --- a/test/tools/tests_posttag_nompi_regression +++ /dev/null @@ -1 +0,0 @@ -smc#4 blc#4 diff --git a/test/tools/tests_pretag_cheyenne_nompi b/test/tools/tests_pretag_cheyenne_nompi deleted file mode 100644 index e92ffaaaad..0000000000 --- a/test/tools/tests_pretag_cheyenne_nompi +++ /dev/null @@ -1,3 +0,0 @@ -smc#4 blc#4 -smba1 blba1 -smbd1 blbd1 diff --git a/test/tools/tests_pretag_derecho_nompi b/test/tools/tests_pretag_derecho_nompi deleted file mode 100644 index 5fdaf335ae..0000000000 --- a/test/tools/tests_pretag_derecho_nompi +++ /dev/null @@ -1,9 +0,0 @@ -smba1 blba1 -smbd1 blbd1 -sm0a1 bl0a1 -sm0c1 bl0c1 -smaa2 blaa2 -smba1 blba1 -smb81 blb81 -smbc1 blbc1 -smbd1 blbd1 diff --git a/test/tools/tests_pretag_nompi_neon b/test/tools/tests_pretag_nompi_neon deleted file mode 100644 index e5fa27e6c4..0000000000 --- a/test/tools/tests_pretag_nompi_neon +++ /dev/null @@ -1,8 +0,0 @@ -sm0a1 bl0a1 -sm0c1 bl0c1 -smaa2 blaa2 -smba1 blba1 -smbb1 blbb1 -smb81 blb81 -smbc1 blbc1 -smbd1 blbd1 From 69dbee8149945c173c66cfa8670adecccf333d16 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 11:08:53 -0600 Subject: [PATCH 157/408] Remove bld/unit_testers/xFail/wrapClmTests.pl --- bld/unit_testers/xFail/wrapClmTests.pl | 128 ------------------------- 1 file changed, 128 deletions(-) delete mode 100755 bld/unit_testers/xFail/wrapClmTests.pl diff --git a/bld/unit_testers/xFail/wrapClmTests.pl b/bld/unit_testers/xFail/wrapClmTests.pl deleted file mode 100755 index 28238b9d5d..0000000000 --- a/bld/unit_testers/xFail/wrapClmTests.pl +++ /dev/null @@ -1,128 +0,0 @@ -#!/usr/bin/env perl - -#-# ========================================================================================= - -=head1 wrapClmTest.pl - -=head1 Overview - -This is a wrapper script that is called from test_driver.sh for either interactive or batch -tests. It calls the CTOR for the xFail::expectedFail.pm module and also parses the td*.status -file to create a new file with xFails listed. - -It takes the following arguments: - - numberOfTests -> number of tests from test_driver.sh - statusFile -> name of the td..status file - callingScript -> name of script calling this. For test_driver.sh it may be one of: - 1) test_driver.sh-i for interactive tests - 2) test_driver.sh for batch tests - -=head1 Notes - -This script may be run standalone which is useful for testing purposes. - -=cut - -#-# ========================================================================================= - -use strict; -use Getopt::Long; -use English; -use Cwd; -use Scalar::Util qw(looks_like_number); - -my $DEBUG=0; - -sub usage { - die < 0, - numberOfTests => undef, - statusFile => undef, - callingScript => undef, - ); - -GetOptions( - "h|help" => \$opts{'help'}, - "numberOfTests=s" => \$opts{'numberOfTests'}, - "statusFile=s" => \$opts{'statusFile'}, - "callingScript=s" => \$opts{'callingScript'}, -) or usage(); - -# Give usage message. -usage() if $opts{'help'}; - -my $statFoo = undef; -my $nTests = undef; -my $script= undef; - -if (defined($opts{'statusFile'})) { - $statFoo = $opts{'statusFile'}; -} -if (defined($opts{'numberOfTests'})) { - $nTests = $opts{'numberOfTests'}; -} -if (defined($opts{'callingScript'})) { - $script = $opts{'callingScript'}; -} - -my ( $self ) = @_; - -#Figure out where configure directory is and where can use the XML/Lite module from -my $ProgName; -($ProgName = $PROGRAM_NAME) =~ s!(.*)/!!; # name of program -my $ProgDir = $1; # name of directory where program lives - -my $cwd = getcwd(); # current working directory -my $cfgdir; - -if ($ProgDir) { $cfgdir = $ProgDir; } -else { $cfgdir = $cwd; } - -#----------------------------------------------------------------------------------------------- -# Add $cfgdir to the list of paths that Perl searches for modules -#----------------------------------------------------------------------------------------------- -my @dirs = ( $cfgdir, - "$cfgdir/../", - "$cfgdir/../../../../../cime/utils/perl5lib"); -unshift @INC, @dirs; -my $result = eval "require expectedFail"; -if ( ! defined($result) ) { - die <<"EOF"; -** Cannot find perl module \"xFail/expectedFail.pm\" from directories: @dirs ** -EOF -} - -#_# ==================================== -#_# setup work complete. Now parse file -#_# ==================================== - -if ($DEBUG) { - print (" wrapClmTests.pl:: calling script $script \n"); - print (" wrapClmTests.pl:: number of tests $nTests \n"); - print (" wrapClmTests.pl:: processing $statFoo \n"); -} - -#_# compGen not used for CLM batch or interactive tests, but we use "compare" as the default in this case -my $compGen="compare"; -my $xFail = xFail::expectedFail->new($script,$compGen,$nTests); - -$xFail->parseOutputCLM($statFoo); - -exit(0); From 8ef1ff4a3a4c2ca4c44c0d59bd654819b32edd62 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 11:19:49 -0600 Subject: [PATCH 158/408] Remove obsolete parts of bld/unit_testers/xFail/expectedFail.pm --- bld/unit_testers/xFail/expectedFail.pm | 119 +------------------------ 1 file changed, 2 insertions(+), 117 deletions(-) diff --git a/bld/unit_testers/xFail/expectedFail.pm b/bld/unit_testers/xFail/expectedFail.pm index 9feaa3e38b..067e3a51d8 100755 --- a/bld/unit_testers/xFail/expectedFail.pm +++ b/bld/unit_testers/xFail/expectedFail.pm @@ -5,7 +5,7 @@ Documentation for expectedFail.pm =head1 Overview The module expectedFail.pm supplies the capability of checking if a failed test is expected to fail. -It is called directly from either test_driver.sh (for batch and interactive tests) or build-namelist_test.pl. +It is called directly from build-namelist_test.pl. Future plans involve integrating this module into cesm tests. =head1 Use Case @@ -112,7 +112,7 @@ sub new { =head1 parseOutput -parseOutput parsese the output from the build-namelist_test.pl script. It is similar +parseOutput parses the output from the build-namelist_test.pl script. It is similar to, but not interchangable with parseOutputCLM. The only argument is that of the reference variable that contains the information dumped @@ -223,119 +223,6 @@ sub parseOutput # ############################################################################## -=head1 parseOutputCLM - -parseOutputCLM parsese the output from the test_driver.sh script. It is similar -to, but not interchangable with parseOutput. - -parseOutputCLM takes one arguments: - $statFoo-> the name of the td..status file - -returns: nothing - -=cut - -############################################################################## -# -############################################################################## -sub parseOutputCLM -{ - - my $report; - my $testId; - my @testName={}; - my $testReason; - - my ($self, $statFoo) = @_ ; - - open(FOO, "< $statFoo"); # open for input - open(FOO_OUT, "> $statFoo.xFail"); # open for input - - my(@reportLines); - - while () { - - my($line) = $_; - - my @outArr=split(/ /,$line); - if (looks_like_number(@outArr[0])) { - - $self->{_numericalTestId}++; - - my $num=sprintf("%03d", $self->{_numericalTestId}); - my $totNum=sprintf("%03d", $self->{_totTests}); - - #_# last element has the pass/fail info. - chomp(@outArr[-1]); - my $repPass=substr(@outArr[-1], -4, 4); - - if ($DEBUG) { - print ("xFail::expectedFail::parseOutput @outArr[0] \n"); - print ("xFail::expectedFail::parseOutput @outArr[1] \n"); - print ("xFail::expectedFail::parseOutput @outArr[2] \n"); - print ("xFail::expectedFail::parseOutput @outArr[3] \n"); - print ("xFail::expectedFail::parseOutput @outArr[4] \n"); - print ("xFail::expectedFail::parseOutput @outArr[5] \n"); - print ("xFail::expectedFail::parseOutput @outArr[6] \n"); - print ("xFail::expectedFail::parseOutput @outArr[-1] \n"); - print ("xFail::expectedFail::parseOutput $repPass \n"); - } - - my $size = @outArr-1; - if ($DEBUG) { - print ("size of line $size \n"); - } - my $endOfDesc=$size-1; - - if ($repPass eq "PASS") { - $report=$pass; - $testId=@outArr[1]; - @testName=@outArr[2..$endOfDesc]; - - my ($retVal,$xFailText)=$self->_searchExpectedFail($testId); - - my $testReason=$self->_testNowPassing($testId,$retVal,$xFailText); - - #_# print out the test results - print FOO_OUT ("$num/$totNum <$report> $testReason \n"); - - } else { - $testId=@outArr[1]; - my ($retVal,$xFailText)=$self->_searchExpectedFail($testId); - - if ($DEBUG) { - print ("xFail::expectedFail::parseOutput Id $retVal,$xFailText \n"); - } - - @testName=@outArr[2..$endOfDesc]; - - if ($retVal eq "TRUE"){ - #_# found an expected FAIL (xFAIL) - $report=$xfail; - $testReason= ""; - } else { - #_# print a regular FAIL - $report=$fail; - $testReason=""; - } - - #_# print out the test results - print FOO_OUT ("$num/$totNum <$report> $testReason \n"); - - } - - } else { - print FOO_OUT $line; - } - } - close(FOO); - close(FOO_OUT); -} - -############################################################################## -# -############################################################################## - =head1 _searchExpectedFail searches the list of expected fails for a match with testId. @@ -608,8 +495,6 @@ sub _getTestType my %testTypes = ( "build-namelist_test.pl" => "namelistTest", - "test_driver.sh-i" => "clmInteractive", - "test_driver.sh" => "clmBatch", "clm-cesm.sh" => "cesm" ); From 0c26697a620292a7dcd69f8eefa55a3ee759332f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 11:22:42 -0600 Subject: [PATCH 159/408] Remove obsolete parts of expectedClmTestFails.xml: DID I rm ENOUGH? --- bld/unit_testers/xFail/expectedClmTestFails.xml | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/bld/unit_testers/xFail/expectedClmTestFails.xml b/bld/unit_testers/xFail/expectedClmTestFails.xml index c7cbfee488..380e614ea1 100644 --- a/bld/unit_testers/xFail/expectedClmTestFails.xml +++ b/bld/unit_testers/xFail/expectedClmTestFails.xml @@ -20,20 +20,6 @@ - - - - - - - - goldbach not recognized - goldbach not recognized - goldbach not recognized - - - - From 882425a205ded67450455466ded69d034f5d39fa Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 11:26:11 -0600 Subject: [PATCH 160/408] Remove mention of test_driver_*.sh in .gitignore --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 1da8072fed..163bfeda2d 100644 --- a/.gitignore +++ b/.gitignore @@ -75,7 +75,6 @@ buildnmlc td.*.status td.*.log td.*.status.xFail -test_driver_*.sh # mksurfdata output surfdata_*.log From 9407ce50522c2a624196fd4b892363cf8505b5ee Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 11:33:48 -0600 Subject: [PATCH 161/408] Remove reference to /test in /doc/.../testing.rst --- doc/source/users_guide/testing/testing.rst | 6 ------ 1 file changed, 6 deletions(-) diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst index bad1183fff..69ca1f7263 100644 --- a/doc/source/users_guide/testing/testing.rst +++ b/doc/source/users_guide/testing/testing.rst @@ -13,12 +13,6 @@ CIME Testing scripts We first introduce the test scripts that work for all CESM components. The CIME script **create_test** runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing `_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also see the `CTSM Wiki on Testing `_. -CTSM Tools Testing -================== - -.. include:: ../../../../test/tools/README - :literal: - CTSM Fortran Unit Tests ======================= From eedbadff362d140cd1f1a34803e525e25fb58236 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 21 May 2024 12:21:32 -0600 Subject: [PATCH 162/408] Check values for a basic run through with default input forcing --- src/biogeochem/DUSTMod.F90 | 54 ++++++++++++++- .../test/DustEmis_test/test_DustEmis.pf | 68 ++++++++++++++++++- 2 files changed, 118 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90 index e0e4e469a1..cd60bd859f 100644 --- a/src/biogeochem/DUSTMod.F90 +++ b/src/biogeochem/DUSTMod.F90 @@ -62,12 +62,14 @@ module DUSTMod contains procedure , public :: Init - procedure , public :: DustEmission ! Dust mobilization - procedure , public :: DustDryDep ! Turbulent dry deposition for dust + procedure , public :: DustEmission ! Dust mobilization + procedure , public :: DustDryDep ! Turbulent dry deposition for dust + procedure , public :: WritePatchToLog ! Write information on the given patch to the log file + procedure , public :: GetPatchVars ! Get important variables on a given patch procedure , private :: InitAllocate procedure , private :: InitHistory procedure , private :: InitCold - procedure , private :: InitDustVars ! Initialize variables used in DustEmission method + procedure , private :: InitDustVars ! Initialize variables used in DustEmission method end type dust_type !------------------------------------------------------------------------ @@ -209,6 +211,52 @@ subroutine InitCold(this, bounds) end subroutine InitCold + !----------------------------------------------------------------------- + + subroutine WritePatchToLog(this, p) + ! + ! !DESCRIPTION: + ! Write out information on dust emisisons for this patch to the log file + ! !ARGUMENTS: + class(dust_type), intent(in) :: this + integer , intent(in) :: p ! Patch to display + + write(iulog,*) 'flx_mss_vrt_dst', this%flx_mss_vrt_dst_patch(p,:) + write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p) + write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p) + write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p) + write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p) + write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p) + write(iulog,*) 'mbl_bsn_fct', this%mbl_bsn_fct_col(p) + end subroutine WritePatchToLog + + !----------------------------------------------------------------------- + + subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, & + vlc_trb_2, vlc_trb_3, vlc_trb_4) + ! + ! !DESCRIPTION: + ! Get important variables on the given patch + ! !ARGUMENTS: + class(dust_type) , intent(in) :: this + integer , intent(in) :: p ! Patch to get + real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst) + real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot + real(r8), optional, intent(out) :: vlc_trb(ndst) + real(r8), optional, intent(out) :: vlc_trb_1 + real(r8), optional, intent(out) :: vlc_trb_2 + real(r8), optional, intent(out) :: vlc_trb_3 + real(r8), optional, intent(out) :: vlc_trb_4 + + if ( present(flx_mss_vrt_dst ) ) flx_mss_vrt_dst = this%flx_mss_vrt_dst_patch(p,:) + if ( present(flx_mss_vrt_dst_tot) ) flx_mss_vrt_dst_tot = this%flx_mss_vrt_dst_tot_patch(p) + if ( present(vlc_trb ) ) vlc_trb = this%vlc_trb_patch(p,:) + if ( present(vlc_trb_1) ) vlc_trb_1 = this%vlc_trb_1_patch(p) + if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p) + if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p) + if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p) +end subroutine GetPatchVars + !------------------------------------------------------------------------ subroutine DustEmission (this, bounds, & num_nolakep, filter_nolakep, & diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index 9be97453b0..08aa683964 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -5,7 +5,7 @@ module test_DustEmis use funit use unittestSubgridMod use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch - use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init + use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit use clm_varcon, only : clm_varcon_init, clm_varcon_clean use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting @@ -19,9 +19,12 @@ module test_DustEmis use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type + use abortutils, only : endrun implicit none + real(r8), parameter :: tol = 1.e-13_r8 + @TestCase type, extends(TestCase) :: TestDustEmis type(dust_type) :: dust_emis @@ -40,6 +43,8 @@ module test_DustEmis procedure :: setupEnvironment procedure :: create_atm2lnd procedure :: create_fv + procedure :: print_patch + procedure :: validate_patch end type TestDustEmis contains @@ -231,11 +236,61 @@ contains end subroutine create_fv + subroutine print_patch(this) + use LandunitType, only : lun + class(TestDustEmis), intent(inout) :: this + integer :: p, c, l + + do l = bounds%begl, bounds%endl + print *, 'landunit type= ', lun%itype(l) + end do + do c = bounds%begc, bounds%endc + print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1) + print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1) + print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c) + end do + do p = bounds%begp, bounds%endp + print *, 'tlai = ', this%canopystate_inst%tlai_patch(p) + call this%dust_emis%WritePatchToLog( p ) + end do + call endrun( "exit early") + end subroutine print_patch + + !----------------------------------------------------------------------- + subroutine validate_patch(this, p) + class(TestDustEmis), intent(inout) :: this + integer, intent(in) :: p + + real(r8) :: flx_mss_vrt_dst(ndst) + real(r8) :: flx_mss_vrt_dst_tot + real(r8) :: vlc_trb(ndst) + real(r8) :: vlc_trb_1 + real(r8) :: vlc_trb_2 + real(r8) :: vlc_trb_3 + real(r8) :: vlc_trb_4 + + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, & + flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, & + vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, & + vlc_trb_4=vlc_trb_4 ) + @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot ) + @assertEqual( vlc_trb(1), vlc_trb_1) + @assertEqual( vlc_trb(2), vlc_trb_2) + @assertEqual( vlc_trb(3), vlc_trb_3) + @assertEqual( vlc_trb(4), vlc_trb_4) + end subroutine validate_patch + !----------------------------------------------------------------------- @Test subroutine check_dust_emis(this) class(TestDustEmis), intent(inout) :: this + integer :: p + real(r8) :: flx_mss_vrt_dst_tot + real(r8) :: vlc_trb_1 + real(r8) :: vlc_trb_2 + real(r8) :: vlc_trb_3 + real(r8) :: vlc_trb_4 call this%create_atm2lnd() call this%create_fv() @@ -243,6 +298,17 @@ contains this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + do p = bounds%begp, bounds%endp + call this%validate_patch(p) + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, & + vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, & + vlc_trb_4=vlc_trb_4) + @assertEqual( 0.0_r8, flx_mss_vrt_dst_tot ) + @assertEqual( 3.319559266672431d-5, vlc_trb_1, tolerance=tol ) + @assertEqual( 1.699714729099379d-5, vlc_trb_2, tolerance=tol ) + @assertEqual( 9.163854318535118d-6, vlc_trb_3, tolerance=tol ) + @assertEqual( 3.614237762488103d-5, vlc_trb_4, tolerance=tol ) + end do end subroutine check_dust_emis From 93c274d7570d8f33002ac0156fc4a977670feef2 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 12:30:38 -0600 Subject: [PATCH 163/408] Update README by removing mention of /test directory --- README | 1 - 1 file changed, 1 deletion(-) diff --git a/README b/README index 4699fec858..af45a14909 100644 --- a/README +++ b/README @@ -47,7 +47,6 @@ doc --------------- Documentation of CTSM. bld --------------- build-namelist scripts for CTSM. src --------------- CTSM Source code. lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model) -test -------------- CTSM Testing scripts for CTSM offline tools (deprecated) tools ------------- CTSM Offline tools to prepare input datasets and process output. cime_config ------- Configuration files of cime for compsets and CTSM settings manage_externals -- Script to manage the external source directories (deprecated) From 802b989d5c408a36bccf07b24f2f8a2724e4ca59 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 May 2024 15:11:29 -0600 Subject: [PATCH 164/408] Second draft of ChangeLog/ChangeSum --- doc/ChangeLog | 37 ++++++++++++++++++++----------------- doc/ChangeSum | 2 +- 2 files changed, 21 insertions(+), 18 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 5644ed295d..d68ef323ac 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,18 +1,18 @@ =============================================================== Tag name: ctsm5.2.006 Originator(s): slevis (Samuel Levis) -Date: Fri May 17 16:17:54 MDT 2024 -One-line Summary: Update externals to cesm2_3_beta17 +Date: Tue 21 May 2024 02:59:05 PM MDT +One-line Summary: Update externals to cesm2_3_beta17, remove mct, retire /test/tools Purpose and description of changes ---------------------------------- -#2493 update externals to beta17 -#2294 remove references to mct but do not remove /src/mct + #2493 update externals to beta17 + #2294 remove mct but not in Externals.cfg + #2279 Retire the /test/tools framework for CESM test system custom tests that do the same thing -Changes unrelated to the tag's title: -#2546 fix error in cam4/cam5 test (ekluzek) -Remove /test/tools/test_driver.sh + Changes unrelated to the tag's title: + #2546 fix error in cam4/cam5 test (ekluzek) Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -36,20 +36,23 @@ Does this tag change answers significantly for any of the following physics conf Bugs fixed ---------- List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: -Fixes #2493 update externals to beta17 -Fixes #2546 fix error in cam4/cam5 test (unrelated) + Fixes #2493 update externals to beta17 + Fixes #2279 Retire the /test/tools framework for CESM test system custom tests that do the same thing + Fixes #2546 fix error in cam4/cam5 test (unrelated) Notes of particular relevance for users --------------------------------------- -Changes to documentation: Remove references to mct and cpl7 +Changes to documentation: + Remove references to mct and cpl7 -Substantial timing or memory changes: Not considered +Substantial timing or memory changes: + Not considered Notes of particular relevance for developers: --------------------------------------------- Changes to tests or testing: -I added a long list of izumi nag debug tests to ExpectedFailures as per -https://github.com/ESCOMP/CMEPS/pull/460 + I added a long list of izumi nag debug tests to ExpectedFailures as per + https://github.com/ESCOMP/CMEPS/pull/460 Testing summary: ---------------- @@ -57,16 +60,16 @@ Testing summary: build-namelist tests (if CLMBuildNamelist.pm has changed): - derecho - + derecho - PASS python testing (if python code has changed; see instructions in python/README.md; document testing done): - (any machine) - + derecho - PASS regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): derecho ----- - izumi ------- IN PROGRESS + izumi ------- OK any other testing (give details below): @@ -98,7 +101,7 @@ Changes answers relative to baseline: Other details ------------- List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): -cism, ccs_config, cime, cmeps, cdeps + cism, ccs_config, cime, cmeps, cdeps Pull Requests that document the changes (include PR ids): https://github.com/ESCOMP/ctsm/pull/2539 diff --git a/doc/ChangeSum b/doc/ChangeSum index c73cb19309..7f8cdaeead 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.006 slevis 05/17/2024 Update externals to cesm2_3_beta17 + ctsm5.2.006 slevis 05/21/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev From ae5dbeae61ef39be636a0293eac5f26defc2a5c5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 21 May 2024 20:04:17 -0600 Subject: [PATCH 165/408] Add more clean routines at the end so can do a different test that shows increasing wind has more dust emission --- src/biogeochem/DUSTMod.F90 | 51 ++++++++-- .../test/DustEmis_test/test_DustEmis.pf | 94 +++++++++++++++---- 2 files changed, 121 insertions(+), 24 deletions(-) diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90 index cd60bd859f..c34f3a6e06 100644 --- a/src/biogeochem/DUSTMod.F90 +++ b/src/biogeochem/DUSTMod.F90 @@ -66,6 +66,8 @@ module DUSTMod procedure , public :: DustDryDep ! Turbulent dry deposition for dust procedure , public :: WritePatchToLog ! Write information on the given patch to the log file procedure , public :: GetPatchVars ! Get important variables on a given patch + procedure , public :: GetConstVars ! Get important constant variables + procedure , public :: Clean ! Deallocate data procedure , private :: InitAllocate procedure , private :: InitHistory procedure , private :: InitCold @@ -94,6 +96,32 @@ subroutine Init(this, bounds, NLFilename) end subroutine Init + + + !------------------------------------------------------------------------ + subroutine Clean(this) + ! + ! !ARGUMENTS: + class (dust_type) :: this + ! + ! !LOCAL VARIABLES: + !------------------------------------------------------------------------ + + deallocate(this%flx_mss_vrt_dst_patch) + deallocate(this%flx_mss_vrt_dst_tot_patch) + deallocate(this%vlc_trb_patch) + deallocate(this%vlc_trb_1_patch) + deallocate(this%vlc_trb_2_patch) + deallocate(this%vlc_trb_3_patch) + deallocate(this%vlc_trb_4_patch) + deallocate(this%mbl_bsn_fct_col) + + deallocate (ovr_src_snk_mss) + deallocate (dmt_vwr) + deallocate (stk_crc) + + end subroutine Clean + !------------------------------------------------------------------------ subroutine InitAllocate(this, bounds) ! @@ -221,19 +249,17 @@ subroutine WritePatchToLog(this, p) class(dust_type), intent(in) :: this integer , intent(in) :: p ! Patch to display - write(iulog,*) 'flx_mss_vrt_dst', this%flx_mss_vrt_dst_patch(p,:) write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p) write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p) write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p) write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p) write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p) - write(iulog,*) 'mbl_bsn_fct', this%mbl_bsn_fct_col(p) - end subroutine WritePatchToLog + end subroutine WritePatchToLog !----------------------------------------------------------------------- - subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, & - vlc_trb_2, vlc_trb_3, vlc_trb_4) + subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, & + vlc_trb_2, vlc_trb_3, vlc_trb_4) ! ! !DESCRIPTION: ! Get important variables on the given patch @@ -255,7 +281,20 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p) if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p) if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p) -end subroutine GetPatchVars + end subroutine GetPatchVars + + !----------------------------------------------------------------------- + + subroutine GetConstVars(this, SaltationFactor ) + ! + ! !DESCRIPTION: + ! Get important constant variables + ! !ARGUMENTS: + class(dust_type) , intent(in) :: this + real(r8) , intent(out) :: SaltationFactor + + SaltationFactor = tmp1 + end subroutine GetConstVars !------------------------------------------------------------------------ subroutine DustEmission (this, bounds, & diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index 08aa683964..4f8f7093d7 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -8,7 +8,7 @@ module test_DustEmis use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit use clm_varcon, only : clm_varcon_init, clm_varcon_clean - use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting + use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean use DUSTMod use shr_kind_mod , only : r8 => shr_kind_r8 use unittestFilterBuilderMod, only : filter_from_range @@ -16,7 +16,7 @@ module test_DustEmis use SoilStateType, only : soilstate_type use CanopyStateType, only : canopystate_type use TemperatureType, only : temperature_type - use WaterType, only : water_type + use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type use abortutils, only : endrun @@ -43,7 +43,7 @@ module test_DustEmis procedure :: setupEnvironment procedure :: create_atm2lnd procedure :: create_fv - procedure :: print_patch + procedure :: print_values procedure :: validate_patch end type TestDustEmis @@ -116,7 +116,9 @@ contains subroutine tearDown(this) class(TestDustEmis), intent(inout) :: this + call this%dust_emis%Clean() call this%water_factory%teardown(this%water_inst) + call SnowHydrologyClean() call unittest_subgrid_teardown() call this%atm2lnd_inst%Clean() call clm_varcon_clean() @@ -163,7 +165,7 @@ contains grc%londeg(:) = 0.0_r8 grc%area(:) = 10.0_r8 - + end subroutine setupEnvironment !----------------------------------------------------------------------- @@ -207,40 +209,43 @@ contains ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets ! fields based on inputs. Excluded inputs are given a default value class(TestDustEmis), intent(inout) :: this - real(r8), intent(in), optional :: fv(:) - real(r8), intent(in), optional :: u10(:) - real(r8), intent(in), optional :: ram1(:) + real(r8), intent(in), optional :: fv + real(r8), intent(in), optional :: u10 + real(r8), intent(in), optional :: ram1 - real(r8), parameter :: fv_default = 0.2_r8 + real(r8), parameter :: fv_default = 2.0_r8 real(r8), parameter :: u10_default = 4._r8 real(r8), parameter :: ram1_default = 200._r8 ! ------------------------------------------------------------------------ if (present(fv)) then - this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv(:) + this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv else this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default end if if (present(u10)) then - this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10(:) + this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10 else this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default end if if (present(ram1)) then - this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1(:) + this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1 else this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default end if end subroutine create_fv - subroutine print_patch(this) + subroutine print_values(this) use LandunitType, only : lun + use PatchType, only : patch class(TestDustEmis), intent(inout) :: this + real(r8) :: SaltationFactor integer :: p, c, l + call this%dust_emis%GetConstVars( SaltationFactor ) do l = bounds%begl, bounds%endl print *, 'landunit type= ', lun%itype(l) end do @@ -248,13 +253,22 @@ contains print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1) print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1) print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c) + print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c) + print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) end do do p = bounds%begp, bounds%endp + print *, 'patch type= ', patch%itype(p) + print *, 'patch weight= ', patch%wtgcell(p) + print *, 'patch active= ', patch%active(p) print *, 'tlai = ', this%canopystate_inst%tlai_patch(p) + print *, 'tsai = ', this%canopystate_inst%tsai_patch(p) + c = patch%column(p) + print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) & + / this%frictionvel_inst%fv_patch(p) call this%dust_emis%WritePatchToLog( p ) end do call endrun( "exit early") - end subroutine print_patch + end subroutine print_values !----------------------------------------------------------------------- subroutine validate_patch(this, p) @@ -284,6 +298,7 @@ contains @Test subroutine check_dust_emis(this) + ! Check dust emissions for default values class(TestDustEmis), intent(inout) :: this integer :: p real(r8) :: flx_mss_vrt_dst_tot @@ -303,15 +318,58 @@ contains call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, & vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, & vlc_trb_4=vlc_trb_4) - @assertEqual( 0.0_r8, flx_mss_vrt_dst_tot ) - @assertEqual( 3.319559266672431d-5, vlc_trb_1, tolerance=tol ) - @assertEqual( 1.699714729099379d-5, vlc_trb_2, tolerance=tol ) - @assertEqual( 9.163854318535118d-6, vlc_trb_3, tolerance=tol ) - @assertEqual( 3.614237762488103d-5, vlc_trb_4, tolerance=tol ) + @assertEqual( flx_mss_vrt_dst_tot, 2.239779135859605d-5, tolerance=tol ) + @assertEqual( vlc_trb_1, 3.407721147709135d-003, tolerance=tol ) + @assertEqual( vlc_trb_2, 4.961153753164878d-003, tolerance=tol ) + @assertEqual( vlc_trb_3, 4.980100969983446d-003, tolerance=tol ) + @assertEqual( vlc_trb_4, 4.977071672163210d-003, tolerance=tol ) end do end subroutine check_dust_emis + @Test + subroutine check_dust_emis_increasing_wind(this) + ! Check dust emissions with increasing wind + class(TestDustEmis), intent(inout) :: this + integer :: p, c + real(r8) :: flx_mss_vrt_dst_tot + real(r8) :: vlc_trb_1 + real(r8) :: vlc_trb_2 + real(r8) :: vlc_trb_3 + real(r8) :: vlc_trb_4 + real(r8) :: fv = 4.0_r8 + real(r8) :: u10 = 10._r8 + real(r8) :: total_dust0, total_dust_higher + + ! Run baseline u10 + call this%create_atm2lnd() + call this%create_fv( u10=u10, fv=fv ) + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + do p = bounds%begp, bounds%endp + call this%validate_patch(p) + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) + total_dust0 = flx_mss_vrt_dst_tot + @assertEqual( flx_mss_vrt_dst_tot, 1.971366884000767d-4, tolerance=tol ) + end do + ! Double u10 and show result is higher + call this%create_fv( u10=u10*2.0_r8, fv=fv) + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + do p = bounds%begp, bounds%endp + call this%validate_patch(p) + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) + total_dust_higher = flx_mss_vrt_dst_tot + @assertEqual( flx_mss_vrt_dst_tot, 3.288208220877217d-4, tolerance=tol ) + end do + @assertGreaterThan( total_dust_higher, total_dust0 ) + + end subroutine check_dust_emis_increasing_wind + !----------------------------------------------------------------------- end module test_DustEmis \ No newline at end of file From f2500c7c6d05db9810b0c8610a7962a2da40064d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 21 May 2024 20:16:06 -0600 Subject: [PATCH 166/408] Tighten the tolerance for numbers on the order of e-3 --- src/biogeochem/test/DustEmis_test/test_DustEmis.pf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index 4f8f7093d7..616fd776fc 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -23,7 +23,7 @@ module test_DustEmis implicit none - real(r8), parameter :: tol = 1.e-13_r8 + real(r8), parameter :: tol = 1.e-18_r8 @TestCase type, extends(TestCase) :: TestDustEmis From 1ba3473c1999073f0ecba7e4cbcf8d0b7d56fae1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 21 May 2024 21:14:01 -0600 Subject: [PATCH 167/408] Add a check that figures out the value of fv where the wind threshold won't be met and dust will be zero --- .../test/DustEmis_test/test_DustEmis.pf | 37 ++++++++++++++++--- 1 file changed, 31 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index 616fd776fc..c7e7566778 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -19,7 +19,6 @@ module test_DustEmis use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type - use abortutils, only : endrun implicit none @@ -267,7 +266,6 @@ contains / this%frictionvel_inst%fv_patch(p) call this%dust_emis%WritePatchToLog( p ) end do - call endrun( "exit early") end subroutine print_values !----------------------------------------------------------------------- @@ -327,16 +325,43 @@ contains end subroutine check_dust_emis + !----------------------------------------------------------------------- + + @Test + subroutine dust_zero_for_fixed_ratio(this) + ! Check dust emissions are zero for a no wind + class(TestDustEmis), intent(inout) :: this + integer :: p + real(r8) :: flx_mss_vrt_dst_tot + real(r8) :: fv + real(r8) :: SaltationFactor + + call this%create_atm2lnd() + call this%dust_emis%GetConstVars( SaltationFactor ) + ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps)) + fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15 + call this%create_fv( fv=fv ) + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%print_values() + do p = bounds%begp, bounds%endp + call this%validate_patch(p) + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) + @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) + end do + + end subroutine dust_zero_for_fixed_ratio + + !----------------------------------------------------------------------- + @Test subroutine check_dust_emis_increasing_wind(this) ! Check dust emissions with increasing wind class(TestDustEmis), intent(inout) :: this integer :: p, c real(r8) :: flx_mss_vrt_dst_tot - real(r8) :: vlc_trb_1 - real(r8) :: vlc_trb_2 - real(r8) :: vlc_trb_3 - real(r8) :: vlc_trb_4 real(r8) :: fv = 4.0_r8 real(r8) :: u10 = 10._r8 real(r8) :: total_dust0, total_dust_higher From 3967d77a17e4e6a02362aec42aa3feb187ba6c72 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 22 May 2024 10:28:47 -0600 Subject: [PATCH 168/408] new fates api 36 paramfile default --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6ef91bb4a0..fdfeba7719 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -481,7 +481,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.35.0.0_12pft_c240326.nc +lnd/clm2/paramdata/fates_params_api.36.0.0_12pft_c240517.nc From 5b30740bd91e421639bb46239f4d921b8e767b54 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 22 May 2024 13:37:16 -0600 Subject: [PATCH 169/408] Pin FATES external to commit a997af5. --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index cfb7beb40f..a8d53e4fdb 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/ckoven/fates -branch = luh2_nocomp_merge +hash = a997af58f38db8ffda259e11f3abcc65478a4903 required = True [externals_description] From 2a7ca01b2177b480e8897fd2921bf00a7ac9c48f Mon Sep 17 00:00:00 2001 From: loaner Date: Wed, 22 May 2024 17:43:48 -0700 Subject: [PATCH 170/408] add systemtest for potential vegetation spin up --- cime_config/SystemTests/pvt.py | 120 ++++++++++++++++++++ cime_config/SystemTests/systemtest_utils.py | 20 +++- 2 files changed, 139 insertions(+), 1 deletion(-) create mode 100644 cime_config/SystemTests/pvt.py diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py new file mode 100644 index 0000000000..e18022220d --- /dev/null +++ b/cime_config/SystemTests/pvt.py @@ -0,0 +1,120 @@ +""" +FATES land use potential vegetation spin up + transient test + +This is a FATES specific test: + +1) conduct a spinup with use_fates_potentialveg on + - write restart file + - use CLM_ACCELERATED_SPINUP? +2) run a transient landuse case with use_fates_lupft + - start from the restart file generated in (1) + +""" +from CIME.XML.standard_module_setup import * +from CIME.SystemTests.system_tests_common import SystemTestsCommon +from systemtest_utils import read_user_nl_clm +import shutil, glob, os + +logger = logging.getLogger(__name__) + +class PVT(SystemTestsCommon): + def __init_(self,case): + SystemTestsCommon.__init__(self,case) + + # Do not allow PVT to be run with certain testmods + # Should this be targeted to a specific testmod for simplicity for now? + # Technically this could be run with the luh fates_harvest_modes + casebaseid = self._case.get_value("CASEBASEID") + casebasid = casebaseid.split("-")[-1] + if casebaseid[0:10] != "FatesLUPFT": + error_message = ( + "Only call PVT with test FatesLUPFT" + ) + logger.error(error_message) + raise RuntimeError(error_message) + + # Only allow to run if resolution is 4x5 for now + # Eventually we could set this up to generate the necessary land use x pft mapping + # on the fly, although this would also require generating the land use timeseries + # regridding on the fly which is a more time consuming endevour currently + lnd_grid = self._case.get_value("LND_GRID") + if lnd_grid != "4x5": + error_message = ( + "PVT can currently only be run with 4x5 resolution" + ) + logger.error(error_message) + raise RuntimeError(error_message) + + def run_phase(self): + # ------------------------------------------------------------------- + # (1) Run FATES spin-up case in potential vegetation mode + # ------------------------------------------------------------------- + orig_case = self._case + orig_casevar = self._case.get_value("CASE") + caseroot = self._case.get_value("CASEROOT") + + # clone the main case to create spinup case + logger.info("PVT log: cloning setup") + clone_path = "{}.potveg".format(caseroot) + if os.path.exists(clone_path): + shutil.rmtree(clone_path) + logger.info("PVT log: cloning") + clone = self._case.create_clone(clone_path, keepexe=True) + logger.info("PVT log: cloning complete") + + # setup the clone case + os.chdir(clone_path) + self._set_active_case(clone) + self._setup_all() + + # Modify the spin up case to use the potential vegetation mode. + # Checks for incompatible cases and necessary mapping files are + # handled in the build case. + # use_fates_lupft should be set to true in the testmod + # save off the harvest mode for reinstating later + found, hmode = self.read_user_nl_clm('fates_harvest_mode') + logger.info("PVT log: modify user_nl_clm file for spin up run") + # TODO: remove fates_harvest_mode if found + self._append_to_user_nl_clm( + [ + "use_fates_potentialveg = .true.", + ] + ) + + stop_n_pveg = 1 + with clone: + # clone.set_value("CLM_ACCELERATED_SPINUP", "on") + clone.set_value("STOP_N", stop_n_pveg) + + # Run the spin up case + # As per SSP test: + # "No history files expected, set suffix=None to avoid compare error" + logger.info("PVT log: starting spin-up run") + dout_sr = clone.get_value("DOUT_S_ROOT") + self._skip_pnl = False + self.run_indv(suffix=None, st_archive=True) + + # ------------------------------------------------------------------- + # (2) Run FATES transient case using restart file from spin-up + # ------------------------------------------------------------------- + os.chdir(caseroot) + self._set_active_case(orig_case) + + # logger.info("PVT log: modify user_nl_clm file for transient run") + # self._append_to_user_nl_clm( + # [ + # "use_fates_potentialveg = .true.", + # ] + # ) + + + self._case.set_value("CLM_ACCELERATED_SPINUP", "off") + self._case.set_value("RUN_TYPE", "hybrid") + self._case.set_value("GET_REFCASE", False) + self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar)) + self._case.set_value("RUN_REFDATE", "1700-01-01") + self._case.set_value("DOUT_S", False) + self._case.flush() + + # do the restart run (short term archiving is off) + self.run_indv() diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index c5ac986abd..8447934797 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -2,7 +2,7 @@ Reduce code duplication by putting reused functions here. """ -import os, subprocess +import os, subprocess, re def cmds_to_setup_conda(caseroot): @@ -84,3 +84,21 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): except: print(f"ERROR trying to run {tool_name}.") raise + +def read_user_nl_clm(self,namelist_option): + user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm") + with open(user_nl_clm_path) as f: + user_nl_clm_text = f.read() + reg = fr'{namelist_option}\s*=\s*([^\n]+)' + find_out = re.findall(reg, user_nl_clm_text) + # This could be more robust + if len(find_out) == 0: + return 0, False + elif len(find_out) > 1: + error_message = ( + "ERROR: read_user_nl_clm: namelist option is set more than once" + ) + # logger.error(error_message) + raise RuntimeError(error_message) + else: + return find_out[0], True From fc1400f5154f86a6d3346aebce677fff506400e8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 22 May 2024 21:31:43 -0600 Subject: [PATCH 171/408] Add a check that when fsno is 1 dust emission is zeroed --- .../test/DustEmis_test/test_DustEmis.pf | 76 ++++++++++++------- 1 file changed, 50 insertions(+), 26 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index c7e7566778..b9b00ae4fa 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -325,34 +325,58 @@ contains end subroutine check_dust_emis - !----------------------------------------------------------------------- + !----------------------------------------------------------------------- + + @Test + subroutine dust_zero_for_fixed_ratio(this) + ! Check dust emissions are zero for a no wind + class(TestDustEmis), intent(inout) :: this + integer :: p + real(r8) :: flx_mss_vrt_dst_tot + real(r8) :: fv + real(r8) :: SaltationFactor + + call this%create_atm2lnd() + call this%dust_emis%GetConstVars( SaltationFactor ) + ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps)) + fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15 + call this%create_fv( fv=fv ) + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%print_values() + do p = bounds%begp, bounds%endp + call this%validate_patch(p) + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) + @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) + end do + + end subroutine dust_zero_for_fixed_ratio - @Test - subroutine dust_zero_for_fixed_ratio(this) - ! Check dust emissions are zero for a no wind - class(TestDustEmis), intent(inout) :: this - integer :: p - real(r8) :: flx_mss_vrt_dst_tot - real(r8) :: fv - real(r8) :: SaltationFactor - - call this%create_atm2lnd() - call this%dust_emis%GetConstVars( SaltationFactor ) - ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps)) - fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15 - call this%create_fv( fv=fv ) - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) - call this%print_values() - do p = bounds%begp, bounds%endp - call this%validate_patch(p) - call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) - @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) - end do + !----------------------------------------------------------------------- - end subroutine dust_zero_for_fixed_ratio + @Test + subroutine dust_zero_when_fsno_one(this) + ! Check dust emissions are zero for a no wind + class(TestDustEmis), intent(inout) :: this + integer :: p + real(r8) :: flx_mss_vrt_dst_tot + + call this%create_atm2lnd() + this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + call this%create_fv( ) + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + do p = bounds%begp, bounds%endp + call this%validate_patch(p) + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) + @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) + end do + + end subroutine dust_zero_when_fsno_one !----------------------------------------------------------------------- From ebdd3267f099fe995c379543a932dfc69b14b969 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 22 May 2024 21:54:28 -0600 Subject: [PATCH 172/408] Add a test that tlai set to 0.3 has zero dust emission --- .../test/DustEmis_test/test_DustEmis.pf | 26 ++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index b9b00ae4fa..764947836d 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -358,7 +358,7 @@ contains @Test subroutine dust_zero_when_fsno_one(this) - ! Check dust emissions are zero for a no wind + ! Check dust emissions are zero when snow fraction is identically 1 class(TestDustEmis), intent(inout) :: this integer :: p real(r8) :: flx_mss_vrt_dst_tot @@ -380,6 +380,30 @@ contains !----------------------------------------------------------------------- + @Test + subroutine dust_zero_when_tlai_high(this) + ! Check dust emissions are zero when LAI is high enough + class(TestDustEmis), intent(inout) :: this + integer :: p + real(r8) :: flx_mss_vrt_dst_tot + + call this%create_atm2lnd() + call this%create_fv( ) + this%canopystate_inst%tlai_patch(:) = 0.3_r8 + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + do p = bounds%begp, bounds%endp + call this%validate_patch(p) + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) + @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) + end do + + end subroutine dust_zero_when_tlai_high + + !----------------------------------------------------------------------- + @Test subroutine check_dust_emis_increasing_wind(this) ! Check dust emissions with increasing wind From 171c981240b2b2c7f614813401f99795fb8c33dc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 22 May 2024 22:58:36 -0600 Subject: [PATCH 173/408] Add test that dust emissions are zero for all non-veg landunits --- .../test/DustEmis_test/test_DustEmis.pf | 29 ++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index 764947836d..a76c724480 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -371,7 +371,6 @@ contains this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) do p = bounds%begp, bounds%endp - call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) end do @@ -380,6 +379,34 @@ contains !----------------------------------------------------------------------- + @Test + subroutine dust_zero_non_veg_lu(this) + ! Check dust emissions are zero for non-veg landunits + use landunit_varcon, only: istcrop, max_lunit + use LandunitType, only : lun + class(TestDustEmis), intent(inout) :: this + integer :: p, l + real(r8) :: flx_mss_vrt_dst_tot + + call this%create_atm2lnd() + call this%create_fv( ) + ! Set the lanunit type for + do l = istcrop+1, max_lunit + lun%itype(bounds%begl:bounds%endl) = l + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + do p = bounds%begp, bounds%endp + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) + @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) + end do + end do + + end subroutine dust_zero_non_veg_lu + + !----------------------------------------------------------------------- + @Test subroutine dust_zero_when_tlai_high(this) ! Check dust emissions are zero when LAI is high enough From b7cf13f6dcfd6c975de294ef90122bb4e2fc0d3e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 23 May 2024 13:47:07 -0700 Subject: [PATCH 174/408] add PVT system test to the config_test xml file --- cime_config/config_tests.xml | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index c0b6afed9d..8a4388c664 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -123,6 +123,18 @@ This defines various CTSM-specific system tests $STOP_N + + FATES potential vegetarion spin-up + land use transient run test + 1 + ndays + startup + 4 + FALSE + FALSE + $STOP_OPTION + $STOP_N + + Generate prescribed maturity requirements, then test with them 1 From 8e35d80baf507185ef0dac47a4adee4bf975d47e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 23 May 2024 14:29:02 -0600 Subject: [PATCH 175/408] add test mode for use_fates_lupft --- .../testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods | 1 + cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm | 1 + 2 files changed, 2 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods new file mode 100644 index 0000000000..4c7aa0f2b4 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/include_user_mods @@ -0,0 +1 @@ +../Fates diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm new file mode 100644 index 0000000000..10044848a0 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/user_nl_clm @@ -0,0 +1 @@ +use_fates_lupft = .true. From a14ab0838951426162b7af5bb1a1a977cf6353cf Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 23 May 2024 14:53:35 -0600 Subject: [PATCH 176/408] Update cmeps to cmeps0.14.63 in Externals.cfg --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 8ef524bf24..70d103a94b 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -48,7 +48,7 @@ tag = cime6.0.238_httpsbranch01 required = True [cmeps] -tag = cmeps0.14.60 +tag = cmeps0.14.63 protocol = git repo_url = https://github.com/ESCOMP/CMEPS.git local_path = components/cmeps From af5451b7e37d53d1192fb87315d01fb16b527ba1 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 23 May 2024 14:39:45 -0700 Subject: [PATCH 177/408] remove tabs and correct whitespace --- bld/CLMBuildNamelist.pm | 58 ++++++++++++++++++++--------------------- 1 file changed, 29 insertions(+), 29 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index acdad5c5cc..b17a245715 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4520,22 +4520,22 @@ sub setup_logic_fates { "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" ); foreach my $var ( @list ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_potentialveg', 'use_fates'=>$nl_flags->{'use_fates'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), - 'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'), - 'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), - 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'}, - 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), - 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_potentialveg', 'use_fates'=>$nl_flags->{'use_fates'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_lupft', 'use_fates'=>$nl_flags->{'use_fates'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), + 'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'), + 'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), + 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_fixed_biogeog', 'use_fates'=>$nl_flags->{'use_fates'}, + 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), + 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); my $suplnitro = $nl->get_value('suplnitro'); my $parteh_mode = $nl->get_value('fates_parteh_mode'); @@ -4564,8 +4564,8 @@ sub setup_logic_fates { # fates landuse can't be on with FATES SP mode is active if ( &value_is_true($nl->get_value('use_fates_luh')) ) { - $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true'); - } + $log->fatal_error('use_fates_luh can NOT be true when use_fates_sp is true'); + } # hydro isn't currently supported to work when FATES SP mode is active if (&value_is_true( $nl->get_value('use_fates_planthydro') )) { @@ -4608,7 +4608,7 @@ sub setup_logic_fates { if ( ! &value_is_true($nl->get_value($var)) ) { $var = "fluh_timeseries"; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, - 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); + 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" ); @@ -4616,21 +4616,21 @@ sub setup_logic_fates { $log->fatal_error("$var does NOT point to a valid filename" ); } } - } + } $var = "use_fates_fixed_biogeog"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { - $var = "flandusepftdat"; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); - my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); - if ( ! defined($nl->get_value($var)) ) { - $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" ); - } elsif ( ! -f "$fname" ) { - $log->fatal_error("$var does NOT point to a valid filename" ); - } - } - } + $var = "flandusepftdat"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, + 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + if ( ! defined($nl->get_value($var)) ) { + $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$var does NOT point to a valid filename" ); + } + } + } } } # check that fates landuse is on and harvest mode is off when potential veg switch is true From 470b279dcc7c2563b719bbbbf67a696cad7f6481 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 23 May 2024 15:55:13 -0600 Subject: [PATCH 178/408] Add a fail test for bad dust mobilization --- src/biogeochem/DUSTMod.F90 | 6 ++++-- .../test/DustEmis_test/test_DustEmis.pf | 21 +++++++++++++++++++ 2 files changed, 25 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DUSTMod.F90 index c34f3a6e06..8de7811aa1 100644 --- a/src/biogeochem/DUSTMod.F90 +++ b/src/biogeochem/DUSTMod.F90 @@ -445,8 +445,10 @@ subroutine DustEmission (this, bounds, & do fp = 1,num_nolakep p = filter_nolakep(fp) if (lnd_frc_mbl(p)>1.0_r8 .or. lnd_frc_mbl(p)<0.0_r8) then - write(iulog,*)'Error dstmbl: pft= ',p,' lnd_frc_mbl(p)= ',lnd_frc_mbl(p) - call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__)) + write(iulog,*)'Error dstmbl: pft= ',p,' lnd_frc_mbl(p)= ',lnd_frc_mbl(p), & + errMsg(sourcefile, __LINE__) + call endrun("Bad value for dust mobilization fraction") + return end if end do diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index a76c724480..a9b72a6e64 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -407,6 +407,27 @@ contains !----------------------------------------------------------------------- + @Test + subroutine aborts_on_bad_dust_mobility(this) + ! Check dust abort when dust mobility is bad + class(TestDustEmis), intent(inout) :: this + real(r8) :: flx_mss_vrt_dst_tot + character(100) :: expected_msg + + call this%create_atm2lnd() + call this%create_fv( ) + ! Dust should abort with an error on dust mobility when snow fraction greater than 1 + this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + 1.e-15_r8 + call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & + this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & + this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + expected_msg = "ABORTED: Bad value for dust mobilization fraction" + @assertExceptionRaised(expected_msg) + + end subroutine aborts_on_bad_dust_mobility + + !----------------------------------------------------------------------- + @Test subroutine dust_zero_when_tlai_high(this) ! Check dust emissions are zero when LAI is high enough From 07918b515c63183135ae85cb43919486b7153ded Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 23 May 2024 16:08:44 -0600 Subject: [PATCH 179/408] Replace DUSTMod with DustEmisZender2003 with VS code --- src/biogeochem/CMakeLists.txt | 2 +- src/biogeochem/CNVegStateType.F90 | 2 +- src/biogeochem/{DUSTMod.F90 => DustEmisZender2003.F90} | 4 ++-- src/biogeochem/test/DustEmis_test/test_DustEmis.pf | 2 +- src/main/clm_driver.F90 | 2 +- src/main/clm_instMod.F90 | 2 +- src/main/lnd2atmMod.F90 | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) rename src/biogeochem/{DUSTMod.F90 => DustEmisZender2003.F90} (99%) diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt index 0f46dc665d..0dd06ac09e 100644 --- a/src/biogeochem/CMakeLists.txt +++ b/src/biogeochem/CMakeLists.txt @@ -6,7 +6,7 @@ list(APPEND clm_sources CNPhenologyMod.F90 CNSpeciesMod.F90 CNDVType.F90 - DUSTMod.F90 + DustEmisZender2003.F90 CropReprPoolsMod.F90 CropType.F90 CNVegStateType.F90 diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index c286c0344f..98c1a6ce3a 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -519,7 +519,7 @@ subroutine InitCold(this, bounds) ! -------------------------------------------------------------------- ! Initialize terms needed for dust model - ! TODO - move these terms to DUSTMod module variables + ! TODO - move these terms to DustEmisZender2003 module variables ! -------------------------------------------------------------------- do c = bounds%begc, bounds%endc diff --git a/src/biogeochem/DUSTMod.F90 b/src/biogeochem/DustEmisZender2003.F90 similarity index 99% rename from src/biogeochem/DUSTMod.F90 rename to src/biogeochem/DustEmisZender2003.F90 index 8de7811aa1..22bbbe0742 100644 --- a/src/biogeochem/DUSTMod.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -1,4 +1,4 @@ -module DUSTMod +module DustEmisZender2003 !----------------------------------------------------------------------- ! !DESCRIPTION: @@ -1033,4 +1033,4 @@ subroutine InitDustVars(this, bounds) end subroutine InitDustVars -end module DUSTMod +end module DustEmisZender2003 diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index a9b72a6e64..ded09f7919 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -9,7 +9,7 @@ module test_DustEmis use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit use clm_varcon, only : clm_varcon_init, clm_varcon_clean use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean - use DUSTMod + use DustEmisZender2003 use shr_kind_mod , only : r8 => shr_kind_r8 use unittestFilterBuilderMod, only : filter_from_range use atm2lndType, only : atm2lnd_type, atm2lnd_params_type diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 00a98e61b4..f9db72e0ed 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -62,7 +62,7 @@ module clm_driver use ndepStreamMod , only : ndep_interp use cropcalStreamMod , only : cropcal_advance, cropcal_interp use ch4Mod , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check - use DUSTMod , only : DustDryDep, DustEmission + use DustEmisZender2003 , only : DustDryDep, DustEmission use VOCEmissionMod , only : VOCEmission ! use filterMod , only : setFilters diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index a24e05b27c..f11805a755 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -45,7 +45,7 @@ module clm_instMod use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use CropType , only : crop_type use DryDepVelocity , only : drydepvel_type - use DUSTMod , only : dust_type + use DustEmisZender2003 , only : dust_type use EnergyFluxType , only : energyflux_type use FrictionVelocityMod , only : frictionvel_type use GlacierSurfaceMassBalanceMod , only : glacier_smb_type diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90 index 1cda0cff91..b91feaabf9 100644 --- a/src/main/lnd2atmMod.F90 +++ b/src/main/lnd2atmMod.F90 @@ -20,7 +20,7 @@ module lnd2atmMod use lnd2atmType , only : lnd2atm_type use atm2lndType , only : atm2lnd_type use ch4Mod , only : ch4_type - use DUSTMod , only : dust_type + use DustEmisZender2003 , only : dust_type use DryDepVelocity , only : drydepvel_type use VocEmissionMod , only : vocemis_type use CNFireEmissionsMod , only : fireemis_type From 00d23e9adb4139847dc5f855ff4ce43bc845b41e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 23 May 2024 16:48:55 -0600 Subject: [PATCH 180/408] correct add default for fluh and flandusepftdat --- bld/CLMBuildNamelist.pm | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index b17a245715..d952e7fe89 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4607,8 +4607,8 @@ sub setup_logic_fates { if ( defined($nl->get_value($var)) ) { if ( ! &value_is_true($nl->get_value($var)) ) { $var = "fluh_timeseries"; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, - 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, + 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" ); @@ -4620,17 +4620,17 @@ sub setup_logic_fates { $var = "use_fates_fixed_biogeog"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { - $var = "flandusepftdat"; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, - 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); - my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); - if ( ! defined($nl->get_value($var)) ) { - $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" ); - } elsif ( ! -f "$fname" ) { - $log->fatal_error("$var does NOT point to a valid filename" ); - } - } - } + $var = "flandusepftdat"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, + 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + if ( ! defined($nl->get_value($var)) ) { + $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$var does NOT point to a valid filename" ); + } + } + } } } # check that fates landuse is on and harvest mode is off when potential veg switch is true From 2ac13bcb7aeec5a1772635edfe7c0f99be9c532d Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 23 May 2024 17:39:57 -0600 Subject: [PATCH 181/408] correct typos causing RunTimeError to be missed --- cime_config/SystemTests/pvt.py | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py index e18022220d..c45c514f39 100644 --- a/cime_config/SystemTests/pvt.py +++ b/cime_config/SystemTests/pvt.py @@ -18,20 +18,17 @@ logger = logging.getLogger(__name__) class PVT(SystemTestsCommon): - def __init_(self,case): + def __init__(self,case): SystemTestsCommon.__init__(self,case) # Do not allow PVT to be run with certain testmods # Should this be targeted to a specific testmod for simplicity for now? # Technically this could be run with the luh fates_harvest_modes + error_message = None casebaseid = self._case.get_value("CASEBASEID") - casebasid = casebaseid.split("-")[-1] + casebaseid = casebaseid.split("-")[-1] if casebaseid[0:10] != "FatesLUPFT": - error_message = ( - "Only call PVT with test FatesLUPFT" - ) - logger.error(error_message) - raise RuntimeError(error_message) + error_message = (f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected.") # Only allow to run if resolution is 4x5 for now # Eventually we could set this up to generate the necessary land use x pft mapping @@ -39,12 +36,11 @@ def __init_(self,case): # regridding on the fly which is a more time consuming endevour currently lnd_grid = self._case.get_value("LND_GRID") if lnd_grid != "4x5": - error_message = ( - "PVT can currently only be run with 4x5 resolution" - ) + error_message = (f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected.") + + if error_message is not None: logger.error(error_message) raise RuntimeError(error_message) - def run_phase(self): # ------------------------------------------------------------------- # (1) Run FATES spin-up case in potential vegetation mode From f4ff559c831533ab9c901d1f44e5744740a8f302 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 23 May 2024 16:45:42 -0700 Subject: [PATCH 182/408] remove tabs again --- bld/CLMBuildNamelist.pm | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index d952e7fe89..0fb7ba9692 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4608,7 +4608,7 @@ sub setup_logic_fates { if ( ! &value_is_true($nl->get_value($var)) ) { $var = "fluh_timeseries"; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, - 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_luh is set and use_fates_potentialveg is false" ); @@ -4620,17 +4620,17 @@ sub setup_logic_fates { $var = "use_fates_fixed_biogeog"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { - $var = "flandusepftdat"; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, - 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); - my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); - if ( ! defined($nl->get_value($var)) ) { - $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" ); - } elsif ( ! -f "$fname" ) { - $log->fatal_error("$var does NOT point to a valid filename" ); - } - } - } + $var = "flandusepftdat"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, + 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, nofail=>1 ); + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); + if ( ! defined($nl->get_value($var)) ) { + $log->fatal_error("$var is required when use_fates_luh and use_fates_fixed_biogeog is set" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$var does NOT point to a valid filename" ); + } + } + } } } # check that fates landuse is on and harvest mode is off when potential veg switch is true From dd5671a824854ab270687cf669ee96656cad2fae Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Fri, 24 May 2024 09:56:34 -0600 Subject: [PATCH 183/408] Update streams file name and global attributes --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 7f9e3de6b4..4b8b7d3571 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1871,15 +1871,15 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_0.9x1.25_simyr1849-2106_c200605.nc /glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc +>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc lnd/clm2/urbandata/CTSM52_tbuildmax_OlesonFeddema_2020_0.9x1.25_simyr1849-2106_c200605.nc /glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc +>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc lnd/clm2/urbandata/CLM50_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc /glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_0.9x1.25_simyr1849-2106_c20230621.nc +>/glade/work/xinchang/02_Explicit_AC_Adoption/02_data_present_day/CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc lnd/clm2/urbandata/CLM45_tbuildmax_Oleson_2016_0.9x1.25_simyr1849-2106_c160923.nc From 8cc00387d6bb131f90ec08334c8e7b132d4388cf Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 11:22:27 -0600 Subject: [PATCH 184/408] Add a unit test shell for SoilStateInitTimeConsst --- src/biogeophys/CMakeLists.txt | 1 + src/biogeophys/test/CMakeLists.txt | 1 + .../CMakeLists.txt | 6 ++++ .../test_dust_soil_clay_functions.pf | 29 +++++++++++++++++++ 4 files changed, 37 insertions(+) create mode 100644 src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt create mode 100644 src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf diff --git a/src/biogeophys/CMakeLists.txt b/src/biogeophys/CMakeLists.txt index 86edcca9f9..07b88b07bf 100644 --- a/src/biogeophys/CMakeLists.txt +++ b/src/biogeophys/CMakeLists.txt @@ -25,6 +25,7 @@ list(APPEND clm_sources SoilHydrologyType.F90 SoilStateType.F90 SoilWaterRetentionCurveMod.F90 + SoilStateInitTimeConstMod.F90 SolarAbsorbedType.F90 PhotosynthesisMod.F90 SurfaceAlbedoType.F90 diff --git a/src/biogeophys/test/CMakeLists.txt b/src/biogeophys/test/CMakeLists.txt index 5c15858210..7a0a1e8fbb 100644 --- a/src/biogeophys/test/CMakeLists.txt +++ b/src/biogeophys/test/CMakeLists.txt @@ -5,6 +5,7 @@ add_subdirectory(HillslopeHydrology_test) add_subdirectory(SnowHydrology_test) add_subdirectory(Photosynthesis_test) add_subdirectory(Balance_test) +add_subdirectory(SoilStateInitTimeConst_test) add_subdirectory(TotalWaterAndHeat_test) add_subdirectory(Wateratm2lnd_test) add_subdirectory(WaterTracerContainerType_test) diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt b/src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt new file mode 100644 index 0000000000..df58da9875 --- /dev/null +++ b/src/biogeophys/test/SoilStateInitTimeConst_test/CMakeLists.txt @@ -0,0 +1,6 @@ +set (pfunit_sources + test_dust_soil_clay_functions.pf) + +add_pfunit_ctest(SoilStateInit + TEST_SOURCES "${pfunit_sources}" + LINK_LIBRARIES clm csm_share) diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf new file mode 100644 index 0000000000..d3d9fc7e7f --- /dev/null +++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf @@ -0,0 +1,29 @@ +module test_dust_soil_clay_functions + + ! Tests of SoilStateInitTimeConst functions for dust emission in regard to clay content + + use funit + use SoilStateInitTimeConstMod + use shr_kind_mod , only : r8 => shr_kind_r8 + + implicit none + + @TestCase + type, extends(TestCase) :: TestDustEmisSoilFunctions + contains + procedure :: setUp + procedure :: tearDown + end type TestDustEmisSoilFunctions + +contains + + subroutine setUp(this) + class(TestDustEmisSoilFunctions), intent(inout) :: this + end subroutine setUp + + subroutine tearDown(this) + class(TestDustEmisSoilFunctions), intent(inout) :: this + + end subroutine tearDown + +end module test_dust_soil_clay_functions From 679ececd1336838b9bcb6e51f900da94fbe91957 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 12:04:33 -0600 Subject: [PATCH 185/408] Add functions needed by dust emissions for soil characteristics --- src/biogeophys/SoilStateInitTimeConstMod.F90 | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90 index 9122b56890..46759cb90b 100644 --- a/src/biogeophys/SoilStateInitTimeConstMod.F90 +++ b/src/biogeophys/SoilStateInitTimeConstMod.F90 @@ -715,4 +715,24 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename) end subroutine SoilStateInitTimeConst + !------------------------------------------------------------------------------ + + real(r8) function ThresholdSoilMoist( clay ) + ! Calculate the threshold soil moisture needed for dust emission, based on clay content + real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%) + + ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 + end function ThresholdSoilMoist + + !------------------------------------------------------------------------------ + + real(r8) function MassFracClay( clay ) + ! Calculate the mass fraction of clay needed for dust emission, based on clay content + real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%) + + MassFracClay = min(clay * 0.01_r8, 0.20_r8) + end function MassFracClay + + !------------------------------------------------------------------------------ + end module SoilStateInitTimeConstMod From 56048af762b22a98dab029a3d5b72f7499e7e058 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 13:26:42 -0600 Subject: [PATCH 186/408] Fill out functions and add unit testing for them, the failure test fails now --- src/biogeophys/SoilStateInitTimeConstMod.F90 | 20 ++++++- .../test_dust_soil_clay_functions.pf | 55 ++++++++++++++++++- 2 files changed, 71 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90 index 46759cb90b..a71a7285aa 100644 --- a/src/biogeophys/SoilStateInitTimeConstMod.F90 +++ b/src/biogeophys/SoilStateInitTimeConstMod.F90 @@ -17,6 +17,11 @@ module SoilStateInitTimeConstMod ! !PUBLIC MEMBER FUNCTIONS: public :: SoilStateInitTimeConst public :: readParams + + ! PRIVATE FUNCTIONS MADE PUBLIC Just for unit-testing: + public :: ThresholdSoilMoist + public :: ThresholdSoilMoistKok2014 + public :: MassFracClay ! ! !PRIVATE MEMBER FUNCTIONS: private :: ReadNL @@ -719,10 +724,19 @@ end subroutine SoilStateInitTimeConst real(r8) function ThresholdSoilMoist( clay ) ! Calculate the threshold soil moisture needed for dust emission, based on clay content - real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%) + real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%) ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 - end function ThresholdSoilMoist + end function ThresholdSoilMoist + + !------------------------------------------------------------------------------ + + real(r8) function ThresholdSoilMoistKok2014( clay ) + ! Calculate the threshold soil moisture needed for dust emission, based on clay content + real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%) + + ThresholdSoilMoistKok2014 = 0.01_r8*(0.17_r8*clay + 0.0014_r8*clay*clay) + end function ThresholdSoilMoistKok2014 !------------------------------------------------------------------------------ @@ -731,7 +745,7 @@ real(r8) function MassFracClay( clay ) real(r8), intent(IN) :: clay ! Fraction of lay in the soil (%) MassFracClay = min(clay * 0.01_r8, 0.20_r8) - end function MassFracClay + end function MassFracClay !------------------------------------------------------------------------------ diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf index d3d9fc7e7f..e612195aff 100644 --- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf +++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf @@ -15,6 +15,8 @@ module test_dust_soil_clay_functions procedure :: tearDown end type TestDustEmisSoilFunctions + real(r8), parameter :: tol = 1.e-15_r8 + contains subroutine setUp(this) @@ -23,7 +25,58 @@ contains subroutine tearDown(this) class(TestDustEmisSoilFunctions), intent(inout) :: this - end subroutine tearDown + @Test + subroutine TestClayOutOfRangeThreshold(this) + class(TestDustEmisSoilFunctions), intent(inout) :: this + real(r8) :: value + character(len=100) :: expected_msg + + value = ThresholdSoilMoist( -1.e-15_r8 ) + expected_msg = "ABORTED: Percent clay is less than zero" + @assertExceptionRaised(expected_msg) + value = ThresholdSoilMoist( 1._r8 + 1.-15_r8 ) + expected_msg = "ABORTED: Percent clay is greater than 100" + @assertExceptionRaised(expected_msg) + end subroutine TestClayOutOfRangeThreshold + + @Test + subroutine TestThresholdValues(this) + class(TestDustEmisSoilFunctions), intent(inout) :: this + real(r8) :: value + + value = ThresholdSoilMoist( 0.0_r8 ) + @assertEqual( value, 0.17_r8, tolerance=tol ) + value = ThresholdSoilMoist( 100.0_r8 ) + @assertEqual( value, 0.31_r8, tolerance=tol ) + end subroutine TestThresholdValues + + @Test + subroutine TestThresholdKok2014Values(this) + class(TestDustEmisSoilFunctions), intent(inout) :: this + real(r8) :: value + + value = ThresholdSoilMoistKok2014( 0.0_r8 ) + @assertEqual( value, 0.0_r8, tolerance=tol ) + value = ThresholdSoilMoistKok2014( 100.0_r8 ) + @assertEqual( value, 0.31_r8, tolerance=tol ) + value = ThresholdSoilMoistKok2014( 1.0_r8 ) + @assertEqual( value, 0.001714_r8, tolerance=tol ) + end subroutine TestThresholdKok2014Values + + @Test + subroutine TestClayMassFracValues(this) + class(TestDustEmisSoilFunctions), intent(inout) :: this + real(r8) :: value + + value = MassFracClay( 0.0_r8 ) + @assertEqual( value, 0.20_r8, tolerance=tol ) + value = MassFracClay( 20.0_r8 ) + @assertEqual( value, 0.20_r8, tolerance=tol ) + value = MassFracClay( 100.0_r8 ) + @assertEqual( value, 1.0_r8, tolerance=tol ) + + end subroutine TestClayMassFracValues + end module test_dust_soil_clay_functions From fc53412192c7fea8980b99fbc93324a10c17ba44 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 24 May 2024 13:49:32 -0600 Subject: [PATCH 187/408] Fix for the LILACSMOKE test to pass --- cime_config/SystemTests/lilacsmoke.py | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/SystemTests/lilacsmoke.py b/cime_config/SystemTests/lilacsmoke.py index 66a94068da..366d5d1176 100644 --- a/cime_config/SystemTests/lilacsmoke.py +++ b/cime_config/SystemTests/lilacsmoke.py @@ -407,6 +407,7 @@ def run_phase(self): # case.get_mpirun_cmd creates a command that runs the executable given by # case.run_exe. So it's important that (elsewhere in this test script) we create a # link pointing from that to the atm_driver.exe executable. + self._case.load_env(reset=True) lid = new_lid() os.environ["OMP_NUM_THREADS"] = str(self._case.thread_count) cmd = self._case.get_mpirun_cmd(allow_unresolved_envvars=False) From de8c0a33315693c9dc66b267bd255e703f9010c0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 24 May 2024 13:53:13 -0600 Subject: [PATCH 188/408] update what new utility function returns as output --- cime_config/SystemTests/systemtest_utils.py | 41 ++++++++++++--------- 1 file changed, 23 insertions(+), 18 deletions(-) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 8447934797..9470799a27 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -2,7 +2,7 @@ Reduce code duplication by putting reused functions here. """ -import os, subprocess, re +import os, subprocess, re, glob def cmds_to_setup_conda(caseroot): @@ -84,21 +84,26 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): except: print(f"ERROR trying to run {tool_name}.") raise +""" +Read a user_nl file and return the namelist option if found +""" +def find_user_nl_option(caseroot, component, namelist_option): + + # This is a copy of the CIME _get_list_of_user_nl_files + # which could be used if this moved into the CIME project + file_pattern = "user_nl_" + component + "*" + file_list = glob.glob(os.path.join(caseroot, file_pattern)) + + # Check that there is at least one file + if len(file_list) == 0: + raise RuntimeError("No user_nl files found for component " + component) -def read_user_nl_clm(self,namelist_option): - user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm") - with open(user_nl_clm_path) as f: - user_nl_clm_text = f.read() - reg = fr'{namelist_option}\s*=\s*([^\n]+)' - find_out = re.findall(reg, user_nl_clm_text) - # This could be more robust - if len(find_out) == 0: - return 0, False - elif len(find_out) > 1: - error_message = ( - "ERROR: read_user_nl_clm: namelist option is set more than once" - ) - # logger.error(error_message) - raise RuntimeError(error_message) - else: - return find_out[0], True + # Read through the file list and look for a match and return the whole entry + output = {} + for one_file in file_list: + with open(one_file, "r") as user_nl_file: + user_nl_text = user_nl_file.read() + reg = fr'{namelist_option}.*?(?=,|\n)' + find_out = re.findall(reg, user_nl_text) + output[one_file] = find_out + return output From b7a0adfa71fa088718df13411e5c04aa83b8add7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 24 May 2024 13:54:29 -0600 Subject: [PATCH 189/408] Rm expected fails associated w https://github.com/ESCOMP/CMEPS/pull/460 --- cime_config/testdefs/ExpectedTestFails.xml | 85 ---------------------- 1 file changed, 85 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index a29e55cc9e..ef6a00993f 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,91 +44,6 @@ - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - - - FAIL - https://github.com/ESCOMP/CMEPS/pull/460 - - - FAIL From 80bfb889db04d56d1b01e24c8102999ef3fe7cf7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 13:58:25 -0600 Subject: [PATCH 190/408] Get the tests passing --- src/biogeophys/SoilStateInitTimeConstMod.F90 | 7 +++++++ .../test_dust_soil_clay_functions.pf | 9 ++++----- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90 index a71a7285aa..3b71efe103 100644 --- a/src/biogeophys/SoilStateInitTimeConstMod.F90 +++ b/src/biogeophys/SoilStateInitTimeConstMod.F90 @@ -724,8 +724,15 @@ end subroutine SoilStateInitTimeConst real(r8) function ThresholdSoilMoist( clay ) ! Calculate the threshold soil moisture needed for dust emission, based on clay content + use abortUtils , only : endrun + use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=) real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%) + if ( clay < 0.0_r8 .or. clay > 100.0_r8 )then + ThresholdSoilMoist = nan + call endrun( 'Clay fraction is out of bounds (0 to 100)') + return + end if ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 end function ThresholdSoilMoist diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf index e612195aff..f753bf1729 100644 --- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf +++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf @@ -34,10 +34,9 @@ contains character(len=100) :: expected_msg value = ThresholdSoilMoist( -1.e-15_r8 ) - expected_msg = "ABORTED: Percent clay is less than zero" + expected_msg = "ABORTED: Clay fraction is out of bounds (0 to 100)" @assertExceptionRaised(expected_msg) value = ThresholdSoilMoist( 1._r8 + 1.-15_r8 ) - expected_msg = "ABORTED: Percent clay is greater than 100" @assertExceptionRaised(expected_msg) end subroutine TestClayOutOfRangeThreshold @@ -71,11 +70,11 @@ contains real(r8) :: value value = MassFracClay( 0.0_r8 ) - @assertEqual( value, 0.20_r8, tolerance=tol ) + @assertEqual( value, 0.0_r8, tolerance=tol ) value = MassFracClay( 20.0_r8 ) @assertEqual( value, 0.20_r8, tolerance=tol ) - value = MassFracClay( 100.0_r8 ) - @assertEqual( value, 1.0_r8, tolerance=tol ) + value = MassFracClay( 25.0_r8 ) + @assertEqual( value, 0.20_r8, tolerance=tol ) end subroutine TestClayMassFracValues From cd04c06c06e1399c262c970180f291d583eaf72b Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 24 May 2024 14:06:36 -0600 Subject: [PATCH 191/408] change dictionary to ordered dict --- cime_config/SystemTests/systemtest_utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 9470799a27..2591ac4223 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -3,6 +3,7 @@ """ import os, subprocess, re, glob +from collections import OrderedDict def cmds_to_setup_conda(caseroot): @@ -99,7 +100,7 @@ def find_user_nl_option(caseroot, component, namelist_option): raise RuntimeError("No user_nl files found for component " + component) # Read through the file list and look for a match and return the whole entry - output = {} + output = OrderedDict() for one_file in file_list: with open(one_file, "r") as user_nl_file: user_nl_text = user_nl_file.read() From 9fc13521793969bd15596a9194353c9dda168349 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 24 May 2024 14:28:48 -0600 Subject: [PATCH 192/408] Correct a testname in ExpectedTestFails.xml --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index ef6a00993f..23e481222b 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -51,7 +51,7 @@ - + FAIL #2542 From bec3291f4bae382f3f89c2c178da7365bc0e4a4f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 14:31:45 -0600 Subject: [PATCH 193/408] Get unit tests passing again --- src/biogeochem/test/DustEmis_test/test_DustEmis.pf | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf index ded09f7919..ff154f3126 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmis.pf @@ -19,6 +19,7 @@ module test_DustEmis use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type + use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay implicit none @@ -155,8 +156,8 @@ contains ! considered bedrock col%nbedrock(c) = nlevsoi - this%soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 - this%soilstate_inst%mss_frc_cly_vld_col(c) = 0.17_r8 + this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay ) + this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) end do @@ -316,7 +317,7 @@ contains call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, & vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, & vlc_trb_4=vlc_trb_4) - @assertEqual( flx_mss_vrt_dst_tot, 2.239779135859605d-5, tolerance=tol ) + @assertEqual( flx_mss_vrt_dst_tot, 2.583480541056971d-6, tolerance=tol ) @assertEqual( vlc_trb_1, 3.407721147709135d-003, tolerance=tol ) @assertEqual( vlc_trb_2, 4.961153753164878d-003, tolerance=tol ) @assertEqual( vlc_trb_3, 4.980100969983446d-003, tolerance=tol ) @@ -473,7 +474,7 @@ contains call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) total_dust0 = flx_mss_vrt_dst_tot - @assertEqual( flx_mss_vrt_dst_tot, 1.971366884000767d-4, tolerance=tol ) + @assertEqual( flx_mss_vrt_dst_tot, 2.273879554711299d-5, tolerance=tol ) end do ! Double u10 and show result is higher call this%create_fv( u10=u10*2.0_r8, fv=fv) @@ -485,7 +486,7 @@ contains call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) total_dust_higher = flx_mss_vrt_dst_tot - @assertEqual( flx_mss_vrt_dst_tot, 3.288208220877217d-4, tolerance=tol ) + @assertEqual( flx_mss_vrt_dst_tot, 3.792794484764924d-5, tolerance=tol ) end do @assertGreaterThan( total_dust_higher, total_dust0 ) From 1e64bc3bfaeec854c09f24da6c9e9afac1135977 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 14:39:58 -0600 Subject: [PATCH 194/408] Increase tolerance a bit, as these numbers are small --- .../test_dust_soil_clay_functions.pf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf index f753bf1729..0e4ac8b3db 100644 --- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf +++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf @@ -15,7 +15,7 @@ module test_dust_soil_clay_functions procedure :: tearDown end type TestDustEmisSoilFunctions - real(r8), parameter :: tol = 1.e-15_r8 + real(r8), parameter :: tol = 1.e-16_r8 contains From 150397c14052ebba30703e7e334078c13626a149 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 15:29:54 -0600 Subject: [PATCH 195/408] Start seperating Dust emis testing into the Base and Zender2003 versions --- .../test/DustEmis_test/CMakeLists.txt | 3 +- .../test/DustEmis_test/test_DustEmisBase.pf | 298 ++++++++++++++++++ ...DustEmis.pf => test_DustEmisZender2003.pf} | 0 3 files changed, 300 insertions(+), 1 deletion(-) create mode 100644 src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf rename src/biogeochem/test/DustEmis_test/{test_DustEmis.pf => test_DustEmisZender2003.pf} (100%) diff --git a/src/biogeochem/test/DustEmis_test/CMakeLists.txt b/src/biogeochem/test/DustEmis_test/CMakeLists.txt index a618489386..49e3c16391 100644 --- a/src/biogeochem/test/DustEmis_test/CMakeLists.txt +++ b/src/biogeochem/test/DustEmis_test/CMakeLists.txt @@ -1,5 +1,6 @@ set (pfunit_sources - test_DustEmis.pf) + test_DustEmisBase.pf + test_DustEmisZender2003.pf) add_pfunit_ctest(DustEmis TEST_SOURCES "${pfunit_sources}" diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf new file mode 100644 index 0000000000..b25ad5c44c --- /dev/null +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf @@ -0,0 +1,298 @@ +module test_DustEmisBase + + ! Tests of DustEmisBase + + use funit + use unittestSubgridMod + use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch + use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst + use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit + use clm_varcon, only : clm_varcon_init, clm_varcon_clean + use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean + use DustEmisZender2003 + use shr_kind_mod , only : r8 => shr_kind_r8 + use unittestFilterBuilderMod, only : filter_from_range + use atm2lndType, only : atm2lnd_type, atm2lnd_params_type + use SoilStateType, only : soilstate_type + use CanopyStateType, only : canopystate_type + use TemperatureType, only : temperature_type + use WaterType, only : water_type + use FrictionVelocityMod, only : frictionvel_type + use unittestWaterTypeFactory, only : unittest_water_type_factory_type + use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay + + implicit none + + real(r8), parameter :: tol = 1.e-18_r8 + + @TestCase + type, extends(TestCase) :: TestDustEmisBase + type(dust_type) :: dust_emis + integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) + integer :: num_nolakep ! number of patches in non-lake filter + type(atm2lnd_type) :: atm2lnd_inst + type(soilstate_type) :: soilstate_inst + type(canopystate_type) :: canopystate_inst + type(temperature_type) :: temperature_inst + type(unittest_water_type_factory_type) :: water_factory + type(water_type) :: water_inst + type(frictionvel_type) :: frictionvel_inst + contains + procedure :: setUp + procedure :: tearDown + procedure :: setupEnvironment + procedure :: create_atm2lnd + procedure :: create_fv + procedure :: print_values + procedure :: validate_patch + end type TestDustEmisBase + +contains + + !----------------------------------------------------------------------- + + subroutine setUp(this) + use ColumnType, only : col + class(TestDustEmisBase), intent(inout) :: this + + character(len=5) :: NLFilename = 'none' + real(r8), allocatable :: snow_depth_col(:) + real(r8), allocatable :: urb_em(:) + integer :: begl, endl, begc, endc + integer :: c + type(atm2lnd_params_type) :: atm2lnd_params + + soil_layerstruct_predefined = '20SL_8.5m' + create_crop_landunit = .true. + use_crop = .false. + call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) + call clm_varcon_init( is_simple_buildtemp=.true.) + call this%water_factory%init() + call this%water_factory%setup_before_subgrid( & + my_nlevsoi = nlevsoi, & + nlevgrnd_additional = nlevgrnd - nlevsoi, & + my_nlevsno = 3) + call setup_single_veg_patch( pft_type=0 ) + begl = bounds%begl + endl = bounds%endl + begc = bounds%begc + endc = bounds%endc + allocate( urb_em(begl:endl) ) + + call this%dust_emis%Init( bounds, NLFilename ) + call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) + atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & + glcmec_downscale_longwave = .false., & + lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) + ) + allocate (snow_depth_col(begc:endc)) + snow_depth_col(begc:endc) = 0.0_r8 + call SnowHydrologySetControlForTesting() + call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc)) + call this%water_factory%setup_after_subgrid(snl = 3) + call this%soilstate_inst%Init(bounds) + do c = begc, endc + this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1) + end do + call this%setupEnvironment( ) + call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) + call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) + call this%canopystate_inst%SetNMLForTesting() + call this%canopystate_inst%Init(bounds) + call this%frictionvel_inst%InitForTesting(bounds) + urb_em(begl:endl) = 0.99_r8 + call this%temperature_inst%Init(bounds, & + em_roof_lun=urb_em(begl:endl), & + em_wall_lun=urb_em(begl:endl), & + em_improad_lun=urb_em(begl:endl), & + em_perroad_lun=urb_em(begl:endl), & + is_simple_buildtemp=.true., is_prog_buildtemp=.false.) + deallocate (snow_depth_col ) + deallocate( urb_em ) + end subroutine setUp + + !----------------------------------------------------------------------- + + subroutine tearDown(this) + class(TestDustEmisBase), intent(inout) :: this + + call this%dust_emis%Clean() + call this%water_factory%teardown(this%water_inst) + call SnowHydrologyClean() + call unittest_subgrid_teardown() + call this%atm2lnd_inst%Clean() + call clm_varcon_clean() + deallocate( this%filter_nolakep ) + end subroutine tearDown + + !----------------------------------------------------------------------- + + subroutine setupEnvironment(this) + ! + ! !DESCRIPTION: + ! Sets up the external environment used by Dust emissions - i.e., things accessed via + ! 'use' statements. + ! + ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has + ! been completed. + ! + use ColumnType, only : col + use GridcellType, only : grc + class(TestDustEmisBase), intent(in) :: this + ! + integer :: c,j + real(r8), parameter :: clay = 10.0_r8 + + !----------------------------------------------------------------------- + col%dz(:,1:nlevgrnd) = 1.0_r8 + do j = 1, nlevgrnd + do c = bounds%begc, bounds%endc + col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j) + end do + end do + + do c = bounds%begc, bounds%endc + ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are + ! considered bedrock + col%nbedrock(c) = nlevsoi + + this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay ) + this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) + end do + + + ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager) + grc%londeg(:) = 0.0_r8 + + grc%area(:) = 10.0_r8 + + end subroutine setupEnvironment + + !----------------------------------------------------------------------- + + subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho ) + ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets + ! forcing fields based on inputs. Excluded inputs are given a default value + class(TestDustEmisBase), intent(inout) :: this + real(r8), intent(in), optional :: forc_t(:) + real(r8), intent(in), optional :: forc_pbot(:) + real(r8), intent(in), optional :: forc_rho(:) + + real(r8), parameter :: forc_t_default = 301._r8 + real(r8), parameter :: forc_pbot_default = 100000._r8 + real(r8), parameter :: forc_rho_default = 1.1_r8 + ! ------------------------------------------------------------------------ + + if (present(forc_t)) then + this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:) + else + this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default + end if + + if (present(forc_pbot)) then + this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:) + else + this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default + end if + + if (present(forc_rho)) then + this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:) + else + this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default + end if + + end subroutine create_atm2lnd + + !----------------------------------------------------------------------- + + subroutine create_fv(this, fv, u10, ram1) + ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets + ! fields based on inputs. Excluded inputs are given a default value + class(TestDustEmisBase), intent(inout) :: this + real(r8), intent(in), optional :: fv + real(r8), intent(in), optional :: u10 + real(r8), intent(in), optional :: ram1 + + real(r8), parameter :: fv_default = 2.0_r8 + real(r8), parameter :: u10_default = 4._r8 + real(r8), parameter :: ram1_default = 200._r8 + ! ------------------------------------------------------------------------ + + if (present(fv)) then + this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv + else + this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default + end if + + if (present(u10)) then + this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10 + else + this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default + end if + + if (present(ram1)) then + this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1 + else + this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default + end if + + end subroutine create_fv + + subroutine print_values(this) + use LandunitType, only : lun + use PatchType, only : patch + class(TestDustEmisBase), intent(inout) :: this + real(r8) :: SaltationFactor + integer :: p, c, l + + call this%dust_emis%GetConstVars( SaltationFactor ) + do l = bounds%begl, bounds%endl + print *, 'landunit type= ', lun%itype(l) + end do + do c = bounds%begc, bounds%endc + print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1) + print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1) + print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c) + print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c) + print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) + end do + do p = bounds%begp, bounds%endp + print *, 'patch type= ', patch%itype(p) + print *, 'patch weight= ', patch%wtgcell(p) + print *, 'patch active= ', patch%active(p) + print *, 'tlai = ', this%canopystate_inst%tlai_patch(p) + print *, 'tsai = ', this%canopystate_inst%tsai_patch(p) + c = patch%column(p) + print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) & + / this%frictionvel_inst%fv_patch(p) + call this%dust_emis%WritePatchToLog( p ) + end do + end subroutine print_values + + !----------------------------------------------------------------------- + subroutine validate_patch(this, p) + class(TestDustEmisBase), intent(inout) :: this + integer, intent(in) :: p + + real(r8) :: flx_mss_vrt_dst(ndst) + real(r8) :: flx_mss_vrt_dst_tot + real(r8) :: vlc_trb(ndst) + real(r8) :: vlc_trb_1 + real(r8) :: vlc_trb_2 + real(r8) :: vlc_trb_3 + real(r8) :: vlc_trb_4 + + call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, & + flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, & + vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, & + vlc_trb_4=vlc_trb_4 ) + @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot ) + @assertEqual( vlc_trb(1), vlc_trb_1) + @assertEqual( vlc_trb(2), vlc_trb_2) + @assertEqual( vlc_trb(3), vlc_trb_3) + @assertEqual( vlc_trb(4), vlc_trb_4) + end subroutine validate_patch + + !----------------------------------------------------------------------- + +end module test_DustEmisBase diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmis.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf similarity index 100% rename from src/biogeochem/test/DustEmis_test/test_DustEmis.pf rename to src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf From a189bb18d80be3ec911a26d7db81773fdfe8e9ca Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 24 May 2024 15:57:26 -0600 Subject: [PATCH 196/408] Get the unit tests to work again --- .../DustEmis_test/test_DustEmisZender2003.pf | 38 +++++++++---------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index ff154f3126..c99f4bd97d 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -1,6 +1,6 @@ -module test_DustEmis +module test_DustEmisZender2003 - ! Tests of DustEmis + ! Tests of DustEmisZender2003 use funit use unittestSubgridMod @@ -26,7 +26,7 @@ module test_DustEmis real(r8), parameter :: tol = 1.e-18_r8 @TestCase - type, extends(TestCase) :: TestDustEmis + type, extends(TestCase) :: TestDustEmisZender2003 type(dust_type) :: dust_emis integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) integer :: num_nolakep ! number of patches in non-lake filter @@ -45,7 +45,7 @@ module test_DustEmis procedure :: create_fv procedure :: print_values procedure :: validate_patch - end type TestDustEmis + end type TestDustEmisZender2003 contains @@ -53,7 +53,7 @@ contains subroutine setUp(this) use ColumnType, only : col - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this character(len=5) :: NLFilename = 'none' real(r8), allocatable :: snow_depth_col(:) @@ -114,7 +114,7 @@ contains !----------------------------------------------------------------------- subroutine tearDown(this) - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this call this%dust_emis%Clean() call this%water_factory%teardown(this%water_inst) @@ -138,7 +138,7 @@ contains ! use ColumnType, only : col use GridcellType, only : grc - class(TestDustEmis), intent(in) :: this + class(TestDustEmisZender2003), intent(in) :: this ! integer :: c,j real(r8), parameter :: clay = 10.0_r8 @@ -173,7 +173,7 @@ contains subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho ) ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets ! forcing fields based on inputs. Excluded inputs are given a default value - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this real(r8), intent(in), optional :: forc_t(:) real(r8), intent(in), optional :: forc_pbot(:) real(r8), intent(in), optional :: forc_rho(:) @@ -208,7 +208,7 @@ contains subroutine create_fv(this, fv, u10, ram1) ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets ! fields based on inputs. Excluded inputs are given a default value - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this real(r8), intent(in), optional :: fv real(r8), intent(in), optional :: u10 real(r8), intent(in), optional :: ram1 @@ -241,7 +241,7 @@ contains subroutine print_values(this) use LandunitType, only : lun use PatchType, only : patch - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this real(r8) :: SaltationFactor integer :: p, c, l @@ -271,7 +271,7 @@ contains !----------------------------------------------------------------------- subroutine validate_patch(this, p) - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this integer, intent(in) :: p real(r8) :: flx_mss_vrt_dst(ndst) @@ -298,7 +298,7 @@ contains @Test subroutine check_dust_emis(this) ! Check dust emissions for default values - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this integer :: p real(r8) :: flx_mss_vrt_dst_tot real(r8) :: vlc_trb_1 @@ -331,7 +331,7 @@ contains @Test subroutine dust_zero_for_fixed_ratio(this) ! Check dust emissions are zero for a no wind - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this integer :: p real(r8) :: flx_mss_vrt_dst_tot real(r8) :: fv @@ -360,7 +360,7 @@ contains @Test subroutine dust_zero_when_fsno_one(this) ! Check dust emissions are zero when snow fraction is identically 1 - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this integer :: p real(r8) :: flx_mss_vrt_dst_tot @@ -385,7 +385,7 @@ contains ! Check dust emissions are zero for non-veg landunits use landunit_varcon, only: istcrop, max_lunit use LandunitType, only : lun - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this integer :: p, l real(r8) :: flx_mss_vrt_dst_tot @@ -411,7 +411,7 @@ contains @Test subroutine aborts_on_bad_dust_mobility(this) ! Check dust abort when dust mobility is bad - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this real(r8) :: flx_mss_vrt_dst_tot character(100) :: expected_msg @@ -432,7 +432,7 @@ contains @Test subroutine dust_zero_when_tlai_high(this) ! Check dust emissions are zero when LAI is high enough - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this integer :: p real(r8) :: flx_mss_vrt_dst_tot @@ -456,7 +456,7 @@ contains @Test subroutine check_dust_emis_increasing_wind(this) ! Check dust emissions with increasing wind - class(TestDustEmis), intent(inout) :: this + class(TestDustEmisZender2003), intent(inout) :: this integer :: p, c real(r8) :: flx_mss_vrt_dst_tot real(r8) :: fv = 4.0_r8 @@ -494,4 +494,4 @@ contains !----------------------------------------------------------------------- -end module test_DustEmis \ No newline at end of file +end module test_DustEmisZender2003 \ No newline at end of file From dab63611a6088551ff2959f1c04bcfbc4b61c2db Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 24 May 2024 16:13:59 -0600 Subject: [PATCH 197/408] pvt system init step update --- cime_config/SystemTests/pvt.py | 149 ++++++++++++++++++--------------- 1 file changed, 82 insertions(+), 67 deletions(-) diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py index c45c514f39..184c5de289 100644 --- a/cime_config/SystemTests/pvt.py +++ b/cime_config/SystemTests/pvt.py @@ -12,7 +12,8 @@ """ from CIME.XML.standard_module_setup import * from CIME.SystemTests.system_tests_common import SystemTestsCommon -from systemtest_utils import read_user_nl_clm +from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files +from systemtest_utils import find_user_nl_option import shutil, glob, os logger = logging.getLogger(__name__) @@ -41,76 +42,90 @@ def __init__(self,case): if error_message is not None: logger.error(error_message) raise RuntimeError(error_message) - def run_phase(self): - # ------------------------------------------------------------------- - # (1) Run FATES spin-up case in potential vegetation mode - # ------------------------------------------------------------------- - orig_case = self._case - orig_casevar = self._case.get_value("CASE") - caseroot = self._case.get_value("CASEROOT") - - # clone the main case to create spinup case - logger.info("PVT log: cloning setup") - clone_path = "{}.potveg".format(caseroot) - if os.path.exists(clone_path): - shutil.rmtree(clone_path) - logger.info("PVT log: cloning") - clone = self._case.create_clone(clone_path, keepexe=True) - logger.info("PVT log: cloning complete") - # setup the clone case - os.chdir(clone_path) - self._set_active_case(clone) - self._setup_all() + # Look to see if a harvest mode has been set in the namelist and save off for the transient run + # If there are more than one entries in the dict, i.e. multiple user_nl_clm's found, abort. + # If there are multiple enteries the user_nl_clm, use the last one as the dict is ordered + caseroot = self._case.get_value("CASEROOT") + harvest_mode_dict = find_user_nl_option(caseroot, 'clm', 'fates_harvest_mode') + harvest_mode = None + if len(harvest_mode_dict) == 1: + hmod = harvest_mode_dict[next(reversed(harvest_mode_dict))] + if len(hmod) != 0: + harvest_mode = hmod[-1] + elif (len(harvest_mode_dict)) > 1: + raise RuntimeError('Multiple user_nl_clm files found. PVT assumes only a single user_nl_clm case') # Modify the spin up case to use the potential vegetation mode. # Checks for incompatible cases and necessary mapping files are # handled in the build case. # use_fates_lupft should be set to true in the testmod - # save off the harvest mode for reinstating later - found, hmode = self.read_user_nl_clm('fates_harvest_mode') - logger.info("PVT log: modify user_nl_clm file for spin up run") - # TODO: remove fates_harvest_mode if found - self._append_to_user_nl_clm( - [ - "use_fates_potentialveg = .true.", - ] - ) - - stop_n_pveg = 1 - with clone: - # clone.set_value("CLM_ACCELERATED_SPINUP", "on") - clone.set_value("STOP_N", stop_n_pveg) - - # Run the spin up case - # As per SSP test: - # "No history files expected, set suffix=None to avoid compare error" - logger.info("PVT log: starting spin-up run") - dout_sr = clone.get_value("DOUT_S_ROOT") - self._skip_pnl = False - self.run_indv(suffix=None, st_archive=True) + # If the testmod has a fates harvest mode, make sure to append 'no_harvest' + # to the spin up case - # ------------------------------------------------------------------- - # (2) Run FATES transient case using restart file from spin-up - # ------------------------------------------------------------------- - os.chdir(caseroot) - self._set_active_case(orig_case) - - # logger.info("PVT log: modify user_nl_clm file for transient run") - # self._append_to_user_nl_clm( - # [ - # "use_fates_potentialveg = .true.", - # ] - # ) - - - self._case.set_value("CLM_ACCELERATED_SPINUP", "off") - self._case.set_value("RUN_TYPE", "hybrid") - self._case.set_value("GET_REFCASE", False) - self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar)) - self._case.set_value("RUN_REFDATE", "1700-01-01") - self._case.set_value("DOUT_S", False) - self._case.flush() - - # do the restart run (short term archiving is off) - self.run_indv() + logger.info("PVT log: modify user_nl_clm file for spin up run") + added_content = ["use_fates_potentialveg = .true."] + if harvest_mode is not None: + added_content.append("fates_harvest_mode = 'no_harvest'") + append_to_user_nl_files(caseroot, "clm", added_content) + +# def run_phase(self): +# # ------------------------------------------------------------------- +# # (1) Run FATES spin-up case in potential vegetation mode +# # ------------------------------------------------------------------- +# orig_case = self._case +# orig_casevar = self._case.get_value("CASE") +# caseroot = self._case.get_value("CASEROOT") +# +# # clone the main case to create spinup case +# logger.info("PVT log: cloning setup") +# clone_path = "{}.potveg".format(caseroot) +# if os.path.exists(clone_path): +# shutil.rmtree(clone_path) +# logger.info("PVT log: cloning") +# clone = self._case.create_clone(clone_path, keepexe=True) +# logger.info("PVT log: cloning complete") +# +# # setup the clone case +# os.chdir(clone_path) +# self._set_active_case(clone) +# self._setup_all() +# +# +# stop_n_pveg = 1 +# with clone: +# # clone.set_value("CLM_ACCELERATED_SPINUP", "on") +# clone.set_value("STOP_N", stop_n_pveg) +# +# # Run the spin up case +# # As per SSP test: +# # "No history files expected, set suffix=None to avoid compare error" +# logger.info("PVT log: starting spin-up run") +# dout_sr = clone.get_value("DOUT_S_ROOT") +# self._skip_pnl = False +# self.run_indv(suffix=None, st_archive=True) +# +# # ------------------------------------------------------------------- +# # (2) Run FATES transient case using restart file from spin-up +# # ------------------------------------------------------------------- +# os.chdir(caseroot) +# self._set_active_case(orig_case) +# +# # logger.info("PVT log: modify user_nl_clm file for transient run") +# # self._append_to_user_nl_clm( +# # [ +# # "use_fates_potentialveg = .true.", +# # ] +# # ) +# +# +# self._case.set_value("CLM_ACCELERATED_SPINUP", "off") +# self._case.set_value("RUN_TYPE", "hybrid") +# self._case.set_value("GET_REFCASE", False) +# self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar)) +# self._case.set_value("RUN_REFDATE", "1700-01-01") +# self._case.set_value("DOUT_S", False) +# self._case.flush() +# +# # do the restart run (short term archiving is off) +# self.run_indv() From 175a3d01082437945f15660f75aca860c626d0a4 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 24 May 2024 18:14:18 -0600 Subject: [PATCH 198/408] pvt system test setup looks correct --- cime_config/SystemTests/pvt.py | 132 +++++++++++++-------------------- 1 file changed, 53 insertions(+), 79 deletions(-) diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py index 184c5de289..6b2a958eaa 100644 --- a/cime_config/SystemTests/pvt.py +++ b/cime_config/SystemTests/pvt.py @@ -43,89 +43,63 @@ def __init__(self,case): logger.error(error_message) raise RuntimeError(error_message) - # Look to see if a harvest mode has been set in the namelist and save off for the transient run - # If there are more than one entries in the dict, i.e. multiple user_nl_clm's found, abort. - # If there are multiple enteries the user_nl_clm, use the last one as the dict is ordered + def run_phase(self): + # ------------------------------------------------------------------- + # (1) Run FATES spin-up case in potential vegetation mode + # ------------------------------------------------------------------- + orig_case = self._case + orig_casevar = self._case.get_value("CASE") caseroot = self._case.get_value("CASEROOT") - harvest_mode_dict = find_user_nl_option(caseroot, 'clm', 'fates_harvest_mode') - harvest_mode = None - if len(harvest_mode_dict) == 1: - hmod = harvest_mode_dict[next(reversed(harvest_mode_dict))] - if len(hmod) != 0: - harvest_mode = hmod[-1] - elif (len(harvest_mode_dict)) > 1: - raise RuntimeError('Multiple user_nl_clm files found. PVT assumes only a single user_nl_clm case') + + # clone the main case to create spinup case + logger.info("PVT log: cloning setup") + clone_path = "{}.potveg".format(caseroot) + if os.path.exists(clone_path): + shutil.rmtree(clone_path) + logger.info("PVT log: cloning") + clone = self._case.create_clone(clone_path, keepexe=True) + logger.info("PVT log: cloning complete") + + # setup the clone case + os.chdir(clone_path) + self._set_active_case(clone) + + # set the clone case values + stop_n_pveg = 1 + with clone: + # clone.set_value("CLM_ACCELERATED_SPINUP", "on") + clone.set_value("STOP_N", stop_n_pveg) # Modify the spin up case to use the potential vegetation mode. # Checks for incompatible cases and necessary mapping files are # handled in the build case. - # use_fates_lupft should be set to true in the testmod - # If the testmod has a fates harvest mode, make sure to append 'no_harvest' - # to the spin up case + # Turn off fates_harvest_mode for the spin up. logger.info("PVT log: modify user_nl_clm file for spin up run") - added_content = ["use_fates_potentialveg = .true."] - if harvest_mode is not None: - added_content.append("fates_harvest_mode = 'no_harvest'") - append_to_user_nl_files(caseroot, "clm", added_content) - -# def run_phase(self): -# # ------------------------------------------------------------------- -# # (1) Run FATES spin-up case in potential vegetation mode -# # ------------------------------------------------------------------- -# orig_case = self._case -# orig_casevar = self._case.get_value("CASE") -# caseroot = self._case.get_value("CASEROOT") -# -# # clone the main case to create spinup case -# logger.info("PVT log: cloning setup") -# clone_path = "{}.potveg".format(caseroot) -# if os.path.exists(clone_path): -# shutil.rmtree(clone_path) -# logger.info("PVT log: cloning") -# clone = self._case.create_clone(clone_path, keepexe=True) -# logger.info("PVT log: cloning complete") -# -# # setup the clone case -# os.chdir(clone_path) -# self._set_active_case(clone) -# self._setup_all() -# -# -# stop_n_pveg = 1 -# with clone: -# # clone.set_value("CLM_ACCELERATED_SPINUP", "on") -# clone.set_value("STOP_N", stop_n_pveg) -# -# # Run the spin up case -# # As per SSP test: -# # "No history files expected, set suffix=None to avoid compare error" -# logger.info("PVT log: starting spin-up run") -# dout_sr = clone.get_value("DOUT_S_ROOT") -# self._skip_pnl = False -# self.run_indv(suffix=None, st_archive=True) -# -# # ------------------------------------------------------------------- -# # (2) Run FATES transient case using restart file from spin-up -# # ------------------------------------------------------------------- -# os.chdir(caseroot) -# self._set_active_case(orig_case) -# -# # logger.info("PVT log: modify user_nl_clm file for transient run") -# # self._append_to_user_nl_clm( -# # [ -# # "use_fates_potentialveg = .true.", -# # ] -# # ) -# -# -# self._case.set_value("CLM_ACCELERATED_SPINUP", "off") -# self._case.set_value("RUN_TYPE", "hybrid") -# self._case.set_value("GET_REFCASE", False) -# self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar)) -# self._case.set_value("RUN_REFDATE", "1700-01-01") -# self._case.set_value("DOUT_S", False) -# self._case.flush() -# -# # do the restart run (short term archiving is off) -# self.run_indv() + added_content = ["use_fates_potentialveg = .true.","fates_harvest_mode = 'no_harvest'"] + append_to_user_nl_files(clone_path, "clm", added_content) + + # Run the spin up case + # As per SSP test: + # "No history files expected, set suffix=None to avoid compare error" + logger.info("PVT log: starting spin-up run") + dout_sr = clone.get_value("DOUT_S_ROOT") + self._skip_pnl = False + self.run_indv(suffix=None, st_archive=True) + + # ------------------------------------------------------------------- + # (2) Run FATES transient case using restart file from spin-up + # ------------------------------------------------------------------- + os.chdir(caseroot) + self._set_active_case(orig_case) + + self._case.set_value("CLM_ACCELERATED_SPINUP", "off") + self._case.set_value("RUN_TYPE", "hybrid") + self._case.set_value("GET_REFCASE", False) + self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar)) + self._case.set_value("RUN_REFDATE", "1700-01-01") + self._case.set_value("DOUT_S", False) + self._case.flush() + + # do the restart run (short term archiving is off) + self.run_indv() From 10728d91c8dcaeeb0719429ba11cf857fec50f68 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 24 May 2024 18:15:04 -0600 Subject: [PATCH 199/408] add non-Cold based testmod for spinup + transient --- .../testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods | 1 + .../testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm | 1 + 2 files changed, 2 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods new file mode 100644 index 0000000000..1ceba4c200 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/include_user_mods @@ -0,0 +1 @@ +../FatesLUPFT diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm new file mode 100644 index 0000000000..426b41b49e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFTAreaHarvest/user_nl_clm @@ -0,0 +1 @@ +fates_harvest_mode = 'luhdata_area' From a7b60fa5539991e0e75fff6c34c1b2f50f3b3e83 Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Mon, 27 May 2024 17:34:56 -0600 Subject: [PATCH 200/408] first remove manage_externals and update docs --- .github/PULL_REQUEST_TEMPLATE.md | 2 +- Externals.cfg | 94 - Externals_CLM.cfg | 9 - README | 6 +- manage_externals/.dir_locals.el | 12 - manage_externals/.github/ISSUE_TEMPLATE.md | 6 - .../.github/PULL_REQUEST_TEMPLATE.md | 17 - .../.github/workflows/bumpversion.yml | 19 - manage_externals/.github/workflows/tests.yml | 30 - manage_externals/.gitignore | 17 - manage_externals/.travis.yml | 18 - manage_externals/LICENSE.txt | 34 - manage_externals/README.md | 231 -- manage_externals/README_FIRST | 54 - manage_externals/checkout_externals | 36 - manage_externals/manic/__init__.py | 9 - manage_externals/manic/checkout.py | 446 ---- .../manic/externals_description.py | 830 -------- manage_externals/manic/externals_status.py | 164 -- manage_externals/manic/global_constants.py | 18 - manage_externals/manic/repository.py | 98 - manage_externals/manic/repository_factory.py | 30 - manage_externals/manic/repository_git.py | 859 -------- manage_externals/manic/repository_svn.py | 291 --- 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manage_externals/test/repos/simple-ext.svn/locks/db-logs.lock delete mode 100644 manage_externals/test/repos/simple-ext.svn/locks/db.lock delete mode 100644 manage_externals/test/requirements.txt delete mode 100755 manage_externals/test/test_sys_checkout.py delete mode 100644 manage_externals/test/test_sys_repository_git.py delete mode 100644 manage_externals/test/test_unit_externals_description.py delete mode 100644 manage_externals/test/test_unit_externals_status.py delete mode 100644 manage_externals/test/test_unit_repository.py delete mode 100644 manage_externals/test/test_unit_repository_git.py delete mode 100755 manage_externals/test/test_unit_repository_svn.py delete mode 100644 manage_externals/test/test_unit_utils.py diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 7c9512c9c3..c4a381383b 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -16,7 +16,7 @@ Testing performed, if any: (List what testing you did to show your changes worked as expected) (This can be manual testing or running of the different test suites) (Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide) -(aux_clm on cheyenne for intel/gnu and izumi for intel/gnu/nag/pgi is the standard for tags on master) +(aux_clm on derecho for intel/gnu and izumi for intel/gnu/nag/nvhpc is the standard for tags on master) **NOTE: Be sure to check your coding style against the standard (https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines) and review diff --git a/Externals.cfg b/Externals.cfg deleted file mode 100644 index 70d103a94b..0000000000 --- a/Externals.cfg +++ /dev/null @@ -1,94 +0,0 @@ -[clm] -local_path = . -protocol = externals_only -externals = Externals_CLM.cfg -required = True - -[cism] -local_path = components/cism -protocol = git -repo_url = https://github.com/ESCOMP/CISM-wrapper -tag = cismwrap_2_1_100 -externals = Externals_CISM.cfg -required = True - -[rtm] -local_path = components/rtm -protocol = git -repo_url = https://github.com/ESCOMP/RTM -tag = rtm1_0_79 -required = True - -[mosart] -local_path = components/mosart -protocol = git -repo_url = https://github.com/ESCOMP/MOSART -tag = mosart1_0_49 -required = True - -[mizuRoute] -tag = cesm-coupling.n02_v2.1.2 -protocol = git -local_path = components/mizuroute -repo_url = https://github.com/ESCOMP/mizuRoute -required = True - -[ccs_config] -tag = ccs_config_cesm0.0.106 -protocol = git -repo_url = https://github.com/ESMCI/ccs_config_cesm.git -local_path = ccs_config -required = True - -[cime] -local_path = cime -protocol = git -repo_url = https://github.com/ESMCI/cime -tag = cime6.0.238_httpsbranch01 -required = True - -[cmeps] -tag = cmeps0.14.63 -protocol = git -repo_url = https://github.com/ESCOMP/CMEPS.git -local_path = components/cmeps -required = True - -[cdeps] -tag = cdeps1.0.33 -protocol = git -repo_url = https://github.com/ESCOMP/CDEPS.git -local_path = components/cdeps -externals = Externals_CDEPS.cfg -required = True - -[share] -tag = share1.0.18 -protocol = git -repo_url = https://github.com/ESCOMP/CESM_share -local_path = share -required = True - -[mct] -tag = MCT_2.11.0 -protocol = git -repo_url = https://github.com/MCSclimate/MCT -local_path = libraries/mct -required = True - -[parallelio] -tag = pio2_6_2 -protocol = git -repo_url = https://github.com/NCAR/ParallelIO -local_path = libraries/parallelio -required = True - -[doc-builder] -local_path = doc/doc-builder -protocol = git -repo_url = https://github.com/ESMCI/doc-builder -tag = v1.0.8 -required = False - -[externals_description] -schema_version = 1.0.0 diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg deleted file mode 100644 index 866b9ac5b2..0000000000 --- a/Externals_CLM.cfg +++ /dev/null @@ -1,9 +0,0 @@ -[fates] -local_path = src/fates -protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.73.0_api.35.0.0 -required = True - -[externals_description] -schema_version = 1.0.0 diff --git a/README b/README index af45a14909..0f1a38edf3 100644 --- a/README +++ b/README @@ -49,7 +49,7 @@ src --------------- CTSM Source code. lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model) tools ------------- CTSM Offline tools to prepare input datasets and process output. cime_config ------- Configuration files of cime for compsets and CTSM settings -manage_externals -- Script to manage the external source directories (deprecated) +bin/git-fleximod -- Script to manage the external source directories py_env_create ----- Script to setup the python environment for CTSM python tools using conda python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts @@ -73,7 +73,6 @@ Top level documentation ($CTSMROOT): README ------------------- This file README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git README.rst --------------- File that displays under the project in github -README_EXTERNALS.rst ----- Information on how to work with manage_externals for CTSM (deprecated) CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project Copyright ---------------- CESM Copyright file doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the @@ -97,9 +96,6 @@ bld/namelist_files/namelist_defaults_ctsm.xml ----- Default values Important files in main directories (under $CTSMROOT): ============================================================================================= -Externals.cfg --------------- File for management of the main high level external (deprecated) -Externals_CLM.cfg ----------- File for management of the CTSM specific externals (i.e. FATES) - run_sys_tests --------------- Python script to send the standard CTSM testing off (submits the create_test test suite for several different compilers on the machines we do standard CTSM testing on). diff --git a/manage_externals/.dir_locals.el b/manage_externals/.dir_locals.el deleted file mode 100644 index a370490e92..0000000000 --- a/manage_externals/.dir_locals.el +++ /dev/null @@ -1,12 +0,0 @@ -; -*- mode: Lisp -*- - -((python-mode - . ( - ;; fill the paragraph to 80 columns when using M-q - (fill-column . 80) - - ;; Use 4 spaces to indent in Python - (python-indent-offset . 4) - (indent-tabs-mode . nil) - ))) - diff --git a/manage_externals/.github/ISSUE_TEMPLATE.md b/manage_externals/.github/ISSUE_TEMPLATE.md deleted file mode 100644 index 8ecb2ae64b..0000000000 --- a/manage_externals/.github/ISSUE_TEMPLATE.md +++ /dev/null @@ -1,6 +0,0 @@ -### Summary of Issue: -### Expected behavior and actual behavior: -### Steps to reproduce the problem (should include model description file(s) or link to publi c repository): -### What is the changeset ID of the code, and the machine you are using: -### have you modified the code? If so, it must be committed and available for testing: -### Screen output or log file showing the error message and context: diff --git a/manage_externals/.github/PULL_REQUEST_TEMPLATE.md b/manage_externals/.github/PULL_REQUEST_TEMPLATE.md deleted file mode 100644 index b68b1fb5e2..0000000000 --- a/manage_externals/.github/PULL_REQUEST_TEMPLATE.md +++ /dev/null @@ -1,17 +0,0 @@ -[ 50 character, one line summary ] - -[ Description of the changes in this commit. It should be enough - information for someone not following this development to understand. - Lines should be wrapped at about 72 characters. ] - -User interface changes?: [ No/Yes ] -[ If yes, describe what changed, and steps taken to ensure backward compatibilty ] - -Fixes: [Github issue #s] And brief description of each issue. - -Testing: - test removed: - unit tests: - system tests: - manual testing: - diff --git a/manage_externals/.github/workflows/bumpversion.yml b/manage_externals/.github/workflows/bumpversion.yml deleted file mode 100644 index f4dc9b7ca5..0000000000 --- a/manage_externals/.github/workflows/bumpversion.yml +++ /dev/null @@ -1,19 +0,0 @@ -name: Bump version -on: - push: - branches: - - main -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Bump version and push tag - id: tag_version - uses: mathieudutour/github-tag-action@v5.5 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - create_annotated_tag: true - default_bump: patch - dry_run: false - tag_prefix: manic- diff --git a/manage_externals/.github/workflows/tests.yml b/manage_externals/.github/workflows/tests.yml deleted file mode 100644 index dd75b91b49..0000000000 --- a/manage_externals/.github/workflows/tests.yml +++ /dev/null @@ -1,30 +0,0 @@ -# This is a workflow to compile the cmeps source without cime -name: Test Manic - -# Controls when the action will run. Triggers the workflow on push or pull request -# events but only for the master branch -on: - push: - branches: [ main ] - pull_request: - branches: [ main ] - -# A workflow run is made up of one or more jobs that can run sequentially or in parallel -jobs: - test-manic: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - name: Test Manic - run: | - pushd test - git config --global user.email "devnull@example.com" - git config --global user.name "GITHUB tester" - git config --global protocol.file.allow always - make utest - make stest - popd - - - name: Setup tmate session - if: ${{ failure() }} - uses: mxschmitt/action-tmate@v3 diff --git a/manage_externals/.gitignore b/manage_externals/.gitignore deleted file mode 100644 index a71ac0cd75..0000000000 --- a/manage_externals/.gitignore +++ /dev/null @@ -1,17 +0,0 @@ -# directories that are checked out by the tool -cime/ -cime_config/ -components/ - -# generated local files -*.log - -# editor files -*~ -*.bak - -# generated python files -*.pyc - -# test tmp file -test/tmp diff --git a/manage_externals/.travis.yml b/manage_externals/.travis.yml deleted file mode 100644 index d9b24c584d..0000000000 --- a/manage_externals/.travis.yml +++ /dev/null @@ -1,18 +0,0 @@ -language: python -os: linux -python: - - "3.4" - - "3.5" - - "3.6" - - "3.7" - - "3.8" -install: - - pip install -r test/requirements.txt -before_script: - - git --version -script: - - cd test; make test - - cd test; make lint -after_success: - - cd test; make coverage - - cd test; coveralls diff --git a/manage_externals/LICENSE.txt b/manage_externals/LICENSE.txt deleted file mode 100644 index 665ee03fbc..0000000000 --- a/manage_externals/LICENSE.txt +++ /dev/null @@ -1,34 +0,0 @@ -Copyright (c) 2017-2018, University Corporation for Atmospheric Research (UCAR) -All rights reserved. - -Developed by: - University Corporation for Atmospheric Research - National Center for Atmospheric Research - https://www2.cesm.ucar.edu/working-groups/sewg - -Permission is hereby granted, free of charge, to any person obtaining -a copy of this software and associated documentation files (the "Software"), -to deal with the Software without restriction, including without limitation -the rights to use, copy, modify, merge, publish, distribute, sublicense, -and/or sell copies of the Software, and to permit persons to whom -the Software is furnished to do so, subject to the following conditions: - - - Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimers. - - Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimers in the documentation - and/or other materials provided with the distribution. - - Neither the names of [Name of Development Group, UCAR], - nor the names of its contributors may be used to endorse or promote - products derived from this Software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE -LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR -CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF -SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS -INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN -CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE -POSSIBILITY OF SUCH DAMAGE. diff --git a/manage_externals/README.md b/manage_externals/README.md deleted file mode 100644 index 9475301b5d..0000000000 --- a/manage_externals/README.md +++ /dev/null @@ -1,231 +0,0 @@ --- AUTOMATICALLY GENERATED FILE. DO NOT EDIT -- - -[![Build Status](https://travis-ci.org/ESMCI/manage_externals.svg?branch=master)](https://travis-ci.org/ESMCI/manage_externals)[![Coverage Status](https://coveralls.io/repos/github/ESMCI/manage_externals/badge.svg?branch=master)](https://coveralls.io/github/ESMCI/manage_externals?branch=master) -``` -usage: checkout_externals [-h] [-e [EXTERNALS]] [-o] [-S] [-v] [--backtrace] - [-d] [--no-logging] - -checkout_externals manages checking out groups of externals from revision -control based on a externals description file. By default only the -required externals are checkout out. - -Operations performed by manage_externals utilities are explicit and -data driven. checkout_externals will always make the working copy *exactly* -match what is in the externals file when modifying the working copy of -a repository. - -If checkout_externals isn't doing what you expected, double check the contents -of the externals description file. - -Running checkout_externals without the '--status' option will always attempt to -synchronize the working copy to exactly match the externals description. - -optional arguments: - -h, --help show this help message and exit - -e [EXTERNALS], --externals [EXTERNALS] - The externals description filename. Default: - Externals.cfg. - -o, --optional By default only the required externals are checked - out. This flag will also checkout the optional - externals. - -S, --status Output status of the repositories managed by - checkout_externals. By default only summary - information is provided. Use verbose output to see - details. - -v, --verbose Output additional information to the screen and log - file. This flag can be used up to two times, - increasing the verbosity level each time. - --backtrace DEVELOPER: show exception backtraces as extra - debugging output - -d, --debug DEVELOPER: output additional debugging information to - the screen and log file. - --no-logging DEVELOPER: disable logging. - -``` -NOTE: checkout_externals *MUST* be run from the root of the source tree it -is managing. For example, if you cloned a repository with: - - $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev - -Then the root of the source tree is /path/to/some-project-dev. If you -obtained a sub-project via a checkout of another project: - - $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev - -and you need to checkout the sub-project externals, then the root of the -source tree is /path/to/some-project-dev. Do *NOT* run checkout_externals -from within /path/to/some-project-dev/sub-project - -The root of the source tree will be referred to as `${SRC_ROOT}` below. - -# Supported workflows - - * Checkout all required components from the default externals - description file: - - $ cd ${SRC_ROOT} - $ ./manage_externals/checkout_externals - - * To update all required components to the current values in the - externals description file, re-run checkout_externals: - - $ cd ${SRC_ROOT} - $ ./manage_externals/checkout_externals - - If there are *any* modifications to *any* working copy according - to the git or svn 'status' command, checkout_externals - will not update any external repositories. Modifications - include: modified files, added files, removed files, or missing - files. - - To avoid this safety check, edit the externals description file - and comment out the modified external block. - - * Checkout all required components from a user specified externals - description file: - - $ cd ${SRC_ROOT} - $ ./manage_externals/checkout_externals --externals my-externals.cfg - - * Status summary of the repositories managed by checkout_externals: - - $ cd ${SRC_ROOT} - $ ./manage_externals/checkout_externals --status - - ./cime - s ./components/cism - ./components/mosart - e-o ./components/rtm - M ./src/fates - e-o ./tools/PTCLM - - where: - * column one indicates the status of the repository in relation - to the externals description file. - * column two indicates whether the working copy has modified files. - * column three shows how the repository is managed, optional or required - - Column one will be one of these values: - * s : out-of-sync : repository is checked out at a different commit - compared with the externals description - * e : empty : directory does not exist - checkout_externals has not been run - * ? : unknown : directory exists but .git or .svn directories are missing - - Column two will be one of these values: - * M : Modified : modified, added, deleted or missing files - * : blank / space : clean - * - : dash : no meaningful state, for empty repositories - - Column three will be one of these values: - * o : optional : optionally repository - * : blank / space : required repository - - * Detailed git or svn status of the repositories managed by checkout_externals: - - $ cd ${SRC_ROOT} - $ ./manage_externals/checkout_externals --status --verbose - -# Externals description file - - The externals description contains a list of the external - repositories that are used and their version control locations. The - file format is the standard ini/cfg configuration file format. Each - external is defined by a section containing the component name in - square brackets: - - * name (string) : component name, e.g. [cime], [cism], etc. - - Each section has the following keyword-value pairs: - - * required (boolean) : whether the component is a required checkout, - 'true' or 'false'. - - * local_path (string) : component path *relative* to where - checkout_externals is called. - - * protoctol (string) : version control protocol that is used to - manage the component. Valid values are 'git', 'svn', - 'externals_only'. - - Switching an external between different protocols is not - supported, e.g. from svn to git. To switch protocols, you need to - manually move the old working copy to a new location. - - Note: 'externals_only' will only process the external's own - external description file without trying to manage a repository - for the component. This is used for retreiving externals for - standalone components like cam and clm. If the source root of the - externals_only component is the same as the main source root, then - the local path must be set to '.', the unix current working - directory, e. g. 'local_path = .' - - * repo_url (string) : URL for the repository location, examples: - * https://svn-ccsm-models.cgd.ucar.edu/glc - * git@github.com:esmci/cime.git - * /path/to/local/repository - * . - - NOTE: To operate on only the local clone and and ignore remote - repositories, set the url to '.' (the unix current path), - i.e. 'repo_url = .' . This can be used to checkout a local branch - instead of the upstream branch. - - If a repo url is determined to be a local path (not a network url) - then user expansion, e.g. ~/, and environment variable expansion, - e.g. $HOME or $REPO_ROOT, will be performed. - - Relative paths are difficult to get correct, especially for mixed - use repos. It is advised that local paths expand to absolute paths. - If relative paths are used, they should be relative to one level - above local_path. If local path is 'src/foo', the the relative url - should be relative to 'src'. - - * tag (string) : tag to checkout - - * hash (string) : the git hash to checkout. Only applies to git - repositories. - - * branch (string) : branch to checkout from the specified - repository. Specifying a branch on a remote repository means that - checkout_externals will checkout the version of the branch in the remote, - not the the version in the local repository (if it exists). - - Note: one and only one of tag, branch hash must be supplied. - - * externals (string) : used to make manage_externals aware of - sub-externals required by an external. This is a relative path to - the external's root directory. For example, the main externals - description has an external checkout out at 'src/useful_library'. - useful_library requires additional externals to be complete. - Those additional externals are managed from the source root by the - externals description file pointed 'useful_library/sub-xternals.cfg', - Then the main 'externals' field in the top level repo should point to - 'sub-externals.cfg'. - Note that by default, `checkout_externals` will clone an external's - submodules. As a special case, the entry, `externals = None`, will - prevent this behavior. For more control over which externals are - checked out, create an externals file (and see the `from_submodule` - configuration entry below). - - * from_submodule (True / False) : used to pull the repo_url, local_path, - and hash properties for this external from the .gitmodules file in - this repository. Note that the section name (the entry in square - brackets) must match the name in the .gitmodules file. - If from_submodule is True, the protocol must be git and no repo_url, - local_path, hash, branch, or tag entries are allowed. - Default: False - - * sparse (string) : used to control a sparse checkout. This optional - entry should point to a filename (path relative to local_path) that - contains instructions on which repository paths to include (or - exclude) from the working tree. - See the "SPARSE CHECKOUT" section of https://git-scm.com/docs/git-read-tree - Default: sparse checkout is disabled - - * Lines begining with '#' or ';' are comments and will be ignored. - -# Obtaining this tool, reporting issues, etc. - - The master repository for manage_externals is - https://github.com/ESMCI/manage_externals. Any issues with this tool - should be reported there. diff --git a/manage_externals/README_FIRST b/manage_externals/README_FIRST deleted file mode 100644 index c8a47d7806..0000000000 --- a/manage_externals/README_FIRST +++ /dev/null @@ -1,54 +0,0 @@ -CESM is comprised of a number of different components that are -developed and managed independently. Each component may have -additional 'external' dependancies and optional parts that are also -developed and managed independently. - -The checkout_externals.py tool manages retreiving and updating the -components and their externals so you have a complete set of source -files for the model. - -checkout_externals.py relies on a model description file that -describes what components are needed, where to find them and where to -put them in the source tree. The default file is called "CESM.xml" -regardless of whether you are checking out CESM or a standalone -component. - -checkout_externals requires access to git and svn repositories that -require authentication. checkout_externals may pass through -authentication requests, but it will not cache them for you. For the -best and most robust user experience, you should have svn and git -working without password authentication. See: - - https://help.github.com/articles/connecting-to-github-with-ssh/ - - ?svn ref? - -NOTE: checkout_externals.py *MUST* be run from the root of the source -tree it is managing. For example, if you cloned CLM with: - - $ git clone git@github.com/ncar/clm clm-dev - -Then the root of the source tree is /path/to/cesm-dev. If you obtained -CLM via an svn checkout of CESM and you need to checkout the CLM -externals, then the root of the source tree for CLM is: - - /path/to/cesm-dev/components/clm - -The root of the source tree will be referred to as ${SRC_ROOT} below. - -To get started quickly, checkout all required components from the -default model description file: - - $ cd ${SRC_ROOT} - $ ./checkout_cesm/checkout_externals.py - -For additional information about using checkout model, please see: - - ${SRC_ROOT}/checkout_cesm/README - -or run: - - $ cd ${SRC_ROOT} - $ ./checkout_cesm/checkout_externals.py --help - - diff --git a/manage_externals/checkout_externals b/manage_externals/checkout_externals deleted file mode 100755 index 48bce24010..0000000000 --- a/manage_externals/checkout_externals +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env python3 - -"""Main driver wrapper around the manic/checkout utility. - -Tool to assemble external respositories represented in an externals -description file. - -""" -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import sys -import traceback - -import manic - -if sys.hexversion < 0x02070000: - print(70 * '*') - print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0])) - print('It appears that you are running python {0}'.format( - '.'.join(str(x) for x in sys.version_info[0:3]))) - print(70 * '*') - sys.exit(1) - - -if __name__ == '__main__': - ARGS = manic.checkout.commandline_arguments() - try: - RET_STATUS, _ = manic.checkout.main(ARGS) - sys.exit(RET_STATUS) - except Exception as error: # pylint: disable=broad-except - manic.printlog(str(error)) - if ARGS.backtrace: - traceback.print_exc() - sys.exit(1) diff --git a/manage_externals/manic/__init__.py b/manage_externals/manic/__init__.py deleted file mode 100644 index 11badedd3b..0000000000 --- a/manage_externals/manic/__init__.py +++ /dev/null @@ -1,9 +0,0 @@ -"""Public API for the manage_externals library -""" - -from manic import checkout -from manic.utils import printlog - -__all__ = [ - 'checkout', 'printlog', -] diff --git a/manage_externals/manic/checkout.py b/manage_externals/manic/checkout.py deleted file mode 100755 index 3f5537adce..0000000000 --- a/manage_externals/manic/checkout.py +++ /dev/null @@ -1,446 +0,0 @@ -#!/usr/bin/env python3 - -""" -Tool to assemble repositories represented in a model-description file. - -If loaded as a module (e.g., in a component's buildcpp), it can be used -to check the validity of existing subdirectories and load missing sources. -""" -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import argparse -import logging -import os -import os.path -import sys - -from manic.externals_description import create_externals_description -from manic.externals_description import read_externals_description_file -from manic.externals_status import check_safe_to_update_repos -from manic.sourcetree import SourceTree -from manic.utils import printlog, fatal_error -from manic.global_constants import VERSION_SEPERATOR, LOG_FILE_NAME - -if sys.hexversion < 0x02070000: - print(70 * '*') - print('ERROR: {0} requires python >= 2.7.x. '.format(sys.argv[0])) - print('It appears that you are running python {0}'.format( - VERSION_SEPERATOR.join(str(x) for x in sys.version_info[0:3]))) - print(70 * '*') - sys.exit(1) - - -# --------------------------------------------------------------------- -# -# User input -# -# --------------------------------------------------------------------- -def commandline_arguments(args=None): - """Process the command line arguments - - Params: args - optional args. Should only be used during systems - testing. - - Returns: processed command line arguments - """ - description = ''' - -%(prog)s manages checking out groups of externals from revision -control based on an externals description file. By default only the -required externals are checkout out. - -Running %(prog)s without the '--status' option will always attempt to -synchronize the working copy to exactly match the externals description. -''' - - epilog = ''' -``` -NOTE: %(prog)s *MUST* be run from the root of the source tree it -is managing. For example, if you cloned a repository with: - - $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev - -Then the root of the source tree is /path/to/some-project-dev. If you -obtained a sub-project via a checkout of another project: - - $ git clone git@github.com/{SOME_ORG}/some-project some-project-dev - -and you need to checkout the sub-project externals, then the root of the -source tree remains /path/to/some-project-dev. Do *NOT* run %(prog)s -from within /path/to/some-project-dev/sub-project - -The root of the source tree will be referred to as `${SRC_ROOT}` below. - - -# Supported workflows - - * Checkout all required components from the default externals - description file: - - $ cd ${SRC_ROOT} - $ ./manage_externals/%(prog)s - - * To update all required components to the current values in the - externals description file, re-run %(prog)s: - - $ cd ${SRC_ROOT} - $ ./manage_externals/%(prog)s - - If there are *any* modifications to *any* working copy according - to the git or svn 'status' command, %(prog)s - will not update any external repositories. Modifications - include: modified files, added files, removed files, or missing - files. - - To avoid this safety check, edit the externals description file - and comment out the modified external block. - - * Checkout all required components from a user specified externals - description file: - - $ cd ${SRC_ROOT} - $ ./manage_externals/%(prog)s --externals my-externals.cfg - - * Status summary of the repositories managed by %(prog)s: - - $ cd ${SRC_ROOT} - $ ./manage_externals/%(prog)s --status - - ./cime - s ./components/cism - ./components/mosart - e-o ./components/rtm - M ./src/fates - e-o ./tools/PTCLM - - - where: - * column one indicates the status of the repository in relation - to the externals description file. - * column two indicates whether the working copy has modified files. - * column three shows how the repository is managed, optional or required - - Column one will be one of these values: - * s : out-of-sync : repository is checked out at a different commit - compared with the externals description - * e : empty : directory does not exist - %(prog)s has not been run - * ? : unknown : directory exists but .git or .svn directories are missing - - Column two will be one of these values: - * M : Modified : modified, added, deleted or missing files - * : blank / space : clean - * - : dash : no meaningful state, for empty repositories - - Column three will be one of these values: - * o : optional : optionally repository - * : blank / space : required repository - - * Detailed git or svn status of the repositories managed by %(prog)s: - - $ cd ${SRC_ROOT} - $ ./manage_externals/%(prog)s --status --verbose - -# Externals description file - - The externals description contains a list of the external - repositories that are used and their version control locations. The - file format is the standard ini/cfg configuration file format. Each - external is defined by a section containing the component name in - square brackets: - - * name (string) : component name, e.g. [cime], [cism], etc. - - Each section has the following keyword-value pairs: - - * required (boolean) : whether the component is a required checkout, - 'true' or 'false'. - - * local_path (string) : component path *relative* to where - %(prog)s is called. - - * protoctol (string) : version control protocol that is used to - manage the component. Valid values are 'git', 'svn', - 'externals_only'. - - Switching an external between different protocols is not - supported, e.g. from svn to git. To switch protocols, you need to - manually move the old working copy to a new location. - - Note: 'externals_only' will only process the external's own - external description file without trying to manage a repository - for the component. This is used for retrieving externals for - standalone components like cam and ctsm which also serve as - sub-components within a larger project. If the source root of the - externals_only component is the same as the main source root, then - the local path must be set to '.', the unix current working - directory, e. g. 'local_path = .' - - * repo_url (string) : URL for the repository location, examples: - * https://svn-ccsm-models.cgd.ucar.edu/glc - * git@github.com:esmci/cime.git - * /path/to/local/repository - * . - - NOTE: To operate on only the local clone and and ignore remote - repositories, set the url to '.' (the unix current path), - i.e. 'repo_url = .' . This can be used to checkout a local branch - instead of the upstream branch. - - If a repo url is determined to be a local path (not a network url) - then user expansion, e.g. ~/, and environment variable expansion, - e.g. $HOME or $REPO_ROOT, will be performed. - - Relative paths are difficult to get correct, especially for mixed - use repos. It is advised that local paths expand to absolute paths. - If relative paths are used, they should be relative to one level - above local_path. If local path is 'src/foo', the the relative url - should be relative to 'src'. - - * tag (string) : tag to checkout - - * hash (string) : the git hash to checkout. Only applies to git - repositories. - - * branch (string) : branch to checkout from the specified - repository. Specifying a branch on a remote repository means that - %(prog)s will checkout the version of the branch in the remote, - not the the version in the local repository (if it exists). - - Note: one and only one of tag, branch hash must be supplied. - - * externals (string) : used to make manage_externals aware of - sub-externals required by an external. This is a relative path to - the external's root directory. For example, if LIBX is often used - as a sub-external, it might have an externals file (for its - externals) called Externals_LIBX.cfg. To use libx as a standalone - checkout, it would have another file, Externals.cfg with the - following entry: - - [ libx ] - local_path = . - protocol = externals_only - externals = Externals_LIBX.cfg - required = True - - Now, %(prog)s will process Externals.cfg and also process - Externals_LIBX.cfg as if it was a sub-external. - - Note that by default, checkout_externals will clone an external's - submodules. As a special case, the entry, "externals = None", will - prevent this behavior. For more control over which externals are - checked out, create an externals file (and see the from_submodule - configuration entry below). - - * from_submodule (True / False) : used to pull the repo_url, local_path, - and hash properties for this external from the .gitmodules file in - this repository. Note that the section name (the entry in square - brackets) must match the name in the .gitmodules file. - If from_submodule is True, the protocol must be git and no repo_url, - local_path, hash, branch, or tag entries are allowed. - Default: False - - * sparse (string) : used to control a sparse checkout. This optional - entry should point to a filename (path relative to local_path) that - contains instructions on which repository paths to include (or - exclude) from the working tree. - See the "SPARSE CHECKOUT" section of https://git-scm.com/docs/git-read-tree - Default: sparse checkout is disabled - - * Lines beginning with '#' or ';' are comments and will be ignored. - -# Obtaining this tool, reporting issues, etc. - - The master repository for manage_externals is - https://github.com/ESMCI/manage_externals. Any issues with this tool - should be reported there. - -# Troubleshooting - -Operations performed by manage_externals utilities are explicit and -data driven. %(prog)s will always attempt to make the working copy -*exactly* match what is in the externals file when modifying the -working copy of a repository. - -If %(prog)s is not doing what you expected, double check the contents -of the externals description file or examine the output of -./manage_externals/%(prog)s --status - -''' - - parser = argparse.ArgumentParser( - description=description, epilog=epilog, - formatter_class=argparse.RawDescriptionHelpFormatter) - - # - # user options - # - parser.add_argument("components", nargs="*", - help="Specific component(s) to checkout. By default, " - "all required externals are checked out.") - - parser.add_argument('-e', '--externals', nargs='?', - default='Externals.cfg', - help='The externals description filename. ' - 'Default: %(default)s.') - - parser.add_argument('-x', '--exclude', nargs='*', - help='Component(s) listed in the externals file which should be ignored.') - - parser.add_argument('-o', '--optional', action='store_true', default=False, - help='By default only the required externals ' - 'are checked out. This flag will also checkout the ' - 'optional externals.') - - parser.add_argument('-S', '--status', action='store_true', default=False, - help='Output the status of the repositories managed by ' - '%(prog)s. By default only summary information ' - 'is provided. Use the verbose option to see details.') - - parser.add_argument('-v', '--verbose', action='count', default=0, - help='Output additional information to ' - 'the screen and log file. This flag can be ' - 'used up to two times, increasing the ' - 'verbosity level each time.') - - parser.add_argument('--svn-ignore-ancestry', action='store_true', default=False, - help='By default, subversion will abort if a component is ' - 'already checked out and there is no common ancestry with ' - 'the new URL. This flag passes the "--ignore-ancestry" flag ' - 'to the svn switch call. (This is not recommended unless ' - 'you are sure about what you are doing.)') - - # - # developer options - # - parser.add_argument('--backtrace', action='store_true', - help='DEVELOPER: show exception backtraces as extra ' - 'debugging output') - - parser.add_argument('-d', '--debug', action='store_true', default=False, - help='DEVELOPER: output additional debugging ' - 'information to the screen and log file.') - - logging_group = parser.add_mutually_exclusive_group() - - logging_group.add_argument('--logging', dest='do_logging', - action='store_true', - help='DEVELOPER: enable logging.') - logging_group.add_argument('--no-logging', dest='do_logging', - action='store_false', default=False, - help='DEVELOPER: disable logging ' - '(this is the default)') - - if args: - options = parser.parse_args(args) - else: - options = parser.parse_args() - return options - -def _dirty_local_repo_msg(program_name, config_file): - return """The external repositories labeled with 'M' above are not in a clean state. -The following are four options for how to proceed: -(1) Go into each external that is not in a clean state and issue either a 'git status' or - an 'svn status' command (depending on whether the external is managed by git or - svn). Either revert or commit your changes so that all externals are in a clean - state. (To revert changes in git, follow the instructions given when you run 'git - status'.) (Note, though, that it is okay to have untracked files in your working - directory.) Then rerun {program_name}. -(2) Alternatively, you do not have to rely on {program_name}. Instead, you can manually - update out-of-sync externals (labeled with 's' above) as described in the - configuration file {config_file}. (For example, run 'git fetch' and 'git checkout' - commands to checkout the appropriate tags for each external, as given in - {config_file}.) -(3) You can also use {program_name} to manage most, but not all externals: You can specify - one or more externals to ignore using the '-x' or '--exclude' argument to - {program_name}. Excluding externals labeled with 'M' will allow {program_name} to - update the other, non-excluded externals. -(4) As a last resort, if you are confident that there is no work that needs to be saved - from a given external, you can remove that external (via "rm -rf [directory]") and - then rerun the {program_name} tool. This option is mainly useful as a workaround for - issues with this tool (such as https://github.com/ESMCI/manage_externals/issues/157). -The external repositories labeled with '?' above are not under version -control using the expected protocol. If you are sure you want to switch -protocols, and you don't have any work you need to save from this -directory, then run "rm -rf [directory]" before rerunning the -{program_name} tool. -""".format(program_name=program_name, config_file=config_file) -# --------------------------------------------------------------------- -# -# main -# -# --------------------------------------------------------------------- -def main(args): - """ - Function to call when module is called from the command line. - Parse externals file and load required repositories or all repositories if - the --all option is passed. - - Returns a tuple (overall_status, tree_status). overall_status is 0 - on success, non-zero on failure. tree_status is a dict mapping local path - to ExternalStatus -- if no checkout is happening. If checkout is happening, tree_status - is None. - """ - if args.do_logging: - logging.basicConfig(filename=LOG_FILE_NAME, - format='%(levelname)s : %(asctime)s : %(message)s', - datefmt='%Y-%m-%d %H:%M:%S', - level=logging.DEBUG) - - program_name = os.path.basename(sys.argv[0]) - logging.info('Beginning of %s', program_name) - - load_all = False - if args.optional: - load_all = True - - root_dir = os.path.abspath(os.getcwd()) - model_data = read_externals_description_file(root_dir, args.externals) - ext_description = create_externals_description( - model_data, components=args.components, exclude=args.exclude) - - for comp in args.components: - if comp not in ext_description.keys(): - # Note we can't print out the list of found externals because - # they were filtered in create_externals_description above. - fatal_error( - "No component {} found in {}".format( - comp, args.externals)) - - source_tree = SourceTree(root_dir, ext_description, svn_ignore_ancestry=args.svn_ignore_ancestry) - if args.components: - components_str = 'specified components' - else: - components_str = 'required & optional components' - printlog('Checking local status of ' + components_str + ': ', end='') - tree_status = source_tree.status(print_progress=True) - printlog('') - - if args.status: - # user requested status-only - for comp in sorted(tree_status): - tree_status[comp].log_status_message(args.verbose) - else: - # checkout / update the external repositories. - safe_to_update = check_safe_to_update_repos(tree_status) - if not safe_to_update: - # print status - for comp in sorted(tree_status): - tree_status[comp].log_status_message(args.verbose) - # exit gracefully - printlog('-' * 70) - printlog(_dirty_local_repo_msg(program_name, args.externals)) - printlog('-' * 70) - else: - if not args.components: - source_tree.checkout(args.verbose, load_all) - for comp in args.components: - source_tree.checkout(args.verbose, load_all, load_comp=comp) - printlog('') - # New tree status is unknown, don't return anything. - tree_status = None - - logging.info('%s completed without exceptions.', program_name) - # NOTE(bja, 2017-11) tree status is used by the systems tests - return 0, tree_status diff --git a/manage_externals/manic/externals_description.py b/manage_externals/manic/externals_description.py deleted file mode 100644 index 546e7fdcb4..0000000000 --- a/manage_externals/manic/externals_description.py +++ /dev/null @@ -1,830 +0,0 @@ -#!/usr/bin/env python3 - -"""Model description - -Model description is the representation of the various externals -included in the model. It processes in input data structure, and -converts it into a standard interface that is used by the rest of the -system. - -To maintain backward compatibility, externals description files should -follow semantic versioning rules, http://semver.org/ - - - -""" -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import logging -import os -import os.path -import re - -# ConfigParser in python2 was renamed to configparser in python3. -# In python2, ConfigParser returns byte strings, str, instead of unicode. -# We need unicode to be compatible with xml and json parser and python3. -try: - # python2 - from ConfigParser import SafeConfigParser as config_parser - from ConfigParser import MissingSectionHeaderError - from ConfigParser import NoSectionError, NoOptionError - - USE_PYTHON2 = True - - def config_string_cleaner(text): - """convert strings into unicode - """ - return text.decode('utf-8') -except ImportError: - # python3 - from configparser import ConfigParser as config_parser - from configparser import MissingSectionHeaderError - from configparser import NoSectionError, NoOptionError - - USE_PYTHON2 = False - - def config_string_cleaner(text): - """Python3 already uses unicode strings, so just return the string - without modification. - - """ - return text - -from .utils import printlog, fatal_error, str_to_bool, expand_local_url -from .utils import execute_subprocess -from .global_constants import EMPTY_STR, PPRINTER, VERSION_SEPERATOR - -# -# Globals -# -DESCRIPTION_SECTION = 'externals_description' -VERSION_ITEM = 'schema_version' - - -def read_externals_description_file(root_dir, file_name): - """Read a file containing an externals description and - create its internal representation. - - """ - root_dir = os.path.abspath(root_dir) - msg = 'In directory : {0}'.format(root_dir) - logging.info(msg) - printlog('Processing externals description file : {0} ({1})'.format(file_name, - root_dir)) - - file_path = os.path.join(root_dir, file_name) - if not os.path.exists(file_name): - if file_name.lower() == "none": - msg = ('INTERNAL ERROR: Attempt to read externals file ' - 'from {0} when not configured'.format(file_path)) - else: - msg = ('ERROR: Model description file, "{0}", does not ' - 'exist at path:\n {1}\nDid you run from the root of ' - 'the source tree?'.format(file_name, file_path)) - - fatal_error(msg) - - externals_description = None - if file_name == ExternalsDescription.GIT_SUBMODULES_FILENAME: - externals_description = _read_gitmodules_file(root_dir, file_name) - else: - try: - config = config_parser() - config.read(file_path) - externals_description = config - except MissingSectionHeaderError: - # not a cfg file - pass - - if externals_description is None: - msg = 'Unknown file format!' - fatal_error(msg) - - return externals_description - -class LstripReader(object): - "LstripReader formats .gitmodules files to be acceptable for configparser" - def __init__(self, filename): - with open(filename, 'r') as infile: - lines = infile.readlines() - self._lines = list() - self._num_lines = len(lines) - self._index = 0 - for line in lines: - self._lines.append(line.lstrip()) - - def readlines(self): - """Return all the lines from this object's file""" - return self._lines - - def readline(self, size=-1): - """Format and return the next line or raise StopIteration""" - try: - line = self.next() - except StopIteration: - line = '' - - if (size > 0) and (len(line) < size): - return line[0:size] - - return line - - def __iter__(self): - """Begin an iteration""" - self._index = 0 - return self - - def next(self): - """Return the next line or raise StopIteration""" - if self._index >= self._num_lines: - raise StopIteration - - self._index = self._index + 1 - return self._lines[self._index - 1] - - def __next__(self): - return self.next() - -def git_submodule_status(repo_dir): - """Run the git submodule status command to obtain submodule hashes. - """ - # This function is here instead of GitRepository to avoid a dependency loop - cmd = 'git -C {repo_dir} submodule status'.format( - repo_dir=repo_dir).split() - git_output = execute_subprocess(cmd, output_to_caller=True) - submodules = {} - submods = git_output.split('\n') - for submod in submods: - if submod: - status = submod[0] - items = submod[1:].split(' ') - if len(items) > 2: - tag = items[2] - else: - tag = None - - submodules[items[1]] = {'hash':items[0], 'status':status, 'tag':tag} - - return submodules - -def parse_submodules_desc_section(section_items, file_path): - """Find the path and url for this submodule description""" - path = None - url = None - for item in section_items: - name = item[0].strip().lower() - if name == 'path': - path = item[1].strip() - elif name == 'url': - url = item[1].strip() - elif name == 'branch': - # We do not care about branch since we have a hash - silently ignore - pass - else: - msg = 'WARNING: Ignoring unknown {} property, in {}' - msg = msg.format(item[0], file_path) # fool pylint - logging.warning(msg) - - return path, url - -def _read_gitmodules_file(root_dir, file_name): - # pylint: disable=deprecated-method - # Disabling this check because the method is only used for python2 - # pylint: disable=too-many-locals - # pylint: disable=too-many-branches - # pylint: disable=too-many-statements - """Read a .gitmodules file and convert it to be compatible with an - externals description. - """ - root_dir = os.path.abspath(root_dir) - msg = 'In directory : {0}'.format(root_dir) - logging.info(msg) - - file_path = os.path.join(root_dir, file_name) - if not os.path.exists(file_name): - msg = ('ERROR: submodules description file, "{0}", does not ' - 'exist in dir:\n {1}'.format(file_name, root_dir)) - fatal_error(msg) - - submodules_description = None - externals_description = None - try: - config = config_parser() - if USE_PYTHON2: - config.readfp(LstripReader(file_path), filename=file_name) - else: - config.read_file(LstripReader(file_path), source=file_name) - - submodules_description = config - except MissingSectionHeaderError: - # not a cfg file - pass - - if submodules_description is None: - msg = 'Unknown file format!' - fatal_error(msg) - else: - # Convert the submodules description to an externals description - externals_description = config_parser() - # We need to grab all the commit hashes for this repo - submods = git_submodule_status(root_dir) - for section in submodules_description.sections(): - if section[0:9] == 'submodule': - sec_name = section[9:].strip(' "') - externals_description.add_section(sec_name) - section_items = submodules_description.items(section) - path, url = parse_submodules_desc_section(section_items, - file_path) - - if path is None: - msg = 'Submodule {} missing path'.format(sec_name) - fatal_error(msg) - - if url is None: - msg = 'Submodule {} missing url'.format(sec_name) - fatal_error(msg) - - externals_description.set(sec_name, - ExternalsDescription.PATH, path) - externals_description.set(sec_name, - ExternalsDescription.PROTOCOL, 'git') - externals_description.set(sec_name, - ExternalsDescription.REPO_URL, url) - externals_description.set(sec_name, - ExternalsDescription.REQUIRED, 'True') - if sec_name in submods: - submod_name = sec_name - else: - # The section name does not have to match the path - submod_name = path - - if submod_name in submods: - git_hash = submods[submod_name]['hash'] - externals_description.set(sec_name, - ExternalsDescription.HASH, - git_hash) - else: - emsg = "submodule status has no section, '{}'" - emsg += "\nCheck section names in externals config file" - fatal_error(emsg.format(submod_name)) - - # Required items - externals_description.add_section(DESCRIPTION_SECTION) - externals_description.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.0') - - return externals_description - -def create_externals_description( - model_data, model_format='cfg', components=None, exclude=None, parent_repo=None): - """Create the a externals description object from the provided data - - components: list of component names to include, None to include all. If a - name isn't found, it is silently omitted from the return value. - exclude: list of component names to skip. - """ - externals_description = None - if model_format == 'dict': - externals_description = ExternalsDescriptionDict( - model_data, components=components, exclude=exclude) - elif model_format == 'cfg': - major, _, _ = get_cfg_schema_version(model_data) - if major == 1: - externals_description = ExternalsDescriptionConfigV1( - model_data, components=components, exclude=exclude, parent_repo=parent_repo) - else: - msg = ('Externals description file has unsupported schema ' - 'version "{0}".'.format(major)) - fatal_error(msg) - else: - msg = 'Unknown model data format "{0}"'.format(model_format) - fatal_error(msg) - return externals_description - - -def get_cfg_schema_version(model_cfg): - """Extract the major, minor, patch version of the config file schema - - Params: - model_cfg - config parser object containing the externas description data - - Returns: - major = integer major version - minor = integer minor version - patch = integer patch version - """ - semver_str = '' - try: - semver_str = model_cfg.get(DESCRIPTION_SECTION, VERSION_ITEM) - except (NoSectionError, NoOptionError): - msg = ('externals description file must have the required ' - 'section: "{0}" and item "{1}"'.format(DESCRIPTION_SECTION, - VERSION_ITEM)) - fatal_error(msg) - - # NOTE(bja, 2017-11) Assume we don't care about the - # build/pre-release metadata for now! - version_list = re.split(r'[-+]', semver_str) - version_str = version_list[0] - version = version_str.split(VERSION_SEPERATOR) - try: - major = int(version[0].strip()) - minor = int(version[1].strip()) - patch = int(version[2].strip()) - except ValueError: - msg = ('Config file schema version must have integer digits for ' - 'major, minor and patch versions. ' - 'Received "{0}"'.format(version_str)) - fatal_error(msg) - return major, minor, patch - - -class ExternalsDescription(dict): - """Base externals description class that is independent of the user input - format. Different input formats can all be converted to this - representation to provide a consistent represtentation for the - rest of the objects in the system. - - NOTE(bja, 2018-03): do NOT define _schema_major etc at the class - level in the base class. The nested/recursive nature of externals - means different schema versions may be present in a single run! - - All inheriting classes must overwrite: - self._schema_major and self._input_major - self._schema_minor and self._input_minor - self._schema_patch and self._input_patch - - where _schema_x is the supported schema, _input_x is the user - input value. - - """ - # keywords defining the interface into the externals description data; these - # are brought together by the schema below. - EXTERNALS = 'externals' # path to externals file. - BRANCH = 'branch' - SUBMODULE = 'from_submodule' - HASH = 'hash' - NAME = 'name' - PATH = 'local_path' - PROTOCOL = 'protocol' - REPO = 'repo' - REPO_URL = 'repo_url' - REQUIRED = 'required' - TAG = 'tag' - SPARSE = 'sparse' - - PROTOCOL_EXTERNALS_ONLY = 'externals_only' - PROTOCOL_GIT = 'git' - PROTOCOL_SVN = 'svn' - GIT_SUBMODULES_FILENAME = '.gitmodules' - KNOWN_PRROTOCOLS = [PROTOCOL_GIT, PROTOCOL_SVN, PROTOCOL_EXTERNALS_ONLY] - - # v1 xml keywords - _V1_TREE_PATH = 'TREE_PATH' - _V1_ROOT = 'ROOT' - _V1_TAG = 'TAG' - _V1_BRANCH = 'BRANCH' - _V1_REQ_SOURCE = 'REQ_SOURCE' - - # Dictionary keys are component names. The corresponding values are laid out - # according to this schema. - _source_schema = {REQUIRED: True, - PATH: 'string', - EXTERNALS: 'string', - SUBMODULE : True, - REPO: {PROTOCOL: 'string', - REPO_URL: 'string', - TAG: 'string', - BRANCH: 'string', - HASH: 'string', - SPARSE: 'string', - } - } - - def __init__(self, parent_repo=None): - """Convert the xml into a standardized dict that can be used to - construct the source objects - - """ - dict.__init__(self) - - self._schema_major = None - self._schema_minor = None - self._schema_patch = None - self._input_major = None - self._input_minor = None - self._input_patch = None - self._parent_repo = parent_repo - - def _verify_schema_version(self): - """Use semantic versioning rules to verify we can process this schema. - - """ - known = '{0}.{1}.{2}'.format(self._schema_major, - self._schema_minor, - self._schema_patch) - received = '{0}.{1}.{2}'.format(self._input_major, - self._input_minor, - self._input_patch) - - if self._input_major != self._schema_major: - # should never get here, the factory should handle this correctly! - msg = ('DEV_ERROR: version "{0}" parser received ' - 'version "{1}" input.'.format(known, received)) - fatal_error(msg) - - if self._input_minor > self._schema_minor: - msg = ('Incompatible schema version:\n' - ' User supplied schema version "{0}" is too new."\n' - ' Can only process version "{1}" files and ' - 'older.'.format(received, known)) - fatal_error(msg) - - if self._input_patch > self._schema_patch: - # NOTE(bja, 2018-03) ignoring for now... Not clear what - # conditions the test is needed. - pass - - def _check_user_input(self): - """Run a series of checks to attempt to validate the user input and - detect errors as soon as possible. - - NOTE(bja, 2018-03) These checks are called *after* the file is - read. That means the schema check can not occur here. - - Note: the order is important. check_optional will create - optional with null data. run check_data first to ensure - required data was provided correctly by the user. - - """ - self._check_data() - self._check_optional() - self._validate() - - def _check_data(self): - # pylint: disable=too-many-branches,too-many-statements - """Check user supplied data is valid where possible. - """ - for ext_name in self.keys(): - if (self[ext_name][self.REPO][self.PROTOCOL] - not in self.KNOWN_PRROTOCOLS): - msg = 'Unknown repository protocol "{0}" in "{1}".'.format( - self[ext_name][self.REPO][self.PROTOCOL], ext_name) - fatal_error(msg) - - if (self[ext_name][self.REPO][self.PROTOCOL] == - self.PROTOCOL_SVN): - if self.HASH in self[ext_name][self.REPO]: - msg = ('In repo description for "{0}". svn repositories ' - 'may not include the "hash" keyword.'.format( - ext_name)) - fatal_error(msg) - - if ((self[ext_name][self.REPO][self.PROTOCOL] != self.PROTOCOL_GIT) - and (self.SUBMODULE in self[ext_name])): - msg = ('self.SUBMODULE is only supported with {0} protocol, ' - '"{1}" is defined as an {2} repository') - fatal_error(msg.format(self.PROTOCOL_GIT, ext_name, - self[ext_name][self.REPO][self.PROTOCOL])) - - if (self[ext_name][self.REPO][self.PROTOCOL] != - self.PROTOCOL_EXTERNALS_ONLY): - ref_count = 0 - found_refs = '' - if self.TAG in self[ext_name][self.REPO]: - ref_count += 1 - found_refs = '"{0} = {1}", {2}'.format( - self.TAG, self[ext_name][self.REPO][self.TAG], - found_refs) - if self.BRANCH in self[ext_name][self.REPO]: - ref_count += 1 - found_refs = '"{0} = {1}", {2}'.format( - self.BRANCH, self[ext_name][self.REPO][self.BRANCH], - found_refs) - if self.HASH in self[ext_name][self.REPO]: - ref_count += 1 - found_refs = '"{0} = {1}", {2}'.format( - self.HASH, self[ext_name][self.REPO][self.HASH], - found_refs) - if (self.SUBMODULE in self[ext_name] and - self[ext_name][self.SUBMODULE]): - ref_count += 1 - found_refs = '"{0} = {1}", {2}'.format( - self.SUBMODULE, - self[ext_name][self.SUBMODULE], found_refs) - - if ref_count > 1: - msg = 'Model description is over specified! ' - if self.SUBMODULE in self[ext_name]: - msg += ('from_submodule is not compatible with ' - '"tag", "branch", or "hash" ') - else: - msg += (' Only one of "tag", "branch", or "hash" ' - 'may be specified ') - - msg += 'for repo description of "{0}".'.format(ext_name) - msg = '{0}\nFound: {1}'.format(msg, found_refs) - fatal_error(msg) - elif ref_count < 1: - msg = ('Model description is under specified! One of ' - '"tag", "branch", or "hash" must be specified for ' - 'repo description of "{0}"'.format(ext_name)) - fatal_error(msg) - - if (self.REPO_URL not in self[ext_name][self.REPO] and - (self.SUBMODULE not in self[ext_name] or - not self[ext_name][self.SUBMODULE])): - msg = ('Model description is under specified! Must have ' - '"repo_url" in repo ' - 'description for "{0}"'.format(ext_name)) - fatal_error(msg) - - if (self.SUBMODULE in self[ext_name] and - self[ext_name][self.SUBMODULE]): - if self.REPO_URL in self[ext_name][self.REPO]: - msg = ('Model description is over specified! ' - 'from_submodule keyword is not compatible ' - 'with {0} keyword for'.format(self.REPO_URL)) - msg = '{0} repo description of "{1}"'.format(msg, - ext_name) - fatal_error(msg) - - if self.PATH in self[ext_name]: - msg = ('Model description is over specified! ' - 'from_submodule keyword is not compatible with ' - '{0} keyword for'.format(self.PATH)) - msg = '{0} repo description of "{1}"'.format(msg, - ext_name) - fatal_error(msg) - - if self.REPO_URL in self[ext_name][self.REPO]: - url = expand_local_url( - self[ext_name][self.REPO][self.REPO_URL], ext_name) - self[ext_name][self.REPO][self.REPO_URL] = url - - def _check_optional(self): - # pylint: disable=too-many-branches - """Some fields like externals, repo:tag repo:branch are - (conditionally) optional. We don't want the user to be - required to enter them in every externals description file, but - still want to validate the input. Check conditions and add - default values if appropriate. - - """ - submod_desc = None # Only load submodules info once - for field in self: - # truely optional - if self.EXTERNALS not in self[field]: - self[field][self.EXTERNALS] = EMPTY_STR - - # git and svn repos must tags and branches for validation purposes. - if self.TAG not in self[field][self.REPO]: - self[field][self.REPO][self.TAG] = EMPTY_STR - if self.BRANCH not in self[field][self.REPO]: - self[field][self.REPO][self.BRANCH] = EMPTY_STR - if self.HASH not in self[field][self.REPO]: - self[field][self.REPO][self.HASH] = EMPTY_STR - if self.REPO_URL not in self[field][self.REPO]: - self[field][self.REPO][self.REPO_URL] = EMPTY_STR - if self.SPARSE not in self[field][self.REPO]: - self[field][self.REPO][self.SPARSE] = EMPTY_STR - - # from_submodule has a complex relationship with other fields - if self.SUBMODULE in self[field]: - # User wants to use submodule information, is it available? - if self._parent_repo is None: - # No parent == no submodule information - PPRINTER.pprint(self[field]) - msg = 'No parent submodule for "{0}"'.format(field) - fatal_error(msg) - elif self._parent_repo.protocol() != self.PROTOCOL_GIT: - PPRINTER.pprint(self[field]) - msg = 'Parent protocol, "{0}", does not support submodules' - fatal_error(msg.format(self._parent_repo.protocol())) - else: - args = self._repo_config_from_submodule(field, submod_desc) - repo_url, repo_path, ref_hash, submod_desc = args - - if repo_url is None: - msg = ('Cannot checkout "{0}" as a submodule, ' - 'repo not found in {1} file') - fatal_error(msg.format(field, - self.GIT_SUBMODULES_FILENAME)) - # Fill in submodule fields - self[field][self.REPO][self.REPO_URL] = repo_url - self[field][self.REPO][self.HASH] = ref_hash - self[field][self.PATH] = repo_path - - if self[field][self.SUBMODULE]: - # We should get everything from the parent submodule - # configuration. - pass - # No else (from _submodule = False is the default) - else: - # Add the default value (not using submodule information) - self[field][self.SUBMODULE] = False - - def _repo_config_from_submodule(self, field, submod_desc): - """Find the external config information for a repository from - its submodule configuration information. - """ - if submod_desc is None: - repo_path = os.getcwd() # Is this always correct? - submod_file = self._parent_repo.submodules_file(repo_path=repo_path) - if submod_file is None: - msg = ('Cannot checkout "{0}" from submodule information\n' - ' Parent repo, "{1}" does not have submodules') - fatal_error(msg.format(field, self._parent_repo.name())) - - printlog( - 'Processing submodules description file : {0} ({1})'.format( - submod_file, repo_path)) - submod_model_data= _read_gitmodules_file(repo_path, submod_file) - submod_desc = create_externals_description(submod_model_data) - - # Can we find our external? - repo_url = None - repo_path = None - ref_hash = None - for ext_field in submod_desc: - if field == ext_field: - ext = submod_desc[ext_field] - repo_url = ext[self.REPO][self.REPO_URL] - repo_path = ext[self.PATH] - ref_hash = ext[self.REPO][self.HASH] - break - - return repo_url, repo_path, ref_hash, submod_desc - - def _validate(self): - """Validate that the parsed externals description contains all necessary - fields. - - """ - def print_compare_difference(data_a, data_b, loc_a, loc_b): - """Look through the data structures and print the differences. - - """ - for item in data_a: - if item in data_b: - if not isinstance(data_b[item], type(data_a[item])): - printlog(" {item}: {loc} = {val} ({val_type})".format( - item=item, loc=loc_a, val=data_a[item], - val_type=type(data_a[item]))) - printlog(" {item} {loc} = {val} ({val_type})".format( - item=' ' * len(item), loc=loc_b, val=data_b[item], - val_type=type(data_b[item]))) - else: - printlog(" {item}: {loc} = {val} ({val_type})".format( - item=item, loc=loc_a, val=data_a[item], - val_type=type(data_a[item]))) - printlog(" {item} {loc} missing".format( - item=' ' * len(item), loc=loc_b)) - - def validate_data_struct(schema, data): - """Compare a data structure against a schema and validate all required - fields are present. - - """ - is_valid = False - in_ref = True - valid = True - if isinstance(schema, dict) and isinstance(data, dict): - # Both are dicts, recursively verify that all fields - # in schema are present in the data. - for key in schema: - in_ref = in_ref and (key in data) - if in_ref: - valid = valid and ( - validate_data_struct(schema[key], data[key])) - - is_valid = in_ref and valid - else: - # non-recursive structure. verify data and schema have - # the same type. - is_valid = isinstance(data, type(schema)) - - if not is_valid: - printlog(" Unmatched schema and input:") - if isinstance(schema, dict): - print_compare_difference(schema, data, 'schema', 'input') - print_compare_difference(data, schema, 'input', 'schema') - else: - printlog(" schema = {0} ({1})".format( - schema, type(schema))) - printlog(" input = {0} ({1})".format(data, type(data))) - - return is_valid - - for field in self: - valid = validate_data_struct(self._source_schema, self[field]) - if not valid: - PPRINTER.pprint(self._source_schema) - PPRINTER.pprint(self[field]) - msg = 'ERROR: source for "{0}" did not validate'.format(field) - fatal_error(msg) - - -class ExternalsDescriptionDict(ExternalsDescription): - """Create a externals description object from a dictionary using the API - representations. Primarily used to simplify creating model - description files for unit testing. - - """ - - def __init__(self, model_data, components=None, exclude=None): - """Parse a native dictionary into a externals description. - """ - ExternalsDescription.__init__(self) - self._schema_major = 1 - self._schema_minor = 0 - self._schema_patch = 0 - self._input_major = 1 - self._input_minor = 0 - self._input_patch = 0 - self._verify_schema_version() - if components: - for key in list(model_data.keys()): - if key not in components: - del model_data[key] - - if exclude: - for key in list(model_data.keys()): - if key in exclude: - del model_data[key] - - self.update(model_data) - self._check_user_input() - - -class ExternalsDescriptionConfigV1(ExternalsDescription): - """Create a externals description object from a config_parser object, - schema version 1. - - """ - - def __init__(self, model_data, components=None, exclude=None, parent_repo=None): - """Convert the config data into a standardized dict that can be used to - construct the source objects - - components: list of component names to include, None to include all. - exclude: list of component names to skip. - """ - ExternalsDescription.__init__(self, parent_repo=parent_repo) - self._schema_major = 1 - self._schema_minor = 1 - self._schema_patch = 0 - self._input_major, self._input_minor, self._input_patch = \ - get_cfg_schema_version(model_data) - self._verify_schema_version() - self._remove_metadata(model_data) - self._parse_cfg(model_data, components=components, exclude=exclude) - self._check_user_input() - - @staticmethod - def _remove_metadata(model_data): - """Remove the metadata section from the model configuration file so - that it is simpler to look through the file and construct the - externals description. - - """ - model_data.remove_section(DESCRIPTION_SECTION) - - def _parse_cfg(self, cfg_data, components=None, exclude=None): - """Parse a config_parser object into a externals description. - - components: list of component names to include, None to include all. - exclude: list of component names to skip. - """ - def list_to_dict(input_list, convert_to_lower_case=True): - """Convert a list of key-value pairs into a dictionary. - """ - output_dict = {} - for item in input_list: - key = config_string_cleaner(item[0].strip()) - value = config_string_cleaner(item[1].strip()) - if convert_to_lower_case: - key = key.lower() - output_dict[key] = value - return output_dict - - for section in cfg_data.sections(): - name = config_string_cleaner(section.lower().strip()) - if (components and name not in components) or (exclude and name in exclude): - continue - self[name] = {} - self[name].update(list_to_dict(cfg_data.items(section))) - self[name][self.REPO] = {} - loop_keys = self[name].copy().keys() - for item in loop_keys: - if item in self._source_schema: - if isinstance(self._source_schema[item], bool): - self[name][item] = str_to_bool(self[name][item]) - elif item in self._source_schema[self.REPO]: - self[name][self.REPO][item] = self[name][item] - del self[name][item] - else: - msg = ('Invalid input: "{sect}" contains unknown ' - 'item "{item}".'.format(sect=name, item=item)) - fatal_error(msg) diff --git a/manage_externals/manic/externals_status.py b/manage_externals/manic/externals_status.py deleted file mode 100644 index 6bc29e9732..0000000000 --- a/manage_externals/manic/externals_status.py +++ /dev/null @@ -1,164 +0,0 @@ -"""ExternalStatus - -Class to store status and state information about repositories and -create a string representation. - -""" -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -from .global_constants import EMPTY_STR -from .utils import printlog, indent_string -from .global_constants import VERBOSITY_VERBOSE, VERBOSITY_DUMP - - -class ExternalStatus(object): - """Class to represent the status of a given source repository or tree. - - Individual repositories determine their own status in the - Repository objects. This object is just resposible for storing the - information and passing it up to a higher level for reporting or - global decisions. - - There are two states of concern: - - * If the repository is in-sync with the externals description file. - - * If the repostiory working copy is clean and there are no pending - transactions (e.g. add, remove, rename, untracked files). - - """ - # sync_state and clean_state can be one of the following: - DEFAULT = '-' # not set yet (sync_state). clean_state can be this if sync_state is EMPTY. - UNKNOWN = '?' - EMPTY = 'e' - MODEL_MODIFIED = 's' # repo version != externals (sync_state only) - DIRTY = 'M' # repo is dirty (clean_state only) - STATUS_OK = ' ' # repo is clean (clean_state) or matches externals version (sync_state) - STATUS_ERROR = '!' - - # source_type can be one of the following: - OPTIONAL = 'o' - STANDALONE = 's' - MANAGED = ' ' - - def __init__(self): - self.sync_state = self.DEFAULT - self.clean_state = self.DEFAULT - self.source_type = self.DEFAULT - self.path = EMPTY_STR - self.current_version = EMPTY_STR - self.expected_version = EMPTY_STR - self.status_output = EMPTY_STR - - def log_status_message(self, verbosity): - """Write status message to the screen and log file - """ - printlog(self._default_status_message()) - if verbosity >= VERBOSITY_VERBOSE: - printlog(self._verbose_status_message()) - if verbosity >= VERBOSITY_DUMP: - printlog(self._dump_status_message()) - - def __repr__(self): - return self._default_status_message() - - def _default_status_message(self): - """Return the default terse status message string - """ - return '{sync}{clean}{src_type} {path}'.format( - sync=self.sync_state, clean=self.clean_state, - src_type=self.source_type, path=self.path) - - def _verbose_status_message(self): - """Return the verbose status message string - """ - clean_str = self.DEFAULT - if self.clean_state == self.STATUS_OK: - clean_str = 'clean sandbox' - elif self.clean_state == self.DIRTY: - clean_str = 'modified sandbox' - - sync_str = 'on {0}'.format(self.current_version) - if self.sync_state != self.STATUS_OK: - sync_str = '{current} --> {expected}'.format( - current=self.current_version, expected=self.expected_version) - return ' {clean}, {sync}'.format(clean=clean_str, sync=sync_str) - - def _dump_status_message(self): - """Return the dump status message string - """ - return indent_string(self.status_output, 12) - - def safe_to_update(self): - """Report if it is safe to update a repository. Safe is defined as: - - * If a repository is empty, it is safe to update. - - * If a repository exists and has a clean working copy state - with no pending transactions. - - """ - safe_to_update = False - repo_exists = self.exists() - if not repo_exists: - safe_to_update = True - else: - # If the repo exists, it must be in ok or modified - # sync_state. Any other sync_state at this point - # represents a logic error that should have been handled - # before now! - sync_safe = ((self.sync_state == ExternalStatus.STATUS_OK) or - (self.sync_state == ExternalStatus.MODEL_MODIFIED)) - if sync_safe: - # The clean_state must be STATUS_OK to update. Otherwise we - # are dirty or there was a missed error previously. - if self.clean_state == ExternalStatus.STATUS_OK: - safe_to_update = True - return safe_to_update - - def exists(self): - """Determine if the repo exists. This is indicated by: - - * sync_state is not EMPTY - - * if the sync_state is empty, then the valid states for - clean_state are default, empty or unknown. Anything else - and there was probably an internal logic error. - - NOTE(bja, 2017-10) For the moment we are considering a - sync_state of default or unknown to require user intervention, - but we may want to relax this convention. This is probably a - result of a network error or internal logic error but more - testing is needed. - - """ - is_empty = (self.sync_state == ExternalStatus.EMPTY) - clean_valid = ((self.clean_state == ExternalStatus.DEFAULT) or - (self.clean_state == ExternalStatus.EMPTY) or - (self.clean_state == ExternalStatus.UNKNOWN)) - - if is_empty and clean_valid: - exists = False - else: - exists = True - return exists - - -def check_safe_to_update_repos(tree_status): - """Check if *ALL* repositories are in a safe state to update. We don't - want to do a partial update of the repositories then die, leaving - the model in an inconsistent state. - - Note: if there is an update to do, the repositories will by - definiation be out of synce with the externals description, so we - can't use that as criteria for updating. - - """ - safe_to_update = True - for comp in tree_status: - stat = tree_status[comp] - safe_to_update &= stat.safe_to_update() - - return safe_to_update diff --git a/manage_externals/manic/global_constants.py b/manage_externals/manic/global_constants.py deleted file mode 100644 index 0e91cffc90..0000000000 --- a/manage_externals/manic/global_constants.py +++ /dev/null @@ -1,18 +0,0 @@ -"""Globals shared across modules -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import pprint - -EMPTY_STR = '' -LOCAL_PATH_INDICATOR = '.' -VERSION_SEPERATOR = '.' -LOG_FILE_NAME = 'manage_externals.log' -PPRINTER = pprint.PrettyPrinter(indent=4) - -VERBOSITY_DEFAULT = 0 -VERBOSITY_VERBOSE = 1 -VERBOSITY_DUMP = 2 diff --git a/manage_externals/manic/repository.py b/manage_externals/manic/repository.py deleted file mode 100644 index ea4230fb7b..0000000000 --- a/manage_externals/manic/repository.py +++ /dev/null @@ -1,98 +0,0 @@ -"""Base class representation of a repository -""" - -from .externals_description import ExternalsDescription -from .utils import fatal_error -from .global_constants import EMPTY_STR - - -class Repository(object): - """ - Class to represent and operate on a repository description. - """ - - def __init__(self, component_name, repo): - """ - Parse repo externals description - """ - self._name = component_name - self._protocol = repo[ExternalsDescription.PROTOCOL] - self._tag = repo[ExternalsDescription.TAG] - self._branch = repo[ExternalsDescription.BRANCH] - self._hash = repo[ExternalsDescription.HASH] - self._url = repo[ExternalsDescription.REPO_URL] - self._sparse = repo[ExternalsDescription.SPARSE] - - if self._url is EMPTY_STR: - fatal_error('repo must have a URL') - - if ((self._tag is EMPTY_STR) and (self._branch is EMPTY_STR) and - (self._hash is EMPTY_STR)): - fatal_error('{0} repo must have a branch, tag or hash element') - - ref_count = 0 - if self._tag is not EMPTY_STR: - ref_count += 1 - if self._branch is not EMPTY_STR: - ref_count += 1 - if self._hash is not EMPTY_STR: - ref_count += 1 - if ref_count != 1: - fatal_error('repo {0} must have exactly one of ' - 'tag, branch or hash.'.format(self._name)) - - def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive): # pylint: disable=unused-argument - """ - If the repo destination directory exists, ensure it is correct (from - correct URL, correct branch or tag), and possibly update the source. - If the repo destination directory does not exist, checkout the correce - branch or tag. - NB: is include as an argument for compatibility with - git functionality (repository_git.py) - """ - msg = ('DEV_ERROR: checkout method must be implemented in all ' - 'repository classes! {0}'.format(self.__class__.__name__)) - fatal_error(msg) - - def status(self, stat, repo_dir_path): # pylint: disable=unused-argument - """Report the status of the repo - - """ - msg = ('DEV_ERROR: status method must be implemented in all ' - 'repository classes! {0}'.format(self.__class__.__name__)) - fatal_error(msg) - - def submodules_file(self, repo_path=None): - # pylint: disable=no-self-use,unused-argument - """Stub for use by non-git VC systems""" - return None - - def url(self): - """Public access of repo url. - """ - return self._url - - def tag(self): - """Public access of repo tag - """ - return self._tag - - def branch(self): - """Public access of repo branch. - """ - return self._branch - - def hash(self): - """Public access of repo hash. - """ - return self._hash - - def name(self): - """Public access of repo name. - """ - return self._name - - def protocol(self): - """Public access of repo protocol. - """ - return self._protocol diff --git a/manage_externals/manic/repository_factory.py b/manage_externals/manic/repository_factory.py deleted file mode 100644 index 18c73ffc4b..0000000000 --- a/manage_externals/manic/repository_factory.py +++ /dev/null @@ -1,30 +0,0 @@ -"""Factory for creating and initializing the appropriate repository class -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -from .repository_git import GitRepository -from .repository_svn import SvnRepository -from .externals_description import ExternalsDescription -from .utils import fatal_error - - -def create_repository(component_name, repo_info, svn_ignore_ancestry=False): - """Determine what type of repository we have, i.e. git or svn, and - create the appropriate object. - - Can return None (e.g. if protocol is 'externals_only'). - """ - protocol = repo_info[ExternalsDescription.PROTOCOL].lower() - if protocol == 'git': - repo = GitRepository(component_name, repo_info) - elif protocol == 'svn': - repo = SvnRepository(component_name, repo_info, ignore_ancestry=svn_ignore_ancestry) - elif protocol == 'externals_only': - repo = None - else: - msg = 'Unknown repo protocol "{0}"'.format(protocol) - fatal_error(msg) - return repo diff --git a/manage_externals/manic/repository_git.py b/manage_externals/manic/repository_git.py deleted file mode 100644 index aab1a468a8..0000000000 --- a/manage_externals/manic/repository_git.py +++ /dev/null @@ -1,859 +0,0 @@ -"""Class for interacting with git repositories -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import copy -import os -import sys - -from .global_constants import EMPTY_STR, LOCAL_PATH_INDICATOR -from .global_constants import VERBOSITY_VERBOSE -from .repository import Repository -from .externals_status import ExternalStatus -from .externals_description import ExternalsDescription, git_submodule_status -from .utils import expand_local_url, split_remote_url, is_remote_url -from .utils import fatal_error, printlog -from .utils import execute_subprocess - - -class GitRepository(Repository): - """Class to represent and operate on a repository description. - - For testing purpose, all system calls to git should: - - * be isolated in separate functions with no application logic - * of the form: - - cmd = 'git -C {dirname} ...'.format(dirname=dirname).split() - - value = execute_subprocess(cmd, output_to_caller={T|F}, - status_to_caller={T|F}) - - return value - * be static methods (not rely on self) - * name as _git_subcommand_args(user_args) - - This convention allows easy unit testing of the repository logic - by mocking the specific calls to return predefined results. - - """ - - def __init__(self, component_name, repo): - """ - repo: ExternalsDescription. - """ - Repository.__init__(self, component_name, repo) - self._gitmodules = None - self._submods = None - - # ---------------------------------------------------------------- - # - # Public API, defined by Repository - # - # ---------------------------------------------------------------- - def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive): - """ - If the repo destination directory exists, ensure it is correct (from - correct URL, correct branch or tag), and possibly update the source. - If the repo destination directory does not exist, checkout the correct - branch or tag. - """ - repo_dir_path = os.path.join(base_dir_path, repo_dir_name) - repo_dir_exists = os.path.exists(repo_dir_path) - if (repo_dir_exists and not os.listdir( - repo_dir_path)) or not repo_dir_exists: - self._clone_repo(base_dir_path, repo_dir_name, verbosity) - self._checkout_ref(repo_dir_path, verbosity, recursive) - gmpath = os.path.join(repo_dir_path, - ExternalsDescription.GIT_SUBMODULES_FILENAME) - if os.path.exists(gmpath): - self._gitmodules = gmpath - self._submods = git_submodule_status(repo_dir_path) - else: - self._gitmodules = None - self._submods = None - - def status(self, stat, repo_dir_path): - """ - If the repo destination directory exists, ensure it is correct (from - correct URL, correct branch or tag), and possibly update the source. - If the repo destination directory does not exist, checkout the correct - branch or tag. - """ - self._check_sync(stat, repo_dir_path) - if os.path.exists(repo_dir_path): - self._status_summary(stat, repo_dir_path) - - def submodules_file(self, repo_path=None): - if repo_path is not None: - gmpath = os.path.join(repo_path, - ExternalsDescription.GIT_SUBMODULES_FILENAME) - if os.path.exists(gmpath): - self._gitmodules = gmpath - self._submods = git_submodule_status(repo_path) - - return self._gitmodules - - # ---------------------------------------------------------------- - # - # Internal work functions - # - # ---------------------------------------------------------------- - def _clone_repo(self, base_dir_path, repo_dir_name, verbosity): - """Clones repo_dir_name into base_dir_path. - """ - self._git_clone(self._url, os.path.join(base_dir_path, repo_dir_name), - verbosity=verbosity) - - def _current_ref(self, dirname): - """Determine the *name* associated with HEAD at dirname. - - If we're on a tag, then returns the tag name; otherwise, returns - the current hash. Returns an empty string if no reference can be - determined (e.g., if we're not actually in a git repository). - - If we're on a branch, then the branch name is also included in - the returned string (in addition to the tag / hash). - """ - ref_found = False - - # If we're exactly at a tag, use that as the current ref - tag_found, tag_name = self._git_current_tag(dirname) - if tag_found: - current_ref = tag_name - ref_found = True - - if not ref_found: - # Otherwise, use current hash as the current ref - hash_found, hash_name = self._git_current_hash(dirname) - if hash_found: - current_ref = hash_name - ref_found = True - - if ref_found: - # If we're on a branch, include branch name in current ref - branch_found, branch_name = self._git_current_branch(dirname) - if branch_found: - current_ref = "{} (branch {})".format(current_ref, branch_name) - else: - # If we still can't find a ref, return empty string. This - # can happen if we're not actually in a git repo - current_ref = '' - - return current_ref - - def _check_sync(self, stat, repo_dir_path): - """Determine whether a git repository is in-sync with the model - description. - - Because repos can have multiple remotes, the only criteria is - whether the branch or tag is the same. - - """ - if not os.path.exists(repo_dir_path): - # NOTE(bja, 2017-10) condition should have been determined - # by _Source() object and should never be here! - stat.sync_state = ExternalStatus.STATUS_ERROR - else: - git_dir = os.path.join(repo_dir_path, '.git') - if not os.path.exists(git_dir): - # NOTE(bja, 2017-10) directory exists, but no git repo - # info.... Can't test with subprocess git command - # because git will move up directory tree until it - # finds the parent repo git dir! - stat.sync_state = ExternalStatus.UNKNOWN - else: - self._check_sync_logic(stat, repo_dir_path) - - def _check_sync_logic(self, stat, repo_dir_path): - """Compare the underlying hashes of the currently checkout ref and the - expected ref. - - Output: sets the sync_state as well as the current and - expected ref in the input status object. - - """ - def compare_refs(current_ref, expected_ref): - """Compare the current and expected ref. - - """ - if current_ref == expected_ref: - status = ExternalStatus.STATUS_OK - else: - status = ExternalStatus.MODEL_MODIFIED - return status - - # get the full hash of the current commit - _, current_ref = self._git_current_hash(repo_dir_path) - - if self._branch: - if self._url == LOCAL_PATH_INDICATOR: - expected_ref = self._branch - else: - remote_name = self._remote_name_for_url(self._url, - repo_dir_path) - if not remote_name: - # git doesn't know about this remote. by definition - # this is a modified state. - expected_ref = "unknown_remote/{0}".format(self._branch) - else: - expected_ref = "{0}/{1}".format(remote_name, self._branch) - elif self._hash: - expected_ref = self._hash - elif self._tag: - expected_ref = self._tag - else: - msg = 'In repo "{0}": none of branch, hash or tag are set'.format( - self._name) - fatal_error(msg) - - # record the *names* of the current and expected branches - stat.current_version = self._current_ref(repo_dir_path) - stat.expected_version = copy.deepcopy(expected_ref) - - if current_ref == EMPTY_STR: - stat.sync_state = ExternalStatus.UNKNOWN - else: - # get the underlying hash of the expected ref - revparse_status, expected_ref_hash = self._git_revparse_commit( - expected_ref, repo_dir_path) - if revparse_status: - # We failed to get the hash associated with - # expected_ref. Maybe we should assign this to some special - # status, but for now we're just calling this out-of-sync to - # remain consistent with how this worked before. - stat.sync_state = ExternalStatus.MODEL_MODIFIED - else: - # compare the underlying hashes - stat.sync_state = compare_refs(current_ref, expected_ref_hash) - - @classmethod - def _remote_name_for_url(cls, remote_url, dirname): - """Return the remote name matching remote_url (or None) - - """ - git_output = cls._git_remote_verbose(dirname) - git_output = git_output.splitlines() - for line in git_output: - data = line.strip() - if not data: - continue - data = data.split() - name = data[0].strip() - url = data[1].strip() - if remote_url == url: - return name - return None - - def _create_remote_name(self): - """The url specified in the externals description file was not known - to git. We need to add it, which means adding a unique and - safe name.... - - The assigned name needs to be safe for git to use, e.g. can't - look like a path 'foo/bar' and work with both remote and local paths. - - Remote paths include but are not limited to: git, ssh, https, - github, gitlab, bitbucket, custom server, etc. - - Local paths can be relative or absolute. They may contain - shell variables, e.g. ${REPO_ROOT}/repo_name, or username - expansion, i.e. ~/ or ~someuser/. - - Relative paths must be at least one layer of redirection, i.e. - container/../ext_repo, but may be many layers deep, e.g. - container/../../../../../ext_repo - - NOTE(bja, 2017-11) - - The base name below may not be unique, for example if the - user has local paths like: - - /path/to/my/repos/nice_repo - /path/to/other/repos/nice_repo - - But the current implementation should cover most common - use cases for remotes and still provide usable names. - - """ - url = copy.deepcopy(self._url) - if is_remote_url(url): - url = split_remote_url(url) - else: - url = expand_local_url(url, self._name) - url = url.split('/') - repo_name = url[-1] - base_name = url[-2] - # repo name should nominally already be something that git can - # deal with. We need to remove other possibly troublesome - # punctuation, e.g. /, $, from the base name. - unsafe_characters = '!@#$%^&*()[]{}\\/,;~' - for unsafe in unsafe_characters: - base_name = base_name.replace(unsafe, '') - remote_name = "{0}_{1}".format(base_name, repo_name) - return remote_name - - def _checkout_ref(self, repo_dir, verbosity, submodules): - """Checkout the user supplied reference - if is True, recursively initialize and update - the repo's submodules - """ - # import pdb; pdb.set_trace() - if self._url.strip() == LOCAL_PATH_INDICATOR: - self._checkout_local_ref(verbosity, submodules, repo_dir) - else: - self._checkout_external_ref(verbosity, submodules, repo_dir) - - if self._sparse: - self._sparse_checkout(repo_dir, verbosity) - - - def _checkout_local_ref(self, verbosity, submodules, dirname): - """Checkout the reference considering the local repo only. Do not - fetch any additional remotes or specify the remote when - checkout out the ref. - if is True, recursively initialize and update - the repo's submodules - """ - if self._tag: - ref = self._tag - elif self._branch: - ref = self._branch - else: - ref = self._hash - - self._check_for_valid_ref(ref, remote_name=None, - dirname=dirname) - self._git_checkout_ref(ref, verbosity, submodules, dirname) - - def _checkout_external_ref(self, verbosity, submodules, dirname): - """Checkout the reference from a remote repository into dirname. - if is True, recursively initialize and update - the repo's submodules. - Note that this results in a 'detached HEAD' state if checking out - a branch, because we check out the remote branch rather than the - local. See https://github.com/ESMCI/manage_externals/issues/34 for - more discussion. - """ - if self._tag: - ref = self._tag - elif self._branch: - ref = self._branch - else: - ref = self._hash - - remote_name = self._remote_name_for_url(self._url, dirname) - if not remote_name: - remote_name = self._create_remote_name() - self._git_remote_add(remote_name, self._url, dirname) - self._git_fetch(remote_name, dirname) - - # NOTE(bja, 2018-03) we need to send separate ref and remote - # name to check_for_vaild_ref, but the combined name to - # checkout_ref! - self._check_for_valid_ref(ref, remote_name, dirname) - - if self._branch: - # Prepend remote name to branch. This means we avoid various - # special cases if the local branch is not tracking the remote or - # cannot be trivially fast-forwarded to match; but, it also - # means we end up in a 'detached HEAD' state. - ref = '{0}/{1}'.format(remote_name, ref) - self._git_checkout_ref(ref, verbosity, submodules, dirname) - - def _sparse_checkout(self, repo_dir, verbosity): - """Use git read-tree to thin the working tree.""" - cmd = ['cp', os.path.join(repo_dir, self._sparse), - os.path.join(repo_dir, - '.git/info/sparse-checkout')] - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - execute_subprocess(cmd) - self._git_sparse_checkout(verbosity, repo_dir) - - def _check_for_valid_ref(self, ref, remote_name, dirname): - """Try some basic sanity checks on the user supplied reference so we - can provide a more useful error message than calledprocess - error... - - remote_name can be NOne - """ - is_tag = self._ref_is_tag(ref, dirname) - is_branch = self._ref_is_branch(ref, remote_name, dirname) - is_hash = self._ref_is_hash(ref, dirname) - is_valid = is_tag or is_branch or is_hash - if not is_valid: - msg = ('In repo "{0}": reference "{1}" does not appear to be a ' - 'valid tag, branch or hash! Please verify the reference ' - 'name (e.g. spelling), is available from: {2} '.format( - self._name, ref, self._url)) - fatal_error(msg) - - if is_tag: - is_unique_tag, msg = self._is_unique_tag(ref, remote_name, - dirname) - if not is_unique_tag: - msg = ('In repo "{0}": tag "{1}" {2}'.format( - self._name, self._tag, msg)) - fatal_error(msg) - - return is_valid - - def _is_unique_tag(self, ref, remote_name, dirname): - """Verify that a reference is a valid tag and is unique (not a branch) - - Tags may be tag names, or SHA id's. It is also possible that a - branch and tag have the some name. - - Note: values returned by git_showref_* and git_revparse are - shell return codes, which are zero for success, non-zero for - error! - - """ - is_tag = self._ref_is_tag(ref, dirname) - is_branch = self._ref_is_branch(ref, remote_name, dirname) - is_hash = self._ref_is_hash(ref, dirname) - - msg = '' - is_unique_tag = False - if is_tag and not is_branch: - # unique tag - msg = 'is ok' - is_unique_tag = True - elif is_tag and is_branch: - msg = ('is both a branch and a tag. git may checkout the branch ' - 'instead of the tag depending on your version of git.') - is_unique_tag = False - elif not is_tag and is_branch: - msg = ('is a branch, and not a tag. If you intended to checkout ' - 'a branch, please change the externals description to be ' - 'a branch. If you intended to checkout a tag, it does not ' - 'exist. Please check the name.') - is_unique_tag = False - else: # not is_tag and not is_branch: - if is_hash: - # probably a sha1 or HEAD, etc, we call it a tag - msg = 'is ok' - is_unique_tag = True - else: - # undetermined state. - msg = ('does not appear to be a valid tag, branch or hash! ' - 'Please check the name and repository.') - is_unique_tag = False - - return is_unique_tag, msg - - def _ref_is_tag(self, ref, dirname): - """Verify that a reference is a valid tag according to git. - - Note: values returned by git_showref_* and git_revparse are - shell return codes, which are zero for success, non-zero for - error! - """ - is_tag = False - value = self._git_showref_tag(ref, dirname) - if value == 0: - is_tag = True - return is_tag - - def _ref_is_branch(self, ref, remote_name, dirname): - """Verify if a ref is any kind of branch (local, tracked remote, - untracked remote). - - remote_name can be None. - """ - local_branch = False - remote_branch = False - if remote_name: - remote_branch = self._ref_is_remote_branch(ref, remote_name, - dirname) - local_branch = self._ref_is_local_branch(ref, dirname) - - is_branch = False - if local_branch or remote_branch: - is_branch = True - return is_branch - - def _ref_is_local_branch(self, ref, dirname): - """Verify that a reference is a valid branch according to git. - - show-ref branch returns local branches that have been - previously checked out. It will not necessarily pick up - untracked remote branches. - - Note: values returned by git_showref_* and git_revparse are - shell return codes, which are zero for success, non-zero for - error! - - """ - is_branch = False - value = self._git_showref_branch(ref, dirname) - if value == 0: - is_branch = True - return is_branch - - def _ref_is_remote_branch(self, ref, remote_name, dirname): - """Verify that a reference is a valid branch according to git. - - show-ref branch returns local branches that have been - previously checked out. It will not necessarily pick up - untracked remote branches. - - Note: values returned by git_showref_* and git_revparse are - shell return codes, which are zero for success, non-zero for - error! - - """ - is_branch = False - value = self._git_lsremote_branch(ref, remote_name, dirname) - if value == 0: - is_branch = True - return is_branch - - def _ref_is_commit(self, ref, dirname): - """Verify that a reference is a valid commit according to git. - - This could be a tag, branch, sha1 id, HEAD and potentially others... - - Note: values returned by git_showref_* and git_revparse are - shell return codes, which are zero for success, non-zero for - error! - """ - is_commit = False - value, _ = self._git_revparse_commit(ref, dirname) - if value == 0: - is_commit = True - return is_commit - - def _ref_is_hash(self, ref, dirname): - """Verify that a reference is a valid hash according to git. - - Git doesn't seem to provide an exact way to determine if user - supplied reference is an actual hash. So we verify that the - ref is a valid commit and return the underlying commit - hash. Then check that the commit hash begins with the user - supplied string. - - Note: values returned by git_showref_* and git_revparse are - shell return codes, which are zero for success, non-zero for - error! - - """ - is_hash = False - status, git_output = self._git_revparse_commit(ref, dirname) - if status == 0: - if git_output.strip().startswith(ref): - is_hash = True - return is_hash - - def _status_summary(self, stat, repo_dir_path): - """Determine the clean/dirty status of a git repository - - """ - git_output = self._git_status_porcelain_v1z(repo_dir_path) - is_dirty = self._status_v1z_is_dirty(git_output) - if is_dirty: - stat.clean_state = ExternalStatus.DIRTY - else: - stat.clean_state = ExternalStatus.STATUS_OK - - # Now save the verbose status output incase the user wants to - # see it. - stat.status_output = self._git_status_verbose(repo_dir_path) - - @staticmethod - def _status_v1z_is_dirty(git_output): - """Parse the git status output from --porcelain=v1 -z and determine if - the repo status is clean or dirty. Dirty means: - - * modified files - * missing files - * added files - * removed - * renamed - * unmerged - - Whether untracked files are considered depends on how the status - command was run (i.e., whether it was run with the '-u' option). - - NOTE: Based on the above definition, the porcelain status - should be an empty string to be considered 'clean'. Of course - this assumes we only get an empty string from an status - command on a clean checkout, and not some error - condition... Could alse use 'git diff --quiet'. - - """ - is_dirty = False - if git_output: - is_dirty = True - return is_dirty - - # ---------------------------------------------------------------- - # - # system call to git for information gathering - # - # ---------------------------------------------------------------- - @staticmethod - def _git_current_hash(dirname): - """Return the full hash of the currently checked-out version. - - Returns a tuple, (hash_found, hash), where hash_found is a - logical specifying whether a hash was found for HEAD (False - could mean we're not in a git repository at all). (If hash_found - is False, then hash is ''.) - """ - status, git_output = GitRepository._git_revparse_commit("HEAD", - dirname) - hash_found = not status - if not hash_found: - git_output = '' - return hash_found, git_output - - @staticmethod - def _git_current_remote_branch(dirname): - """Determines the name of the current remote branch, if any. - - if dir is None, uses the cwd. - - Returns a tuple, (branch_found, branch_name), where branch_found - is a bool specifying whether a branch name was found for - HEAD. (If branch_found is False, then branch_name is ''). - branch_name is in the format '$remote/$branch', e.g. 'origin/foo'. - """ - branch_found = False - branch_name = '' - - cmd = 'git -C {dirname} log -n 1 --pretty=%d HEAD'.format( - dirname=dirname).split() - status, git_output = execute_subprocess(cmd, - output_to_caller=True, - status_to_caller=True) - branch_found = 'HEAD,' in git_output - if branch_found: - # git_output is of the form " (HEAD, origin/blah)" - branch_name = git_output.split(',')[1].strip()[:-1] - return branch_found, branch_name - - @staticmethod - def _git_current_branch(dirname): - """Determines the name of the current local branch. - - Returns a tuple, (branch_found, branch_name), where branch_found - is a bool specifying whether a branch name was found for - HEAD. (If branch_found is False, then branch_name is ''.) - Note that currently we check out the remote branch rather than - the local, so this command does not return the just-checked-out - branch. See _git_current_remote_branch. - """ - cmd = 'git -C {dirname} symbolic-ref --short -q HEAD'.format( - dirname=dirname).split() - status, git_output = execute_subprocess(cmd, - output_to_caller=True, - status_to_caller=True) - branch_found = not status - if branch_found: - git_output = git_output.strip() - else: - git_output = '' - return branch_found, git_output - - @staticmethod - def _git_current_tag(dirname): - """Determines the name tag corresponding to HEAD (if any). - - if dirname is None, uses the cwd. - - Returns a tuple, (tag_found, tag_name), where tag_found is a - bool specifying whether we found a tag name corresponding to - HEAD. (If tag_found is False, then tag_name is ''.) - """ - cmd = 'git -C {dirname} describe --exact-match --tags HEAD'.format( - dirname=dirname).split() - status, git_output = execute_subprocess(cmd, - output_to_caller=True, - status_to_caller=True) - tag_found = not status - if tag_found: - git_output = git_output.strip() - else: - git_output = '' - return tag_found, git_output - - @staticmethod - def _git_showref_tag(ref, dirname): - """Run git show-ref check if the user supplied ref is a tag. - - could also use git rev-parse --quiet --verify tagname^{tag} - """ - cmd = ('git -C {dirname} show-ref --quiet --verify refs/tags/{ref}' - .format(dirname=dirname, ref=ref).split()) - status = execute_subprocess(cmd, status_to_caller=True) - return status - - @staticmethod - def _git_showref_branch(ref, dirname): - """Run git show-ref check if the user supplied ref is a local or - tracked remote branch. - - """ - cmd = ('git -C {dirname} show-ref --quiet --verify refs/heads/{ref}' - .format(dirname=dirname, ref=ref).split()) - status = execute_subprocess(cmd, status_to_caller=True) - return status - - @staticmethod - def _git_lsremote_branch(ref, remote_name, dirname): - """Run git ls-remote to check if the user supplied ref is a remote - branch that is not being tracked - - """ - cmd = ('git -C {dirname} ls-remote --exit-code --heads ' - '{remote_name} {ref}').format( - dirname=dirname, remote_name=remote_name, ref=ref).split() - status, output = execute_subprocess(cmd, status_to_caller=True, output_to_caller=True) - if not status and not f"refs/heads/{ref}" in output: - # In this case the ref is contained in the branch name but is not the complete branch name - return -1 - return status - - @staticmethod - def _git_revparse_commit(ref, dirname): - """Run git rev-parse to detect if a reference is a SHA, HEAD or other - valid commit. - - """ - cmd = ('git -C {dirname} rev-parse --quiet --verify {ref}^{commit}' - .format(dirname=dirname, ref=ref, commit='{commit}').split()) - status, git_output = execute_subprocess(cmd, status_to_caller=True, - output_to_caller=True) - git_output = git_output.strip() - return status, git_output - - @staticmethod - def _git_status_porcelain_v1z(dirname): - """Run git status to obtain repository information. - - This is run with '--untracked=no' to ignore untracked files. - - The machine-portable format that is guaranteed not to change - between git versions or *user configuration*. - - """ - cmd = ('git -C {dirname} status --untracked-files=no --porcelain -z' - .format(dirname=dirname)).split() - git_output = execute_subprocess(cmd, output_to_caller=True) - return git_output - - @staticmethod - def _git_status_verbose(dirname): - """Run the git status command to obtain repository information. - """ - cmd = 'git -C {dirname} status'.format(dirname=dirname).split() - git_output = execute_subprocess(cmd, output_to_caller=True) - return git_output - - @staticmethod - def _git_remote_verbose(dirname): - """Run the git remote command to obtain repository information. - - Returned string is of the form: - myfork git@github.com:johnpaulalex/manage_externals_jp.git (fetch) - myfork git@github.com:johnpaulalex/manage_externals_jp.git (push) - """ - cmd = 'git -C {dirname} remote --verbose'.format( - dirname=dirname).split() - return execute_subprocess(cmd, output_to_caller=True) - - @staticmethod - def has_submodules(repo_dir_path): - """Return True iff the repository at has a - '.gitmodules' file - """ - fname = os.path.join(repo_dir_path, - ExternalsDescription.GIT_SUBMODULES_FILENAME) - - return os.path.exists(fname) - - # ---------------------------------------------------------------- - # - # system call to git for sideffects modifying the working tree - # - # ---------------------------------------------------------------- - @staticmethod - def _git_clone(url, repo_dir_name, verbosity): - """Clones url into repo_dir_name. - """ - cmd = 'git clone --quiet {url} {repo_dir_name}'.format( - url=url, repo_dir_name=repo_dir_name).split() - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - execute_subprocess(cmd) - - @staticmethod - def _git_remote_add(name, url, dirname): - """Run the git remote command for the side effect of adding a remote - """ - cmd = 'git -C {dirname} remote add {name} {url}'.format( - dirname=dirname, name=name, url=url).split() - execute_subprocess(cmd) - - @staticmethod - def _git_fetch(remote_name, dirname): - """Run the git fetch command for the side effect of updating the repo - """ - cmd = 'git -C {dirname} fetch --quiet --tags {remote_name}'.format( - dirname=dirname, remote_name=remote_name).split() - execute_subprocess(cmd) - - @staticmethod - def _git_checkout_ref(ref, verbosity, submodules, dirname): - """Run the git checkout command for the side effect of updating the repo - - Param: ref is a reference to a local or remote object in the - form 'origin/my_feature', or 'tag1'. - - """ - cmd = 'git -C {dirname} checkout --quiet {ref}'.format( - dirname=dirname, ref=ref).split() - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - execute_subprocess(cmd) - if submodules: - GitRepository._git_update_submodules(verbosity, dirname) - - @staticmethod - def _git_sparse_checkout(verbosity, dirname): - """Configure repo via read-tree.""" - cmd = 'git -C {dirname} config core.sparsecheckout true'.format( - dirname=dirname).split() - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - execute_subprocess(cmd) - cmd = 'git -C {dirname} read-tree -mu HEAD'.format( - dirname=dirname).split() - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - execute_subprocess(cmd) - - @staticmethod - def _git_update_submodules(verbosity, dirname): - """Run git submodule update for the side effect of updating this - repo's submodules. - """ - # due to https://vielmetti.typepad.com/logbook/2022/10/git-security-fixes-lead-to-fatal-transport-file-not-allowed-error-in-ci-systems-cve-2022-39253.html - # submodules from file doesn't work without overriding the protocol, this is done - # for testing submodule support but should not be done in practice - file_protocol = "" - if 'unittest' in sys.modules.keys(): - file_protocol = "-c protocol.file.allow=always" - - # First, verify that we have a .gitmodules file - if os.path.exists( - os.path.join(dirname, - ExternalsDescription.GIT_SUBMODULES_FILENAME)): - cmd = ('git {file_protocol} -C {dirname} submodule update --init --recursive' - .format(file_protocol=file_protocol, dirname=dirname)).split() - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - - execute_subprocess(cmd) diff --git a/manage_externals/manic/repository_svn.py b/manage_externals/manic/repository_svn.py deleted file mode 100644 index 32a71184b4..0000000000 --- a/manage_externals/manic/repository_svn.py +++ /dev/null @@ -1,291 +0,0 @@ -"""Class for interacting with svn repositories -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import os -import re -import xml.etree.ElementTree as ET - -from .global_constants import EMPTY_STR, VERBOSITY_VERBOSE -from .repository import Repository -from .externals_status import ExternalStatus -from .utils import fatal_error, indent_string, printlog -from .utils import execute_subprocess - - -class SvnRepository(Repository): - """ - Class to represent and operate on a repository description. - - For testing purpose, all system calls to svn should: - - * be isolated in separate functions with no application logic - * of the form: - - cmd = ['svn', ...] - - value = execute_subprocess(cmd, output_to_caller={T|F}, - status_to_caller={T|F}) - - return value - * be static methods (not rely on self) - * name as _svn_subcommand_args(user_args) - - This convention allows easy unit testing of the repository logic - by mocking the specific calls to return predefined results. - - """ - RE_URLLINE = re.compile(r'^URL:') - - def __init__(self, component_name, repo, ignore_ancestry=False): - """ - Parse repo (a XML element). - """ - Repository.__init__(self, component_name, repo) - if 'github.com' in self._url: - msg = "SVN access to github.com is no longer supported" - fatal_error(msg) - self._ignore_ancestry = ignore_ancestry - if self._url.endswith('/'): - # there is already a '/' separator in the URL; no need to add another - url_sep = '' - else: - url_sep = '/' - if self._branch: - self._url = self._url + url_sep + self._branch - elif self._tag: - self._url = self._url + url_sep + self._tag - else: - msg = "DEV_ERROR in svn repository. Shouldn't be here!" - fatal_error(msg) - - # ---------------------------------------------------------------- - # - # Public API, defined by Repository - # - # ---------------------------------------------------------------- - def checkout(self, base_dir_path, repo_dir_name, verbosity, recursive): # pylint: disable=unused-argument - """Checkout or update the working copy - - If the repo destination directory exists, switch the sandbox to - match the externals description. - - If the repo destination directory does not exist, checkout the - correct branch or tag. - NB: is include as an argument for compatibility with - git functionality (repository_git.py) - - """ - repo_dir_path = os.path.join(base_dir_path, repo_dir_name) - if os.path.exists(repo_dir_path): - cwd = os.getcwd() - os.chdir(repo_dir_path) - self._svn_switch(self._url, self._ignore_ancestry, verbosity) - # svn switch can lead to a conflict state, but it gives a - # return code of 0. So now we need to make sure that we're - # in a clean (non-conflict) state. - self._abort_if_dirty(repo_dir_path, - "Expected clean state following switch") - os.chdir(cwd) - else: - self._svn_checkout(self._url, repo_dir_path, verbosity) - - def status(self, stat, repo_dir_path): - """ - Check and report the status of the repository - """ - self._check_sync(stat, repo_dir_path) - if os.path.exists(repo_dir_path): - self._status_summary(stat, repo_dir_path) - - # ---------------------------------------------------------------- - # - # Internal work functions - # - # ---------------------------------------------------------------- - def _check_sync(self, stat, repo_dir_path): - """Check to see if repository directory exists and is at the expected - url. Return: status object - - """ - if not os.path.exists(repo_dir_path): - # NOTE(bja, 2017-10) this state should have been handled by - # the source object and we never get here! - stat.sync_state = ExternalStatus.STATUS_ERROR - else: - svn_output = self._svn_info(repo_dir_path) - if not svn_output: - # directory exists, but info returned nothing. .svn - # directory removed or incomplete checkout? - stat.sync_state = ExternalStatus.UNKNOWN - else: - stat.sync_state, stat.current_version = \ - self._check_url(svn_output, self._url) - stat.expected_version = '/'.join(self._url.split('/')[3:]) - - def _abort_if_dirty(self, repo_dir_path, message): - """Check if the repo is in a dirty state; if so, abort with a - helpful message. - - """ - - stat = ExternalStatus() - self._status_summary(stat, repo_dir_path) - if stat.clean_state != ExternalStatus.STATUS_OK: - status = self._svn_status_verbose(repo_dir_path) - status = indent_string(status, 4) - errmsg = """In directory - {cwd} - -svn status now shows: -{status} - -ERROR: {message} - -One possible cause of this problem is that there may have been untracked -files in your working directory that had the same name as tracked files -in the new revision. - -To recover: Clean up the above directory (resolving conflicts, etc.), -then rerun checkout_externals. -""".format(cwd=repo_dir_path, message=message, status=status) - - fatal_error(errmsg) - - @staticmethod - def _check_url(svn_output, expected_url): - """Determine the svn url from svn info output and return whether it - matches the expected value. - - """ - url = None - for line in svn_output.splitlines(): - if SvnRepository.RE_URLLINE.match(line): - url = line.split(': ')[1].strip() - break - if not url: - status = ExternalStatus.UNKNOWN - elif url == expected_url: - status = ExternalStatus.STATUS_OK - else: - status = ExternalStatus.MODEL_MODIFIED - - if url: - current_version = '/'.join(url.split('/')[3:]) - else: - current_version = EMPTY_STR - - return status, current_version - - def _status_summary(self, stat, repo_dir_path): - """Report whether the svn repository is in-sync with the model - description and whether the sandbox is clean or dirty. - - """ - svn_output = self._svn_status_xml(repo_dir_path) - is_dirty = self.xml_status_is_dirty(svn_output) - if is_dirty: - stat.clean_state = ExternalStatus.DIRTY - else: - stat.clean_state = ExternalStatus.STATUS_OK - - # Now save the verbose status output incase the user wants to - # see it. - stat.status_output = self._svn_status_verbose(repo_dir_path) - - @staticmethod - def xml_status_is_dirty(svn_output): - """Parse svn status xml output and determine if the working copy is - clean or dirty. Dirty is defined as: - - * modified files - * added files - * deleted files - * missing files - - Unversioned files do not affect the clean/dirty status. - - 'external' is also an acceptable state - - """ - # pylint: disable=invalid-name - SVN_EXTERNAL = 'external' - SVN_UNVERSIONED = 'unversioned' - # pylint: enable=invalid-name - - is_dirty = False - try: - xml_status = ET.fromstring(svn_output) - except BaseException: - fatal_error( - "SVN returned invalid XML message {}".format(svn_output)) - xml_target = xml_status.find('./target') - entries = xml_target.findall('./entry') - for entry in entries: - status = entry.find('./wc-status') - item = status.get('item') - if item == SVN_EXTERNAL: - continue - if item == SVN_UNVERSIONED: - continue - is_dirty = True - break - return is_dirty - - # ---------------------------------------------------------------- - # - # system call to svn for information gathering - # - # ---------------------------------------------------------------- - @staticmethod - def _svn_info(repo_dir_path): - """Return results of svn info command - """ - cmd = ['svn', 'info', repo_dir_path] - output = execute_subprocess(cmd, output_to_caller=True) - return output - - @staticmethod - def _svn_status_verbose(repo_dir_path): - """capture the full svn status output - """ - cmd = ['svn', 'status', repo_dir_path] - svn_output = execute_subprocess(cmd, output_to_caller=True) - return svn_output - - @staticmethod - def _svn_status_xml(repo_dir_path): - """ - Get status of the subversion sandbox in repo_dir - """ - cmd = ['svn', 'status', '--xml', repo_dir_path] - svn_output = execute_subprocess(cmd, output_to_caller=True) - return svn_output - - # ---------------------------------------------------------------- - # - # system call to svn for sideffects modifying the working tree - # - # ---------------------------------------------------------------- - @staticmethod - def _svn_checkout(url, repo_dir_path, verbosity): - """ - Checkout a subversion repository (repo_url) to checkout_dir. - """ - cmd = ['svn', 'checkout', '--quiet', url, repo_dir_path] - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - execute_subprocess(cmd) - - @staticmethod - def _svn_switch(url, ignore_ancestry, verbosity): - """ - Switch branches for in an svn sandbox - """ - cmd = ['svn', 'switch', '--quiet'] - if ignore_ancestry: - cmd.append('--ignore-ancestry') - cmd.append(url) - if verbosity >= VERBOSITY_VERBOSE: - printlog(' {0}'.format(' '.join(cmd))) - execute_subprocess(cmd) diff --git a/manage_externals/manic/sourcetree.py b/manage_externals/manic/sourcetree.py deleted file mode 100644 index cf2a5b7569..0000000000 --- a/manage_externals/manic/sourcetree.py +++ /dev/null @@ -1,425 +0,0 @@ -""" -Classes to represent an externals config file (SourceTree) and the components -within it (_External). -""" - -import errno -import logging -import os - -from .externals_description import ExternalsDescription -from .externals_description import read_externals_description_file -from .externals_description import create_externals_description -from .repository_factory import create_repository -from .repository_git import GitRepository -from .externals_status import ExternalStatus -from .utils import fatal_error, printlog -from .global_constants import EMPTY_STR, LOCAL_PATH_INDICATOR -from .global_constants import VERBOSITY_VERBOSE - -class _External(object): - """ - A single component hosted in an external repository (and any children). - - The component may or may not be checked-out upon construction. - """ - # pylint: disable=R0902 - - def __init__(self, root_dir, name, local_path, required, subexternals_path, - repo, svn_ignore_ancestry, subexternal_sourcetree): - """Create a single external component (checked out or not). - - Input: - root_dir : string - the (checked-out) parent repo's root dir. - local_path : string - this external's (checked-out) subdir relative - to root_dir, e.g. "components/mom" - repo: Repository - the repo object for this external. Can be None (e.g. if this external just refers to another external file). - - name : string - name of this external (as named by the parent - reference). May or may not correspond to something in the path. - - ext_description : dict - source ExternalsDescription object - - svn_ignore_ancestry : bool - use --ignore-externals with svn switch - - subexternals_path: string - path to sub-externals config file, if any. Relative to local_path, or special value 'none'. - subexternal_sourcetree: SourceTree - corresponding to subexternals_path, if subexternals_path exists (it might not, if it is not checked out yet). - """ - self._name = name - self._required = required - - self._stat = None # Populated in status() - - self._local_path = local_path - # _repo_dir_path : full repository directory, e.g. - # "/components/mom" - repo_dir = os.path.join(root_dir, local_path) - self._repo_dir_path = os.path.abspath(repo_dir) - # _base_dir_path : base directory *containing* the repository, e.g. - # "/components" - self._base_dir_path = os.path.dirname(self._repo_dir_path) - # _repo_dir_name : base_dir_path + repo_dir_name = repo_dir_path - # e.g., "mom" - self._repo_dir_name = os.path.basename(self._repo_dir_path) - self._repo = repo - - # Does this component have subcomponents aka an externals config? - self._subexternals_path = subexternals_path - self._subexternal_sourcetree = subexternal_sourcetree - - - def get_name(self): - """ - Return the external object's name - """ - return self._name - - def get_local_path(self): - """ - Return the external object's path - """ - return self._local_path - - def get_repo_dir_path(self): - return self._repo_dir_path - - def get_subexternals_path(self): - return self._subexternals_path - - def get_repo(self): - return self._repo - - def status(self, force=False, print_progress=False): - """ - Returns status of this component and all subcomponents. - - Returns a dict mapping our local path (not component name!) to an - ExternalStatus dict. Any subcomponents will have their own top-level - path keys. Note the return value includes entries for this and all - subcomponents regardless of whether they are locally installed or not. - - Side-effect: If self._stat is empty or force is True, calculates _stat. - """ - calc_stat = force or not self._stat - - if calc_stat: - self._stat = ExternalStatus() - self._stat.path = self.get_local_path() - if not self._required: - self._stat.source_type = ExternalStatus.OPTIONAL - elif self._local_path == LOCAL_PATH_INDICATOR: - # LOCAL_PATH_INDICATOR, '.' paths, are standalone - # component directories that are not managed by - # checkout_subexternals. - self._stat.source_type = ExternalStatus.STANDALONE - else: - # managed by checkout_subexternals - self._stat.source_type = ExternalStatus.MANAGED - - subcomponent_stats = {} - if not os.path.exists(self._repo_dir_path): - if calc_stat: - # No local repository. - self._stat.sync_state = ExternalStatus.EMPTY - msg = ('status check: repository directory for "{0}" does not ' - 'exist.'.format(self._name)) - logging.info(msg) - self._stat.current_version = 'not checked out' - # NOTE(bja, 2018-01) directory doesn't exist, so we cannot - # use repo to determine the expected version. We just take - # a best-guess based on the assumption that only tag or - # branch should be set, but not both. - if not self._repo: - self._stat.expected_version = 'unknown' - else: - self._stat.expected_version = self._repo.tag() + self._repo.branch() - else: - # Merge local repository state (e.g. clean/dirty) into self._stat. - if calc_stat and self._repo: - self._repo.status(self._stat, self._repo_dir_path) - - # Status of subcomponents, if any. - if self._subexternals_path and self._subexternal_sourcetree: - cwd = os.getcwd() - # SourceTree.status() expects to be called from the correct - # root directory. - os.chdir(self._repo_dir_path) - subcomponent_stats = self._subexternal_sourcetree.status(self._local_path, force=force, print_progress=print_progress) - os.chdir(cwd) - - # Merge our status + subcomponent statuses into one return dict keyed - # by component path. - all_stats = {} - # don't add the root component because we don't manage it - # and can't provide useful info about it. - if self._local_path != LOCAL_PATH_INDICATOR: - # store the stats under the local_path, not comp name so - # it will be sorted correctly - all_stats[self._stat.path] = self._stat - - if subcomponent_stats: - all_stats.update(subcomponent_stats) - - return all_stats - - def checkout(self, verbosity): - """ - If the repo destination directory exists, ensure it is correct (from - correct URL, correct branch or tag), and possibly updateit. - If the repo destination directory does not exist, checkout the correct - branch or tag. - Does not check out sub-externals, see SourceTree.checkout(). - """ - # Make sure we are in correct location - if not os.path.exists(self._repo_dir_path): - # repository directory doesn't exist. Need to check it - # out, and for that we need the base_dir_path to exist - try: - os.makedirs(self._base_dir_path) - except OSError as error: - if error.errno != errno.EEXIST: - msg = 'Could not create directory "{0}"'.format( - self._base_dir_path) - fatal_error(msg) - - if not self._stat: - self.status() - assert self._stat - - if self._stat.source_type != ExternalStatus.STANDALONE: - if verbosity >= VERBOSITY_VERBOSE: - # NOTE(bja, 2018-01) probably do not want to pass - # verbosity in this case, because if (verbosity == - # VERBOSITY_DUMP), then the previous status output would - # also be dumped, adding noise to the output. - self._stat.log_status_message(VERBOSITY_VERBOSE) - - if self._repo: - if self._stat.sync_state == ExternalStatus.STATUS_OK: - # If we're already in sync, avoid showing verbose output - # from the checkout command, unless the verbosity level - # is 2 or more. - checkout_verbosity = verbosity - 1 - else: - checkout_verbosity = verbosity - - self._repo.checkout(self._base_dir_path, self._repo_dir_name, - checkout_verbosity, self.clone_recursive()) - - def replace_subexternal_sourcetree(self, sourcetree): - self._subexternal_sourcetree = sourcetree - - def clone_recursive(self): - 'Return True iff any .gitmodules files should be processed' - # Try recursive .gitmodules unless there is an externals entry - recursive = not self._subexternals_path - - return recursive - - -class SourceTree(object): - """ - SourceTree represents a group of managed externals. - - Those externals may not be checked out locally yet, they might only - have Repository objects pointing to their respective repositories. - """ - - @classmethod - def from_externals_file(cls, parent_repo_dir_path, parent_repo, - externals_path): - """Creates a SourceTree representing the given externals file. - - Looks up a git submodules file as an optional backup if there is no - externals file specified. - - Returns None if there is no externals file (i.e. it's None or 'none'), - or if the externals file hasn't been checked out yet. - - parent_repo_dir_path: parent repo root dir - parent_repo: parent repo. - externals_path: path to externals file, relative to parent_repo_dir_path. - """ - if not os.path.exists(parent_repo_dir_path): - # NOTE(bja, 2017-10) repository has not been checked out - # yet, can't process the externals file. Assume we are - # checking status before code is checkoud out and this - # will be handled correctly later. - return None - - if externals_path.lower() == 'none': - # With explicit 'none', do not look for git submodules file. - return None - - cwd = os.getcwd() - os.chdir(parent_repo_dir_path) - - if not externals_path: - if GitRepository.has_submodules(parent_repo_dir_path): - externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME - else: - return None - - if not os.path.exists(externals_path): - # NOTE(bja, 2017-10) this check is redundant with the one - # in read_externals_description_file! - msg = ('Externals description file "{0}" ' - 'does not exist! In directory: {1}'.format( - externals_path, parent_repo_dir_path)) - fatal_error(msg) - - externals_root = parent_repo_dir_path - # model_data is a dict-like object which mirrors the file format. - model_data = read_externals_description_file(externals_root, - externals_path) - # ext_description is another dict-like object (see ExternalsDescription) - ext_description = create_externals_description(model_data, - parent_repo=parent_repo) - externals_sourcetree = SourceTree(externals_root, ext_description) - os.chdir(cwd) - return externals_sourcetree - - def __init__(self, root_dir, ext_description, svn_ignore_ancestry=False): - """ - Build a SourceTree object from an ExternalDescription. - - root_dir: the (checked-out) parent repo root dir. - """ - self._root_dir = os.path.abspath(root_dir) - self._all_components = {} # component_name -> _External - self._required_compnames = [] - for comp, desc in ext_description.items(): - local_path = desc[ExternalsDescription.PATH] - required = desc[ExternalsDescription.REQUIRED] - repo_info = desc[ExternalsDescription.REPO] - subexternals_path = desc[ExternalsDescription.EXTERNALS] - - repo = create_repository(comp, - repo_info, - svn_ignore_ancestry=svn_ignore_ancestry) - - sourcetree = None - # Treat a .gitmodules file as a backup externals config - if not subexternals_path: - parent_repo_dir_path = os.path.abspath(os.path.join(root_dir, - local_path)) - if GitRepository.has_submodules(parent_repo_dir_path): - subexternals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME - - # Might return None (if the subexternal isn't checked out yet, or subexternal is None or 'none') - subexternal_sourcetree = SourceTree.from_externals_file( - os.path.join(self._root_dir, local_path), - repo, - subexternals_path) - src = _External(self._root_dir, comp, local_path, required, - subexternals_path, repo, svn_ignore_ancestry, - subexternal_sourcetree) - - self._all_components[comp] = src - if required: - self._required_compnames.append(comp) - - def status(self, relative_path_base=LOCAL_PATH_INDICATOR, - force=False, print_progress=False): - """Return a dictionary of local path->ExternalStatus. - - Notes about the returned dictionary: - * It is keyed by local path (e.g. 'components/mom'), not by - component name (e.g. 'mom'). - * It contains top-level keys for all traversed components, whether - discovered by recursion or top-level. - * It contains entries for all components regardless of whether they - are locally installed or not, or required or optional. -x """ - load_comps = self._all_components.keys() - - summary = {} # Holds merged statuses from all components. - for comp in load_comps: - if print_progress: - printlog('{0}, '.format(comp), end='') - stat = self._all_components[comp].status(force=force, - print_progress=print_progress) - - # Returned status dictionary is keyed by local path; prepend - # relative_path_base if not already there. - stat_final = {} - for name in stat.keys(): - if stat[name].path.startswith(relative_path_base): - stat_final[name] = stat[name] - else: - modified_path = os.path.join(relative_path_base, - stat[name].path) - stat_final[modified_path] = stat[name] - stat_final[modified_path].path = modified_path - summary.update(stat_final) - - return summary - - def _find_installed_optional_components(self): - """Returns a list of installed optional component names, if any.""" - installed_comps = [] - for comp_name, ext in self._all_components.items(): - if comp_name in self._required_compnames: - continue - # Note that in practice we expect this status to be cached. - path_to_stat = ext.status() - - # If any part of this component exists locally, consider it - # installed and therefore eligible for updating. - if any(s.sync_state != ExternalStatus.EMPTY - for s in path_to_stat.values()): - installed_comps.append(comp_name) - return installed_comps - - def checkout(self, verbosity, load_all, load_comp=None): - """ - Checkout or update indicated components into the configured subdirs. - - If load_all is True, checkout all externals (required + optional), recursively. - If load_all is False and load_comp is set, checkout load_comp (and any required subexternals, plus any optional subexternals that are already checked out, recursively) - If load_all is False and load_comp is None, checkout all required externals, plus any optionals that are already checked out, recursively. - """ - if load_all: - tmp_comps = self._all_components.keys() - elif load_comp is not None: - tmp_comps = [load_comp] - else: - local_optional_compnames = self._find_installed_optional_components() - tmp_comps = self._required_compnames + local_optional_compnames - if local_optional_compnames: - printlog('Found locally installed optional components: ' + - ', '.join(local_optional_compnames)) - bad_compnames = set(local_optional_compnames) - set(self._all_components.keys()) - if bad_compnames: - printlog('Internal error: found locally installed components that are not in the global list of all components: ' + ','.join(bad_compnames)) - - if verbosity >= VERBOSITY_VERBOSE: - printlog('Checking out externals: ') - else: - printlog('Checking out externals: ', end='') - - # Sort by path so that if paths are nested the - # parent repo is checked out first. - load_comps = sorted(tmp_comps, key=lambda comp: self._all_components[comp].get_local_path()) - - # checkout. - for comp_name in load_comps: - if verbosity < VERBOSITY_VERBOSE: - printlog('{0}, '.format(comp_name), end='') - else: - # verbose output handled by the _External object, just - # output a newline - printlog(EMPTY_STR) - c = self._all_components[comp_name] - # Does not recurse. - c.checkout(verbosity) - # Recursively check out subexternals, if any. Returns None - # if there's no subexternals path. - component_subexternal_sourcetree = SourceTree.from_externals_file( - c.get_repo_dir_path(), - c.get_repo(), - c.get_subexternals_path()) - c.replace_subexternal_sourcetree(component_subexternal_sourcetree) - if component_subexternal_sourcetree: - component_subexternal_sourcetree.checkout(verbosity, load_all) - printlog('') diff --git a/manage_externals/manic/utils.py b/manage_externals/manic/utils.py deleted file mode 100644 index 9c63ffe65e..0000000000 --- a/manage_externals/manic/utils.py +++ /dev/null @@ -1,330 +0,0 @@ -#!/usr/bin/env python3 -""" -Common public utilities for manic package - -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import logging -import os -import subprocess -import sys -from threading import Timer - -from .global_constants import LOCAL_PATH_INDICATOR - -# --------------------------------------------------------------------- -# -# screen and logging output and functions to massage text for output -# -# --------------------------------------------------------------------- - - -def log_process_output(output): - """Log each line of process output at debug level so it can be - filtered if necessary. By default, output is a single string, and - logging.debug(output) will only put log info heading on the first - line. This makes it hard to filter with grep. - - """ - output = output.split('\n') - for line in output: - logging.debug(line) - - -def printlog(msg, **kwargs): - """Wrapper script around print to ensure that everything printed to - the screen also gets logged. - - """ - logging.info(msg) - if kwargs: - print(msg, **kwargs) - else: - print(msg) - sys.stdout.flush() - - -def last_n_lines(the_string, n_lines, truncation_message=None): - """Returns the last n lines of the given string - - Args: - the_string: str - n_lines: int - truncation_message: str, optional - - Returns a string containing the last n lines of the_string - - If truncation_message is provided, the returned string begins with - the given message if and only if the string is greater than n lines - to begin with. - """ - - lines = the_string.splitlines(True) - if len(lines) <= n_lines: - return_val = the_string - else: - lines_subset = lines[-n_lines:] - str_truncated = ''.join(lines_subset) - if truncation_message: - str_truncated = truncation_message + '\n' + str_truncated - return_val = str_truncated - - return return_val - - -def indent_string(the_string, indent_level): - """Indents the given string by a given number of spaces - - Args: - the_string: str - indent_level: int - - Returns a new string that is the same as the_string, except that - each line is indented by 'indent_level' spaces. - - In python3, this can be done with textwrap.indent. - """ - - lines = the_string.splitlines(True) - padding = ' ' * indent_level - lines_indented = [padding + line for line in lines] - return ''.join(lines_indented) - -# --------------------------------------------------------------------- -# -# error handling -# -# --------------------------------------------------------------------- - - -def fatal_error(message): - """ - Error output function - """ - logging.error(message) - raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message)) - - -# --------------------------------------------------------------------- -# -# Data conversion / manipulation -# -# --------------------------------------------------------------------- -def str_to_bool(bool_str): - """Convert a sting representation of as boolean into a true boolean. - - Conversion should be case insensitive. - """ - value = None - str_lower = bool_str.lower() - if str_lower in ('true', 't'): - value = True - elif str_lower in ('false', 'f'): - value = False - if value is None: - msg = ('ERROR: invalid boolean string value "{0}". ' - 'Must be "true" or "false"'.format(bool_str)) - fatal_error(msg) - return value - - -REMOTE_PREFIXES = ['http://', 'https://', 'ssh://', 'git@'] - - -def is_remote_url(url): - """check if the user provided a local file path instead of a - remote. If so, it must be expanded to an absolute - path. - - """ - remote_url = False - for prefix in REMOTE_PREFIXES: - if url.startswith(prefix): - remote_url = True - return remote_url - - -def split_remote_url(url): - """check if the user provided a local file path or a - remote. If remote, try to strip off protocol info. - - """ - remote_url = is_remote_url(url) - if not remote_url: - return url - - for prefix in REMOTE_PREFIXES: - url = url.replace(prefix, '') - - if '@' in url: - url = url.split('@')[1] - - if ':' in url: - url = url.split(':')[1] - - return url - - -def expand_local_url(url, field): - """check if the user provided a local file path instead of a - remote. If so, it must be expanded to an absolute - path. - - Note: local paths of LOCAL_PATH_INDICATOR have special meaning and - represent local copy only, don't work with the remotes. - - """ - remote_url = is_remote_url(url) - if not remote_url: - if url.strip() == LOCAL_PATH_INDICATOR: - pass - else: - url = os.path.expandvars(url) - url = os.path.expanduser(url) - if not os.path.isabs(url): - msg = ('WARNING: Externals description for "{0}" contains a ' - 'url that is not remote and does not expand to an ' - 'absolute path. Version control operations may ' - 'fail.\n\nurl={1}'.format(field, url)) - printlog(msg) - else: - url = os.path.normpath(url) - return url - - -# --------------------------------------------------------------------- -# -# subprocess -# -# --------------------------------------------------------------------- - -# Give the user a helpful message if we detect that a command seems to -# be hanging. -_HANGING_SEC = 300 - - -def _hanging_msg(working_directory, command): - print(""" - -Command '{command}' -from directory {working_directory} -has taken {hanging_sec} seconds. It may be hanging. - -The command will continue to run, but you may want to abort -manage_externals with ^C and investigate. A possible cause of hangs is -when svn or git require authentication to access a private -repository. On some systems, svn and git requests for authentication -information will not be displayed to the user. In this case, the program -will appear to hang. Ensure you can run svn and git manually and access -all repositories without entering your authentication information. - -""".format(command=command, - working_directory=working_directory, - hanging_sec=_HANGING_SEC)) - - -def execute_subprocess(commands, status_to_caller=False, - output_to_caller=False): - """Wrapper around subprocess.check_output to handle common - exceptions. - - check_output runs a command with arguments and waits - for it to complete. - - check_output raises an exception on a nonzero return code. if - status_to_caller is true, execute_subprocess returns the subprocess - return code, otherwise execute_subprocess treats non-zero return - status as an error and raises an exception. - - """ - cwd = os.getcwd() - msg = 'In directory: {0}\nexecute_subprocess running command:'.format(cwd) - logging.info(msg) - commands_str = ' '.join(commands) - logging.info(commands_str) - return_to_caller = status_to_caller or output_to_caller - status = -1 - output = '' - hanging_timer = Timer(_HANGING_SEC, _hanging_msg, - kwargs={"working_directory": cwd, - "command": commands_str}) - hanging_timer.start() - try: - output = subprocess.check_output(commands, stderr=subprocess.STDOUT, - universal_newlines=True) - log_process_output(output) - status = 0 - except OSError as error: - msg = failed_command_msg( - 'Command execution failed. Does the executable exist?', - commands) - logging.error(error) - fatal_error(msg) - except ValueError as error: - msg = failed_command_msg( - 'DEV_ERROR: Invalid arguments trying to run subprocess', - commands) - logging.error(error) - fatal_error(msg) - except subprocess.CalledProcessError as error: - # Only report the error if we are NOT returning to the - # caller. If we are returning to the caller, then it may be a - # simple status check. If returning, it is the callers - # responsibility determine if an error occurred and handle it - # appropriately. - if not return_to_caller: - msg_context = ('Process did not run successfully; ' - 'returned status {0}'.format(error.returncode)) - msg = failed_command_msg(msg_context, commands, - output=error.output) - logging.error(error) - logging.error(msg) - log_process_output(error.output) - fatal_error(msg) - status = error.returncode - finally: - hanging_timer.cancel() - - if status_to_caller and output_to_caller: - ret_value = (status, output) - elif status_to_caller: - ret_value = status - elif output_to_caller: - ret_value = output - else: - ret_value = None - - return ret_value - - -def failed_command_msg(msg_context, command, output=None): - """Template for consistent error messages from subprocess calls. - - If 'output' is given, it should provide the output from the failed - command - """ - - if output: - output_truncated = last_n_lines(output, 20, - truncation_message='[... Output truncated for brevity ...]') - errmsg = ('Failed with output:\n' + - indent_string(output_truncated, 4) + - '\nERROR: ') - else: - errmsg = '' - - command_str = ' '.join(command) - errmsg += """In directory - {cwd} -{context}: - {command} -""".format(cwd=os.getcwd(), context=msg_context, command=command_str) - - if output: - errmsg += 'See above for output from failed command.\n' - - return errmsg diff --git a/manage_externals/test/.coveragerc b/manage_externals/test/.coveragerc deleted file mode 100644 index 8b681888b8..0000000000 --- a/manage_externals/test/.coveragerc +++ /dev/null @@ -1,7 +0,0 @@ -[run] -branch = True -omit = test_unit_*.py - test_sys_*.py - /usr/* - .local/* - */site-packages/* \ No newline at end of file diff --git a/manage_externals/test/.gitignore b/manage_externals/test/.gitignore deleted file mode 100644 index dd5795998f..0000000000 --- a/manage_externals/test/.gitignore +++ /dev/null @@ -1,7 +0,0 @@ -# virtual environments -env_python* - -# python code coverage tool output -.coverage -htmlcov - diff --git a/manage_externals/test/.pylint.rc b/manage_externals/test/.pylint.rc deleted file mode 100644 index 64abd03e42..0000000000 --- a/manage_externals/test/.pylint.rc +++ /dev/null @@ -1,426 +0,0 @@ -[MASTER] - -# A comma-separated list of package or module names from where C extensions may -# be loaded. Extensions are loading into the active Python interpreter and may -# run arbitrary code -extension-pkg-whitelist= - -# Add files or directories to the blacklist. They should be base names, not -# paths. -ignore=.git,.svn,env2 - -# Add files or directories matching the regex patterns to the blacklist. The -# regex matches against base names, not paths. -ignore-patterns= - -# Python code to execute, usually for sys.path manipulation such as -# pygtk.require(). -#init-hook= - -# Use multiple processes to speed up Pylint. -jobs=1 - -# List of plugins (as comma separated values of python modules names) to load, -# usually to register additional checkers. -load-plugins= - -# Pickle collected data for later comparisons. -persistent=yes - -# Specify a configuration file. -#rcfile= - -# Allow loading of arbitrary C extensions. Extensions are imported into the -# active Python interpreter and may run arbitrary code. -unsafe-load-any-extension=no - - -[MESSAGES CONTROL] - -# Only show warnings with the listed confidence levels. Leave empty to show -# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED -confidence= - -# Disable the message, report, category or checker with the given id(s). You -# can either give multiple identifiers separated by comma (,) or put this -# option multiple times (only on the command line, not in the configuration -# file where it should appear only once).You can also use "--disable=all" to -# disable everything first and then reenable specific checks. For example, if -# you want to run only the similarities checker, you can use "--disable=all -# --enable=similarities". If you want to run only the classes checker, but have -# no Warning level messages displayed, use"--disable=all --enable=classes -# --disable=W" -disable=bad-continuation,useless-object-inheritance - - -# Enable the message, report, category or checker with the given id(s). You can -# either give multiple identifier separated by comma (,) or put this option -# multiple time (only on the command line, not in the configuration file where -# it should appear only once). See also the "--disable" option for examples. -enable= - - -[REPORTS] - -# Python expression which should return a note less than 10 (10 is the highest -# note). You have access to the variables errors warning, statement which -# respectively contain the number of errors / warnings messages and the total -# number of statements analyzed. This is used by the global evaluation report -# (RP0004). -evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10) - -# Template used to display messages. This is a python new-style format string -# used to format the message information. See doc for all details -msg-template={msg_id}:{line:3d},{column:2d}: {msg} ({symbol}) - -# Set the output format. Available formats are text, parseable, colorized, json -# and msvs (visual studio).You can also give a reporter class, eg -# mypackage.mymodule.MyReporterClass. -output-format=text - -# Tells whether to display a full report or only the messages -#reports=yes - -# Activate the evaluation score. -score=yes - - -[REFACTORING] - -# Maximum number of nested blocks for function / method body -max-nested-blocks=5 - - -[BASIC] - -# Naming hint for argument names -argument-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Regular expression matching correct argument names -argument-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Naming hint for attribute names -attr-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Regular expression matching correct attribute names -attr-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Bad variable names which should always be refused, separated by a comma -bad-names=foo,bar,baz,toto,tutu,tata - -# Naming hint for class attribute names -class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$ - -# Regular expression matching correct class attribute names -class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$ - -# Naming hint for class names -class-name-hint=[A-Z_][a-zA-Z0-9]+$ - -# Regular expression matching correct class names -class-rgx=[A-Z_][a-zA-Z0-9]+$ - -# Naming hint for constant names -const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$ - -# Regular expression matching correct constant names -const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$ - -# Minimum line length for functions/classes that require docstrings, shorter -# ones are exempt. -docstring-min-length=-1 - -# Naming hint for function names -function-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Regular expression matching correct function names -function-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Good variable names which should always be accepted, separated by a comma -good-names=i,j,k,ex,Run,_ - -# Include a hint for the correct naming format with invalid-name -include-naming-hint=no - -# Naming hint for inline iteration names -inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$ - -# Regular expression matching correct inline iteration names -inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$ - -# Naming hint for method names -method-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Regular expression matching correct method names -method-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Naming hint for module names -module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$ - -# Regular expression matching correct module names -module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$ - -# Colon-delimited sets of names that determine each other's naming style when -# the name regexes allow several styles. -name-group= - -# Regular expression which should only match function or class names that do -# not require a docstring. -no-docstring-rgx=^_ - -# List of decorators that produce properties, such as abc.abstractproperty. Add -# to this list to register other decorators that produce valid properties. -property-classes=abc.abstractproperty - -# Naming hint for variable names -variable-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - -# Regular expression matching correct variable names -variable-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$ - - -[FORMAT] - -# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. -expected-line-ending-format= - -# Regexp for a line that is allowed to be longer than the limit. -ignore-long-lines=^\s*(# )??$ - -# Number of spaces of indent required inside a hanging or continued line. -indent-after-paren=4 - -# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 -# tab). -indent-string=' ' - -# Maximum number of characters on a single line. -max-line-length=100 - -# Maximum number of lines in a module -max-module-lines=1000 - -# List of optional constructs for which whitespace checking is disabled. `dict- -# separator` is used to allow tabulation in dicts, etc.: {1 : 1,\n222: 2}. -# `trailing-comma` allows a space between comma and closing bracket: (a, ). -# `empty-line` allows space-only lines. -no-space-check=trailing-comma,dict-separator - -# Allow the body of a class to be on the same line as the declaration if body -# contains single statement. -single-line-class-stmt=no - -# Allow the body of an if to be on the same line as the test if there is no -# else. -single-line-if-stmt=no - - -[LOGGING] - -# Logging modules to check that the string format arguments are in logging -# function parameter format -logging-modules=logging - - -[MISCELLANEOUS] - -# List of note tags to take in consideration, separated by a comma. -notes=FIXME,XXX,TODO - - -[SIMILARITIES] - -# Ignore comments when computing similarities. -ignore-comments=yes - -# Ignore docstrings when computing similarities. -ignore-docstrings=yes - -# Ignore imports when computing similarities. -ignore-imports=no - -# Minimum lines number of a similarity. -min-similarity-lines=4 - - -[SPELLING] - -# Spelling dictionary name. Available dictionaries: none. To make it working -# install python-enchant package. -spelling-dict= - -# List of comma separated words that should not be checked. -spelling-ignore-words= - -# A path to a file that contains private dictionary; one word per line. -spelling-private-dict-file= - -# Tells whether to store unknown words to indicated private dictionary in -# --spelling-private-dict-file option instead of raising a message. -spelling-store-unknown-words=no - - -[TYPECHECK] - -# List of decorators that produce context managers, such as -# contextlib.contextmanager. Add to this list to register other decorators that -# produce valid context managers. -contextmanager-decorators=contextlib.contextmanager - -# List of members which are set dynamically and missed by pylint inference -# system, and so shouldn't trigger E1101 when accessed. Python regular -# expressions are accepted. -generated-members= - -# Tells whether missing members accessed in mixin class should be ignored. A -# mixin class is detected if its name ends with "mixin" (case insensitive). -ignore-mixin-members=yes - -# This flag controls whether pylint should warn about no-member and similar -# checks whenever an opaque object is returned when inferring. The inference -# can return multiple potential results while evaluating a Python object, but -# some branches might not be evaluated, which results in partial inference. In -# that case, it might be useful to still emit no-member and other checks for -# the rest of the inferred objects. -ignore-on-opaque-inference=yes - -# List of class names for which member attributes should not be checked (useful -# for classes with dynamically set attributes). This supports the use of -# qualified names. -ignored-classes=optparse.Values,thread._local,_thread._local - -# List of module names for which member attributes should not be checked -# (useful for modules/projects where namespaces are manipulated during runtime -# and thus existing member attributes cannot be deduced by static analysis. It -# supports qualified module names, as well as Unix pattern matching. -ignored-modules= - -# Show a hint with possible names when a member name was not found. The aspect -# of finding the hint is based on edit distance. -missing-member-hint=yes - -# The minimum edit distance a name should have in order to be considered a -# similar match for a missing member name. -missing-member-hint-distance=1 - -# The total number of similar names that should be taken in consideration when -# showing a hint for a missing member. -missing-member-max-choices=1 - - -[VARIABLES] - -# List of additional names supposed to be defined in builtins. Remember that -# you should avoid to define new builtins when possible. -additional-builtins= - -# Tells whether unused global variables should be treated as a violation. -allow-global-unused-variables=yes - -# List of strings which can identify a callback function by name. A callback -# name must start or end with one of those strings. -callbacks=cb_,_cb - -# A regular expression matching the name of dummy variables (i.e. expectedly -# not used). -dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_ - -# Argument names that match this expression will be ignored. Default to name -# with leading underscore -ignored-argument-names=_.*|^ignored_|^unused_ - -# Tells whether we should check for unused import in __init__ files. -init-import=no - -# List of qualified module names which can have objects that can redefine -# builtins. -redefining-builtins-modules=six.moves,future.builtins - - -[CLASSES] - -# List of method names used to declare (i.e. assign) instance attributes. -defining-attr-methods=__init__,__new__,setUp - -# List of member names, which should be excluded from the protected access -# warning. -exclude-protected=_asdict,_fields,_replace,_source,_make - -# List of valid names for the first argument in a class method. -valid-classmethod-first-arg=cls - -# List of valid names for the first argument in a metaclass class method. -valid-metaclass-classmethod-first-arg=mcs - - -[DESIGN] - -# Maximum number of arguments for function / method -max-args=5 - -# Maximum number of attributes for a class (see R0902). -max-attributes=7 - -# Maximum number of boolean expressions in a if statement -max-bool-expr=5 - -# Maximum number of branch for function / method body -max-branches=12 - -# Maximum number of locals for function / method body -max-locals=15 - -# Maximum number of parents for a class (see R0901). -max-parents=7 - -# Maximum number of public methods for a class (see R0904). -max-public-methods=20 - -# Maximum number of return / yield for function / method body -max-returns=6 - -# Maximum number of statements in function / method body -max-statements=50 - -# Minimum number of public methods for a class (see R0903). -min-public-methods=2 - - -[IMPORTS] - -# Allow wildcard imports from modules that define __all__. -allow-wildcard-with-all=no - -# Analyse import fallback blocks. This can be used to support both Python 2 and -# 3 compatible code, which means that the block might have code that exists -# only in one or another interpreter, leading to false positives when analysed. -analyse-fallback-blocks=no - -# Deprecated modules which should not be used, separated by a comma -deprecated-modules=regsub,TERMIOS,Bastion,rexec - -# Create a graph of external dependencies in the given file (report RP0402 must -# not be disabled) -ext-import-graph= - -# Create a graph of every (i.e. internal and external) dependencies in the -# given file (report RP0402 must not be disabled) -import-graph= - -# Create a graph of internal dependencies in the given file (report RP0402 must -# not be disabled) -int-import-graph= - -# Force import order to recognize a module as part of the standard -# compatibility libraries. -known-standard-library= - -# Force import order to recognize a module as part of a third party library. -known-third-party=enchant - - -[EXCEPTIONS] - -# Exceptions that will emit a warning when being caught. Defaults to -# "Exception" -overgeneral-exceptions=Exception diff --git a/manage_externals/test/Makefile b/manage_externals/test/Makefile deleted file mode 100644 index 293e360757..0000000000 --- a/manage_externals/test/Makefile +++ /dev/null @@ -1,124 +0,0 @@ -python = not-set -verbose = not-set -debug = not-set - -ifneq ($(python), not-set) -PYTHON=$(python) -else -PYTHON=python -endif - -# we need the python path to point one level up to access the package -# and executables -PYPATH=PYTHONPATH=..: - -# common args for running tests -TEST_ARGS=-m unittest discover - -ifeq ($(debug), not-set) - ifeq ($(verbose), not-set) - # summary only output - TEST_ARGS+=--buffer - else - # show individual test summary - TEST_ARGS+=--buffer --verbose - endif -else - # show detailed test output - TEST_ARGS+=--verbose -endif - - -# auto reformat the code -AUTOPEP8=autopep8 -AUTOPEP8_ARGS=--aggressive --in-place - -# run lint -PYLINT=pylint -PYLINT_ARGS=-j 2 --rcfile=.pylint.rc - -# code coverage -COVERAGE=coverage -COVERAGE_ARGS=--rcfile=.coveragerc - -# source files -SRC = \ - ../checkout_externals \ - ../manic/*.py - -CHECKOUT_EXE = ../checkout_externals - -TEST_DIR = . - -README = ../README.md - -# -# testing -# -.PHONY : utest -utest : FORCE - $(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_unit_*.py' - -.PHONY : stest -stest : FORCE - $(PYPATH) $(PYTHON) $(TEST_ARGS) --pattern 'test_sys_*.py' - -.PHONY : test -test : utest stest - -# -# documentation -# -.PHONY : readme -readme : $(CHECKOUT_EXE) - printf "%s\n\n" "-- AUTOMATICALLY GENERATED FILE. DO NOT EDIT --" > $(README) - printf "%s" '[![Build Status](https://travis-ci.org/ESMCI/manage_externals.svg?branch=master)](https://travis-ci.org/ESMCI/manage_externals)' >> $(README) - printf "%s" '[![Coverage Status](https://coveralls.io/repos/github/ESMCI/manage_externals/badge.svg?branch=master)](https://coveralls.io/github/ESMCI/manage_externals?branch=master)' >> $(README) - printf "\n%s\n" '```' >> $(README) - $(CHECKOUT_EXE) --help >> $(README) - -# -# coding standards -# -.PHONY : style -style : FORCE - $(AUTOPEP8) $(AUTOPEP8_ARGS) --recursive $(SRC) $(TEST_DIR)/test_*.py - -.PHONY : lint -lint : FORCE - $(PYLINT) $(PYLINT_ARGS) $(SRC) $(TEST_DIR)/test_*.py - -.PHONY : stylint -stylint : style lint - -.PHONY : coverage -# Need to use a single coverage run with a single pattern rather than -# using two separate commands with separate patterns for test_unit_*.py -# and test_sys_*.py: The latter clobbers some results from the first -# run, even if we use the --append flag to 'coverage run'. -coverage : FORCE - $(PYPATH) $(COVERAGE) erase - $(PYPATH) $(COVERAGE) run $(COVERAGE_ARGS) $(TEST_ARGS) --pattern 'test_*.py' - $(PYPATH) $(COVERAGE) html - -# -# virtual environment creation -# -.PHONY : env -env : FORCE - $(PYPATH) virtualenv --python $(PYTHON) $@_$(PYTHON) - . $@_$(PYTHON)/bin/activate; pip install -r requirements.txt - -# -# utilites -# -.PHONY : clean -clean : FORCE - -rm -rf *~ *.pyc tmp fake htmlcov - -.PHONY : clobber -clobber : clean - -rm -rf env_* - -FORCE : - diff --git a/manage_externals/test/README.md b/manage_externals/test/README.md deleted file mode 100644 index 1e8f2eaa77..0000000000 --- a/manage_externals/test/README.md +++ /dev/null @@ -1,53 +0,0 @@ -# Testing for checkout_externals - -## Unit tests - -```SH - cd checkout_externals/test - make utest -``` - -## System tests - -```SH - cd checkout_externals/test - make stest -``` - -Example to run a single test: -```SH - cd checkout_externals - python -m unittest test.test_sys_checkout.TestSysCheckout.test_container_simple_required -``` - -## Static analysis - -checkout_externals is difficult to test thoroughly because it relies -on git and svn, and svn requires a live network connection and -repository. Static analysis will help catch bugs in code paths that -are not being executed, but it requires conforming to community -standards and best practices. autopep8 and pylint should be run -regularly for automatic code formatting and linting. - -```SH - cd checkout_externals/test - make lint -``` - -The canonical formatting for the code is whatever autopep8 -generates. All issues identified by pylint should be addressed. - - -## Code coverage - -All changes to the code should include maintaining existing tests and -writing new tests for new or changed functionality. To ensure test -coverage, run the code coverage tool: - -```SH - cd checkout_externals/test - make coverage - open -a Firefox.app htmlcov/index.html -``` - - diff --git a/manage_externals/test/doc/.gitignore b/manage_externals/test/doc/.gitignore deleted file mode 100644 index d4e11e5ea0..0000000000 --- a/manage_externals/test/doc/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -_build - diff --git a/manage_externals/test/doc/Makefile b/manage_externals/test/doc/Makefile deleted file mode 100644 index 18f4d5bf99..0000000000 --- a/manage_externals/test/doc/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SPHINXPROJ = ManageExternals -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) \ No newline at end of file diff --git a/manage_externals/test/doc/conf.py b/manage_externals/test/doc/conf.py deleted file mode 100644 index 469c0b0dc5..0000000000 --- a/manage_externals/test/doc/conf.py +++ /dev/null @@ -1,172 +0,0 @@ -# -*- coding: utf-8 -*- -# -# Manage Externals documentation build configuration file, created by -# sphinx-quickstart on Wed Nov 29 10:53:25 2017. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) - - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -# -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = ['sphinx.ext.autodoc', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.viewcode', - 'sphinx.ext.githubpages'] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'Manage Externals' -copyright = u'2017, CSEG at NCAR' -author = u'CSEG at NCAR' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = u'1.0.0' -# The full version, including alpha/beta/rc tags. -release = u'1.0.0' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = True - - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'alabaster' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -# html_theme_options = {} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# This is required for the alabaster theme -# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars -html_sidebars = { - '**': [ - 'relations.html', # needs 'show_related': True theme option to display - 'searchbox.html', - ] -} - - -# -- Options for HTMLHelp output ------------------------------------------ - -# Output file base name for HTML help builder. -htmlhelp_basename = 'ManageExternalsdoc' - - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'ManageExternals.tex', u'Manage Externals Documentation', - u'CSEG at NCAR', 'manual'), -] - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'manageexternals', u'Manage Externals Documentation', - [author], 1) -] - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'ManageExternals', u'Manage Externals Documentation', - author, 'ManageExternals', 'One line description of project.', - 'Miscellaneous'), -] - - - diff --git a/manage_externals/test/doc/develop.rst b/manage_externals/test/doc/develop.rst deleted file mode 100644 index b817b7b093..0000000000 --- a/manage_externals/test/doc/develop.rst +++ /dev/null @@ -1,202 +0,0 @@ -Developer Guidelines -==================== - -The manage externals utilities are a light weight replacement for svn -externals that will work with git repositories pulling in a mixture of -git and svn dependencies. - -Given an externals description and a working copy: - -* *checkout_externals* attempts to make the working copy agree with the - externals description - -* *generate_externals* attempts to make the externals description agree - with the working copy. - -For these operations utilities should: - -* operate consistently across git and svn - -* operate simply with minimal user complexity - -* robustly across a wide range of repository states - -* provide explicit error messages when a problem occurs - -* leave the working copy in a valid state - -The utilities in manage externals are **NOT** generic wrappers around -revision control operations or a replacement for common tasks. Users -are expected to: - -* create branches prior to starting development - -* add remotes and push changes - -* create tags - -* delete branches - -These types of tasks are often highly workflow dependent, e.g. branch -naming conventions may vary between repositories, have the potential -to destroy user data, introduce significant code complexit and 'edge -cases' that are extremely difficult to detect and test, and often -require subtle decision making, especially if a problem occurs. - -Users who want to automate these types are encouraged to create their -own tools. The externals description files are explicitly versioned -and the internal APIs are intended to be stable for these purposes. - -Core Design Principles ------------------------ - -1. Users can, and are actively encouraged to, modify the externals - directories using revision control outside of manage_externals - tools. You can't make any assumptions about the state of the - working copy. Examples: adding a remote, creating a branch, - switching to a branch, deleting the directory entirely. - -2. Give that the user can do anything, the manage externals library - can not preserve state between calls. The only information it can - rely on is what it expectes based on the content of the externals - description file, and what the actual state of the directory tree - is. - -3. Do *not* do anything that will possibly destroy user data! - - a. Do not remove files from the file system. We are operating on - user supplied input. If you don't call 'rm', you can't - accidentally remove the user's data. Thinking of calling - ``shutil.rmtree(user_input)``? What if the user accidentally - specified user_input such that it resolves to their home - directory.... Yeah. Don't go there. - - b. Rely on git and svn to do their job as much as possible. Don't - duplicate functionality. Examples: - - i. We require the working copies to be 'clean' as reported by - ``git status`` and ``svn status``. What if there are misc - editor files floating around that prevent an update? Use the - git and svn ignore functionality so they are not - reported. Don't try to remove them from manage_externals or - determine if they are 'safe' to ignore. - - ii. Do not use '--force'. Ever. This is a sign you are doing - something dangerous, it may not be what the user - wants. Remember, they are encouraged to modify their repo. - -4. There are often multiple ways to obtain a particular piece of - information from git. Scraping screen output is brittle and - generally not considered a stable API across different versions of - git. Given a choice between: - - a. a lower level git 'plumbing' command that processes a - specific request and returns a sucess/failure status. - - b. high level git command that produces a bunch of output - that must be processed. - - We always prefer the former. It almost always involves - writing and maintaining less code and is more likely to be - stable. - -5. Backward compatibility is critical. We have *nested* - repositories. They are trivially easy to change versions. They may - have very different versions of the top level manage_externals. The - ability to read and work with old model description files is - critical to avoid problems for users. We also have automated tools - (testdb) that must generate and read external description - files. Backward compatibility will make staging changes vastly - simpler. - -Model Users ------------ - -Consider the needs of the following model userswhen developing manage_externals: - -* Users who will checkout the code once, and never change versions. - -* Users who will checkout the code once, then work for several years, - never updating. before trying to update or request integration. - -* Users develope code but do not use revision control beyond the - initial checkout. If they have modified or untracked files in the - repo, they may be irreplacable. Don't destroy user data. - -* Intermediate users who are working with multiple repos or branches - on a regular basis. They may only use manage_externals weekly or - monthly. Keep the user interface and documentation simple and - explicit. The more command line options they have to remember or - look up, the more frustrated they git. - -* Software engineers who use the tools multiple times a day. It should - get out of their way. - -User Interface --------------- - -Basic operation for the most standard use cases should be kept as -simple as possible. Many users will only rarely run the manage -utilities. Even advanced users don't like reading a lot of help -documentation or struggling to remember commands and piece together -what they need to run. Having many command line options, even if not -needed, is exteremly frustrating and overwhelming for most users. A few -simple, explicitly named commands are better than a single command -with many options. - -How will users get help if something goes wrong? This is a custom, -one-off solution. Searching the internet for manage_externals, will -only return the user doc for this project at best. There isn't likely -to be a stackoverflow question or blog post where someone else already -answered a user's question. And very few people outside this community -will be able to provide help if something goes wrong. The sooner we -kick users out of these utilities and into standard version control -tools, the better off they are going to be if they run into a problem. - -Repositories ------------- - -There are three basic types of repositories that must be considered: - -* container repositories - repositories that are always top level - repositories, and have a group of externals that must be managed. - -* simple repositories - repositories that are externals to another - repository, and do not have any of their own externals that will be - managed. - -* mixed use repositories - repositories that can act as a top level - container repository or as an external to a top level - container. They may also have their own sub-externals that are - required. They may have different externals needs depening on - whether they are top level or not. - -Repositories must be able to checkout and switch to both branches and -tags. - -Development -=========== - -The functionality to manage externals is broken into a library of core -functionality and applications built with the library. - -The core library is called 'manic', pseduo-homophone of (man)age -(ex)ternals that is: short, pronounceable and spell-checkable. It is -also no more or less meaningful to an unfamiliar user than a random -jumble of letters forming an acronym. - -The core architecture of manic is: - -* externals description - an abstract description on an external, - including of how to obtain it, where to obtain it, where it goes in - the working tree. - -* externals - the software object representing an external. - -* source trees - collection of externals - -* repository wrappers - object oriented wrappers around repository - operations. So the higher level management of the soure tree and - external does not have to be concerned with how a particular - external is obtained and managed. - diff --git a/manage_externals/test/doc/index.rst b/manage_externals/test/doc/index.rst deleted file mode 100644 index 9ab287ad8c..0000000000 --- a/manage_externals/test/doc/index.rst +++ /dev/null @@ -1,22 +0,0 @@ -.. Manage Externals documentation master file, created by - sphinx-quickstart on Wed Nov 29 10:53:25 2017. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to Manage Externals's documentation! -============================================ - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - - develop.rst - testing.rst - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/manage_externals/test/doc/testing.rst b/manage_externals/test/doc/testing.rst deleted file mode 100644 index 623f0e431c..0000000000 --- a/manage_externals/test/doc/testing.rst +++ /dev/null @@ -1,123 +0,0 @@ -Testing -======= - -The manage_externals package has an automated test suite. All pull -requests are expected to pass 100% of the automated tests, as well as -be pep8 and lint 'clean' and maintain approximately constant (at a -minimum) level of code coverage. - -Quick Start ------------ - -Do nothing approach -~~~~~~~~~~~~~~~~~~~ - -When you create a pull request on GitHub, Travis-CI continuous -integration testing will run the test suite in both python2 and -python3. Test results, lint results, and code coverage results are -available online. - -Do something approach -~~~~~~~~~~~~~~~~~~~~~ - -In the test directory, run: - -.. code-block:: shell - - make env - make lint - make test - make coverage - - -Automated Testing ------------------ - -The manage_externals manic library and executables are developed to be -python2 and python3 compatible using only the standard library. The -test suites meet the same requirements. But additional tools are -required to provide lint and code coverage metrics and generate -documentation. The requirements are maintained in the requirements.txt -file, and can be automatically installed into an isolated environment -via Makefile. - -Bootstrap requirements: - -* python2 - version 2.7.x or later - -* python3 - version 3.6 tested other versions may work - -* pip and virtualenv for python2 and python3 - -Note: all make rules can be of the form ``make python=pythonX rule`` -or ``make rule`` depending if you want to use the default system -python or specify a specific version. - -The Makefile in the test directory has the following rules: - -* ``make python=pythonX env`` - create a python virtual environment - for python2 or python3 and install all required packages. These - packages are required to run lint or coverage. - -* ``make style`` - runs autopep8 - -* ``make lint`` - runs autopep8 and pylint - -* ``make test`` - run the full test suite - -* ``make utest`` - run jus the unit tests - -* ``make stest`` - run jus the system integration tests - -* ``make coverage`` - run the full test suite through the code - coverage tool and generate an html report. - -* ``make readme`` - automatically generate the README files. - -* ``make clean`` - remove editor and pyc files - -* ``make clobber`` - remove all generated test files, including - virtual environments, coverage reports, and temporary test - repository directories. - -Unit Tests ----------- - -Unit tests are probably not 'true unit tests' for the pedantic, but -are pragmatic unit tests. They cover small practicle code blocks: -functions, class methods, and groups of functions and class methods. - -System Integration Tests ------------------------- - -NOTE(bja, 2017-11) The systems integration tests currently do not include svn repositories. - -The manage_externals package is extremely tedious and error prone to test manually. - -Combinations that must be tested to ensure basic functionality are: - -* container repository pulling in simple externals - -* container repository pulling in mixed externals with sub-externals. - -* mixed repository acting as a container, pulling in simple externals and sub-externals - -Automatic system tests are handled the same way manual testing is done: - -* clone a test repository - -* create an externals description file for the test - -* run the executable with the desired args - -* check the results - -* potentially modify the repo (checkout a different branch) - -* rerun and test - -* etc - -The automated system stores small test repositories in the main repo -by adding them as bare repositories. These repos are cloned via a -subprocess call to git and manipulated during the tests. diff --git a/manage_externals/test/repos/README.md b/manage_externals/test/repos/README.md deleted file mode 100644 index 026b684ea3..0000000000 --- a/manage_externals/test/repos/README.md +++ /dev/null @@ -1,33 +0,0 @@ -Git and svn repositories for testing git and svn-related behavior. For usage and terminology notes, see test/test_sys_checkout.py. - -For git repos: To list files and view file contents at HEAD: -``` -cd -git ls-tree --full-tree -r --name-only HEAD -git cat-file -p HEAD: -``` - -File contents at a glance: -``` -container.git/ - readme.txt - -simple-ext.git/ - (has branches: feature2, feature3) - (has tags: tag1, tag2) - readme.txt - simple_subdir/subdir_file.txt - -simple-ext-fork.git/ - (has tags: abandoned-feature, forked-feature-v1, tag1) - (has branch: feature2) - readme.txt - -mixed-cont-ext.git/ - (has branch: new-feature) - readme.txt - sub-externals.cfg ('simp_branch' section refers to 'feature2' branch in simple-ext.git/ repo) - -error/ - (no git repo here, just a readme.txt in the clear) -``` diff --git a/manage_externals/test/repos/container.git/HEAD b/manage_externals/test/repos/container.git/HEAD deleted file mode 100644 index cb089cd89a..0000000000 --- a/manage_externals/test/repos/container.git/HEAD +++ /dev/null @@ -1 +0,0 @@ -ref: refs/heads/master diff --git a/manage_externals/test/repos/container.git/config b/manage_externals/test/repos/container.git/config deleted file mode 100644 index e6da231579..0000000000 --- a/manage_externals/test/repos/container.git/config +++ /dev/null @@ -1,6 +0,0 @@ -[core] - repositoryformatversion = 0 - filemode = true - bare = true - ignorecase = true - precomposeunicode = true diff --git a/manage_externals/test/repos/container.git/description b/manage_externals/test/repos/container.git/description deleted file mode 100644 index 498b267a8c..0000000000 --- a/manage_externals/test/repos/container.git/description +++ /dev/null @@ -1 +0,0 @@ -Unnamed repository; edit this file 'description' to name the repository. diff --git a/manage_externals/test/repos/container.git/info/exclude b/manage_externals/test/repos/container.git/info/exclude deleted file mode 100644 index a5196d1be8..0000000000 --- a/manage_externals/test/repos/container.git/info/exclude +++ /dev/null @@ -1,6 +0,0 @@ -# git ls-files --others --exclude-from=.git/info/exclude -# Lines that start with '#' are comments. -# For a project mostly in C, the following would be a good set of -# exclude patterns (uncomment them if you want to use them): -# *.[oa] -# *~ diff --git a/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801 b/manage_externals/test/repos/container.git/objects/41/1de5d96ee418c1c55f3e96e6e6e7c06bb95801 deleted file mode 100644 index f65234e17f32800b1be0aa9908cc706458b14605..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 133 zcmV;00DAv;0acB$4#OY}L_6~pma=t7)Fr=DfpLNr2P1F?mVSF_r3_t8x_fuJAR6GY zuD1yyS3=Xu)WDKA@Ra});Xx7fWf1zv2~1TS@=422pQw4`eHcB9X3EwU=O)-GQ}s5s nqUZ%S7HaN3i|$`ck;m7Sz6S{Y_}`UoN%K{iOGozsJ+C?sZtFeC diff --git a/manage_externals/test/repos/container.git/objects/71/5b8f3e4afe1802a178e1d603af404ba45d59de b/manage_externals/test/repos/container.git/objects/71/5b8f3e4afe1802a178e1d603af404ba45d59de deleted file mode 100644 index 9759965b1ba440f1899216c1c82c0780fb65f46e..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 136 zcmV;30C)d*0hNtQ3c@fDKwak)a{8g?ULFizQ5yOj!O$#BY{3QX>9e{j4e8<)

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100644 index 607e80d1bc..0000000000 --- a/manage_externals/test/repos/mixed-cont-ext.git/refs/heads/new-feature +++ /dev/null @@ -1 +0,0 @@ -9580ecc12f16334ce44e42287d5d46f927bb7b75 diff --git a/manage_externals/test/repos/simple-ext-fork.git/HEAD b/manage_externals/test/repos/simple-ext-fork.git/HEAD deleted file mode 100644 index cb089cd89a..0000000000 --- a/manage_externals/test/repos/simple-ext-fork.git/HEAD +++ /dev/null @@ -1 +0,0 @@ -ref: refs/heads/master diff --git a/manage_externals/test/repos/simple-ext-fork.git/config b/manage_externals/test/repos/simple-ext-fork.git/config deleted file mode 100644 index 04eba17870..0000000000 --- a/manage_externals/test/repos/simple-ext-fork.git/config +++ /dev/null @@ -1,8 +0,0 @@ -[core] - repositoryformatversion = 0 - filemode = true - bare = true - ignorecase = true - precomposeunicode = true -[remote "origin"] - url = 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a/manage_externals/test/repos/simple-ext-fork.git/objects/3d/ec1fdf8e2f5edba28148c5db2fe8d7a842360b +++ /dev/null @@ -1,2 +0,0 @@ -x•ŽKnÃ0 ³Ö)x”,ÊI½EÑŸ´–A¹Ü#t7o€ŒìÛ¶vp.žzS…ÁšÆƒ&oÑ„©d¦8¹xLd@™Ì‹›ÖCð6f¯% -œpt$‰m&ŽJd…¦¡øhøÝ—½Á—VxÔÒ®ùÉpŸ7^/²o7°d­K1ÂGDsØ#¯ë¿æ{o?Z 7®²€,\g½˜AV=y!@Ff%bx&`ZxO$xP47FG^)_lznAV=y!@Ff%bx&`ZxO$xP47FG^)_lznvGy0&Z${j?E8>6rD10GHRYE2d diff --git a/manage_externals/test/repos/simple-ext-fork.git/objects/5f/1d4786d12e52d7ab28d2f2f1118c1059a9f1ae b/manage_externals/test/repos/simple-ext-fork.git/objects/5f/1d4786d12e52d7ab28d2f2f1118c1059a9f1ae deleted file mode 100644 index 25488b7bfe52fd0d530e20393b752815d9aaf16f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 93 zcmV-j0HXhR0S(JB4ue1p1i;kyiv0l8%LNPZurX=iP=VtPL2T>`g? zkh3=;83|{%kTn0{lH8#Nev_`XVPmImRbRpwOIgehnBL{IWwXg diff --git a/manage_externals/test/repos/simple-ext-fork.git/objects/67/136e5ab4d5c1c65d10c8048763b96b0e53c1d6 b/manage_externals/test/repos/simple-ext-fork.git/objects/67/136e5ab4d5c1c65d10c8048763b96b0e53c1d6 deleted file mode 100644 index d3dfe31113715fe07ea6833f0c2a25e868ac20b2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 165 zcmV;W09yZe0hNwR4#F@DL|Nw)z5pm6r*$QSfIWwB8k=t$6s6+&lq0Ykjo#?ZSf=UT zz+~D012)4Gj)~xM%ugTv-b1AFi TQ|c4S3@Y4~D&BknM3zUWvn5b3 diff --git a/manage_externals/test/repos/simple-ext-fork.git/objects/7b/0bd630ac13865735a1dff3437a137d8ab50663 b/manage_externals/test/repos/simple-ext-fork.git/objects/7b/0bd630ac13865735a1dff3437a137d8ab50663 deleted file mode 100644 index 0a2ec0494bc1600144cb54b61a6d7b43c7f3e806..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 119 zcmV--0Eqv10X50d4FVw$MNz-0;#IJTYiz*^YyjkKAhHY@MpwI+#E{&tb3>7U^YwDN zr`$2}=y`92Fm{8oNzW$w#gQ$c3ivT<^#zfQHTwFÁ©¹£rPkÖSèkJ´^ë \ No newline at end of file diff --git a/manage_externals/test/repos/simple-ext-fork.git/objects/a4/2fe9144f5707bc1e9515ce1b44681f7aba6f95 b/manage_externals/test/repos/simple-ext-fork.git/objects/a4/2fe9144f5707bc1e9515ce1b44681f7aba6f95 deleted file mode 100644 index d8ba654548..0000000000 --- a/manage_externals/test/repos/simple-ext-fork.git/objects/a4/2fe9144f5707bc1e9515ce1b44681f7aba6f95 +++ /dev/null @@ -1,3 +0,0 @@ -xUÌ[ -Â0…aŸ³ŠÙ@%Is+ˆ¨;™¤c/˜DÂq÷VðÅ×Ã>Æ ”w‡WJ Ú˜>8ò!¤!&'ƒS=)í±×CòF+ÑI2‚ßO‚Ts^Xðn`Ä2ÖBcw'ä­Ñw¨Á -\ËØNqÝ›F—)ãò8îç3(«¬Œ2:é¥ÿü0x-<×!6,i ª9 \ No newline at end of file diff --git a/manage_externals/test/repos/simple-ext-fork.git/objects/b9/3737be3ea6b19f6255983748a0a0f4d622f936 b/manage_externals/test/repos/simple-ext-fork.git/objects/b9/3737be3ea6b19f6255983748a0a0f4d622f936 deleted file mode 100644 index 9b40a0afa00b93a318cd503d3b29db1162978b03..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 89 zcmV-f0H*(V0V^p=O;s>AV=y!@Ff%bx&`ZxO$xP47FG^)_lznD—}ÂD>£Nƒv“{ŠZ¼M˜I…¥?jƒ‹Ìpžs8ÄgøÓ½„qÚ¥ZŽ€qo j†­f­ÕJ×{]þÕµÓ¥®¥Om/¨3Ü$ô¥‰Q_@ÞH© \ No newline at end of file diff --git a/manage_externals/test/repos/simple-ext-fork.git/packed-refs b/manage_externals/test/repos/simple-ext-fork.git/packed-refs deleted file mode 100644 index b8f9e86308..0000000000 --- a/manage_externals/test/repos/simple-ext-fork.git/packed-refs +++ /dev/null @@ -1,5 +0,0 @@ -# pack-refs with: peeled fully-peeled sorted -36418b4e5665956a90725c9a1b5a8e551c5f3d48 refs/heads/feature2 -9b75494003deca69527bb64bcaa352e801611dd2 refs/heads/master -11a76e3d9a67313dec7ce1230852ab5c86352c5c refs/tags/tag1 -^9b75494003deca69527bb64bcaa352e801611dd2 diff --git a/manage_externals/test/repos/simple-ext-fork.git/refs/heads/feature2 b/manage_externals/test/repos/simple-ext-fork.git/refs/heads/feature2 deleted file mode 100644 index d223b0362d..0000000000 --- a/manage_externals/test/repos/simple-ext-fork.git/refs/heads/feature2 +++ /dev/null @@ -1 +0,0 @@ -f268d4e56d067da9bd1d85e55bdc40a8bd2b0bca diff --git a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/abandoned-feature b/manage_externals/test/repos/simple-ext-fork.git/refs/tags/abandoned-feature deleted file mode 100644 index 8a18bf08e9..0000000000 --- a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/abandoned-feature +++ /dev/null @@ -1 +0,0 @@ -a42fe9144f5707bc1e9515ce1b44681f7aba6f95 diff --git a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1 b/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1 deleted file mode 100644 index 2764b552d5..0000000000 --- a/manage_externals/test/repos/simple-ext-fork.git/refs/tags/forked-feature-v1 +++ /dev/null @@ -1 +0,0 @@ -8d2b3b35126224c975d23f109aa1e3cbac452989 diff --git a/manage_externals/test/repos/simple-ext.git/HEAD b/manage_externals/test/repos/simple-ext.git/HEAD deleted file mode 100644 index cb089cd89a..0000000000 --- a/manage_externals/test/repos/simple-ext.git/HEAD +++ /dev/null @@ -1 +0,0 @@ -ref: refs/heads/master diff --git a/manage_externals/test/repos/simple-ext.git/config b/manage_externals/test/repos/simple-ext.git/config deleted file mode 100644 index e6da231579..0000000000 --- a/manage_externals/test/repos/simple-ext.git/config +++ /dev/null @@ -1,6 +0,0 @@ -[core] - repositoryformatversion = 0 - filemode = true - bare = true - ignorecase = true - precomposeunicode = true diff --git a/manage_externals/test/repos/simple-ext.git/description b/manage_externals/test/repos/simple-ext.git/description deleted file mode 100644 index 498b267a8c..0000000000 --- a/manage_externals/test/repos/simple-ext.git/description +++ /dev/null @@ -1 +0,0 @@ -Unnamed repository; edit this file 'description' to name the repository. diff --git a/manage_externals/test/repos/simple-ext.git/info/exclude b/manage_externals/test/repos/simple-ext.git/info/exclude deleted file mode 100644 index a5196d1be8..0000000000 --- a/manage_externals/test/repos/simple-ext.git/info/exclude +++ /dev/null @@ -1,6 +0,0 @@ -# git ls-files --others --exclude-from=.git/info/exclude -# Lines that start with '#' are comments. -# For a project mostly in C, the following would be a good set of -# exclude patterns (uncomment them if you want to use them): -# *.[oa] -# *~ diff --git a/manage_externals/test/repos/simple-ext.git/objects/00/fd13e76189f9134b0506b4b8ed3172723b467f b/manage_externals/test/repos/simple-ext.git/objects/00/fd13e76189f9134b0506b4b8ed3172723b467f deleted file mode 100644 index ae28c037e5e8773bab7a7f9b6b050a01c3c8402a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 89 zcmV-f0H*(V0V^p=O;s>AV=y!@Ff%bx&`ZxO$xP47FG^)_lznbW_*ltIGSP}@rN;eRaRvTe4jec)&9#mV ztc{ztsDi^RDN|POQ7IsM3R)Zn^fb6Ap%fNDG*4c1YCyeUO2}@P$+4Hjj2b9dvLb3- zmJ-WQ2E*@mn-@6i1g9x43VXTpcO0*k$48gudH@`(^)|-1gKbZJZ&teIHT_#Om*271 ST(#ZC=?eOIX=gtC)=0=UK}@j# diff --git 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binary patch literal 0 HcmV?d00001 literal 816 zcmZvZJ!lj`6vt;bpA3nm2sW<~jBwfc+L_sFOu`))jUhw{0gGh577vfyac(dHi+~?R zh?R}CT|}_e+9r*qV5N;MStC{G3)m;lNk zCm~lv(?C<68Ar-%YL%o`uYzC#rkyZdVR9kD9Q-!%}%S;O#unUwLYMU_)@exaSbTJeGis^rnsBF zpQ$A6r{xuTL@SSJeWQcholp+qxI~k*M^FFKr;u_G6ohjsvpQAEc$GQHnKxDmExDoA zqy#EZIZ5|4d3k=%Gb>dAc}$Wl&XYP%bKGo< zTmjWejYqZH7n7Q%0^8yGT2lbUjl12Rz=7w$2rz4bdULXUmfC*4ic;URV zT5%(!r#bby^on`qSY{66?ef&aVF)RMbPpw2dC8>a+6zOarB*P`g_V_4QdROm3)2?cKX5He8X8kD zRTa09dUI>+4($Ie?{8&&x)?7E=6hH1%;vc$isp`@N5_6ekGpR>52FX2McUt&KhAE3 z8yY={3bg&={dRN#qtCB?emH(VI)R>Tecg&qWAyFm%XhPPH2SpjWe4}>(DxsApLgH< zK6?@&t~A)(Gf_HKN~e|J&g9-2E__xI=82{tXa=RNLR*{|XCxC^W?VX{y(YOLf>dnb E4; /dev/null || exit 1 - -# Check that the author of this commit has the rights to perform -# the commit on the files and directories being modified. -commit-access-control.pl "$REPOS" "$TXN" commit-access-control.cfg || exit 1 - -# All checks passed, so allow the commit. -exit 0 diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/pre-lock.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/pre-lock.tmpl deleted file mode 100755 index 148582a689..0000000000 --- a/manage_externals/test/repos/simple-ext.svn/hooks/pre-lock.tmpl +++ /dev/null @@ -1,95 +0,0 @@ -#!/bin/sh - -# PRE-LOCK HOOK -# -# The pre-lock hook is invoked before an exclusive lock is -# created. Subversion runs this hook by invoking a program -# (script, executable, binary, etc.) named 'pre-lock' (for which -# this file is a template), with the following ordered arguments: -# -# [1] REPOS-PATH (the path to this repository) -# [2] PATH (the path in the repository about to be locked) -# [3] USER (the user creating the lock) -# [4] COMMENT (the comment of the lock) -# [5] STEAL-LOCK (1 if the user is trying to steal the lock, else 0) -# -# If the hook program outputs anything on stdout, the output string will -# be used as the lock token for this lock operation. If you choose to use -# this feature, you must guarantee the tokens generated are unique across -# the repository each time. -# -# If the hook program exits with success, the lock is created; but -# if it exits with failure (non-zero), the lock action is aborted -# and STDERR is returned to the client. -# -# The default working directory for the invocation is undefined, so -# the program should set one explicitly if it cares. -# -# On a Unix system, the normal procedure is to have 'pre-lock' -# invoke other programs to do the real work, though it may do the -# work itself too. -# -# Note that 'pre-lock' must be executable by the user(s) who will -# invoke it (typically the user httpd runs as), and that user must -# have filesystem-level permission to access the repository. -# -# On a Windows system, you should name the hook program -# 'pre-lock.bat' or 'pre-lock.exe', -# but the basic idea is the same. -# -# The hook program runs in an empty environment, unless the server is -# explicitly configured otherwise. For example, a common problem is for -# the PATH environment variable to not be set to its usual value, so -# that subprograms fail to launch unless invoked via absolute path. -# If you're having unexpected problems with a hook program, the -# culprit may be unusual (or missing) environment variables. -# -# CAUTION: -# For security reasons, you MUST always properly quote arguments when -# you use them, as those arguments could contain whitespace or other -# problematic characters. Additionally, you should delimit the list -# of options with "--" before passing the arguments, so malicious -# clients cannot bootleg unexpected options to the commands your -# script aims to execute. -# For similar reasons, you should also add a trailing @ to URLs which -# are passed to SVN commands accepting URLs with peg revisions. -# -# Here is an example hook script, for a Unix /bin/sh interpreter. -# For more examples and pre-written hooks, see those in -# the Subversion repository at -# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and -# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/ - - -REPOS="$1" -PATH="$2" -USER="$3" -COMMENT="$4" -STEAL="$5" - -# If a lock exists and is owned by a different person, don't allow it -# to be stolen (e.g., with 'svn lock --force ...'). - -# (Maybe this script could send email to the lock owner?) -SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook -GREP=/bin/grep -SED=/bin/sed - -LOCK_OWNER=`$SVNLOOK lock "$REPOS" "$PATH" | \ - $GREP '^Owner: ' | $SED 's/Owner: //'` - -# If we get no result from svnlook, there's no lock, allow the lock to -# happen: -if [ "$LOCK_OWNER" = "" ]; then - exit 0 -fi - -# If the person locking matches the lock's owner, allow the lock to -# happen: -if [ "$LOCK_OWNER" = "$USER" ]; then - exit 0 -fi - -# Otherwise, we've got an owner mismatch, so return failure: -echo "Error: $PATH already locked by ${LOCK_OWNER}." 1>&2 -exit 1 diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl deleted file mode 100755 index 8b065d7c79..0000000000 --- a/manage_externals/test/repos/simple-ext.svn/hooks/pre-revprop-change.tmpl +++ /dev/null @@ -1,79 +0,0 @@ -#!/bin/sh - -# PRE-REVPROP-CHANGE HOOK -# -# The pre-revprop-change hook is invoked before a revision property -# is added, modified or deleted. Subversion runs this hook by invoking -# a program (script, executable, binary, etc.) named 'pre-revprop-change' -# (for which this file is a template), with the following ordered -# arguments: -# -# [1] REPOS-PATH (the path to this repository) -# [2] REV (the revision being tweaked) -# [3] USER (the username of the person tweaking the property) -# [4] PROPNAME (the property being set on the revision) -# [5] ACTION (the property is being 'A'dded, 'M'odified, or 'D'eleted) -# -# [STDIN] PROPVAL ** the new property value is passed via STDIN. -# -# If the hook program exits with success, the propchange happens; but -# if it exits with failure (non-zero), the propchange doesn't happen. -# The hook program can use the 'svnlook' utility to examine the -# existing value of the revision property. -# -# WARNING: unlike other hooks, this hook MUST exist for revision -# properties to be changed. If the hook does not exist, Subversion -# will behave as if the hook were present, but failed. The reason -# for this is that revision properties are UNVERSIONED, meaning that -# a successful propchange is destructive; the old value is gone -# forever. We recommend the hook back up the old value somewhere. -# -# The default working directory for the invocation is undefined, so -# the program should set one explicitly if it cares. -# -# On a Unix system, the normal procedure is to have 'pre-revprop-change' -# invoke other programs to do the real work, though it may do the -# work itself too. -# -# Note that 'pre-revprop-change' must be executable by the user(s) who will -# invoke it (typically the user httpd runs as), and that user must -# have filesystem-level permission to access the repository. -# -# On a Windows system, you should name the hook program -# 'pre-revprop-change.bat' or 'pre-revprop-change.exe', -# but the basic idea is the same. -# -# The hook program runs in an empty environment, unless the server is -# explicitly configured otherwise. For example, a common problem is for -# the PATH environment variable to not be set to its usual value, so -# that subprograms fail to launch unless invoked via absolute path. -# If you're having unexpected problems with a hook program, the -# culprit may be unusual (or missing) environment variables. -# -# CAUTION: -# For security reasons, you MUST always properly quote arguments when -# you use them, as those arguments could contain whitespace or other -# problematic characters. Additionally, you should delimit the list -# of options with "--" before passing the arguments, so malicious -# clients cannot bootleg unexpected options to the commands your -# script aims to execute. -# For similar reasons, you should also add a trailing @ to URLs which -# are passed to SVN commands accepting URLs with peg revisions. -# -# Here is an example hook script, for a Unix /bin/sh interpreter. -# For more examples and pre-written hooks, see those in -# the Subversion repository at -# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and -# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/ - - -REPOS="$1" -REV="$2" -USER="$3" -PROPNAME="$4" -ACTION="$5" - -if [ "$ACTION" = "M" -a "$PROPNAME" = "svn:log" ]; then exit 0; fi - -echo "Changing revision properties other than svn:log is prohibited" >&2 -exit 1 diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl deleted file mode 100755 index 9ba99d071b..0000000000 --- a/manage_externals/test/repos/simple-ext.svn/hooks/pre-unlock.tmpl +++ /dev/null @@ -1,87 +0,0 @@ -#!/bin/sh - -# PRE-UNLOCK HOOK -# -# The pre-unlock hook is invoked before an exclusive lock is -# destroyed. Subversion runs this hook by invoking a program -# (script, executable, binary, etc.) named 'pre-unlock' (for which -# this file is a template), with the following ordered arguments: -# -# [1] REPOS-PATH (the path to this repository) -# [2] PATH (the path in the repository about to be unlocked) -# [3] USER (the user destroying the lock) -# [4] TOKEN (the lock token to be destroyed) -# [5] BREAK-UNLOCK (1 if the user is breaking the lock, else 0) -# -# If the hook program exits with success, the lock is destroyed; but -# if it exits with failure (non-zero), the unlock action is aborted -# and STDERR is returned to the client. -# -# The default working directory for the invocation is undefined, so -# the program should set one explicitly if it cares. -# -# On a Unix system, the normal procedure is to have 'pre-unlock' -# invoke other programs to do the real work, though it may do the -# work itself too. -# -# Note that 'pre-unlock' must be executable by the user(s) who will -# invoke it (typically the user httpd runs as), and that user must -# have filesystem-level permission to access the repository. -# -# On a Windows system, you should name the hook program -# 'pre-unlock.bat' or 'pre-unlock.exe', -# but the basic idea is the same. -# -# The hook program runs in an empty environment, unless the server is -# explicitly configured otherwise. For example, a common problem is for -# the PATH environment variable to not be set to its usual value, so -# that subprograms fail to launch unless invoked via absolute path. -# If you're having unexpected problems with a hook program, the -# culprit may be unusual (or missing) environment variables. -# -# CAUTION: -# For security reasons, you MUST always properly quote arguments when -# you use them, as those arguments could contain whitespace or other -# problematic characters. Additionally, you should delimit the list -# of options with "--" before passing the arguments, so malicious -# clients cannot bootleg unexpected options to the commands your -# script aims to execute. -# For similar reasons, you should also add a trailing @ to URLs which -# are passed to SVN commands accepting URLs with peg revisions. -# -# Here is an example hook script, for a Unix /bin/sh interpreter. -# For more examples and pre-written hooks, see those in -# the Subversion repository at -# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and -# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/ - - -REPOS="$1" -PATH="$2" -USER="$3" -TOKEN="$4" -BREAK="$5" - -# If a lock is owned by a different person, don't allow it be broken. -# (Maybe this script could send email to the lock owner?) - -SVNLOOK=/opt/homebrew/Cellar/subversion/1.14.2_1/bin/svnlook -GREP=/bin/grep -SED=/bin/sed - -LOCK_OWNER=`$SVNLOOK lock "$REPOS" "$PATH" | \ - $GREP '^Owner: ' | $SED 's/Owner: //'` - -# If we get no result from svnlook, there's no lock, return success: -if [ "$LOCK_OWNER" = "" ]; then - exit 0 -fi - -# If the person unlocking matches the lock's owner, return success: -if [ "$LOCK_OWNER" = "$USER" ]; then - exit 0 -fi - -# Otherwise, we've got an owner mismatch, so return failure: -echo "Error: $PATH locked by ${LOCK_OWNER}." 1>&2 -exit 1 diff --git a/manage_externals/test/repos/simple-ext.svn/hooks/start-commit.tmpl b/manage_externals/test/repos/simple-ext.svn/hooks/start-commit.tmpl deleted file mode 100755 index 1395e8315a..0000000000 --- a/manage_externals/test/repos/simple-ext.svn/hooks/start-commit.tmpl +++ /dev/null @@ -1,81 +0,0 @@ -#!/bin/sh - -# START-COMMIT HOOK -# -# The start-commit hook is invoked immediately after a Subversion txn is -# created and populated with initial revprops in the process of doing a -# commit. Subversion runs this hook by invoking a program (script, -# executable, binary, etc.) named 'start-commit' (for which this file -# is a template) with the following ordered arguments: -# -# [1] REPOS-PATH (the path to this repository) -# [2] USER (the authenticated user attempting to commit) -# [3] CAPABILITIES (a colon-separated list of capabilities reported -# by the client; see note below) -# [4] TXN-NAME (the name of the commit txn just created) -# -# Note: The CAPABILITIES parameter is new in Subversion 1.5, and 1.5 -# clients will typically report at least the "mergeinfo" capability. -# If there are other capabilities, then the list is colon-separated, -# e.g.: "mergeinfo:some-other-capability" (the order is undefined). -# -# The list is self-reported by the client. Therefore, you should not -# make security assumptions based on the capabilities list, nor should -# you assume that clients reliably report every capability they have. -# -# Note: The TXN-NAME parameter is new in Subversion 1.8. Prior to version -# 1.8, the start-commit hook was invoked before the commit txn was even -# created, so the ability to inspect the commit txn and its metadata from -# within the start-commit hook was not possible. -# -# If the hook program exits with success, the commit continues; but -# if it exits with failure (non-zero), the commit is stopped before -# a Subversion txn is created, and STDERR is returned to the client. -# -# The default working directory for the invocation is undefined, so -# the program should set one explicitly if it cares. -# -# On a Unix system, the normal procedure is to have 'start-commit' -# invoke other programs to do the real work, though it may do the -# work itself too. -# -# Note that 'start-commit' must be executable by the user(s) who will -# invoke it (typically the user httpd runs as), and that user must -# have filesystem-level permission to access the repository. -# -# On a Windows system, you should name the hook program -# 'start-commit.bat' or 'start-commit.exe', -# but the basic idea is the same. -# -# The hook program runs in an empty environment, unless the server is -# explicitly configured otherwise. For example, a common problem is for -# the PATH environment variable to not be set to its usual value, so -# that subprograms fail to launch unless invoked via absolute path. -# If you're having unexpected problems with a hook program, the -# culprit may be unusual (or missing) environment variables. -# -# CAUTION: -# For security reasons, you MUST always properly quote arguments when -# you use them, as those arguments could contain whitespace or other -# problematic characters. Additionally, you should delimit the list -# of options with "--" before passing the arguments, so malicious -# clients cannot bootleg unexpected options to the commands your -# script aims to execute. -# For similar reasons, you should also add a trailing @ to URLs which -# are passed to SVN commands accepting URLs with peg revisions. -# -# Here is an example hook script, for a Unix /bin/sh interpreter. -# For more examples and pre-written hooks, see those in -# the Subversion repository at -# http://svn.apache.org/repos/asf/subversion/trunk/tools/hook-scripts/ and -# http://svn.apache.org/repos/asf/subversion/trunk/contrib/hook-scripts/ - - -REPOS="$1" -USER="$2" - -commit-allower.pl --repository "$REPOS" --user "$USER" || exit 1 -special-auth-check.py --user "$USER" --auth-level 3 || exit 1 - -# All checks passed, so allow the commit. -exit 0 diff --git a/manage_externals/test/repos/simple-ext.svn/locks/db-logs.lock b/manage_externals/test/repos/simple-ext.svn/locks/db-logs.lock deleted file mode 100644 index 20dd6369be..0000000000 --- a/manage_externals/test/repos/simple-ext.svn/locks/db-logs.lock +++ /dev/null @@ -1,3 +0,0 @@ -This file is not used by Subversion 1.3.x or later. -However, its existence is required for compatibility with -Subversion 1.2.x or earlier. diff --git a/manage_externals/test/repos/simple-ext.svn/locks/db.lock b/manage_externals/test/repos/simple-ext.svn/locks/db.lock deleted file mode 100644 index 20dd6369be..0000000000 --- a/manage_externals/test/repos/simple-ext.svn/locks/db.lock +++ /dev/null @@ -1,3 +0,0 @@ -This file is not used by Subversion 1.3.x or later. -However, its existence is required for compatibility with -Subversion 1.2.x or earlier. diff --git a/manage_externals/test/requirements.txt b/manage_externals/test/requirements.txt deleted file mode 100644 index d66f6f1e67..0000000000 --- a/manage_externals/test/requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -pylint>=1.7.0 -autopep8>=1.3.0 -coverage>=4.4.0 -coveralls>=1.2.0 -sphinx>=1.6.0 diff --git a/manage_externals/test/test_sys_checkout.py b/manage_externals/test/test_sys_checkout.py deleted file mode 100755 index 664160dc99..0000000000 --- a/manage_externals/test/test_sys_checkout.py +++ /dev/null @@ -1,1871 +0,0 @@ -#!/usr/bin/env python3 - -"""Unit test driver for checkout_externals - -Terminology: - * 'container': a repo that has externals - * 'simple': a repo that has no externals, but is referenced as an external by another repo. - * 'mixed': a repo that both has externals and is referenced as an external by another repo. - - * 'clean': the local repo matches the version in the externals and has no local modifications. - * 'empty': the external isn't checked out at all. - -Note: this script assume the path to the manic and -checkout_externals module is already in the python path. This is -usually handled by the makefile. If you call it directly, you may need -to adjust your path. - -NOTE(bja, 2017-11) If a test fails, we want to keep the repo for that -test. But the tests will keep running, so we need a unique name. Also, -tearDown is always called after each test. I haven't figured out how -to determine if an assertion failed and whether it is safe to clean up -the test repos. - -So the solution is: - -* assign a unique id to each test repo. - -* never cleanup during the run. - -* Erase any existing repos at the begining of the module in -setUpModule. -""" - -# NOTE(bja, 2017-11) pylint complains that the module is too big, but -# I'm still working on how to break up the tests and still have the -# temporary directory be preserved.... -# pylint: disable=too-many-lines - - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import logging -import os -import os.path -import shutil -import unittest - -from manic.externals_description import ExternalsDescription -from manic.externals_description import DESCRIPTION_SECTION, VERSION_ITEM -from manic.externals_description import git_submodule_status -from manic.externals_status import ExternalStatus -from manic.repository_git import GitRepository -from manic.utils import printlog, execute_subprocess -from manic.global_constants import LOCAL_PATH_INDICATOR, VERBOSITY_DEFAULT -from manic.global_constants import LOG_FILE_NAME -from manic import checkout - -# ConfigParser was renamed in python2 to configparser. In python2, -# ConfigParser returns byte strings, str, instead of unicode. We need -# unicode to be compatible with xml and json parser and python3. -try: - # python2 - from ConfigParser import SafeConfigParser as config_parser -except ImportError: - # python3 - from configparser import ConfigParser as config_parser - -# --------------------------------------------------------------------- -# -# Global constants -# -# --------------------------------------------------------------------- - - -# Module-wide root directory for all the per-test subdirs we'll create on -# the fly (which are placed under wherever $CWD is when the test runs). -# Set by setupModule(). -module_tmp_root_dir = None -TMP_REPO_DIR_NAME = 'tmp' # subdir under $CWD - -# subdir under test/ that holds all of our checked-in repositories (which we -# will clone for these tests). -BARE_REPO_ROOT_NAME = 'repos' - -# Environment var referenced by checked-in externals file in mixed-cont-ext.git, -# which should be pointed to the fully-resolved BARE_REPO_ROOT_NAME directory. -# We explicitly clear this after every test, via tearDown(). -MIXED_CONT_EXT_ROOT_ENV_VAR = 'MANIC_TEST_BARE_REPO_ROOT' - -# Subdirs under bare repo root, each holding a repository. For more info -# on the contents of these repositories, see test/repos/README.md. In these -# tests the 'parent' repos are cloned as a starting point, whereas the 'child' -# repos are checked out when the tests run checkout_externals. -CONTAINER_REPO = 'container.git' # Parent repo -SIMPLE_REPO = 'simple-ext.git' # Child repo -SIMPLE_FORK_REPO = 'simple-ext-fork.git' # Child repo -MIXED_REPO = 'mixed-cont-ext.git' # Both parent and child -SVN_TEST_REPO = 'simple-ext.svn' # Subversion repository - -# Standard (arbitrary) external names for test configs -TAG_SECTION = 'simp_tag' -BRANCH_SECTION = 'simp_branch' -HASH_SECTION = 'simp_hash' - -# All the configs we construct check out their externals into these local paths. -EXTERNALS_PATH = 'externals' -SUB_EXTERNALS_PATH = 'src' # For mixed test repos, - -# For testing behavior with '.' instead of an explicit paths. -SIMPLE_LOCAL_ONLY_NAME = '.' - -# Externals files. -CFG_NAME = 'externals.cfg' # We construct this on a per-test basis. -CFG_SUB_NAME = 'sub-externals.cfg' # Already exists in mixed-cont-ext repo. - -# Arbitrary text file in all the test repos. -README_NAME = 'readme.txt' - -# Branch that exists in both the simple and simple-fork repos. -REMOTE_BRANCH_FEATURE2 = 'feature2' - -# Disable too-many-public-methods error -# pylint: disable=R0904 - -def setUpModule(): # pylint: disable=C0103 - """Setup for all tests in this module. It is called once per module! - """ - logging.basicConfig(filename=LOG_FILE_NAME, - format='%(levelname)s : %(asctime)s : %(message)s', - datefmt='%Y-%m-%d %H:%M:%S', - level=logging.DEBUG) - repo_root = os.path.join(os.getcwd(), TMP_REPO_DIR_NAME) - repo_root = os.path.abspath(repo_root) - # delete if it exists from previous runs - try: - shutil.rmtree(repo_root) - except BaseException: - pass - # create clean dir for this run - os.mkdir(repo_root) - - # Make available to all tests in this file. - global module_tmp_root_dir - assert module_tmp_root_dir == None, module_tmp_root_dir - module_tmp_root_dir = repo_root - - -class RepoUtils(object): - """Convenience methods for interacting with git repos.""" - @staticmethod - def create_branch(repo_base_dir, external_name, branch, with_commit=False): - """Create branch and optionally (with_commit) add a single commit. - """ - # pylint: disable=R0913 - cwd = os.getcwd() - repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name) - os.chdir(repo_root) - cmd = ['git', 'checkout', '-b', branch, ] - execute_subprocess(cmd) - if with_commit: - msg = 'start work on {0}'.format(branch) - with open(README_NAME, 'a') as handle: - handle.write(msg) - cmd = ['git', 'add', README_NAME, ] - execute_subprocess(cmd) - cmd = ['git', 'commit', '-m', msg, ] - execute_subprocess(cmd) - os.chdir(cwd) - - @staticmethod - def create_commit(repo_base_dir, external_name): - """Make a commit to the given external. - - This is used to test sync state changes from local commits on - detached heads and tracking branches. - """ - cwd = os.getcwd() - repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name) - os.chdir(repo_root) - - msg = 'work on great new feature!' - with open(README_NAME, 'a') as handle: - handle.write(msg) - cmd = ['git', 'add', README_NAME, ] - execute_subprocess(cmd) - cmd = ['git', 'commit', '-m', msg, ] - execute_subprocess(cmd) - os.chdir(cwd) - - @staticmethod - def clone_test_repo(bare_root, test_id, parent_repo_name, dest_dir_in): - """Clone repo at / into dest_dir_in or local per-test-subdir. - - Returns output dir. - """ - parent_repo_dir = os.path.join(bare_root, parent_repo_name) - if dest_dir_in is None: - # create unique subdir for this test - test_dir_name = test_id - print("Test repository name: {0}".format(test_dir_name)) - dest_dir = os.path.join(module_tmp_root_dir, test_dir_name) - else: - dest_dir = dest_dir_in - - # pylint: disable=W0212 - GitRepository._git_clone(parent_repo_dir, dest_dir, VERBOSITY_DEFAULT) - return dest_dir - - @staticmethod - def add_file_to_repo(under_test_dir, filename, tracked): - """Add a file to the repository so we can put it into a dirty state - - """ - cwd = os.getcwd() - os.chdir(under_test_dir) - with open(filename, 'w') as tmp: - tmp.write('Hello, world!') - - if tracked: - # NOTE(bja, 2018-01) brittle hack to obtain repo dir and - # file name - path_data = filename.split('/') - repo_dir = os.path.join(path_data[0], path_data[1]) - os.chdir(repo_dir) - tracked_file = path_data[2] - cmd = ['git', 'add', tracked_file] - execute_subprocess(cmd) - - os.chdir(cwd) - -class GenerateExternalsDescriptionCfgV1(object): - """Building blocks to create ExternalsDescriptionCfgV1 files. - - Basic usage: create_config() multiple create_*(), then write_config(). - Optionally after that: write_with_*(). - """ - - def __init__(self, bare_root): - self._schema_version = '1.1.0' - self._config = None - - # directory where we have test repositories (which we will clone for - # tests) - self._bare_root = bare_root - - def write_config(self, dest_dir, filename=CFG_NAME): - """Write self._config to disk - - """ - dest_path = os.path.join(dest_dir, filename) - with open(dest_path, 'w') as configfile: - self._config.write(configfile) - - def create_config(self): - """Create an config object and add the required metadata section - - """ - self._config = config_parser() - self.create_metadata() - - def create_metadata(self): - """Create the metadata section of the config file - """ - self._config.add_section(DESCRIPTION_SECTION) - - self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, - self._schema_version) - - def url_for_repo_path(self, repo_path, repo_path_abs=None): - if repo_path_abs is not None: - return repo_path_abs - else: - return os.path.join(self._bare_root, repo_path) - - def create_section(self, repo_path, name, tag='', branch='', - ref_hash='', required=True, path=EXTERNALS_PATH, - sub_externals='', repo_path_abs=None, from_submodule=False, - sparse='', nested=False): - # pylint: disable=too-many-branches - """Create a config ExternalsDescription section with the given name. - - Autofills some items and handles some optional items. - - repo_path_abs overrides repo_path (which is relative to the bare repo) - path is a subdir under repo_path to check out to. - """ - # pylint: disable=R0913 - self._config.add_section(name) - if not from_submodule: - if nested: - self._config.set(name, ExternalsDescription.PATH, path) - else: - self._config.set(name, ExternalsDescription.PATH, - os.path.join(path, name)) - - self._config.set(name, ExternalsDescription.PROTOCOL, - ExternalsDescription.PROTOCOL_GIT) - - # from_submodules is incompatible with some other options, turn them off - if (from_submodule and - ((repo_path_abs is not None) or tag or ref_hash or branch)): - printlog('create_section: "from_submodule" is incompatible with ' - '"repo_url", "tag", "hash", and "branch" options;\n' - 'Ignoring those options for {}'.format(name)) - repo_url = None - tag = '' - ref_hash = '' - branch = '' - - repo_url = self.url_for_repo_path(repo_path, repo_path_abs) - - if not from_submodule: - self._config.set(name, ExternalsDescription.REPO_URL, repo_url) - - self._config.set(name, ExternalsDescription.REQUIRED, str(required)) - - if tag: - self._config.set(name, ExternalsDescription.TAG, tag) - - if branch: - self._config.set(name, ExternalsDescription.BRANCH, branch) - - if ref_hash: - self._config.set(name, ExternalsDescription.HASH, ref_hash) - - if sub_externals: - self._config.set(name, ExternalsDescription.EXTERNALS, - sub_externals) - - if sparse: - self._config.set(name, ExternalsDescription.SPARSE, sparse) - - if from_submodule: - self._config.set(name, ExternalsDescription.SUBMODULE, "True") - - def create_section_reference_to_subexternal(self, name): - """Just a reference to another externals file. - - """ - # pylint: disable=R0913 - self._config.add_section(name) - self._config.set(name, ExternalsDescription.PATH, LOCAL_PATH_INDICATOR) - - self._config.set(name, ExternalsDescription.PROTOCOL, - ExternalsDescription.PROTOCOL_EXTERNALS_ONLY) - - self._config.set(name, ExternalsDescription.REPO_URL, - LOCAL_PATH_INDICATOR) - - self._config.set(name, ExternalsDescription.REQUIRED, str(True)) - - self._config.set(name, ExternalsDescription.EXTERNALS, CFG_SUB_NAME) - - def create_svn_external(self, name, url, tag='', branch=''): - """Create a config section for an svn repository. - - """ - self._config.add_section(name) - self._config.set(name, ExternalsDescription.PATH, - os.path.join(EXTERNALS_PATH, name)) - - self._config.set(name, ExternalsDescription.PROTOCOL, - ExternalsDescription.PROTOCOL_SVN) - - self._config.set(name, ExternalsDescription.REPO_URL, url) - - self._config.set(name, ExternalsDescription.REQUIRED, str(True)) - - if tag: - self._config.set(name, ExternalsDescription.TAG, tag) - - if branch: - self._config.set(name, ExternalsDescription.BRANCH, branch) - - def write_with_git_branch(self, dest_dir, name, branch, new_remote_repo_path=None): - """Update fields in our config and write it to disk. - - name is the key of the ExternalsDescription in self._config to update. - """ - # pylint: disable=R0913 - self._config.set(name, ExternalsDescription.BRANCH, branch) - - if new_remote_repo_path: - if new_remote_repo_path == SIMPLE_LOCAL_ONLY_NAME: - repo_url = SIMPLE_LOCAL_ONLY_NAME - else: - repo_url = os.path.join(self._bare_root, new_remote_repo_path) - self._config.set(name, ExternalsDescription.REPO_URL, repo_url) - - try: - # remove the tag if it existed - self._config.remove_option(name, ExternalsDescription.TAG) - except BaseException: - pass - - self.write_config(dest_dir) - - def write_with_svn_branch(self, dest_dir, name, branch): - """Update a repository branch, and potentially the remote. - """ - # pylint: disable=R0913 - self._config.set(name, ExternalsDescription.BRANCH, branch) - - try: - # remove the tag if it existed - self._config.remove_option(name, ExternalsDescription.TAG) - except BaseException: - pass - - self.write_config(dest_dir) - - def write_with_tag_and_remote_repo(self, dest_dir, name, tag, new_remote_repo_path, - remove_branch=True): - """Update a repository tag and the remote. - - NOTE(bja, 2017-11) remove_branch=False should result in an - overspecified external with both a branch and tag. This is - used for error condition testing. - - """ - # pylint: disable=R0913 - self._config.set(name, ExternalsDescription.TAG, tag) - - if new_remote_repo_path: - repo_url = os.path.join(self._bare_root, new_remote_repo_path) - self._config.set(name, ExternalsDescription.REPO_URL, repo_url) - - try: - # remove the branch if it existed - if remove_branch: - self._config.remove_option(name, ExternalsDescription.BRANCH) - except BaseException: - pass - - self.write_config(dest_dir) - - def write_without_branch_tag(self, dest_dir, name): - """Update a repository protocol, and potentially the remote - """ - # pylint: disable=R0913 - try: - # remove the branch if it existed - self._config.remove_option(name, ExternalsDescription.BRANCH) - except BaseException: - pass - - try: - # remove the tag if it existed - self._config.remove_option(name, ExternalsDescription.TAG) - except BaseException: - pass - - self.write_config(dest_dir) - - def write_without_repo_url(self, dest_dir, name): - """Update a repository protocol, and potentially the remote - """ - # pylint: disable=R0913 - try: - # remove the repo url if it existed - self._config.remove_option(name, ExternalsDescription.REPO_URL) - except BaseException: - pass - - self.write_config(dest_dir) - - def write_with_protocol(self, dest_dir, name, protocol, repo_path=None): - """Update a repository protocol, and potentially the remote - """ - # pylint: disable=R0913 - self._config.set(name, ExternalsDescription.PROTOCOL, protocol) - - if repo_path: - repo_url = os.path.join(self._bare_root, repo_path) - self._config.set(name, ExternalsDescription.REPO_URL, repo_url) - - self.write_config(dest_dir) - - -def _execute_checkout_in_dir(dirname, args, debug_env=''): - """Execute the checkout command in the appropriate repo dir with the - specified additional args. - - args should be a list of strings. - debug_env shuld be a string of the form 'FOO=bar' or the empty string. - - Note that we are calling the command line processing and main - routines and not using a subprocess call so that we get code - coverage results! Note this means that environment variables are passed - to checkout_externals via os.environ; debug_env is just used to aid - manual reproducibility of a given call. - - Returns (overall_status, tree_status) - where overall_status is 0 for success, nonzero otherwise. - and tree_status is set if --status was passed in, None otherwise. - - Note this command executes the checkout command, it doesn't - necessarily do any checking out (e.g. if --status is passed in). - """ - cwd = os.getcwd() - - # Construct a command line for reproducibility; this command is not - # actually executed in the test. - os.chdir(dirname) - cmdline = ['--externals', CFG_NAME, ] - cmdline += args - manual_cmd = ('Running equivalent of:\n' - 'pushd {dirname}; ' - '{debug_env} /path/to/checkout_externals {args}'.format( - dirname=dirname, debug_env=debug_env, - args=' '.join(cmdline))) - printlog(manual_cmd) - options = checkout.commandline_arguments(cmdline) - overall_status, tree_status = checkout.main(options) - os.chdir(cwd) - return overall_status, tree_status - -class BaseTestSysCheckout(unittest.TestCase): - """Base class of reusable systems level test setup for - checkout_externals - - """ - # NOTE(bja, 2017-11) pylint complains about long method names, but - # it is hard to differentiate tests without making them more - # cryptic. - # pylint: disable=invalid-name - - # Command-line args for checkout_externals, used in execute_checkout_in_dir() - status_args = ['--status'] - checkout_args = [] - optional_args = ['--optional'] - verbose_args = ['--status', '--verbose'] - - def setUp(self): - """Setup for all individual checkout_externals tests - """ - # directory we want to return to after the test system and - # checkout_externals are done cd'ing all over the place. - self._return_dir = os.getcwd() - - self._test_id = self.id().split('.')[-1] - - # find root - if os.path.exists(os.path.join(os.getcwd(), 'checkout_externals')): - root_dir = os.path.abspath(os.getcwd()) - else: - # maybe we are in a subdir, search up - root_dir = os.path.abspath(os.path.join(os.getcwd(), os.pardir)) - while os.path.basename(root_dir): - if os.path.exists(os.path.join(root_dir, 'checkout_externals')): - break - root_dir = os.path.dirname(root_dir) - - if not os.path.exists(os.path.join(root_dir, 'checkout_externals')): - raise RuntimeError('Cannot find checkout_externals') - - # path to the executable - self._checkout = os.path.join(root_dir, 'checkout_externals') - - # directory where we have test repositories (which we will clone for - # tests) - self._bare_root = os.path.abspath( - os.path.join(root_dir, 'test', BARE_REPO_ROOT_NAME)) - - # set the input file generator - self._generator = GenerateExternalsDescriptionCfgV1(self._bare_root) - # set the input file generator for secondary externals - self._sub_generator = GenerateExternalsDescriptionCfgV1(self._bare_root) - - def tearDown(self): - """Tear down for individual tests - """ - # return to our common starting point - os.chdir(self._return_dir) - - # (in case this was set) Don't pollute environment of other tests. - os.environ.pop(MIXED_CONT_EXT_ROOT_ENV_VAR, - None) # Don't care if key wasn't set. - - def clone_test_repo(self, parent_repo_name, dest_dir_in=None): - """Clones repo under self._bare_root""" - return RepoUtils.clone_test_repo(self._bare_root, self._test_id, - parent_repo_name, dest_dir_in) - - def execute_checkout_in_dir(self, dirname, args, debug_env=''): - overall_status, tree_status = _execute_checkout_in_dir(dirname, args, - debug_env=debug_env) - self.assertEqual(overall_status, 0) - return tree_status - - def execute_checkout_with_status(self, dirname, args, debug_env=''): - """Calls checkout a second time to get status if needed.""" - tree_status = self.execute_checkout_in_dir( - dirname, args, debug_env=debug_env) - if tree_status is None: - tree_status = self.execute_checkout_in_dir(dirname, - self.status_args, - debug_env=debug_env) - self.assertNotEqual(tree_status, None) - return tree_status - - def _check_sync_clean(self, ext_status, expected_sync_state, - expected_clean_state): - self.assertEqual(ext_status.sync_state, expected_sync_state) - self.assertEqual(ext_status.clean_state, expected_clean_state) - - @staticmethod - def _external_path(section_name, base_path=EXTERNALS_PATH): - return './{0}/{1}'.format(base_path, section_name) - - def _check_file_exists(self, repo_dir, pathname): - "Check that exists in " - self.assertTrue(os.path.exists(os.path.join(repo_dir, pathname))) - - def _check_file_absent(self, repo_dir, pathname): - "Check that does not exist in " - self.assertFalse(os.path.exists(os.path.join(repo_dir, pathname))) - - -class TestSysCheckout(BaseTestSysCheckout): - """Run systems level tests of checkout_externals - """ - # NOTE(bja, 2017-11) pylint complains about long method names, but - # it is hard to differentiate tests without making them more - # cryptic. - # pylint: disable=invalid-name - - # ---------------------------------------------------------------- - # - # Run systems tests - # - # ---------------------------------------------------------------- - def test_required_bytag(self): - """Check out a required external pointing to a git tag.""" - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, - tag='tag1') - self._generator.write_config(cloned_repo_dir) - - # externals start out 'empty' aka not checked out. - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - local_path_rel = self._external_path(TAG_SECTION) - self._check_sync_clean(tree[local_path_rel], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - local_path_abs = os.path.join(cloned_repo_dir, local_path_rel) - self.assertFalse(os.path.exists(local_path_abs)) - - # after checkout, the external is 'clean' aka at the correct version. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[local_path_rel], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # Actually checked out the desired repo. - self.assertEqual('origin', GitRepository._remote_name_for_url( - # Which url to look up - self._generator.url_for_repo_path(SIMPLE_REPO), - # Which directory has the local checked-out repo. - dirname=local_path_abs)) - - # Actually checked out the desired tag. - (tag_found, tag_name) = GitRepository._git_current_tag(local_path_abs) - self.assertEqual(tag_name, 'tag1') - - # Check existence of some simp_tag files - tag_path = os.path.join('externals', TAG_SECTION) - self._check_file_exists(cloned_repo_dir, - os.path.join(tag_path, README_NAME)) - # Subrepo should not exist (not referenced by configs). - self._check_file_absent(cloned_repo_dir, os.path.join(tag_path, - 'simple_subdir', - 'subdir_file.txt')) - - def test_required_bybranch(self): - """Check out a required external pointing to a git branch.""" - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # externals start out 'empty' aka not checked out. - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - local_path_rel = self._external_path(BRANCH_SECTION) - self._check_sync_clean(tree[local_path_rel], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - local_path_abs = os.path.join(cloned_repo_dir, local_path_rel) - self.assertFalse(os.path.exists(local_path_abs)) - - # after checkout, the external is 'clean' aka at the correct version. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[local_path_rel], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self.assertTrue(os.path.exists(local_path_abs)) - - # Actually checked out the desired repo. - self.assertEqual('origin', GitRepository._remote_name_for_url( - # Which url to look up - self._generator.url_for_repo_path(SIMPLE_REPO), - # Which directory has the local checked-out repo. - dirname=local_path_abs)) - - # Actually checked out the desired branch. - (branch_found, branch_name) = GitRepository._git_current_remote_branch( - local_path_abs) - self.assertEquals(branch_name, 'origin/' + REMOTE_BRANCH_FEATURE2) - - def test_required_byhash(self): - """Check out a required external pointing to a git hash.""" - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, HASH_SECTION, - ref_hash='60b1cc1a38d63') - self._generator.write_config(cloned_repo_dir) - - # externals start out 'empty' aka not checked out. - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - local_path_rel = self._external_path(HASH_SECTION) - self._check_sync_clean(tree[local_path_rel], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - local_path_abs = os.path.join(cloned_repo_dir, local_path_rel) - self.assertFalse(os.path.exists(local_path_abs)) - - # after checkout, the externals are 'clean' aka at their correct version. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[local_path_rel], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # Actually checked out the desired repo. - self.assertEqual('origin', GitRepository._remote_name_for_url( - # Which url to look up - self._generator.url_for_repo_path(SIMPLE_REPO), - # Which directory has the local checked-out repo. - dirname=local_path_abs)) - - # Actually checked out the desired hash. - (hash_found, hash_name) = GitRepository._git_current_hash( - local_path_abs) - self.assertTrue(hash_name.startswith('60b1cc1a38d63'), - msg=hash_name) - - def test_container_nested_required(self): - """Verify that a container with nested subrepos generates the correct initial status. - Tests over all possible permutations - """ - # Output subdirs for each of the externals, to test that one external can be - # checked out in a subdir of another. - NESTED_SUBDIR = ['./fred', './fred/wilma', './fred/wilma/barney'] - - # Assert that each type of external (e.g. tag vs branch) can be at any parent level - # (e.g. child/parent/grandparent). - orders = [[0, 1, 2], [1, 2, 0], [2, 0, 1], - [0, 2, 1], [2, 1, 0], [1, 0, 2]] - for n, order in enumerate(orders): - dest_dir = os.path.join(module_tmp_root_dir, self._test_id, - "test"+str(n)) - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO, - dest_dir_in=dest_dir) - self._generator.create_config() - # We happen to check out each section via a different reference (tag/branch/hash) but - # those don't really matter, we just need to check out three repos into a nested set of - # directories. - self._generator.create_section( - SIMPLE_REPO, TAG_SECTION, nested=True, - tag='tag1', path=NESTED_SUBDIR[order[0]]) - self._generator.create_section( - SIMPLE_REPO, BRANCH_SECTION, nested=True, - branch=REMOTE_BRANCH_FEATURE2, path=NESTED_SUBDIR[order[1]]) - self._generator.create_section( - SIMPLE_REPO, HASH_SECTION, nested=True, - ref_hash='60b1cc1a38d63', path=NESTED_SUBDIR[order[2]]) - self._generator.write_config(cloned_repo_dir) - - # all externals start out 'empty' aka not checked out. - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - - # after checkout, all the repos are 'clean'. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_simple_optional(self): - """Verify that container with an optional simple subrepos generates - the correct initial status. - - """ - # create repo and externals config. - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, 'simp_req', - tag='tag1') - - self._generator.create_section(SIMPLE_REPO, 'simp_opt', - tag='tag1', required=False) - - self._generator.write_config(cloned_repo_dir) - - # all externals start out 'empty' aka not checked out. - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - req_status = tree[self._external_path('simp_req')] - self._check_sync_clean(req_status, - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self.assertEqual(req_status.source_type, ExternalStatus.MANAGED) - - opt_status = tree[self._external_path('simp_opt')] - self._check_sync_clean(opt_status, - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL) - - # after checkout, required external is clean, optional is still empty. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - req_status = tree[self._external_path('simp_req')] - self._check_sync_clean(req_status, - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self.assertEqual(req_status.source_type, ExternalStatus.MANAGED) - - opt_status = tree[self._external_path('simp_opt')] - self._check_sync_clean(opt_status, - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL) - - # after checking out optionals, the optional external is also clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.optional_args) - req_status = tree[self._external_path('simp_req')] - self._check_sync_clean(req_status, - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self.assertEqual(req_status.source_type, ExternalStatus.MANAGED) - - opt_status = tree[self._external_path('simp_opt')] - self._check_sync_clean(opt_status, - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL) - - def test_container_simple_verbose(self): - """Verify that verbose status matches non-verbose. - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, - tag='tag1') - self._generator.write_config(cloned_repo_dir) - - # after checkout, all externals should be 'clean'. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # 'Verbose' status should tell the same story. - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.verbose_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_simple_dirty(self): - """Verify that a container with a new tracked file is marked dirty. - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, - tag='tag1') - self._generator.write_config(cloned_repo_dir) - - # checkout, should start out clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # add a tracked file to the simp_tag external, should be dirty. - RepoUtils.add_file_to_repo(cloned_repo_dir, - 'externals/{0}/tmp.txt'.format(TAG_SECTION), - tracked=True) - tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.DIRTY) - - # Re-checkout; simp_tag should still be dirty. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.DIRTY) - - def test_container_simple_untracked(self): - """Verify that a container with simple subrepos and a untracked files - is not considered 'dirty' and will attempt an update. - - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, - tag='tag1') - self._generator.write_config(cloned_repo_dir) - - # checkout, should start out clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # add an untracked file to the simp_tag external, should stay clean. - RepoUtils.add_file_to_repo(cloned_repo_dir, - 'externals/{0}/tmp.txt'.format(TAG_SECTION), - tracked=False) - tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # After checkout, the external should still be 'clean'. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_simple_detached_sync(self): - """Verify that a container with simple subrepos generates the correct - out of sync status when making commits from a detached head - state. - - For more info about 'detached head' state: https://www.cloudbees.com/blog/git-detached-head - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, - tag='tag1') - - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - - self._generator.create_section(SIMPLE_REPO, 'simp_hash', - ref_hash='60b1cc1a38d63') - - self._generator.write_config(cloned_repo_dir) - - # externals start out 'empty' aka not checked out. - tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self._check_sync_clean(tree[self._external_path(HASH_SECTION)], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - - # checkout - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - # Commit on top of the tag and hash (creating the detached head state in those two - # externals' repos) - # The branch commit does not create the detached head state, but here for completeness. - RepoUtils.create_commit(cloned_repo_dir, TAG_SECTION) - RepoUtils.create_commit(cloned_repo_dir, HASH_SECTION) - RepoUtils.create_commit(cloned_repo_dir, BRANCH_SECTION) - - # sync status of all three should be 'modified' (uncommitted changes) - # clean status is 'ok' (matches externals version) - tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.MODEL_MODIFIED, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.MODEL_MODIFIED, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(HASH_SECTION)], - ExternalStatus.MODEL_MODIFIED, - ExternalStatus.STATUS_OK) - - # after checkout, all externals should be totally clean (no uncommitted changes, - # and matches externals version). - tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(HASH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_remote_branch(self): - """Verify that a container with remote branch change works - - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # initial checkout - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - # update the branch external to point to a different remote with the same branch, - # then simp_branch should be out of sync - self._generator.write_with_git_branch(cloned_repo_dir, - name=BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2, - new_remote_repo_path=SIMPLE_FORK_REPO) - tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.MODEL_MODIFIED, - ExternalStatus.STATUS_OK) - - # checkout new externals, now simp_branch should be clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_remote_tag_same_branch(self): - """Verify that a container with remote tag change works. The new tag - should not be in the original repo, only the new remote - fork. The new tag is automatically fetched because it is on - the branch. - - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # initial checkout - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - # update the config file to point to a different remote with - # the new tag replacing the old branch. Tag MUST NOT be in the original - # repo! status of simp_branch should then be out of sync - self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, - tag='forked-feature-v1', - new_remote_repo_path=SIMPLE_FORK_REPO) - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.MODEL_MODIFIED, - ExternalStatus.STATUS_OK) - - # checkout new externals, then should be synced. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_remote_tag_fetch_all(self): - """Verify that a container with remote tag change works. The new tag - should not be in the original repo, only the new remote - fork. It should also not be on a branch that will be fetched, - and therefore not fetched by default with 'git fetch'. It will - only be retrieved by 'git fetch --tags' - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # initial checkout - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - # update the config file to point to a different remote with - # the new tag instead of the old branch. Tag MUST NOT be in the original - # repo! status of simp_branch should then be out of sync. - self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, - tag='abandoned-feature', - new_remote_repo_path=SIMPLE_FORK_REPO) - tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.MODEL_MODIFIED, - ExternalStatus.STATUS_OK) - - # checkout new externals, should be clean again. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_preserve_dot(self): - """Verify that after inital checkout, modifying an external git repo - url to '.' and the current branch will leave it unchanged. - - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # initial checkout - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - # update the config file to point to a different remote with - # the same branch. - self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2, - new_remote_repo_path=SIMPLE_FORK_REPO) - # after checkout, should be clean again. - tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # update branch to point to a new branch that only exists in - # the local fork - RepoUtils.create_branch(cloned_repo_dir, external_name=BRANCH_SECTION, - branch='private-feature', with_commit=True) - self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION, - branch='private-feature', - new_remote_repo_path=SIMPLE_LOCAL_ONLY_NAME) - # after checkout, should be clean again. - tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_mixed_subrepo(self): - """Verify container with mixed subrepo. - - The mixed subrepo has a sub-externals file with different - sub-externals on different branches. - - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - - self._generator.create_config() - self._generator.create_section(MIXED_REPO, 'mixed_req', - branch='master', sub_externals=CFG_SUB_NAME) - self._generator.write_config(cloned_repo_dir) - - # The subrepo has a repo_url that uses this environment variable. - # It'll be cleared in tearDown(). - os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root - debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root - - # inital checkout: all requireds are clean, and optional is empty. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args, - debug_env=debug_env) - mixed_req_path = self._external_path('mixed_req') - self._check_sync_clean(tree[mixed_req_path], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - sub_ext_base_path = "{0}/{1}/{2}".format(EXTERNALS_PATH, 'mixed_req', SUB_EXTERNALS_PATH) - # The already-checked-in subexternals file has a 'simp_branch' section - self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # update the mixed-use external to point to different branch - # status should become out of sync for mixed_req, but sub-externals - # are still in sync - self._generator.write_with_git_branch(cloned_repo_dir, name='mixed_req', - branch='new-feature', - new_remote_repo_path=MIXED_REPO) - tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args, - debug_env=debug_env) - self._check_sync_clean(tree[mixed_req_path], - ExternalStatus.MODEL_MODIFIED, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # run the checkout. Now the mixed use external and its sub-externals should be clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args, - debug_env=debug_env) - self._check_sync_clean(tree[mixed_req_path], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_component(self): - """Verify that optional component checkout works - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - - # create the top level externals file - self._generator.create_config() - # Optional external, by tag. - self._generator.create_section(SIMPLE_REPO, 'simp_opt', - tag='tag1', required=False) - - # Required external, by branch. - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - - # Required external, by hash. - self._generator.create_section(SIMPLE_REPO, HASH_SECTION, - ref_hash='60b1cc1a38d63') - self._generator.write_config(cloned_repo_dir) - - # inital checkout, first try a nonexistent component argument noref - checkout_args = ['simp_opt', 'noref'] - checkout_args.extend(self.checkout_args) - - with self.assertRaises(RuntimeError): - self.execute_checkout_in_dir(cloned_repo_dir, checkout_args) - - # Now explicitly check out one optional component.. - # Explicitly listed component (opt) should be present, the other two not. - checkout_args = ['simp_opt'] - checkout_args.extend(self.checkout_args) - tree = self.execute_checkout_with_status(cloned_repo_dir, - checkout_args) - self._check_sync_clean(tree[self._external_path('simp_opt')], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self._check_sync_clean(tree[self._external_path(HASH_SECTION)], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - - # Check out a second component, this one required. - # Explicitly listed component (branch) should be present, the still-unlisted one (tag) not. - checkout_args.append(BRANCH_SECTION) - tree = self.execute_checkout_with_status(cloned_repo_dir, - checkout_args) - self._check_sync_clean(tree[self._external_path('simp_opt')], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(HASH_SECTION)], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - - - def test_container_exclude_component(self): - """Verify that exclude component checkout works - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, - tag='tag1') - - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - - self._generator.create_section(SIMPLE_REPO, 'simp_hash', - ref_hash='60b1cc1a38d63') - - self._generator.write_config(cloned_repo_dir) - - # inital checkout should result in all externals being clean except excluded TAG_SECTION. - checkout_args = ['--exclude', TAG_SECTION] - checkout_args.extend(self.checkout_args) - tree = self.execute_checkout_with_status(cloned_repo_dir, checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.EMPTY, - ExternalStatus.DEFAULT) - self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path(HASH_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_subexternal(self): - """Verify that an externals file can be brought in as a reference. - - """ - cloned_repo_dir = self.clone_test_repo(MIXED_REPO) - - self._generator.create_config() - self._generator.create_section_reference_to_subexternal('mixed_base') - self._generator.write_config(cloned_repo_dir) - - # The subrepo has a repo_url that uses this environment variable. - # It'll be cleared in tearDown(). - os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root - debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root - - # After checkout, confirm required's are clean and the referenced - # subexternal's contents are also clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args, - debug_env=debug_env) - - self._check_sync_clean( - tree[self._external_path(BRANCH_SECTION, base_path=SUB_EXTERNALS_PATH)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def test_container_sparse(self): - """Verify that 'full' container with simple subrepo - can run a sparse checkout and generate the correct initial status. - - """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - - # Create a file to list filenames to checkout. - sparse_filename = 'sparse_checkout' - with open(os.path.join(cloned_repo_dir, sparse_filename), 'w') as sfile: - sfile.write(README_NAME) - - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, - tag='tag2') - - # Same tag as above, but with a sparse file too. - sparse_relpath = '../../' + sparse_filename - self._generator.create_section(SIMPLE_REPO, 'simp_sparse', - tag='tag2', sparse=sparse_relpath) - - self._generator.write_config(cloned_repo_dir) - - # inital checkout, confirm required's are clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._external_path('simp_sparse')], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - # Check existence of some files - full set in TAG_SECTION, and sparse set - # in 'simp_sparse'. - subrepo_path = os.path.join('externals', TAG_SECTION) - self._check_file_exists(cloned_repo_dir, - os.path.join(subrepo_path, README_NAME)) - self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path, - 'simple_subdir', - 'subdir_file.txt')) - subrepo_path = os.path.join('externals', 'simp_sparse') - self._check_file_exists(cloned_repo_dir, - os.path.join(subrepo_path, README_NAME)) - self._check_file_absent(cloned_repo_dir, os.path.join(subrepo_path, - 'simple_subdir', - 'subdir_file.txt')) - -class TestSysCheckoutSVN(BaseTestSysCheckout): - """Run systems level tests of checkout_externals accessing svn repositories - - SVN tests - these tests use the svn repository interface. - """ - - @staticmethod - def _svn_branch_name(): - return './{0}/svn_branch'.format(EXTERNALS_PATH) - - @staticmethod - def _svn_tag_name(): - return './{0}/svn_tag'.format(EXTERNALS_PATH) - - def _svn_test_repo_url(self): - return 'file://' + os.path.join(self._bare_root, SVN_TEST_REPO) - - def _check_tag_branch_svn_tag_clean(self, tree): - self._check_sync_clean(tree[self._external_path(TAG_SECTION)], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._svn_branch_name()], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - self._check_sync_clean(tree[self._svn_tag_name()], - ExternalStatus.STATUS_OK, - ExternalStatus.STATUS_OK) - - def _have_svn_access(self): - """Check if we have svn access so we can enable tests that use svn. - - """ - have_svn = False - cmd = ['svn', 'ls', self._svn_test_repo_url(), ] - try: - execute_subprocess(cmd) - have_svn = True - except BaseException: - pass - return have_svn - - def _skip_if_no_svn_access(self): - """Function decorator to disable svn tests when svn isn't available - """ - have_svn = self._have_svn_access() - if not have_svn: - raise unittest.SkipTest("No svn access") - - def test_container_simple_svn(self): - """Verify that a container repo can pull in an svn branch and svn tag. - - """ - self._skip_if_no_svn_access() - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - - self._generator.create_config() - # Git repo. - self._generator.create_section(SIMPLE_REPO, TAG_SECTION, tag='tag1') - - # Svn repos. - self._generator.create_svn_external('svn_branch', self._svn_test_repo_url(), branch='trunk') - self._generator.create_svn_external('svn_tag', self._svn_test_repo_url(), tag='tags/cesm2.0.beta07') - - self._generator.write_config(cloned_repo_dir) - - # checkout, make sure all sections are clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_tag_branch_svn_tag_clean(tree) - - # update description file to make the tag into a branch and - # trigger a switch - self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag', - 'trunk') - - # checkout, again the results should be clean. - tree = self.execute_checkout_with_status(cloned_repo_dir, - self.checkout_args) - self._check_tag_branch_svn_tag_clean(tree) - - # add an untracked file to the repo - tracked = False - RepoUtils.add_file_to_repo(cloned_repo_dir, - 'externals/svn_branch/tmp.txt', tracked) - - # run a no-op checkout. - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - # update description file to make the branch into a tag and - # trigger a modified sync status - self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag', - 'tags/cesm2.0.beta07') - - self.execute_checkout_in_dir(cloned_repo_dir,self.checkout_args) - - # verify status is still clean and unmodified, last - # checkout modified the working dir state. - tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.verbose_args) - self._check_tag_branch_svn_tag_clean(tree) - -class TestSubrepoCheckout(BaseTestSysCheckout): - # Need to store information at setUp time for checking - # pylint: disable=too-many-instance-attributes - """Run tests to ensure proper handling of repos with submodules. - - By default, submodules in git repositories are checked out. A git - repository checked out as a submodule is treated as if it was - listed in an external with the same properties as in the source - .gitmodules file. - """ - - def setUp(self): - """Setup for all submodule checkout tests - Create a repo with two submodule repositories. - """ - - # Run the basic setup - super().setUp() - # create test repo - # We need to do this here (rather than have a static repo) because - # git submodules do not allow for variables in .gitmodules files - self._test_repo_name = 'test_repo_with_submodules' - self._bare_branch_name = 'subrepo_branch' - self._config_branch_name = 'subrepo_config_branch' - self._container_extern_name = 'externals_container.cfg' - self._my_test_dir = os.path.join(module_tmp_root_dir, self._test_id) - self._repo_dir = os.path.join(self._my_test_dir, self._test_repo_name) - self._checkout_dir = 'repo_with_submodules' - check_dir = self.clone_test_repo(CONTAINER_REPO, - dest_dir_in=self._repo_dir) - self.assertTrue(self._repo_dir == check_dir) - # Add the submodules - cwd = os.getcwd() - fork_repo_dir = os.path.join(self._bare_root, SIMPLE_FORK_REPO) - simple_repo_dir = os.path.join(self._bare_root, SIMPLE_REPO) - self._simple_ext_fork_name = os.path.splitext(SIMPLE_FORK_REPO)[0] - self._simple_ext_name = os.path.join('sourc', - os.path.splitext(SIMPLE_REPO)[0]) - os.chdir(self._repo_dir) - # Add a branch with a subrepo - cmd = ['git', 'branch', self._bare_branch_name, 'master'] - execute_subprocess(cmd) - cmd = ['git', 'checkout', self._bare_branch_name] - execute_subprocess(cmd) - cmd = ['git', '-c', 'protocol.file.allow=always','submodule', 'add', fork_repo_dir] - execute_subprocess(cmd) - cmd = ['git', 'commit', '-am', "'Added simple-ext-fork as a submodule'"] - execute_subprocess(cmd) - # Save the fork repo hash for comparison - os.chdir(self._simple_ext_fork_name) - self._fork_hash_check = self.get_git_hash() - os.chdir(self._repo_dir) - # Now, create a branch to test from_sbmodule - cmd = ['git', 'branch', - self._config_branch_name, self._bare_branch_name] - execute_subprocess(cmd) - cmd = ['git', 'checkout', self._config_branch_name] - execute_subprocess(cmd) - cmd = ['git', '-c', 'protocol.file.allow=always', 'submodule', 'add', '--name', SIMPLE_REPO, - simple_repo_dir, self._simple_ext_name] - execute_subprocess(cmd) - # Checkout feature2 - os.chdir(self._simple_ext_name) - cmd = ['git', 'branch', 'feature2', 'origin/feature2'] - execute_subprocess(cmd) - cmd = ['git', 'checkout', 'feature2'] - execute_subprocess(cmd) - # Save the fork repo hash for comparison - self._simple_hash_check = self.get_git_hash() - os.chdir(self._repo_dir) - self.write_externals_config(filename=self._container_extern_name, - dest_dir=self._repo_dir, from_submodule=True) - cmd = ['git', 'add', self._container_extern_name] - execute_subprocess(cmd) - cmd = ['git', 'commit', '-am', "'Added simple-ext as a submodule'"] - execute_subprocess(cmd) - # Reset to master - cmd = ['git', 'checkout', 'master'] - execute_subprocess(cmd) - os.chdir(cwd) - - @staticmethod - def get_git_hash(revision="HEAD"): - """Return the hash for """ - cmd = ['git', 'rev-parse', revision] - git_out = execute_subprocess(cmd, output_to_caller=True) - return git_out.strip() - - def write_externals_config(self, name='', dest_dir=None, - filename=CFG_NAME, - branch_name=None, sub_externals=None, - from_submodule=False): - # pylint: disable=too-many-arguments - """Create a container externals file with only simple externals. - - """ - self._generator.create_config() - - if dest_dir is None: - dest_dir = self._my_test_dir - - if from_submodule: - self._generator.create_section(SIMPLE_FORK_REPO, - self._simple_ext_fork_name, - from_submodule=True) - self._generator.create_section(SIMPLE_REPO, - self._simple_ext_name, - branch='feature3', path='', - from_submodule=False) - else: - if branch_name is None: - branch_name = 'master' - - self._generator.create_section(self._test_repo_name, - self._checkout_dir, - branch=branch_name, - path=name, sub_externals=sub_externals, - repo_path_abs=self._repo_dir) - - self._generator.write_config(dest_dir, filename=filename) - - def idempotence_check(self, checkout_dir): - """Verify that calling checkout_externals and - checkout_externals --status does not cause errors""" - cwd = os.getcwd() - os.chdir(checkout_dir) - self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - self.execute_checkout_in_dir(self._my_test_dir, - self.status_args) - os.chdir(cwd) - - def test_submodule_checkout_bare(self): - """Verify that a git repo with submodule is properly checked out - This test if for where there is no 'externals' keyword in the - parent repo. - Correct behavior is that the submodule is checked out using - normal git submodule behavior. - """ - simple_ext_fork_tag = "(tag1)" - simple_ext_fork_status = " " - self.write_externals_config(branch_name=self._bare_branch_name) - self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - cwd = os.getcwd() - checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) - fork_file = os.path.join(checkout_dir, - self._simple_ext_fork_name, "readme.txt") - self.assertTrue(os.path.exists(fork_file)) - - submods = git_submodule_status(checkout_dir) - print('checking status of', checkout_dir, ':', submods) - self.assertEqual(len(submods.keys()), 1) - self.assertTrue(self._simple_ext_fork_name in submods) - submod = submods[self._simple_ext_fork_name] - self.assertTrue('hash' in submod) - self.assertEqual(submod['hash'], self._fork_hash_check) - self.assertTrue('status' in submod) - self.assertEqual(submod['status'], simple_ext_fork_status) - self.assertTrue('tag' in submod) - self.assertEqual(submod['tag'], simple_ext_fork_tag) - self.idempotence_check(checkout_dir) - - def test_submodule_checkout_none(self): - """Verify that a git repo with submodule is properly checked out - This test is for when 'externals=None' is in parent repo's - externals cfg file. - Correct behavior is the submodle is not checked out. - """ - self.write_externals_config(branch_name=self._bare_branch_name, - sub_externals="none") - self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - cwd = os.getcwd() - checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) - fork_file = os.path.join(checkout_dir, - self._simple_ext_fork_name, "readme.txt") - self.assertFalse(os.path.exists(fork_file)) - os.chdir(cwd) - self.idempotence_check(checkout_dir) - - def test_submodule_checkout_config(self): # pylint: disable=too-many-locals - """Verify that a git repo with submodule is properly checked out - This test if for when the 'from_submodule' keyword is used in the - parent repo. - Correct behavior is that the submodule is checked out using - normal git submodule behavior. - """ - tag_check = None # Not checked out as submodule - status_check = "-" # Not checked out as submodule - self.write_externals_config(branch_name=self._config_branch_name, - sub_externals=self._container_extern_name) - self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - cwd = os.getcwd() - checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) - fork_file = os.path.join(checkout_dir, - self._simple_ext_fork_name, "readme.txt") - self.assertTrue(os.path.exists(fork_file)) - os.chdir(checkout_dir) - # Check submodule status - submods = git_submodule_status(checkout_dir) - self.assertEqual(len(submods.keys()), 2) - self.assertTrue(self._simple_ext_fork_name in submods) - submod = submods[self._simple_ext_fork_name] - self.assertTrue('hash' in submod) - self.assertEqual(submod['hash'], self._fork_hash_check) - self.assertTrue('status' in submod) - self.assertEqual(submod['status'], status_check) - self.assertTrue('tag' in submod) - self.assertEqual(submod['tag'], tag_check) - self.assertTrue(self._simple_ext_name in submods) - submod = submods[self._simple_ext_name] - self.assertTrue('hash' in submod) - self.assertEqual(submod['hash'], self._simple_hash_check) - self.assertTrue('status' in submod) - self.assertEqual(submod['status'], status_check) - self.assertTrue('tag' in submod) - self.assertEqual(submod['tag'], tag_check) - # Check fork repo status - os.chdir(self._simple_ext_fork_name) - self.assertEqual(self.get_git_hash(), self._fork_hash_check) - os.chdir(checkout_dir) - os.chdir(self._simple_ext_name) - hash_check = self.get_git_hash('origin/feature3') - self.assertEqual(self.get_git_hash(), hash_check) - os.chdir(cwd) - self.idempotence_check(checkout_dir) - -class TestSysCheckoutErrors(BaseTestSysCheckout): - """Run systems level tests of error conditions in checkout_externals - - Error conditions - these tests are designed to trigger specific - error conditions and ensure that they are being handled as - runtime errors (and hopefully usefull error messages) instead of - the default internal message that won't mean anything to the - user, e.g. key error, called process error, etc. - - These are not 'expected failures'. They are pass when a - RuntimeError is raised, fail if any other error is raised (or no - error is raised). - - """ - - # NOTE(bja, 2017-11) pylint complains about long method names, but - # it is hard to differentiate tests without making them more - # cryptic. - # pylint: disable=invalid-name - - def test_error_unknown_protocol(self): - """Verify that a runtime error is raised when the user specified repo - protocol is not known. - - """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION, - 'this-protocol-does-not-exist') - - with self.assertRaises(RuntimeError): - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - def test_error_switch_protocol(self): - """Verify that a runtime error is raised when the user switches - protocols, git to svn. - - TODO(bja, 2017-11) This correctly results in an error, but it - isn't a helpful error message. - - """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION, 'svn') - with self.assertRaises(RuntimeError): - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - def test_error_unknown_tag(self): - """Verify that a runtime error is raised when the user specified tag - does not exist. - - """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, - tag='this-tag-does-not-exist', - new_remote_repo_path=SIMPLE_REPO) - - with self.assertRaises(RuntimeError): - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - def test_error_overspecify_tag_branch(self): - """Verify that a runtime error is raised when the user specified both - tag and a branch - - """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, - tag='this-tag-does-not-exist', - new_remote_repo_path=SIMPLE_REPO, - remove_branch=False) - - with self.assertRaises(RuntimeError): - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - def test_error_underspecify_tag_branch(self): - """Verify that a runtime error is raised when the user specified - neither a tag or a branch - - """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_without_branch_tag(cloned_repo_dir, BRANCH_SECTION) - - with self.assertRaises(RuntimeError): - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - def test_error_missing_url(self): - """Verify that a runtime error is raised when the user specified - neither a tag or a branch - - """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - self._generator.create_config() - self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, - branch=REMOTE_BRANCH_FEATURE2) - self._generator.write_config(cloned_repo_dir) - - # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_without_repo_url(cloned_repo_dir, - BRANCH_SECTION) - - with self.assertRaises(RuntimeError): - self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) - - -if __name__ == '__main__': - unittest.main() diff --git a/manage_externals/test/test_sys_repository_git.py b/manage_externals/test/test_sys_repository_git.py deleted file mode 100644 index 7e5fb5020d..0000000000 --- a/manage_externals/test/test_sys_repository_git.py +++ /dev/null @@ -1,238 +0,0 @@ -#!/usr/bin/env python3 - -"""Tests of some of the functionality in repository_git.py that actually -interacts with git repositories. - -We're calling these "system" tests because we expect them to be a lot -slower than most of the unit tests. - -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import os -import shutil -import tempfile -import unittest - -from manic.repository_git import GitRepository -from manic.externals_description import ExternalsDescription -from manic.externals_description import ExternalsDescriptionDict -from manic.utils import execute_subprocess - -# NOTE(wjs, 2018-04-09) I find a mix of camel case and underscores to be -# more readable for unit test names, so I'm disabling pylint's naming -# convention check -# pylint: disable=C0103 - -# Allow access to protected members -# pylint: disable=W0212 - - -class GitTestCase(unittest.TestCase): - """Adds some git-specific unit test functionality on top of TestCase""" - - def assertIsHash(self, maybe_hash): - """Assert that the string given by maybe_hash really does look - like a git hash. - """ - - # Ensure it is non-empty - self.assertTrue(maybe_hash, msg="maybe_hash is empty") - - # Ensure it has a single string - self.assertEqual(1, len(maybe_hash.split()), - msg="maybe_hash has multiple strings: {}".format(maybe_hash)) - - # Ensure that the only characters in the string are ones allowed - # in hashes - allowed_chars_set = set('0123456789abcdef') - self.assertTrue(set(maybe_hash) <= allowed_chars_set, - msg="maybe_hash has non-hash characters: {}".format(maybe_hash)) - - -class TestGitTestCase(GitTestCase): - """Tests GitTestCase""" - - def test_assertIsHash_true(self): - """Ensure that assertIsHash passes for something that looks - like a hash""" - self.assertIsHash('abc123') - - def test_assertIsHash_empty(self): - """Ensure that assertIsHash raises an AssertionError for an - empty string""" - with self.assertRaises(AssertionError): - self.assertIsHash('') - - def test_assertIsHash_multipleStrings(self): - """Ensure that assertIsHash raises an AssertionError when - given multiple strings""" - with self.assertRaises(AssertionError): - self.assertIsHash('abc123 def456') - - def test_assertIsHash_badChar(self): - """Ensure that assertIsHash raises an AssertionError when given a - string that has a character that doesn't belong in a hash - """ - with self.assertRaises(AssertionError): - self.assertIsHash('abc123g') - - -class TestGitRepositoryGitCommands(GitTestCase): - """Test some git commands in RepositoryGit - - It's silly that we need to create a repository in order to test - these git commands. Much or all of the git functionality that is - currently in repository_git.py should eventually be moved to a - separate module that is solely responsible for wrapping git - commands; that would allow us to test it independently of this - repository class. - """ - - # ======================================================================== - # Test helper functions - # ======================================================================== - - def setUp(self): - # directory we want to return to after the test system and - # checkout_externals are done cd'ing all over the place. - self._return_dir = os.getcwd() - - self._tmpdir = tempfile.mkdtemp() - os.chdir(self._tmpdir) - - self._name = 'component' - rdata = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: - '/path/to/local/repo', - ExternalsDescription.TAG: - 'tag1', - } - - data = {self._name: - { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: 'junk', - ExternalsDescription.EXTERNALS: '', - ExternalsDescription.REPO: rdata, - }, - } - model = ExternalsDescriptionDict(data) - repo = model[self._name][ExternalsDescription.REPO] - self._repo = GitRepository('test', repo) - - def tearDown(self): - # return to our common starting point - os.chdir(self._return_dir) - - shutil.rmtree(self._tmpdir, ignore_errors=True) - - @staticmethod - def make_cwd_git_repo(): - """Turn the current directory into an empty git repository""" - execute_subprocess(['git', 'init']) - - @staticmethod - def add_cwd_git_commit(): - """Add a git commit in the current directory""" - with open('README', 'a') as myfile: - myfile.write('more info') - execute_subprocess(['git', 'add', 'README']) - execute_subprocess(['git', 'commit', '-m', 'my commit message']) - - @staticmethod - def checkout_cwd_git_branch(branchname): - """Checkout a new branch in the current directory""" - execute_subprocess(['git', 'checkout', '-b', branchname]) - - @staticmethod - def make_cwd_git_tag(tagname): - """Make a lightweight tag at the current commit""" - execute_subprocess(['git', 'tag', '-m', 'making a tag', tagname]) - - @staticmethod - def checkout_cwd_ref(refname): - """Checkout the given refname in the current directory""" - execute_subprocess(['git', 'checkout', refname]) - - # ======================================================================== - # Begin actual tests - # ======================================================================== - - def test_currentHash_returnsHash(self): - """Ensure that the _git_current_hash function returns a hash""" - self.make_cwd_git_repo() - self.add_cwd_git_commit() - hash_found, myhash = self._repo._git_current_hash(os.getcwd()) - self.assertTrue(hash_found) - self.assertIsHash(myhash) - - def test_currentHash_outsideGitRepo(self): - """Ensure that the _git_current_hash function returns False when - outside a git repository""" - hash_found, myhash = self._repo._git_current_hash(os.getcwd()) - self.assertFalse(hash_found) - self.assertEqual('', myhash) - - def test_currentBranch_onBranch(self): - """Ensure that the _git_current_branch function returns the name - of the branch""" - self.make_cwd_git_repo() - self.add_cwd_git_commit() - self.checkout_cwd_git_branch('foo') - branch_found, mybranch = self._repo._git_current_branch(os.getcwd()) - self.assertTrue(branch_found) - self.assertEqual('foo', mybranch) - - def test_currentBranch_notOnBranch(self): - """Ensure that the _git_current_branch function returns False - when not on a branch""" - self.make_cwd_git_repo() - self.add_cwd_git_commit() - self.make_cwd_git_tag('mytag') - self.checkout_cwd_ref('mytag') - branch_found, mybranch = self._repo._git_current_branch(os.getcwd()) - self.assertFalse(branch_found) - self.assertEqual('', mybranch) - - def test_currentBranch_outsideGitRepo(self): - """Ensure that the _git_current_branch function returns False - when outside a git repository""" - branch_found, mybranch = self._repo._git_current_branch(os.getcwd()) - self.assertFalse(branch_found) - self.assertEqual('', mybranch) - - def test_currentTag_onTag(self): - """Ensure that the _git_current_tag function returns the name of - the tag""" - self.make_cwd_git_repo() - self.add_cwd_git_commit() - self.make_cwd_git_tag('some_tag') - tag_found, mytag = self._repo._git_current_tag(os.getcwd()) - self.assertTrue(tag_found) - self.assertEqual('some_tag', mytag) - - def test_currentTag_notOnTag(self): - """Ensure tha the _git_current_tag function returns False when - not on a tag""" - self.make_cwd_git_repo() - self.add_cwd_git_commit() - self.make_cwd_git_tag('some_tag') - self.add_cwd_git_commit() - tag_found, mytag = self._repo._git_current_tag(os.getcwd()) - self.assertFalse(tag_found) - self.assertEqual('', mytag) - - def test_currentTag_outsideGitRepo(self): - """Ensure that the _git_current_tag function returns False when - outside a git repository""" - tag_found, mytag = self._repo._git_current_tag(os.getcwd()) - self.assertFalse(tag_found) - self.assertEqual('', mytag) - - -if __name__ == '__main__': - unittest.main() diff --git a/manage_externals/test/test_unit_externals_description.py b/manage_externals/test/test_unit_externals_description.py deleted file mode 100644 index 30e5288499..0000000000 --- a/manage_externals/test/test_unit_externals_description.py +++ /dev/null @@ -1,478 +0,0 @@ -#!/usr/bin/env python3 - -"""Unit test driver for checkout_externals - -Note: this script assume the path to the checkout_externals.py module is -already in the python path. - -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import os -import os.path -import shutil -import unittest - -try: - # python2 - from ConfigParser import SafeConfigParser as config_parser - - def config_string_cleaner(text): - """convert strings into unicode - """ - return text.decode('utf-8') -except ImportError: - # python3 - from configparser import ConfigParser as config_parser - - def config_string_cleaner(text): - """Python3 already uses unicode strings, so just return the string - without modification. - - """ - return text - -from manic.externals_description import DESCRIPTION_SECTION, VERSION_ITEM -from manic.externals_description import ExternalsDescription -from manic.externals_description import ExternalsDescriptionDict -from manic.externals_description import ExternalsDescriptionConfigV1 -from manic.externals_description import get_cfg_schema_version -from manic.externals_description import read_externals_description_file -from manic.externals_description import create_externals_description - -from manic.global_constants import EMPTY_STR - - -class TestCfgSchemaVersion(unittest.TestCase): - """Test that schema identification for the externals description - returns the correct results. - - """ - - def setUp(self): - """Reusable config object - """ - self._config = config_parser() - self._config.add_section('section1') - self._config.set('section1', 'keword', 'value') - - self._config.add_section(DESCRIPTION_SECTION) - - def test_schema_version_valid(self): - """Test that schema identification returns the correct version for a - valid tag. - - """ - version_str = '2.1.3' - self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, version_str) - major, minor, patch = get_cfg_schema_version(self._config) - expected_major = 2 - expected_minor = 1 - expected_patch = 3 - self.assertEqual(expected_major, major) - self.assertEqual(expected_minor, minor) - self.assertEqual(expected_patch, patch) - - def test_schema_section_missing(self): - """Test that an error is returned if the schema section is missing - from the input file. - - """ - self._config.remove_section(DESCRIPTION_SECTION) - with self.assertRaises(RuntimeError): - get_cfg_schema_version(self._config) - - def test_schema_version_missing(self): - """Test that a externals description file without a version raises a - runtime error. - - """ - # Note: the default setup method shouldn't include a version - # keyword, but remove it just to be future proof.... - self._config.remove_option(DESCRIPTION_SECTION, VERSION_ITEM) - with self.assertRaises(RuntimeError): - get_cfg_schema_version(self._config) - - def test_schema_version_not_int(self): - """Test that a externals description file a version that doesn't - decompose to integer major, minor and patch versions raises - runtime error. - - """ - self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, 'unknown') - with self.assertRaises(RuntimeError): - get_cfg_schema_version(self._config) - - -class TestModelDescritionConfigV1(unittest.TestCase): - """Test that parsing config/ini fileproduces a correct dictionary - for the externals description. - - """ - # pylint: disable=R0902 - - def setUp(self): - """Boiler plate construction of string containing xml for multiple components. - """ - self._comp1_name = 'comp1' - self._comp1_path = 'path/to/comp1' - self._comp1_protocol = 'svn' - self._comp1_url = 'https://svn.somewhere.com/path/of/comp1' - self._comp1_tag = 'a_nice_tag_v1' - self._comp1_is_required = 'True' - self._comp1_externals = '' - - self._comp2_name = 'comp2' - self._comp2_path = 'path/to/comp2' - self._comp2_protocol = 'git' - self._comp2_url = '/local/clone/of/comp2' - self._comp2_branch = 'a_very_nice_branch' - self._comp2_is_required = 'False' - self._comp2_externals = 'path/to/comp2.cfg' - - def _setup_comp1(self, config): - """Boiler plate construction of xml string for componet 1 - """ - config.add_section(self._comp1_name) - config.set(self._comp1_name, 'local_path', self._comp1_path) - config.set(self._comp1_name, 'protocol', self._comp1_protocol) - config.set(self._comp1_name, 'repo_url', self._comp1_url) - config.set(self._comp1_name, 'tag', self._comp1_tag) - config.set(self._comp1_name, 'required', self._comp1_is_required) - - def _setup_comp2(self, config): - """Boiler plate construction of xml string for componet 2 - """ - config.add_section(self._comp2_name) - config.set(self._comp2_name, 'local_path', self._comp2_path) - config.set(self._comp2_name, 'protocol', self._comp2_protocol) - config.set(self._comp2_name, 'repo_url', self._comp2_url) - config.set(self._comp2_name, 'branch', self._comp2_branch) - config.set(self._comp2_name, 'required', self._comp2_is_required) - config.set(self._comp2_name, 'externals', self._comp2_externals) - - @staticmethod - def _setup_externals_description(config): - """Add the required exernals description section - """ - - config.add_section(DESCRIPTION_SECTION) - config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.1') - - def _check_comp1(self, model): - """Test that component one was constructed correctly. - """ - self.assertTrue(self._comp1_name in model) - comp1 = model[self._comp1_name] - self.assertEqual(comp1[ExternalsDescription.PATH], self._comp1_path) - self.assertTrue(comp1[ExternalsDescription.REQUIRED]) - repo = comp1[ExternalsDescription.REPO] - self.assertEqual(repo[ExternalsDescription.PROTOCOL], - self._comp1_protocol) - self.assertEqual(repo[ExternalsDescription.REPO_URL], self._comp1_url) - self.assertEqual(repo[ExternalsDescription.TAG], self._comp1_tag) - self.assertEqual(EMPTY_STR, comp1[ExternalsDescription.EXTERNALS]) - - def _check_comp2(self, model): - """Test that component two was constucted correctly. - """ - self.assertTrue(self._comp2_name in model) - comp2 = model[self._comp2_name] - self.assertEqual(comp2[ExternalsDescription.PATH], self._comp2_path) - self.assertFalse(comp2[ExternalsDescription.REQUIRED]) - repo = comp2[ExternalsDescription.REPO] - self.assertEqual(repo[ExternalsDescription.PROTOCOL], - self._comp2_protocol) - self.assertEqual(repo[ExternalsDescription.REPO_URL], self._comp2_url) - self.assertEqual(repo[ExternalsDescription.BRANCH], self._comp2_branch) - self.assertEqual(self._comp2_externals, - comp2[ExternalsDescription.EXTERNALS]) - - def test_one_tag_required(self): - """Test that a component source with a tag is correctly parsed. - """ - config = config_parser() - self._setup_comp1(config) - self._setup_externals_description(config) - model = ExternalsDescriptionConfigV1(config) - print(model) - self._check_comp1(model) - - def test_one_branch_externals(self): - """Test that a component source with a branch is correctly parsed. - """ - config = config_parser() - self._setup_comp2(config) - self._setup_externals_description(config) - model = ExternalsDescriptionConfigV1(config) - print(model) - self._check_comp2(model) - - def test_two_sources(self): - """Test that multiple component sources are correctly parsed. - """ - config = config_parser() - self._setup_comp1(config) - self._setup_comp2(config) - self._setup_externals_description(config) - model = ExternalsDescriptionConfigV1(config) - print(model) - self._check_comp1(model) - self._check_comp2(model) - - def test_cfg_v1_reject_unknown_item(self): - """Test that a v1 description object will reject unknown items - """ - config = config_parser() - self._setup_comp1(config) - self._setup_externals_description(config) - config.set(self._comp1_name, 'junk', 'foobar') - with self.assertRaises(RuntimeError): - ExternalsDescriptionConfigV1(config) - - def test_cfg_v1_reject_v2(self): - """Test that a v1 description object won't try to parse a v2 file. - """ - config = config_parser() - self._setup_comp1(config) - self._setup_externals_description(config) - config.set(DESCRIPTION_SECTION, VERSION_ITEM, '2.0.1') - with self.assertRaises(RuntimeError): - ExternalsDescriptionConfigV1(config) - - def test_cfg_v1_reject_v1_too_new(self): - """Test that a v1 description object won't try to parse a v2 file. - """ - config = config_parser() - self._setup_comp1(config) - self._setup_externals_description(config) - config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.100.0') - with self.assertRaises(RuntimeError): - ExternalsDescriptionConfigV1(config) - - -class TestReadExternalsDescription(unittest.TestCase): - """Test the application logic of read_externals_description_file - """ - TMP_FAKE_DIR = 'fake' - - def setUp(self): - """Setup directory for tests - """ - if not os.path.exists(self.TMP_FAKE_DIR): - os.makedirs(self.TMP_FAKE_DIR) - - def tearDown(self): - """Cleanup tmp stuff on the file system - """ - if os.path.exists(self.TMP_FAKE_DIR): - shutil.rmtree(self.TMP_FAKE_DIR) - - def test_no_file_error(self): - """Test that a runtime error is raised when the file does not exist - - """ - root_dir = os.getcwd() - filename = 'this-file-should-not-exist' - with self.assertRaises(RuntimeError): - read_externals_description_file(root_dir, filename) - - def test_no_dir_error(self): - """Test that a runtime error is raised when the file does not exist - - """ - root_dir = '/path/to/some/repo' - filename = 'externals.cfg' - with self.assertRaises(RuntimeError): - read_externals_description_file(root_dir, filename) - - def test_no_invalid_error(self): - """Test that a runtime error is raised when the file format is invalid - - """ - root_dir = os.getcwd() - filename = 'externals.cfg' - file_path = os.path.join(root_dir, filename) - file_path = os.path.abspath(file_path) - contents = """ - -invalid file format -""" - with open(file_path, 'w') as fhandle: - fhandle.write(contents) - with self.assertRaises(RuntimeError): - read_externals_description_file(root_dir, filename) - os.remove(file_path) - - -class TestCreateExternalsDescription(unittest.TestCase): - """Test the application logic of creat_externals_description - """ - - def setUp(self): - """Create config object used as basis for all tests - """ - self._config = config_parser() - self._gmconfig = config_parser() - self.setup_config() - - def setup_config(self): - """Boiler plate construction of xml string for componet 1 - """ - # Create a standard externals config with a single external - name = 'test' - self._config.add_section(name) - self._config.set(name, ExternalsDescription.PATH, 'externals') - self._config.set(name, ExternalsDescription.PROTOCOL, 'git') - self._config.set(name, ExternalsDescription.REPO_URL, '/path/to/repo') - self._config.set(name, ExternalsDescription.TAG, 'test_tag') - self._config.set(name, ExternalsDescription.REQUIRED, 'True') - - self._config.add_section(DESCRIPTION_SECTION) - self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.0') - - # Create a .gitmodules test - name = 'submodule "gitmodules_test"' - self._gmconfig.add_section(name) - self._gmconfig.set(name, "path", 'externals/test') - self._gmconfig.set(name, "url", '/path/to/repo') - # NOTE(goldy, 2019-03) Should test other possible keywords such as - # fetchRecurseSubmodules, ignore, and shallow - - @staticmethod - def setup_dict_config(): - """Create the full container dictionary with simple and mixed use - externals - - """ - rdatat = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: 'simple-ext.git', - ExternalsDescription.TAG: 'tag1'} - rdatab = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: 'simple-ext.git', - ExternalsDescription.BRANCH: 'feature2'} - rdatam = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: 'mixed-cont-ext.git', - ExternalsDescription.BRANCH: 'master'} - desc = {'simp_tag': {ExternalsDescription.REQUIRED: True, - ExternalsDescription.PATH: 'simp_tag', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdatat}, - 'simp_branch' : {ExternalsDescription.REQUIRED: True, - ExternalsDescription.PATH: 'simp_branch', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdatab}, - 'simp_opt': {ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: 'simp_opt', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdatat}, - 'mixed_req': {ExternalsDescription.REQUIRED: True, - ExternalsDescription.PATH: 'mixed_req', - ExternalsDescription.EXTERNALS: 'sub-ext.cfg', - ExternalsDescription.REPO: rdatam}} - - return desc - - def test_cfg_v1_ok(self): - """Test that a correct cfg v1 object is created by create_externals_description - - """ - self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '1.0.3') - ext = create_externals_description(self._config, model_format='cfg') - self.assertIsInstance(ext, ExternalsDescriptionConfigV1) - - def test_cfg_v1_unknown_version(self): - """Test that a config file with unknown schema version is rejected by - create_externals_description. - - """ - self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '100.0.3') - with self.assertRaises(RuntimeError): - create_externals_description(self._config, model_format='cfg') - - def test_dict(self): - """Test that a correct cfg v1 object is created by create_externals_description - - """ - rdata = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: '/path/to/repo', - ExternalsDescription.TAG: 'tagv1', - } - - desc = { - 'test': { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: '../fake', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdata, }, - } - - ext = create_externals_description(desc, model_format='dict') - self.assertIsInstance(ext, ExternalsDescriptionDict) - - def test_cfg_component_dict(self): - """Verify that create_externals_description works with a dictionary - """ - # create the top level externals file - desc = self.setup_dict_config() - # Check external with all repos - external = create_externals_description(desc, model_format='dict') - self.assertIsInstance(external, ExternalsDescriptionDict) - self.assertTrue('simp_tag' in external) - self.assertTrue('simp_branch' in external) - self.assertTrue('simp_opt' in external) - self.assertTrue('mixed_req' in external) - - def test_cfg_exclude_component_dict(self): - """Verify that exclude component checkout works with a dictionary - """ - # create the top level externals file - desc = self.setup_dict_config() - # Test an excluded repo - external = create_externals_description(desc, model_format='dict', - exclude=['simp_tag', - 'simp_opt']) - self.assertIsInstance(external, ExternalsDescriptionDict) - self.assertFalse('simp_tag' in external) - self.assertTrue('simp_branch' in external) - self.assertFalse('simp_opt' in external) - self.assertTrue('mixed_req' in external) - - def test_cfg_opt_component_dict(self): - """Verify that exclude component checkout works with a dictionary - """ - # create the top level externals file - desc = self.setup_dict_config() - # Test an excluded repo - external = create_externals_description(desc, model_format='dict', - components=['simp_tag', - 'simp_opt']) - self.assertIsInstance(external, ExternalsDescriptionDict) - self.assertTrue('simp_tag' in external) - self.assertFalse('simp_branch' in external) - self.assertTrue('simp_opt' in external) - self.assertFalse('mixed_req' in external) - - def test_cfg_unknown_version(self): - """Test that a runtime error is raised when an unknown file version is - received - - """ - self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, '123.456.789') - with self.assertRaises(RuntimeError): - create_externals_description(self._config, model_format='cfg') - - def test_cfg_unknown_format(self): - """Test that a runtime error is raised when an unknown format string is - received - - """ - with self.assertRaises(RuntimeError): - create_externals_description(self._config, model_format='unknown') - - -if __name__ == '__main__': - unittest.main() diff --git a/manage_externals/test/test_unit_externals_status.py b/manage_externals/test/test_unit_externals_status.py deleted file mode 100644 index f019514e9e..0000000000 --- a/manage_externals/test/test_unit_externals_status.py +++ /dev/null @@ -1,299 +0,0 @@ -#!/usr/bin/env python3 - -"""Unit test driver for the manic external status reporting module. - -Note: this script assumes the path to the manic package is already in -the python path. - -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import unittest - -from manic.externals_status import ExternalStatus - - -class TestStatusObject(unittest.TestCase): - """Verify that the Status object behaives as expected. - """ - - def test_exists_empty_all(self): - """If the repository sync-state is empty (doesn't exist), and there is no - clean state, then it is considered not to exist. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.EMPTY - stat.clean_state = ExternalStatus.DEFAULT - exists = stat.exists() - self.assertFalse(exists) - - stat.clean_state = ExternalStatus.EMPTY - exists = stat.exists() - self.assertFalse(exists) - - stat.clean_state = ExternalStatus.UNKNOWN - exists = stat.exists() - self.assertFalse(exists) - - # this state represtens an internal logic error in how the - # repo status was determined. - stat.clean_state = ExternalStatus.STATUS_OK - exists = stat.exists() - self.assertTrue(exists) - - # this state represtens an internal logic error in how the - # repo status was determined. - stat.clean_state = ExternalStatus.DIRTY - exists = stat.exists() - self.assertTrue(exists) - - def test_exists_default_all(self): - """If the repository sync-state is default, then it is considered to exist - regardless of clean state. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.DEFAULT - stat.clean_state = ExternalStatus.DEFAULT - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.EMPTY - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.UNKNOWN - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.STATUS_OK - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.DIRTY - exists = stat.exists() - self.assertTrue(exists) - - def test_exists_unknown_all(self): - """If the repository sync-state is unknown, then it is considered to exist - regardless of clean state. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.UNKNOWN - stat.clean_state = ExternalStatus.DEFAULT - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.EMPTY - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.UNKNOWN - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.STATUS_OK - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.DIRTY - exists = stat.exists() - self.assertTrue(exists) - - def test_exists_modified_all(self): - """If the repository sync-state is modified, then it is considered to exist - regardless of clean state. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.MODEL_MODIFIED - stat.clean_state = ExternalStatus.DEFAULT - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.EMPTY - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.UNKNOWN - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.STATUS_OK - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.DIRTY - exists = stat.exists() - self.assertTrue(exists) - - def test_exists_ok_all(self): - """If the repository sync-state is ok, then it is considered to exist - regardless of clean state. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.STATUS_OK - stat.clean_state = ExternalStatus.DEFAULT - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.EMPTY - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.UNKNOWN - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.STATUS_OK - exists = stat.exists() - self.assertTrue(exists) - - stat.clean_state = ExternalStatus.DIRTY - exists = stat.exists() - self.assertTrue(exists) - - def test_update_ok_all(self): - """If the repository in-sync is ok, then it is safe to - update only if clean state is ok - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.STATUS_OK - stat.clean_state = ExternalStatus.DEFAULT - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.EMPTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.UNKNOWN - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.STATUS_OK - safe_to_update = stat.safe_to_update() - self.assertTrue(safe_to_update) - - stat.clean_state = ExternalStatus.DIRTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - def test_update_modified_all(self): - """If the repository in-sync is modified, then it is safe to - update only if clean state is ok - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.MODEL_MODIFIED - stat.clean_state = ExternalStatus.DEFAULT - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.EMPTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.UNKNOWN - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.STATUS_OK - safe_to_update = stat.safe_to_update() - self.assertTrue(safe_to_update) - - stat.clean_state = ExternalStatus.DIRTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - def test_update_unknown_all(self): - """If the repository in-sync is unknown, then it is not safe to - update, regardless of the clean state. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.UNKNOWN - stat.clean_state = ExternalStatus.DEFAULT - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.EMPTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.UNKNOWN - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.STATUS_OK - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.DIRTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - def test_update_default_all(self): - """If the repository in-sync is default, then it is not safe to - update, regardless of the clean state. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.UNKNOWN - stat.clean_state = ExternalStatus.DEFAULT - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.EMPTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.UNKNOWN - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.STATUS_OK - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.DIRTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - def test_update_empty_all(self): - """If the repository in-sync is empty, then it is not safe to - update, regardless of the clean state. - - """ - stat = ExternalStatus() - stat.sync_state = ExternalStatus.UNKNOWN - stat.clean_state = ExternalStatus.DEFAULT - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.EMPTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.UNKNOWN - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.STATUS_OK - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - stat.clean_state = ExternalStatus.DIRTY - safe_to_update = stat.safe_to_update() - self.assertFalse(safe_to_update) - - -if __name__ == '__main__': - unittest.main() diff --git a/manage_externals/test/test_unit_repository.py b/manage_externals/test/test_unit_repository.py deleted file mode 100644 index 1b93861834..0000000000 --- a/manage_externals/test/test_unit_repository.py +++ /dev/null @@ -1,208 +0,0 @@ -#!/usr/bin/env python3 - -"""Unit test driver for checkout_externals - -Note: this script assume the path to the checkout_externals.py module is -already in the python path. - -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import unittest - -from manic.repository_factory import create_repository -from manic.repository_git import GitRepository -from manic.repository_svn import SvnRepository -from manic.repository import Repository -from manic.externals_description import ExternalsDescription -from manic.global_constants import EMPTY_STR - - -class TestCreateRepositoryDict(unittest.TestCase): - """Test the create_repository functionality to ensure it returns the - propper type of repository and errors for unknown repository - types. - - """ - - def setUp(self): - """Common data needed for all tests in this class - """ - self._name = 'test_name' - self._repo = {ExternalsDescription.PROTOCOL: None, - ExternalsDescription.REPO_URL: 'junk_root', - ExternalsDescription.TAG: 'junk_tag', - ExternalsDescription.BRANCH: EMPTY_STR, - ExternalsDescription.HASH: EMPTY_STR, - ExternalsDescription.SPARSE: EMPTY_STR, } - - def test_create_repo_git(self): - """Verify that several possible names for the 'git' protocol - create git repository objects. - - """ - protocols = ['git', 'GIT', 'Git', ] - for protocol in protocols: - self._repo[ExternalsDescription.PROTOCOL] = protocol - repo = create_repository(self._name, self._repo) - self.assertIsInstance(repo, GitRepository) - - def test_create_repo_svn(self): - """Verify that several possible names for the 'svn' protocol - create svn repository objects. - """ - protocols = ['svn', 'SVN', 'Svn', ] - for protocol in protocols: - self._repo[ExternalsDescription.PROTOCOL] = protocol - repo = create_repository(self._name, self._repo) - self.assertIsInstance(repo, SvnRepository) - - def test_create_repo_externals_only(self): - """Verify that an externals only repo returns None. - """ - protocols = ['externals_only', ] - for protocol in protocols: - self._repo[ExternalsDescription.PROTOCOL] = protocol - repo = create_repository(self._name, self._repo) - self.assertEqual(None, repo) - - def test_create_repo_unsupported(self): - """Verify that an unsupported protocol generates a runtime error. - """ - protocols = ['not_a_supported_protocol', ] - for protocol in protocols: - self._repo[ExternalsDescription.PROTOCOL] = protocol - with self.assertRaises(RuntimeError): - create_repository(self._name, self._repo) - - -class TestRepository(unittest.TestCase): - """Test the externals description processing used to create the Repository - base class shared by protocol specific repository classes. - - """ - - def test_tag(self): - """Test creation of a repository object with a tag - """ - name = 'test_repo' - protocol = 'test_protocol' - url = 'test_url' - tag = 'test_tag' - repo_info = {ExternalsDescription.PROTOCOL: protocol, - ExternalsDescription.REPO_URL: url, - ExternalsDescription.TAG: tag, - ExternalsDescription.BRANCH: EMPTY_STR, - ExternalsDescription.HASH: EMPTY_STR, - ExternalsDescription.SPARSE: EMPTY_STR, } - repo = Repository(name, repo_info) - print(repo.__dict__) - self.assertEqual(repo.tag(), tag) - self.assertEqual(repo.url(), url) - - def test_branch(self): - """Test creation of a repository object with a branch - """ - name = 'test_repo' - protocol = 'test_protocol' - url = 'test_url' - branch = 'test_branch' - repo_info = {ExternalsDescription.PROTOCOL: protocol, - ExternalsDescription.REPO_URL: url, - ExternalsDescription.BRANCH: branch, - ExternalsDescription.TAG: EMPTY_STR, - ExternalsDescription.HASH: EMPTY_STR, - ExternalsDescription.SPARSE: EMPTY_STR, } - repo = Repository(name, repo_info) - print(repo.__dict__) - self.assertEqual(repo.branch(), branch) - self.assertEqual(repo.url(), url) - - def test_hash(self): - """Test creation of a repository object with a hash - """ - name = 'test_repo' - protocol = 'test_protocol' - url = 'test_url' - ref = 'deadc0de' - sparse = EMPTY_STR - repo_info = {ExternalsDescription.PROTOCOL: protocol, - ExternalsDescription.REPO_URL: url, - ExternalsDescription.BRANCH: EMPTY_STR, - ExternalsDescription.TAG: EMPTY_STR, - ExternalsDescription.HASH: ref, - ExternalsDescription.SPARSE: sparse, } - repo = Repository(name, repo_info) - print(repo.__dict__) - self.assertEqual(repo.hash(), ref) - self.assertEqual(repo.url(), url) - - def test_tag_branch(self): - """Test creation of a repository object with a tag and branch raises a - runtimer error. - - """ - name = 'test_repo' - protocol = 'test_protocol' - url = 'test_url' - branch = 'test_branch' - tag = 'test_tag' - ref = EMPTY_STR - sparse = EMPTY_STR - repo_info = {ExternalsDescription.PROTOCOL: protocol, - ExternalsDescription.REPO_URL: url, - ExternalsDescription.BRANCH: branch, - ExternalsDescription.TAG: tag, - ExternalsDescription.HASH: ref, - ExternalsDescription.SPARSE: sparse, } - with self.assertRaises(RuntimeError): - Repository(name, repo_info) - - def test_tag_branch_hash(self): - """Test creation of a repository object with a tag, branch and hash raises a - runtimer error. - - """ - name = 'test_repo' - protocol = 'test_protocol' - url = 'test_url' - branch = 'test_branch' - tag = 'test_tag' - ref = 'deadc0de' - sparse = EMPTY_STR - repo_info = {ExternalsDescription.PROTOCOL: protocol, - ExternalsDescription.REPO_URL: url, - ExternalsDescription.BRANCH: branch, - ExternalsDescription.TAG: tag, - ExternalsDescription.HASH: ref, - ExternalsDescription.SPARSE: sparse, } - with self.assertRaises(RuntimeError): - Repository(name, repo_info) - - def test_no_tag_no_branch(self): - """Test creation of a repository object without a tag or branch raises a - runtimer error. - - """ - name = 'test_repo' - protocol = 'test_protocol' - url = 'test_url' - branch = EMPTY_STR - tag = EMPTY_STR - ref = EMPTY_STR - sparse = EMPTY_STR - repo_info = {ExternalsDescription.PROTOCOL: protocol, - ExternalsDescription.REPO_URL: url, - ExternalsDescription.BRANCH: branch, - ExternalsDescription.TAG: tag, - ExternalsDescription.HASH: ref, - ExternalsDescription.SPARSE: sparse, } - with self.assertRaises(RuntimeError): - Repository(name, repo_info) - - -if __name__ == '__main__': - unittest.main() diff --git a/manage_externals/test/test_unit_repository_git.py b/manage_externals/test/test_unit_repository_git.py deleted file mode 100644 index 1c01098acf..0000000000 --- a/manage_externals/test/test_unit_repository_git.py +++ /dev/null @@ -1,811 +0,0 @@ -#!/usr/bin/env python3 - -"""Unit test driver for checkout_externals - -Note: this script assume the path to the checkout_externals.py module is -already in the python path. - -""" -# pylint: disable=too-many-lines,protected-access - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import os -import shutil -import unittest - -from manic.repository_git import GitRepository -from manic.externals_status import ExternalStatus -from manic.externals_description import ExternalsDescription -from manic.externals_description import ExternalsDescriptionDict -from manic.global_constants import EMPTY_STR - -# NOTE(bja, 2017-11) order is important here. origin should be a -# subset of other to trap errors on processing remotes! -GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM = ''' -upstream /path/to/other/repo (fetch) -upstream /path/to/other/repo (push) -other /path/to/local/repo2 (fetch) -other /path/to/local/repo2 (push) -origin /path/to/local/repo (fetch) -origin /path/to/local/repo (push) -''' - - -class TestGitRepositoryCurrentRef(unittest.TestCase): - """test the current_ref command on a git repository - """ - - def setUp(self): - self._name = 'component' - rdata = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: - '/path/to/local/repo', - ExternalsDescription.TAG: - 'tag1', - } - - data = {self._name: - { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: 'junk', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdata, - }, - } - - model = ExternalsDescriptionDict(data) - repo = model[self._name][ExternalsDescription.REPO] - self._repo = GitRepository('test', repo) - - # - # mock methods replacing git system calls - # - @staticmethod - def _git_current_branch(branch_found, branch_name): - """Return a function that takes the place of - repo._git_current_branch, which returns the given output.""" - def my_git_current_branch(dirname): - """mock function that can take the place of repo._git_current_branch""" - return branch_found, branch_name - return my_git_current_branch - - @staticmethod - def _git_current_tag(tag_found, tag_name): - """Return a function that takes the place of - repo._git_current_tag, which returns the given output.""" - def my_git_current_tag(dirname): - """mock function that can take the place of repo._git_current_tag""" - return tag_found, tag_name - return my_git_current_tag - - @staticmethod - def _git_current_hash(hash_found, hash_name): - """Return a function that takes the place of - repo._git_current_hash, which returns the given output.""" - def my_git_current_hash(dirname): - """mock function that can take the place of repo._git_current_hash""" - return hash_found, hash_name - return my_git_current_hash - - # ------------------------------------------------------------------------ - # Begin tests - # ------------------------------------------------------------------------ - - def test_ref_branch(self): - """Test that we correctly identify we are on a branch - """ - self._repo._git_current_branch = self._git_current_branch( - True, 'feature3') - self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag') - self._repo._git_current_hash = self._git_current_hash(True, 'abc123') - expected = 'foo_tag (branch feature3)' - result = self._repo._current_ref(os.getcwd()) - self.assertEqual(result, expected) - - def test_ref_detached_tag(self): - """Test that we correctly identify that the ref is detached at a tag - """ - self._repo._git_current_branch = self._git_current_branch(False, '') - self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag') - self._repo._git_current_hash = self._git_current_hash(True, 'abc123') - expected = 'foo_tag' - result = self._repo._current_ref(os.getcwd()) - self.assertEqual(result, expected) - - def test_ref_detached_hash(self): - """Test that we can identify ref is detached at a hash - - """ - self._repo._git_current_branch = self._git_current_branch(False, '') - self._repo._git_current_tag = self._git_current_tag(False, '') - self._repo._git_current_hash = self._git_current_hash(True, 'abc123') - expected = 'abc123' - result = self._repo._current_ref(os.getcwd()) - self.assertEqual(result, expected) - - def test_ref_none(self): - """Test that we correctly identify that we're not in a git repo. - """ - self._repo._git_current_branch = self._git_current_branch(False, '') - self._repo._git_current_tag = self._git_current_tag(False, '') - self._repo._git_current_hash = self._git_current_hash(False, '') - result = self._repo._current_ref(os.getcwd()) - self.assertEqual(result, EMPTY_STR) - - -class TestGitRepositoryCheckSync(unittest.TestCase): - """Test whether the GitRepository _check_sync_logic functionality is - correct. - - Note: there are a lot of combinations of state: - - - external description - tag, branch - - - working copy - - doesn't exist (not checked out) - - exists, no git info - incorrect protocol, e.g. svn, or tarball? - - exists, git info - - as expected: - - different from expected: - - detached tag, - - detached hash, - - detached branch (compare remote and branch), - - tracking branch (compare remote and branch), - - same remote - - different remote - - untracked branch - - Test list: - - doesn't exist - - exists no git info - - - num_external * (working copy expected + num_working copy different) - - total tests = 16 - - """ - - # NOTE(bja, 2017-11) pylint complains about long method names, but - # it is hard to differentiate tests without making them more - # cryptic. Also complains about too many public methods, but it - # doesn't really make sense to break this up. - # pylint: disable=invalid-name,too-many-public-methods - - TMP_FAKE_DIR = 'fake' - TMP_FAKE_GIT_DIR = os.path.join(TMP_FAKE_DIR, '.git') - - def setUp(self): - """Setup reusable git repository object - """ - self._name = 'component' - rdata = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: - '/path/to/local/repo', - ExternalsDescription.TAG: 'tag1', - } - - data = {self._name: - { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: self.TMP_FAKE_DIR, - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdata, - }, - } - - model = ExternalsDescriptionDict(data) - repo = model[self._name][ExternalsDescription.REPO] - self._repo = GitRepository('test', repo) - # The unit tests here don't care about the result of - # _current_ref, but we replace it here so that we don't need to - # worry about calling a possibly slow and possibly - # error-producing command (since _current_ref calls various git - # functions): - self._repo._current_ref = self._current_ref_empty - self._create_tmp_git_dir() - - # We have to override this class method rather than the self._repo - # instance method because it is called via - # GitRepository._remote_name_for_url, which is itself a @classmethod - # calls cls._git_remote_verbose(). - self._orignal_git_remote_verbose = GitRepository._git_remote_verbose - GitRepository._git_remote_verbose = self._git_remote_origin_upstream - def tearDown(self): - """Cleanup tmp stuff on the file system - """ - self._remove_tmp_git_dir() - - GitRepository._git_remote_verbose = self._orignal_git_remote_verbose - - def _create_tmp_git_dir(self): - """Create a temporary fake git directory for testing purposes. - """ - if not os.path.exists(self.TMP_FAKE_GIT_DIR): - os.makedirs(self.TMP_FAKE_GIT_DIR) - - def _remove_tmp_git_dir(self): - """Remove the temporary fake git directory - """ - if os.path.exists(self.TMP_FAKE_DIR): - shutil.rmtree(self.TMP_FAKE_DIR) - - # - # mock methods replacing git system calls - # - @staticmethod - def _current_ref_empty(dirname): - """Return an empty string. - - Drop-in for GitRepository._current_ref - """ - return EMPTY_STR - - @staticmethod - def _git_remote_origin_upstream(dirname): - """Return an info string that is a checkout hash. - - Drop-in for GitRepository._git_remote_verbose. - """ - return GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM - - @staticmethod - def _git_current_hash(myhash): - """Return a function that takes the place of repo._git_current_hash, - which returns the given hash - """ - def my_git_current_hash(dirname): - """mock function that can take the place of repo._git_current_hash""" - return 0, myhash - return my_git_current_hash - - def _git_revparse_commit(self, expected_ref, mystatus, myhash): - """Return a function that takes the place of - repo._git_revparse_commit, which returns a tuple: - (mystatus, myhash). - - Expects the passed-in ref to equal expected_ref - - status = 0 implies success, non-zero implies failure - """ - def my_git_revparse_commit(ref, dirname): - """mock function that can take the place of repo._git_revparse_commit""" - self.assertEqual(expected_ref, ref) - return mystatus, myhash - return my_git_revparse_commit - - # ---------------------------------------------------------------- - # - # Tests where working copy doesn't exist or is invalid - # - # ---------------------------------------------------------------- - def test_sync_dir_not_exist(self): - """Test that a directory that doesn't exist returns an error status - - Note: the Repository classes should be prevented from ever - working on an empty directory by the _Source object. - - """ - stat = ExternalStatus() - self._repo._check_sync(stat, 'invalid_directory_name') - self.assertEqual(stat.sync_state, ExternalStatus.STATUS_ERROR) - # check_dir should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_sync_dir_exist_no_git_info(self): - """Test that a non-existent git repo returns an unknown status - """ - stat = ExternalStatus() - self._repo._tag = 'tag1' - self._repo._git_current_hash = self._git_current_hash('') - self._repo._git_revparse_commit = self._git_revparse_commit( - 'tag1', 1, '') - self._repo._check_sync(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.UNKNOWN) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - # ------------------------------------------------------------------------ - # - # Tests where version in configuration file is not a valid reference - # - # ------------------------------------------------------------------------ - - def test_sync_invalid_reference(self): - """Test that an invalid reference returns out-of-sync - """ - stat = ExternalStatus() - self._repo._tag = 'tag1' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = self._git_revparse_commit( - 'tag1', 1, '') - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - # ---------------------------------------------------------------- - # - # Tests where external description specifies a tag - # - # ---------------------------------------------------------------- - def test_sync_tag_on_same_hash(self): - """Test expect tag on same hash --> status ok - - """ - stat = ExternalStatus() - self._repo._tag = 'tag1' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = self._git_revparse_commit( - 'tag1', 0, 'abc123') - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_sync_tag_on_different_hash(self): - """Test expect tag on a different hash --> status modified - - """ - stat = ExternalStatus() - self._repo._tag = 'tag1' - self._repo._git_current_hash = self._git_current_hash('def456') - self._repo._git_revparse_commit = self._git_revparse_commit( - 'tag1', 0, 'abc123') - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - # ---------------------------------------------------------------- - # - # Tests where external description specifies a hash - # - # ---------------------------------------------------------------- - def test_sync_hash_on_same_hash(self): - """Test expect hash on same hash --> status ok - - """ - stat = ExternalStatus() - self._repo._tag = '' - self._repo._hash = 'abc' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = self._git_revparse_commit( - 'abc', 0, 'abc123') - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_sync_hash_on_different_hash(self): - """Test expect hash on a different hash --> status modified - - """ - stat = ExternalStatus() - self._repo._tag = '' - self._repo._hash = 'abc' - self._repo._git_current_hash = self._git_current_hash('def456') - self._repo._git_revparse_commit = self._git_revparse_commit( - 'abc', 0, 'abc123') - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - # ---------------------------------------------------------------- - # - # Tests where external description specifies a branch - # - # ---------------------------------------------------------------- - def test_sync_branch_on_same_hash(self): - """Test expect branch on same hash --> status ok - - """ - stat = ExternalStatus() - self._repo._branch = 'feature-2' - self._repo._tag = '' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = ( - self._git_revparse_commit('origin/feature-2', 0, 'abc123')) - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_sync_branch_on_diff_hash(self): - """Test expect branch on diff hash --> status modified - - """ - stat = ExternalStatus() - self._repo._branch = 'feature-2' - self._repo._tag = '' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = ( - self._git_revparse_commit('origin/feature-2', 0, 'def456')) - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_sync_branch_diff_remote(self): - """Test _remote_name_for_url with a different remote - - """ - stat = ExternalStatus() - self._repo._branch = 'feature-2' - self._repo._tag = '' - self._repo._url = '/path/to/other/repo' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = ( - self._git_revparse_commit('upstream/feature-2', 0, 'def456')) - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - # The test passes if _git_revparse_commit is called with the - # expected argument - - def test_sync_branch_diff_remote2(self): - """Test _remote_name_for_url with a different remote - - """ - stat = ExternalStatus() - self._repo._branch = 'feature-2' - self._repo._tag = '' - self._repo._url = '/path/to/local/repo2' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = ( - self._git_revparse_commit('other/feature-2', 0, 'def789')) - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - # The test passes if _git_revparse_commit is called with the - # expected argument - - def test_sync_branch_on_unknown_remote(self): - """Test expect branch, but remote is unknown --> status modified - - """ - stat = ExternalStatus() - self._repo._branch = 'feature-2' - self._repo._tag = '' - self._repo._url = '/path/to/unknown/repo' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = ( - self._git_revparse_commit('unknown_remote/feature-2', 1, '')) - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_sync_branch_on_untracked_local(self): - """Test expect branch, on untracked branch in local repo --> status ok - - Setting the externals description to '.' indicates that the - user only wants to consider the current local repo state - without fetching from remotes. This is required to preserve - the current branch of a repository during an update. - - """ - stat = ExternalStatus() - self._repo._branch = 'feature3' - self._repo._tag = '' - self._repo._url = '.' - self._repo._git_current_hash = self._git_current_hash('abc123') - self._repo._git_revparse_commit = ( - self._git_revparse_commit('feature3', 0, 'abc123')) - self._repo._check_sync_logic(stat, self.TMP_FAKE_DIR) - self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK) - # check_sync should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - -class TestGitStatusPorcelain(unittest.TestCase): - """Test parsing of output from git status --porcelain=v1 -z - """ - # pylint: disable=C0103 - GIT_STATUS_PORCELAIN_V1_ALL = ( - r' D INSTALL\0MM Makefile\0M README.md\0R cmakelists.txt\0' - r'CMakeLists.txt\0D commit-message-template.txt\0A stuff.txt\0' - r'?? junk.txt') - - GIT_STATUS_PORCELAIN_CLEAN = r'' - - def test_porcelain_status_dirty(self): - """Verify that git status output is considered dirty when there are - listed files. - - """ - git_output = self.GIT_STATUS_PORCELAIN_V1_ALL - is_dirty = GitRepository._status_v1z_is_dirty(git_output) - self.assertTrue(is_dirty) - - def test_porcelain_status_clean(self): - """Verify that git status output is considered clean when there are no - listed files. - - """ - git_output = self.GIT_STATUS_PORCELAIN_CLEAN - is_dirty = GitRepository._status_v1z_is_dirty(git_output) - self.assertFalse(is_dirty) - - -class TestGitCreateRemoteName(unittest.TestCase): - """Test the create_remote_name method on the GitRepository class - """ - - def setUp(self): - """Common infrastructure for testing _create_remote_name - """ - self._rdata = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: - 'empty', - ExternalsDescription.TAG: - 'very_useful_tag', - ExternalsDescription.BRANCH: EMPTY_STR, - ExternalsDescription.HASH: EMPTY_STR, - ExternalsDescription.SPARSE: EMPTY_STR, } - self._repo = GitRepository('test', self._rdata) - - def test_remote_git_proto(self): - """Test remote with git protocol - """ - self._repo._url = 'git@git.github.com:very_nice_org/useful_repo' - remote_name = self._repo._create_remote_name() - self.assertEqual(remote_name, 'very_nice_org_useful_repo') - - def test_remote_https_proto(self): - """Test remote with git protocol - """ - self._repo._url = 'https://www.github.com/very_nice_org/useful_repo' - remote_name = self._repo._create_remote_name() - self.assertEqual(remote_name, 'very_nice_org_useful_repo') - - def test_remote_local_abs(self): - """Test remote with git protocol - """ - self._repo._url = '/path/to/local/repositories/useful_repo' - remote_name = self._repo._create_remote_name() - self.assertEqual(remote_name, 'repositories_useful_repo') - - def test_remote_local_rel(self): - """Test remote with git protocol - """ - os.environ['TEST_VAR'] = '/my/path/to/repos' - self._repo._url = '${TEST_VAR}/../../useful_repo' - remote_name = self._repo._create_remote_name() - self.assertEqual(remote_name, 'path_useful_repo') - del os.environ['TEST_VAR'] - - -class TestVerifyTag(unittest.TestCase): - """Test logic verifying that a tag exists and is unique - - """ - - def setUp(self): - """Setup reusable git repository object - """ - self._name = 'component' - rdata = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: - '/path/to/local/repo', - ExternalsDescription.TAG: 'tag1', - } - - data = {self._name: - { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: 'tmp', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdata, - }, - } - - model = ExternalsDescriptionDict(data) - repo = model[self._name][ExternalsDescription.REPO] - self._repo = GitRepository('test', repo) - - @staticmethod - def _shell_true(*args, **kwargs): - return 0 - - @staticmethod - def _shell_false(*args, **kwargs): - return 1 - - @staticmethod - def _mock_revparse_commit(ref, dirname): - _ = ref - return (TestValidRef._shell_true, '97ebc0e0deadc0de') - - @staticmethod - def _mock_revparse_commit_false(ref, dirname): - _ = ref - return (TestValidRef._shell_false, '97ebc0e0deadc0de') - - def test_tag_not_tag_branch_commit(self): - """Verify a non-tag returns false - """ - self._repo._git_showref_tag = self._shell_false - self._repo._git_showref_branch = self._shell_false - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_revparse_commit_false - self._repo._tag = 'something' - remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, - os.getcwd()) - self.assertFalse(received) - - def test_tag_not_tag(self): - """Verify a non-tag, untracked remote returns false - """ - self._repo._git_showref_tag = self._shell_false - self._repo._git_showref_branch = self._shell_true - self._repo._git_lsremote_branch = self._shell_true - self._repo._git_revparse_commit = self._mock_revparse_commit_false - self._repo._tag = 'tag1' - remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, - os.getcwd()) - self.assertFalse(received) - - def test_tag_indeterminant(self): - """Verify an indeterminant tag/branch returns false - """ - self._repo._git_showref_tag = self._shell_true - self._repo._git_showref_branch = self._shell_true - self._repo._git_lsremote_branch = self._shell_true - self._repo._git_revparse_commit = self._mock_revparse_commit - self._repo._tag = 'something' - remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, - os.getcwd()) - self.assertFalse(received) - - def test_tag_is_unique(self): - """Verify a unique tag match returns true - """ - self._repo._git_showref_tag = self._shell_true - self._repo._git_showref_branch = self._shell_false - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_revparse_commit - self._repo._tag = 'tag1' - remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, - os.getcwd()) - self.assertTrue(received) - - def test_tag_is_not_hash(self): - """Verify a commit hash is not classified as a tag - """ - self._repo._git_showref_tag = self._shell_false - self._repo._git_showref_branch = self._shell_false - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_revparse_commit - self._repo._tag = '97ebc0e0' - remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, - os.getcwd()) - self.assertFalse(received) - - def test_hash_is_commit(self): - """Verify a commit hash is not classified as a tag - """ - self._repo._git_showref_tag = self._shell_false - self._repo._git_showref_branch = self._shell_false - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_revparse_commit - self._repo._tag = '97ebc0e0' - remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, - os.getcwd()) - self.assertFalse(received) - - -class TestValidRef(unittest.TestCase): - """Test logic verifying that a reference is a valid tag, branch or sha1 - - """ - - def setUp(self): - """Setup reusable git repository object - """ - self._name = 'component' - rdata = {ExternalsDescription.PROTOCOL: 'git', - ExternalsDescription.REPO_URL: - '/path/to/local/repo', - ExternalsDescription.TAG: 'tag1', - } - - data = {self._name: - { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: 'tmp', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdata, - }, - } - - model = ExternalsDescriptionDict(data) - repo = model[self._name][ExternalsDescription.REPO] - self._repo = GitRepository('test', repo) - - @staticmethod - def _shell_true(url, remote=None): - _ = url - _ = remote - return 0 - - @staticmethod - def _shell_false(url, remote=None): - _ = url - _ = remote - return 1 - - @staticmethod - def _mock_revparse_commit_false(ref, dirname): - _ = ref - return (TestValidRef._shell_false, '') - - @staticmethod - def _mock_revparse_commit_true(ref, dirname): - _ = ref - _ = dirname - return (TestValidRef._shell_true, '') - - def test_valid_ref_is_invalid(self): - """Verify an invalid reference raises an exception - """ - self._repo._git_showref_tag = self._shell_false - self._repo._git_showref_branch = self._shell_false - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_revparse_commit_false - self._repo._tag = 'invalid_ref' - with self.assertRaises(RuntimeError): - self._repo._check_for_valid_ref(self._repo._tag, - remote_name=None, - dirname=os.getcwd()) - - def test_valid_tag(self): - """Verify a valid tag return true - """ - self._repo._git_showref_tag = self._shell_true - self._repo._git_showref_branch = self._shell_false - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_revparse_commit_true - self._repo._tag = 'tag1' - received = self._repo._check_for_valid_ref(self._repo._tag, - remote_name=None, - dirname=os.getcwd()) - self.assertTrue(received) - - def test_valid_branch(self): - """Verify a valid tag return true - """ - self._repo._git_showref_tag = self._shell_false - self._repo._git_showref_branch = self._shell_true - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_revparse_commit_true - self._repo._tag = 'tag1' - received = self._repo._check_for_valid_ref(self._repo._tag, - remote_name=None, - dirname=os.getcwd()) - self.assertTrue(received) - - def test_valid_hash(self): - """Verify a valid hash return true - """ - def _mock_revparse_commit_true(ref, dirname): - _ = ref - return (0, '56cc0b539426eb26810af9e') - - self._repo._git_showref_tag = self._shell_false - self._repo._git_showref_branch = self._shell_false - self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = _mock_revparse_commit_true - self._repo._hash = '56cc0b5394' - received = self._repo._check_for_valid_ref(self._repo._hash, - remote_name=None, - dirname=os.getcwd()) - self.assertTrue(received) - - -if __name__ == '__main__': - unittest.main() diff --git a/manage_externals/test/test_unit_repository_svn.py b/manage_externals/test/test_unit_repository_svn.py deleted file mode 100755 index d9309df7f6..0000000000 --- a/manage_externals/test/test_unit_repository_svn.py +++ /dev/null @@ -1,501 +0,0 @@ -#!/usr/bin/env python3 - -"""Unit test driver for checkout_externals - -Note: this script assume the path to the checkout_externals.py module is -already in the python path. - -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import unittest - -from manic.repository_svn import SvnRepository -from manic.externals_status import ExternalStatus -from manic.externals_description import ExternalsDescription -from manic.externals_description import ExternalsDescriptionDict -from manic.global_constants import EMPTY_STR - -# pylint: disable=W0212 - -SVN_INFO_MOSART = """Path: components/mosart -Working Copy Root Path: /Users/andreb/projects/ncar/git-conversion/clm-dev-experimental/components/mosart -URL: https://svn-ccsm-models.cgd.ucar.edu/mosart/trunk_tags/mosart1_0_26 -Relative URL: ^/mosart/trunk_tags/mosart1_0_26 -Repository Root: https://svn-ccsm-models.cgd.ucar.edu -Repository UUID: fe37f545-8307-0410-aea5-b40df96820b5 -Revision: 86711 -Node Kind: directory -Schedule: normal -Last Changed Author: erik -Last Changed Rev: 86031 -Last Changed Date: 2017-07-07 12:28:10 -0600 (Fri, 07 Jul 2017) -""" -SVN_INFO_CISM = """ -Path: components/cism -Working Copy Root Path: /Users/andreb/projects/ncar/git-conversion/clm-dev-experimental/components/cism -URL: https://svn-ccsm-models.cgd.ucar.edu/glc/trunk_tags/cism2_1_37 -Relative URL: ^/glc/trunk_tags/cism2_1_37 -Repository Root: https://svn-ccsm-models.cgd.ucar.edu -Repository UUID: fe37f545-8307-0410-aea5-b40df96820b5 -Revision: 86711 -Node Kind: directory -Schedule: normal -Last Changed Author: sacks -Last Changed Rev: 85704 -Last Changed Date: 2017-06-15 05:59:28 -0600 (Thu, 15 Jun 2017) -""" - - -class TestSvnRepositoryCheckURL(unittest.TestCase): - """Verify that the svn_check_url function is working as expected. - """ - - def setUp(self): - """Setup reusable svn repository object - """ - self._name = 'component' - rdata = {ExternalsDescription.PROTOCOL: 'svn', - ExternalsDescription.REPO_URL: - 'https://svn-ccsm-models.cgd.ucar.edu', - ExternalsDescription.TAG: - 'mosart/trunk_tags/mosart1_0_26', - } - - data = {self._name: - { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: 'junk', - ExternalsDescription.EXTERNALS: '', - ExternalsDescription.REPO: rdata, - }, - } - - model = ExternalsDescriptionDict(data) - repo = model[self._name][ExternalsDescription.REPO] - self._repo = SvnRepository('test', repo) - - def test_check_url_same(self): - """Test that we correctly identify that the correct URL. - """ - svn_output = SVN_INFO_MOSART - expected_url = self._repo.url() - result, current_version = \ - self._repo._check_url(svn_output, expected_url) - self.assertEqual(result, ExternalStatus.STATUS_OK) - self.assertEqual(current_version, 'mosart/trunk_tags/mosart1_0_26') - - def test_check_url_different(self): - """Test that we correctly reject an incorrect URL. - """ - svn_output = SVN_INFO_CISM - expected_url = self._repo.url() - result, current_version = \ - self._repo._check_url(svn_output, expected_url) - self.assertEqual(result, ExternalStatus.MODEL_MODIFIED) - self.assertEqual(current_version, 'glc/trunk_tags/cism2_1_37') - - def test_check_url_none(self): - """Test that we can handle an empty string for output, e.g. not an svn - repo. - - """ - svn_output = EMPTY_STR - expected_url = self._repo.url() - result, current_version = \ - self._repo._check_url(svn_output, expected_url) - self.assertEqual(result, ExternalStatus.UNKNOWN) - self.assertEqual(current_version, '') - - -class TestSvnRepositoryCheckSync(unittest.TestCase): - """Test whether the SvnRepository svn_check_sync functionality is - correct. - - """ - - def setUp(self): - """Setup reusable svn repository object - """ - self._name = "component" - rdata = {ExternalsDescription.PROTOCOL: 'svn', - ExternalsDescription.REPO_URL: - 'https://svn-ccsm-models.cgd.ucar.edu/', - ExternalsDescription.TAG: - 'mosart/trunk_tags/mosart1_0_26', - } - - data = {self._name: - { - ExternalsDescription.REQUIRED: False, - ExternalsDescription.PATH: 'junk', - ExternalsDescription.EXTERNALS: EMPTY_STR, - ExternalsDescription.REPO: rdata, - }, - } - - model = ExternalsDescriptionDict(data) - repo = model[self._name][ExternalsDescription.REPO] - self._repo = SvnRepository('test', repo) - - @staticmethod - def _svn_info_empty(*_): - """Return an empty info string. Simulates svn info failing. - """ - return '' - - @staticmethod - def _svn_info_synced(*_): - """Return an info sting that is synced with the setUp data - """ - return SVN_INFO_MOSART - - @staticmethod - def _svn_info_modified(*_): - """Return and info string that is modified from the setUp data - """ - return SVN_INFO_CISM - - def test_repo_dir_not_exist(self): - """Test that a directory that doesn't exist returns an error status - - Note: the Repository classes should be prevented from ever - working on an empty directory by the _Source object. - - """ - stat = ExternalStatus() - self._repo._check_sync(stat, 'junk') - self.assertEqual(stat.sync_state, ExternalStatus.STATUS_ERROR) - # check_dir should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_repo_dir_exist_no_svn_info(self): - """Test that an empty info string returns an unknown status - """ - stat = ExternalStatus() - # Now we over-ride the _svn_info method on the repo to return - # a known value without requiring access to svn. - self._repo._svn_info = self._svn_info_empty - self._repo._check_sync(stat, '.') - self.assertEqual(stat.sync_state, ExternalStatus.UNKNOWN) - # check_dir should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_repo_dir_synced(self): - """Test that a valid info string that is synced to the repo in the - externals description returns an ok status. - - """ - stat = ExternalStatus() - # Now we over-ride the _svn_info method on the repo to return - # a known value without requiring access to svn. - self._repo._svn_info = self._svn_info_synced - self._repo._check_sync(stat, '.') - self.assertEqual(stat.sync_state, ExternalStatus.STATUS_OK) - # check_dir should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - def test_repo_dir_modified(self): - """Test that a valid svn info string that is out of sync with the - externals description returns a modified status. - - """ - stat = ExternalStatus() - # Now we over-ride the _svn_info method on the repo to return - # a known value without requiring access to svn. - self._repo._svn_info = self._svn_info_modified - self._repo._check_sync(stat, '.') - self.assertEqual(stat.sync_state, ExternalStatus.MODEL_MODIFIED) - # check_dir should only modify the sync_state, not clean_state - self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) - - -class TestSVNStatusXML(unittest.TestCase): - """Test parsing of svn status xml output - """ - SVN_STATUS_XML_DIRTY_ALL = ''' - - - - - -sacks -2017-06-15T11:59:00.355419Z - - - - - - -sacks -2013-02-07T16:17:56.412878Z - - - - - - -sacks -2017-05-01T16:48:27.893741Z - - - - - - - - - - - - - - - - -''' - - SVN_STATUS_XML_DIRTY_MISSING = ''' - - - - - -sacks -2017-06-15T11:59:00.355419Z - - - - - - - - -''' - - SVN_STATUS_XML_DIRTY_MODIFIED = ''' - - - - - -sacks -2013-02-07T16:17:56.412878Z - - - - - - - - -''' - - SVN_STATUS_XML_DIRTY_DELETED = ''' - - - - - -sacks -2017-05-01T16:48:27.893741Z - - - - - - - - -''' - - SVN_STATUS_XML_DIRTY_UNVERSION = ''' - - - - - - - - - - - -''' - - SVN_STATUS_XML_DIRTY_ADDED = ''' - - - - - - - - - - - -''' - - SVN_STATUS_XML_CLEAN = ''' - - - - - - - - - - - -''' - - def test_xml_status_dirty_missing(self): - """Verify that svn status output is consindered dirty when there is a - missing file. - - """ - svn_output = self.SVN_STATUS_XML_DIRTY_MISSING - is_dirty = SvnRepository.xml_status_is_dirty( - svn_output) - self.assertTrue(is_dirty) - - def test_xml_status_dirty_modified(self): - """Verify that svn status output is consindered dirty when there is a - modified file. - """ - svn_output = self.SVN_STATUS_XML_DIRTY_MODIFIED - is_dirty = SvnRepository.xml_status_is_dirty( - svn_output) - self.assertTrue(is_dirty) - - def test_xml_status_dirty_deleted(self): - """Verify that svn status output is consindered dirty when there is a - deleted file. - """ - svn_output = self.SVN_STATUS_XML_DIRTY_DELETED - is_dirty = SvnRepository.xml_status_is_dirty( - svn_output) - self.assertTrue(is_dirty) - - def test_xml_status_dirty_unversion(self): - """Verify that svn status output ignores unversioned files when making - the clean/dirty decision. - - """ - svn_output = self.SVN_STATUS_XML_DIRTY_UNVERSION - is_dirty = SvnRepository.xml_status_is_dirty( - svn_output) - self.assertFalse(is_dirty) - - def test_xml_status_dirty_added(self): - """Verify that svn status output is consindered dirty when there is a - added file. - """ - svn_output = self.SVN_STATUS_XML_DIRTY_ADDED - is_dirty = SvnRepository.xml_status_is_dirty( - svn_output) - self.assertTrue(is_dirty) - - def test_xml_status_dirty_all(self): - """Verify that svn status output is consindered dirty when there are - multiple dirty files.. - - """ - svn_output = self.SVN_STATUS_XML_DIRTY_ALL - is_dirty = SvnRepository.xml_status_is_dirty( - svn_output) - self.assertTrue(is_dirty) - - def test_xml_status_dirty_clean(self): - """Verify that svn status output is consindered clean when there are - no 'dirty' files. This means accepting untracked and externals. - - """ - svn_output = self.SVN_STATUS_XML_CLEAN - is_dirty = SvnRepository.xml_status_is_dirty( - svn_output) - self.assertFalse(is_dirty) - - -if __name__ == '__main__': - unittest.main() diff --git a/manage_externals/test/test_unit_utils.py b/manage_externals/test/test_unit_utils.py deleted file mode 100644 index 80e1636649..0000000000 --- a/manage_externals/test/test_unit_utils.py +++ /dev/null @@ -1,350 +0,0 @@ -#!/usr/bin/env python3 - -"""Unit test driver for checkout_externals - -Note: this script assume the path to the checkout_externals.py module is -already in the python path. - -""" - -from __future__ import absolute_import -from __future__ import unicode_literals -from __future__ import print_function - -import os -import unittest - -from manic.utils import last_n_lines, indent_string -from manic.utils import str_to_bool, execute_subprocess -from manic.utils import is_remote_url, split_remote_url, expand_local_url - - -class TestExecuteSubprocess(unittest.TestCase): - """Test the application logic of execute_subprocess wrapper - """ - - def test_exesub_return_stat_err(self): - """Test that execute_subprocess returns a status code when caller - requests and the executed subprocess fails. - - """ - cmd = ['false'] - status = execute_subprocess(cmd, status_to_caller=True) - self.assertEqual(status, 1) - - def test_exesub_return_stat_ok(self): - """Test that execute_subprocess returns a status code when caller - requests and the executed subprocess succeeds. - - """ - cmd = ['true'] - status = execute_subprocess(cmd, status_to_caller=True) - self.assertEqual(status, 0) - - def test_exesub_except_stat_err(self): - """Test that execute_subprocess raises an exception on error when - caller doesn't request return code - - """ - cmd = ['false'] - with self.assertRaises(RuntimeError): - execute_subprocess(cmd, status_to_caller=False) - - -class TestLastNLines(unittest.TestCase): - """Test the last_n_lines function. - - """ - - def test_last_n_lines_short(self): - """With a message with <= n lines, result of last_n_lines should - just be the original message. - - """ - mystr = """three -line -string -""" - - mystr_truncated = last_n_lines( - mystr, 3, truncation_message='[truncated]') - self.assertEqual(mystr, mystr_truncated) - - def test_last_n_lines_long(self): - """With a message with > n lines, result of last_n_lines should - be a truncated string. - - """ - mystr = """a -big -five -line -string -""" - expected = """[truncated] -five -line -string -""" - - mystr_truncated = last_n_lines( - mystr, 3, truncation_message='[truncated]') - self.assertEqual(expected, mystr_truncated) - - -class TestIndentStr(unittest.TestCase): - """Test the indent_string function. - - """ - - def test_indent_string_singleline(self): - """Test the indent_string function with a single-line string - - """ - mystr = 'foo' - result = indent_string(mystr, 4) - expected = ' foo' - self.assertEqual(expected, result) - - def test_indent_string_multiline(self): - """Test the indent_string function with a multi-line string - - """ - mystr = """hello -hi -goodbye -""" - result = indent_string(mystr, 2) - expected = """ hello - hi - goodbye -""" - self.assertEqual(expected, result) - - -class TestStrToBool(unittest.TestCase): - """Test the string to boolean conversion routine. - - """ - - def test_case_insensitive_true(self): - """Verify that case insensitive variants of 'true' returns the True - boolean. - - """ - values = ['true', 'TRUE', 'True', 'tRuE', 't', 'T', ] - for value in values: - received = str_to_bool(value) - self.assertTrue(received) - - def test_case_insensitive_false(self): - """Verify that case insensitive variants of 'false' returns the False - boolean. - - """ - values = ['false', 'FALSE', 'False', 'fAlSe', 'f', 'F', ] - for value in values: - received = str_to_bool(value) - self.assertFalse(received) - - def test_invalid_str_error(self): - """Verify that a non-true/false string generates a runtime error. - """ - values = ['not_true_or_false', 'A', '1', '0', - 'false_is_not_true', 'true_is_not_false'] - for value in values: - with self.assertRaises(RuntimeError): - str_to_bool(value) - - -class TestIsRemoteURL(unittest.TestCase): - """Crude url checking to determine if a url is local or remote. - - """ - - def test_url_remote_git(self): - """verify that a remote git url is identified. - """ - url = 'git@somewhere' - is_remote = is_remote_url(url) - self.assertTrue(is_remote) - - def test_url_remote_ssh(self): - """verify that a remote ssh url is identified. - """ - url = 'ssh://user@somewhere' - is_remote = is_remote_url(url) - self.assertTrue(is_remote) - - def test_url_remote_http(self): - """verify that a remote http url is identified. - """ - url = 'http://somewhere' - is_remote = is_remote_url(url) - self.assertTrue(is_remote) - - def test_url_remote_https(self): - """verify that a remote https url is identified. - """ - url = 'https://somewhere' - is_remote = is_remote_url(url) - self.assertTrue(is_remote) - - def test_url_local_user(self): - """verify that a local path with '~/path/to/repo' gets rejected - - """ - url = '~/path/to/repo' - is_remote = is_remote_url(url) - self.assertFalse(is_remote) - - def test_url_local_var_curly(self): - """verify that a local path with env var '${HOME}' gets rejected - """ - url = '${HOME}/path/to/repo' - is_remote = is_remote_url(url) - self.assertFalse(is_remote) - - def test_url_local_var(self): - """verify that a local path with an env var '$HOME' gets rejected - """ - url = '$HOME/path/to/repo' - is_remote = is_remote_url(url) - self.assertFalse(is_remote) - - def test_url_local_abs(self): - """verify that a local abs path gets rejected - """ - url = '/path/to/repo' - is_remote = is_remote_url(url) - self.assertFalse(is_remote) - - def test_url_local_rel(self): - """verify that a local relative path gets rejected - """ - url = '../../path/to/repo' - is_remote = is_remote_url(url) - self.assertFalse(is_remote) - - -class TestSplitRemoteURL(unittest.TestCase): - """Crude url checking to determine if a url is local or remote. - - """ - - def test_url_remote_git(self): - """verify that a remote git url is identified. - """ - url = 'git@somewhere.com:org/repo' - received = split_remote_url(url) - self.assertEqual(received, "org/repo") - - def test_url_remote_ssh(self): - """verify that a remote ssh url is identified. - """ - url = 'ssh://user@somewhere.com/path/to/repo' - received = split_remote_url(url) - self.assertEqual(received, 'somewhere.com/path/to/repo') - - def test_url_remote_http(self): - """verify that a remote http url is identified. - """ - url = 'http://somewhere.org/path/to/repo' - received = split_remote_url(url) - self.assertEqual(received, 'somewhere.org/path/to/repo') - - def test_url_remote_https(self): - """verify that a remote http url is identified. - """ - url = 'http://somewhere.gov/path/to/repo' - received = split_remote_url(url) - self.assertEqual(received, 'somewhere.gov/path/to/repo') - - def test_url_local_url_unchanged(self): - """verify that a local path is unchanged - - """ - url = '/path/to/repo' - received = split_remote_url(url) - self.assertEqual(received, url) - - -class TestExpandLocalURL(unittest.TestCase): - """Crude url checking to determine if a url is local or remote. - - Remote should be unmodified. - - Local, should perform user and variable expansion. - - """ - - def test_url_local_user1(self): - """verify that a local path with '~/path/to/repo' gets expanded to an - absolute path. - - NOTE(bja, 2017-11) we can't test for something like: - '~user/path/to/repo' because the user has to be in the local - machine password directory and we don't know a user name that - is valid on every system....? - - """ - field = 'test' - url = '~/path/to/repo' - received = expand_local_url(url, field) - print(received) - self.assertTrue(os.path.isabs(received)) - - def test_url_local_expand_curly(self): - """verify that a local path with '${HOME}' gets expanded to an absolute path. - """ - field = 'test' - url = '${HOME}/path/to/repo' - received = expand_local_url(url, field) - self.assertTrue(os.path.isabs(received)) - - def test_url_local_expand_var(self): - """verify that a local path with '$HOME' gets expanded to an absolute path. - """ - field = 'test' - url = '$HOME/path/to/repo' - received = expand_local_url(url, field) - self.assertTrue(os.path.isabs(received)) - - def test_url_local_env_missing(self): - """verify that a local path with env var that is missing gets left as-is - - """ - field = 'test' - url = '$TMP_VAR/path/to/repo' - received = expand_local_url(url, field) - print(received) - self.assertEqual(received, url) - - def test_url_local_expand_env(self): - """verify that a local path with another env var gets expanded to an - absolute path. - - """ - field = 'test' - os.environ['TMP_VAR'] = '/some/absolute' - url = '$TMP_VAR/path/to/repo' - received = expand_local_url(url, field) - del os.environ['TMP_VAR'] - print(received) - self.assertTrue(os.path.isabs(received)) - self.assertEqual(received, '/some/absolute/path/to/repo') - - def test_url_local_normalize_rel(self): - """verify that a local path with another env var gets expanded to an - absolute path. - - """ - field = 'test' - url = '/this/is/a/long/../path/to/a/repo' - received = expand_local_url(url, field) - print(received) - self.assertEqual(received, '/this/is/a/path/to/a/repo') - - -if __name__ == '__main__': - unittest.main() From 0f7d429f0071995504ef41a91215724c957e2fb6 Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Mon, 27 May 2024 17:40:56 -0600 Subject: [PATCH 201/408] add submodules --- .gitignore | 11 ----------- .gitmodules | 39 +++++++++++++++++++++++++++++++++++++++ ccs_config | 1 + cime | 1 + components/cdeps | 1 + components/cism | 1 + components/cmeps | 1 + components/mizuRoute | 1 + components/mosart | 1 + components/rtm | 1 + doc/doc-builder | 1 + libraries/mct | 1 + libraries/parallelio | 1 + share | 1 + src/fates | 1 + 15 files changed, 52 insertions(+), 11 deletions(-) create mode 100644 .gitmodules create mode 160000 ccs_config create mode 160000 cime create mode 160000 components/cdeps create mode 160000 components/cism create mode 160000 components/cmeps create mode 160000 components/mizuRoute create mode 160000 components/mosart create mode 160000 components/rtm create mode 160000 doc/doc-builder create mode 160000 libraries/mct create mode 160000 libraries/parallelio create mode 160000 share create mode 160000 src/fates diff --git a/.gitignore b/.gitignore index 163bfeda2d..a083a7853f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,14 +1,3 @@ -# directories checked out by manage_externals, and other files created -# by manage_externals -manage_externals.log -ccs_config -/src/fates/ -/cime/ -/components/ -/libraries/ -/share/ -/doc/doc-builder/ - # ignore svn directories **/.svn/** .svn/ diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000000..329ed2e748 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,39 @@ +[submodule "fates"] + path = src/fates + url = https://github.com/NGEET/fates +[submodule "cism"] + path = components/cism + url = https://github.com/ESCOMP/CISM-wrapper +[submodule "mosart"] + path = components/mosart + url = https://github.com/ESCOMP/MOSART +[submodule "rtm"] + path = components/rtm + url = https://github.com/ESCOMP/RTM +[submodule "mizuRoute"] + path = components/mizuRoute + url = https://github.com/ESCOMP/mizuRoute +[submodule "ccs_config"] + path = ccs_config + url = https://github.com/ESMCI/ccs_config_cesm.git +[submodule "cime"] + path = cime + url = https://github.com/ESMCI/cime +[submodule "cmeps"] + path = components/cmeps + url = https://github.com/ESCOMP/CMEPS.git +[submodule "cdeps"] + path = components/cdeps + url = https://github.com/ESCOMP/CDEPS.git +[submodule "share"] + path = share + url = https://github.com/ESCOMP/CESM_share +[submodule "mct"] + path = libraries/mct + url = https://github.com/MCSclimate/MCT +[submodule "parallelio"] + path = libraries/parallelio + url = https://github.com/NCAR/ParallelIO +[submodule "doc-builder"] + path = doc/doc-builder + url = https://github.com/ESMCI/doc-builder diff --git a/ccs_config b/ccs_config new file mode 160000 index 0000000000..f90e10502c --- /dev/null +++ b/ccs_config @@ -0,0 +1 @@ +Subproject commit f90e10502c7246c2b45e373b7dd5e0da6cba0828 diff --git a/cime b/cime new file mode 160000 index 0000000000..422ddaa770 --- /dev/null +++ b/cime @@ -0,0 +1 @@ +Subproject commit 422ddaa770a3cea6e83a60c9700ebce77acaceed diff --git a/components/cdeps b/components/cdeps new file mode 160000 index 0000000000..7a522c828c --- /dev/null +++ b/components/cdeps @@ -0,0 +1 @@ +Subproject commit 7a522c828c32dc35777992653f281ec525509c4a diff --git a/components/cism b/components/cism new file mode 160000 index 0000000000..c05dd5c4fc --- /dev/null +++ b/components/cism @@ -0,0 +1 @@ +Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928 diff --git a/components/cmeps b/components/cmeps new file mode 160000 index 0000000000..6384ff4e4a --- /dev/null +++ b/components/cmeps @@ -0,0 +1 @@ +Subproject commit 6384ff4e4a6bc82a678f9419a43ffbd5d53ac209 diff --git a/components/mizuRoute b/components/mizuRoute new file mode 160000 index 0000000000..0a62ee6185 --- /dev/null +++ b/components/mizuRoute @@ -0,0 +1 @@ +Subproject commit 0a62ee6185bdc9b99cd88ed5f15ea850602c43a2 diff --git a/components/mosart b/components/mosart new file mode 160000 index 0000000000..1c22a8c547 --- /dev/null +++ b/components/mosart @@ -0,0 +1 @@ +Subproject commit 1c22a8c5478b714cf5b7c54b3e5cf7bad09fd9b2 diff --git a/components/rtm b/components/rtm new file mode 160000 index 0000000000..88503adbc2 --- /dev/null +++ b/components/rtm @@ -0,0 +1 @@ +Subproject commit 88503adbc275fb2ccbb6b598e460deaeb140e515 diff --git a/doc/doc-builder b/doc/doc-builder new file mode 160000 index 0000000000..ab9bc93dd0 --- /dev/null +++ b/doc/doc-builder @@ -0,0 +1 @@ +Subproject commit ab9bc93dd09d0173f8097c7a18c7d061c1cd3b79 diff --git a/libraries/mct b/libraries/mct new file mode 160000 index 0000000000..e36024c5dd --- /dev/null +++ b/libraries/mct @@ -0,0 +1 @@ +Subproject commit e36024c5ddf482625ae6bd9474eff7d8f393f87c diff --git a/libraries/parallelio b/libraries/parallelio new file mode 160000 index 0000000000..6539ef05ae --- /dev/null +++ b/libraries/parallelio @@ -0,0 +1 @@ +Subproject commit 6539ef05ae7584ec570a56fdab9f7dfb336c2b80 diff --git a/share b/share new file mode 160000 index 0000000000..4b9dc4871a --- /dev/null +++ b/share @@ -0,0 +1 @@ +Subproject commit 4b9dc4871a259f00f35bb47708d876cb7dcdf75c diff --git a/src/fates b/src/fates new file mode 160000 index 0000000000..f0185f7c70 --- /dev/null +++ b/src/fates @@ -0,0 +1 @@ +Subproject commit f0185f7c7033fa69c80d1ddb07cbcbf1f8be1adc From aa544736634b4e095b691c2d5168dbd3c8de9cef Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Mon, 27 May 2024 17:43:00 -0600 Subject: [PATCH 202/408] update submodules --- .gitmodules | 105 ++- .../git-fleximod/.github/workflows/pre-commit | 13 + .../.github/workflows/pytest.yaml | 77 ++ .lib/git-fleximod/.pre-commit-config.yaml | 18 + .lib/git-fleximod/License | 20 + .lib/git-fleximod/README.md | 110 +++ .lib/git-fleximod/doc/Makefile | 20 + .lib/git-fleximod/doc/conf.py | 26 + .lib/git-fleximod/doc/index.rst | 24 + .lib/git-fleximod/doc/make.bat | 35 + .lib/git-fleximod/escomp_install | 25 + .lib/git-fleximod/git_fleximod/__init__.py | 0 .lib/git-fleximod/git_fleximod/cli.py | 119 +++ .../git-fleximod/git_fleximod/git_fleximod.py | 601 +++++++++++++++ .../git-fleximod/git_fleximod/gitinterface.py | 79 ++ .lib/git-fleximod/git_fleximod/gitmodules.py | 97 +++ .../git-fleximod/git_fleximod/lstripreader.py | 43 ++ .lib/git-fleximod/git_fleximod/metoflexi.py | 236 ++++++ .lib/git-fleximod/git_fleximod/utils.py | 365 +++++++++ .lib/git-fleximod/poetry.lock | 693 ++++++++++++++++++ .lib/git-fleximod/pyproject.toml | 41 ++ .lib/git-fleximod/tbump.toml | 43 ++ .lib/git-fleximod/tests/__init__.py | 3 + .lib/git-fleximod/tests/conftest.py | 138 ++++ .lib/git-fleximod/tests/test_a_import.py | 8 + .lib/git-fleximod/tests/test_b_update.py | 26 + .lib/git-fleximod/tests/test_c_required.py | 30 + .lib/git-fleximod/tests/test_d_complex.py | 67 ++ bin/git-fleximod | 8 + ccs_config | 2 +- components/cdeps | 2 +- components/mizuRoute | 2 +- components/mosart | 2 +- libraries/mct | 2 +- libraries/parallelio | 2 +- src/fates | 2 +- 36 files changed, 3050 insertions(+), 34 deletions(-) create mode 100644 .lib/git-fleximod/.github/workflows/pre-commit create mode 100644 .lib/git-fleximod/.github/workflows/pytest.yaml create mode 100644 .lib/git-fleximod/.pre-commit-config.yaml create mode 100644 .lib/git-fleximod/License create mode 100644 .lib/git-fleximod/README.md create mode 100644 .lib/git-fleximod/doc/Makefile create mode 100644 .lib/git-fleximod/doc/conf.py create mode 100644 .lib/git-fleximod/doc/index.rst create mode 100644 .lib/git-fleximod/doc/make.bat create mode 100644 .lib/git-fleximod/escomp_install create mode 100644 .lib/git-fleximod/git_fleximod/__init__.py create mode 100644 .lib/git-fleximod/git_fleximod/cli.py create mode 100755 .lib/git-fleximod/git_fleximod/git_fleximod.py create mode 100644 .lib/git-fleximod/git_fleximod/gitinterface.py create mode 100644 .lib/git-fleximod/git_fleximod/gitmodules.py create mode 100644 .lib/git-fleximod/git_fleximod/lstripreader.py create mode 100755 .lib/git-fleximod/git_fleximod/metoflexi.py create mode 100644 .lib/git-fleximod/git_fleximod/utils.py create mode 100644 .lib/git-fleximod/poetry.lock create mode 100644 .lib/git-fleximod/pyproject.toml create mode 100644 .lib/git-fleximod/tbump.toml create mode 100644 .lib/git-fleximod/tests/__init__.py create mode 100644 .lib/git-fleximod/tests/conftest.py create mode 100644 .lib/git-fleximod/tests/test_a_import.py create mode 100644 .lib/git-fleximod/tests/test_b_update.py create mode 100644 .lib/git-fleximod/tests/test_c_required.py create mode 100644 .lib/git-fleximod/tests/test_d_complex.py create mode 100755 bin/git-fleximod diff --git a/.gitmodules b/.gitmodules index 329ed2e748..699ad22969 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,39 +1,90 @@ [submodule "fates"] - path = src/fates - url = https://github.com/NGEET/fates +path = src/fates +url = https://github.com/NGEET/fates +fxtag = sci.1.73.0_api.35.0.0 +fxrequired = AlwaysRequired +fxDONOTUSEurl = https://github.com/NCAR/fates-release + [submodule "cism"] - path = components/cism - url = https://github.com/ESCOMP/CISM-wrapper -[submodule "mosart"] - path = components/mosart - url = https://github.com/ESCOMP/MOSART +path = components/cism +url = https://github.com/ESCOMP/CISM-wrapper +fxtag = cismwrap_2_2_001 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper + [submodule "rtm"] - path = components/rtm - url = https://github.com/ESCOMP/RTM +path = components/rtm +url = https://github.com/ESCOMP/RTM +fxtag = rtm1_0_79 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESCOMP/RTM + +[submodule "mosart"] +path = components/mosart +url = https://github.com/ESCOMP/MOSART +fxtag = mosart1_0_49 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESCOMP/MOSART + [submodule "mizuRoute"] - path = components/mizuRoute - url = https://github.com/ESCOMP/mizuRoute +path = components/mizuRoute +url = https://github.com/ESCOMP/mizuRoute +fxtag = cesm-coupling.n02_v2.1.2 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute + [submodule "ccs_config"] - path = ccs_config - url = https://github.com/ESMCI/ccs_config_cesm.git +path = ccs_config +url = https://github.com/ESMCI/ccs_config_cesm.git +fxtag = ccs_config_cesm0.0.106 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git + [submodule "cime"] - path = cime - url = https://github.com/ESMCI/cime +path = cime +url = https://github.com/ESMCI/cime +fxtag = cime6.0.246 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESMCI/cime + [submodule "cmeps"] - path = components/cmeps - url = https://github.com/ESCOMP/CMEPS.git +path = components/cmeps +url = https://github.com/ESCOMP/CMEPS.git +fxtag = cmeps0.14.63 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git + [submodule "cdeps"] - path = components/cdeps - url = https://github.com/ESCOMP/CDEPS.git +path = components/cdeps +url = https://github.com/ESCOMP/CDEPS.git +fxtag = cdeps1.0.34 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git + [submodule "share"] - path = share - url = https://github.com/ESCOMP/CESM_share +path = share +url = https://github.com/ESCOMP/CESM_share +fxtag = share1.0.19 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share + [submodule "mct"] - path = libraries/mct - url = https://github.com/MCSclimate/MCT +path = libraries/mct +url = https://github.com/MCSclimate/MCT +fxtag = MCT_2.11.0 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/MCSclimate/MCT + [submodule "parallelio"] - path = libraries/parallelio - url = https://github.com/NCAR/ParallelIO +path = libraries/parallelio +url = https://github.com/NCAR/ParallelIO +fxtag = pio2_6_2 +fxrequired = ToplevelRequired +fxDONOTUSEurl = https://github.com/NCAR/ParallelIO + [submodule "doc-builder"] - path = doc/doc-builder - url = https://github.com/ESMCI/doc-builder +path = doc/doc-builder +url = https://github.com/ESMCI/doc-builder +fxtag = v1.0.8 +fxrequired = ToplevelOptional +fxDONOTUSEurl = https://github.com/ESMCI/doc-builder diff --git a/.lib/git-fleximod/.github/workflows/pre-commit b/.lib/git-fleximod/.github/workflows/pre-commit new file mode 100644 index 0000000000..1a6ad0082a --- /dev/null +++ b/.lib/git-fleximod/.github/workflows/pre-commit @@ -0,0 +1,13 @@ +name: pre-commit +on: + pull_request: + push: + branches: [main] + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v3 + - uses: pre-commit/action@v3.0.0 diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml new file mode 100644 index 0000000000..0868dd9a33 --- /dev/null +++ b/.lib/git-fleximod/.github/workflows/pytest.yaml @@ -0,0 +1,77 @@ +# Run this job on pushes to `main`, and for pull requests. If you don't specify +# `branches: [main], then this actions runs _twice_ on pull requests, which is +# annoying. + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and + # reference the matrixe python version here. + - uses: actions/setup-python@v5 + with: + python-version: '3.9' + + # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow + # from installing Poetry every time, which can be slow. Note the use of the Poetry version + # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache + # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be + # mildly cleaner by using an environment variable, but I don't really care. + - name: cache poetry install + uses: actions/cache@v4 + with: + path: ~/.local + key: poetry-1.7.1 + + # Install Poetry. You could do this manually, or there are several actions that do this. + # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to + # Poetry's default install script, which feels correct. I pin the Poetry version here + # because Poetry does occasionally change APIs between versions and I don't want my + # actions to break if it does. + # + # The key configuration value here is `virtualenvs-in-project: true`: this creates the + # venv as a `.venv` in your testing directory, which allows the next step to easily + # cache it. + - uses: snok/install-poetry@v1 + with: + version: 1.7.1 + virtualenvs-create: true + virtualenvs-in-project: true + + # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache + # key: if you're using multiple Python versions, or multiple OSes, you'd need to include + # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock. + - name: cache deps + id: cache-deps + uses: actions/cache@v4 + with: + path: .venv + key: pydeps-${{ hashFiles('**/poetry.lock') }} + + # Install dependencies. `--no-root` means "install all dependencies but not the project + # itself", which is what you want to avoid caching _your_ code. The `if` statement + # ensures this only runs on a cache miss. + - run: poetry install --no-interaction --no-root + if: steps.cache-deps.outputs.cache-hit != 'true' + + # Now install _your_ project. This isn't necessary for many types of projects -- particularly + # things like Django apps don't need this. But it's a good idea since it fully-exercises the + # pyproject.toml and makes that if you add things like console-scripts at some point that + # they'll be installed and working. + - run: poetry install --no-interaction + + # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml` + # so this line is super-simple. But it could be as complex as you need. + - run: | + git config --global user.name "${GITHUB_ACTOR}" + git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com" + poetry run pytest + diff --git a/.lib/git-fleximod/.pre-commit-config.yaml b/.lib/git-fleximod/.pre-commit-config.yaml new file mode 100644 index 0000000000..2f6089da72 --- /dev/null +++ b/.lib/git-fleximod/.pre-commit-config.yaml @@ -0,0 +1,18 @@ +exclude: ^utils/.*$ + +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.0.1 + hooks: + - id: end-of-file-fixer + - id: trailing-whitespace + - repo: https://github.com/psf/black + rev: 22.3.0 + hooks: + - id: black + - repo: https://github.com/PyCQA/pylint + rev: v2.11.1 + hooks: + - id: pylint + args: + - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member diff --git a/.lib/git-fleximod/License b/.lib/git-fleximod/License new file mode 100644 index 0000000000..2c6fe768c2 --- /dev/null +++ b/.lib/git-fleximod/License @@ -0,0 +1,20 @@ +Copyright 2024 National Center for Atmospheric Sciences (NCAR) + +Permission is hereby granted, free of charge, to any person obtaining +a copy of this software and associated documentation files (the +“Softwareâ€), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED “AS ISâ€, WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE +LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/.lib/git-fleximod/README.md b/.lib/git-fleximod/README.md new file mode 100644 index 0000000000..d1ef632f28 --- /dev/null +++ b/.lib/git-fleximod/README.md @@ -0,0 +1,110 @@ +# git-fleximod + +Flexible, Enhanced Submodule Management for Git + +## Overview + +Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way. + +## Installation + +#TODO Install using pip: +# pip install git-fleximod + If you choose to locate git-fleximod in your path you can access it via command: git fleximod + +## Usage + + Basic Usage: + git fleximod [options] + Available Commands: + status: Display the status of submodules. + update: Update submodules to the tag indicated in .gitmodules variable fxtag. + test: Make sure that fxtags and submodule hashes are consistant, + make sure that official urls (as defined by fxDONOTUSEurl) are set + make sure that fxtags are defined for all submodules + Additional Options: + See git fleximod --help for more details. + +## Supported .gitmodules Variables + + fxtag: Specify a specific tag or branch to checkout for a submodule. + fxrequired: Mark a submodule's checkout behavior, with allowed values: + - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module). + - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module). + - AlwaysRequired: Always required (always checked out). + - AlwaysOptional: Always optional (checked out with --optional flag). + fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths. + fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks + **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be + changed by users. Use the url variable to change to a fork if desired. + +## Sparse Checkouts + + To enable sparse checkout for a submodule, set the fxsparse variable + in the .gitmodules file to the path of a file containing the desired + sparse checkout paths. Git-fleximod will automatically configure + sparse checkout based on this file when applicable commands are run. + See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set) + for details on the format of this file. + +## Tests + + The git fleximod test action is designed to be used by, for example, github workflows + to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags + +## Examples + +Here are some common usage examples: + +Update all submodules, including optional ones: +```bash + git fleximod update --optional +``` + +Updating a specific submodule to the fxtag indicated in .gitmodules: + +```bash + git fleximod update submodule-name +``` +Example .gitmodules entry: +```ini, toml + [submodule "cosp2"] + path = src/physics/cosp2/src + url = https://github.com/CFMIP/COSPv2.0 + fxsparse = ../.cosp_sparse_checkout + fxrequired = AlwaysRequired + fxtag = v2.1.4cesm +``` +Explanation: + +This entry indicates that the submodule named cosp2 at tag v2.1.4cesm +should be checked out into the directory src/physics/cosp2/src +relative to the .gitmodules directory. It should be checked out from +the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as +described in the file ../.cosp_sparse_checkout relative to the path +directory. It should be checked out anytime this .gitmodules entry is +read. + +Additional example: +```ini, toml + [submodule "cime"] + path = cime + url = https://github.com/jedwards4b/cime + fxrequired = ToplevelRequired + fxtag = cime6.0.198_rme01 +``` + +Explanation: + +This entry indicates that the submodule cime should be checked out +into a directory named cime at tag cime6.0.198_rme01 from the URL +https://github.com/jedwards4b/cime. This should only be done if +the .gitmodules file is at the top level of the repository clone. + +## Contributing + +We welcome contributions! Please see the CONTRIBUTING.md file for guidelines. + +## License + +Git-fleximod is released under the MIT License. diff --git a/.lib/git-fleximod/doc/Makefile b/.lib/git-fleximod/doc/Makefile new file mode 100644 index 0000000000..d4bb2cbb9e --- /dev/null +++ b/.lib/git-fleximod/doc/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/.lib/git-fleximod/doc/conf.py b/.lib/git-fleximod/doc/conf.py new file mode 100644 index 0000000000..423099eec9 --- /dev/null +++ b/.lib/git-fleximod/doc/conf.py @@ -0,0 +1,26 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = "git-fleximod" +author = "Jim Edwards " +release = "0.4.0" + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = ["sphinx_argparse_cli"] + +templates_path = ["_templates"] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = "alabaster" +html_static_path = ["_static"] diff --git a/.lib/git-fleximod/doc/index.rst b/.lib/git-fleximod/doc/index.rst new file mode 100644 index 0000000000..0f9c1a7f7e --- /dev/null +++ b/.lib/git-fleximod/doc/index.rst @@ -0,0 +1,24 @@ +.. git-fleximod documentation master file, created by + sphinx-quickstart on Sat Feb 3 12:02:22 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to git-fleximod's documentation! +======================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: +.. module:: sphinxcontrib.autoprogram +.. sphinx_argparse_cli:: + :module: git_fleximod.cli + :func: get_parser + :prog: git-fleximod + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/.lib/git-fleximod/doc/make.bat b/.lib/git-fleximod/doc/make.bat new file mode 100644 index 0000000000..32bb24529f --- /dev/null +++ b/.lib/git-fleximod/doc/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/.lib/git-fleximod/escomp_install b/.lib/git-fleximod/escomp_install new file mode 100644 index 0000000000..ae782e72a4 --- /dev/null +++ b/.lib/git-fleximod/escomp_install @@ -0,0 +1,25 @@ +#!/usr/bin/env python +# updates git-fleximod in an ESCOMP model +# this script should be run from the model root directory, it expects +# git-fleximod to already be installed with the script in bin +# and the classes in lib/python/site-packages +import sys +import shutil +import os + +from glob import iglob + +fleximod_root = sys.argv[1] +fleximod_path = os.path.join(fleximod_root,"src","git-fleximod") +if os.path.isfile(fleximod_path): + with open(fleximod_path,"r") as f: + fleximod = f.readlines() + with open(os.path.join(".","bin","git-fleximod"),"w") as f: + for line in fleximod: + f.write(line) + if "import argparse" in line: + f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n') + + for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")): + shutil.copy(file, + os.path.join("lib","python","site-packages","fleximod",os.path.basename(file))) diff --git a/.lib/git-fleximod/git_fleximod/__init__.py b/.lib/git-fleximod/git_fleximod/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py new file mode 100644 index 0000000000..1fb959dad0 --- /dev/null +++ b/.lib/git-fleximod/git_fleximod/cli.py @@ -0,0 +1,119 @@ +from pathlib import Path +import argparse + +__version__ = "0.7.4" + +def find_root_dir(filename=".git"): + d = Path.cwd() + root = Path(d.root) + while d != root: + attempt = d / filename + if attempt.is_dir(): + return attempt + d = d.parent + return None + + +def get_parser(): + description = """ + %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models + """ + parser = argparse.ArgumentParser( + description=description, formatter_class=argparse.RawDescriptionHelpFormatter + ) + + # + # user options + # + choices = ["update", "status", "test"] + parser.add_argument( + "action", + choices=choices, + default="update", + help=f"Subcommand of git-fleximod, choices are {choices[:-1]}", + ) + + parser.add_argument( + "components", + nargs="*", + help="Specific component(s) to checkout. By default, " + "all required submodules are checked out.", + ) + + parser.add_argument( + "-C", + "--path", + default=find_root_dir(), + help="Toplevel repository directory. Defaults to top git directory relative to current.", + ) + + parser.add_argument( + "-g", + "--gitmodules", + nargs="?", + default=".gitmodules", + help="The submodule description filename. " "Default: %(default)s.", + ) + + parser.add_argument( + "-x", + "--exclude", + nargs="*", + help="Component(s) listed in the gitmodules file which should be ignored.", + ) + parser.add_argument( + "-f", + "--force", + action="store_true", + default=False, + help="Override cautions and update or checkout over locally modified repository.", + ) + + parser.add_argument( + "-o", + "--optional", + action="store_true", + default=False, + help="By default only the required submodules " + "are checked out. This flag will also checkout the " + "optional submodules relative to the toplevel directory.", + ) + + parser.add_argument( + "-v", + "--verbose", + action="count", + default=0, + help="Output additional information to " + "the screen and log file. This flag can be " + "used up to two times, increasing the " + "verbosity level each time.", + ) + + parser.add_argument( + "-V", + "--version", + action="version", + version=f"%(prog)s {__version__}", + help="Print version and exit.", + ) + + # + # developer options + # + parser.add_argument( + "--backtrace", + action="store_true", + help="DEVELOPER: show exception backtraces as extra " "debugging output", + ) + + parser.add_argument( + "-d", + "--debug", + action="store_true", + default=False, + help="DEVELOPER: output additional debugging " + "information to the screen and log file.", + ) + + return parser diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py new file mode 100755 index 0000000000..103cc82a50 --- /dev/null +++ b/.lib/git-fleximod/git_fleximod/git_fleximod.py @@ -0,0 +1,601 @@ +#!/usr/bin/env python +import sys + +MIN_PYTHON = (3, 7) +if sys.version_info < MIN_PYTHON: + sys.exit("Python %s.%s or later is required." % MIN_PYTHON) + +import os +import shutil +import logging +import textwrap +from git_fleximod import utils +from git_fleximod import cli +from git_fleximod.gitinterface import GitInterface +from git_fleximod.gitmodules import GitModules +from configparser import NoOptionError + +# logger variable is global +logger = None + + +def fxrequired_allowed_values(): + return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"] + + +def commandline_arguments(args=None): + parser = cli.get_parser() + + if args: + options = parser.parse_args(args) + else: + options = parser.parse_args() + + # explicitly listing a component overrides the optional flag + if options.optional or options.components: + fxrequired = [ + "ToplevelRequired", + "ToplevelOptional", + "AlwaysRequired", + "AlwaysOptional", + ] + else: + fxrequired = ["ToplevelRequired", "AlwaysRequired"] + + action = options.action + if not action: + action = "update" + handlers = [logging.StreamHandler()] + + if options.debug: + try: + open("fleximod.log", "w") + except PermissionError: + sys.exit("ABORT: Could not write file fleximod.log") + level = logging.DEBUG + handlers.append(logging.FileHandler("fleximod.log")) + elif options.verbose: + level = logging.INFO + else: + level = logging.WARNING + # Configure the root logger + logging.basicConfig( + level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers + ) + + if hasattr(options, "version"): + exit() + + return ( + options.path, + options.gitmodules, + fxrequired, + options.components, + options.exclude, + options.force, + action, + ) + + +def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"): + """ + This function performs a sparse checkout of a git submodule. It does so by first creating the .git/info/sparse-checkout fileq + in the submodule and then checking out the desired tag. If the submodule is already checked out, it will not be checked out again. + Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed. This is important + because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time + and disk space consuming. + + Parameters: + root_dir (str): The root directory for the git operation. + name (str): The name of the submodule. + url (str): The URL of the submodule. + path (str): The path to the submodule. + sparsefile (str): The sparse file for the submodule. + tag (str, optional): The tag to checkout. Defaults to "master". + + Returns: + None + """ + logger.info("Called sparse_checkout for {}".format(name)) + rgit = GitInterface(root_dir, logger) + superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree") + if superroot: + gitroot = superroot.strip() + else: + gitroot = root_dir.strip() + assert os.path.isdir(os.path.join(gitroot, ".git")) + # first create the module directory + if not os.path.isdir(os.path.join(root_dir, path)): + os.makedirs(os.path.join(root_dir, path)) + + # initialize a new git repo and set the sparse checkout flag + sprep_repo = os.path.join(root_dir, path) + sprepo_git = GitInterface(sprep_repo, logger) + if os.path.exists(os.path.join(sprep_repo, ".git")): + try: + logger.info("Submodule {} found".format(name)) + chk = sprepo_git.config_get_value("core", "sparseCheckout") + if chk == "true": + logger.info("Sparse submodule {} already checked out".format(name)) + return + except NoOptionError: + logger.debug("Sparse submodule {} not present".format(name)) + except Exception as e: + utils.fatal_error("Unexpected error {} occured.".format(e)) + + sprepo_git.config_set_value("core", "sparseCheckout", "true") + + # set the repository remote + + logger.info("Setting remote origin in {}/{}".format(root_dir, path)) + status = sprepo_git.git_operation("remote", "-v") + if url not in status: + sprepo_git.git_operation("remote", "add", "origin", url) + + topgit = os.path.join(gitroot, ".git") + + if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")): + with open(os.path.join(root_dir, ".git")) as f: + gitpath = os.path.relpath( + os.path.join(root_dir, f.read().split()[1]), + start=os.path.join(root_dir, path), + ) + topgit = os.path.join(gitpath, "modules") + else: + topgit = os.path.relpath( + os.path.join(root_dir, ".git", "modules"), + start=os.path.join(root_dir, path), + ) + + with utils.pushd(sprep_repo): + if not os.path.isdir(topgit): + os.makedirs(topgit) + topgit += os.sep + name + + if os.path.isdir(os.path.join(root_dir, path, ".git")): + with utils.pushd(sprep_repo): + shutil.move(".git", topgit) + with open(".git", "w") as f: + f.write("gitdir: " + os.path.relpath(topgit)) + # assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo))) + gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout")) + if os.path.isfile(gitsparse): + logger.warning( + "submodule {} is already initialized {}".format(name, topgit) + ) + return + + with utils.pushd(sprep_repo): + shutil.copy(sparsefile, gitsparse) + + # Finally checkout the repo + sprepo_git.git_operation("fetch", "origin", "--tags") + sprepo_git.git_operation("checkout", tag) + + print(f"Successfully checked out {name:>20} at {tag}") + rgit.config_set_value(f'submodule "{name}"', "active", "true") + rgit.config_set_value(f'submodule "{name}"', "url", url) + + +def single_submodule_checkout( + root, name, path, url=None, tag=None, force=False, optional=False +): + """ + This function checks out a single git submodule. + + Parameters: + root (str): The root directory for the git operation. + name (str): The name of the submodule. + path (str): The path to the submodule. + url (str, optional): The URL of the submodule. Defaults to None. + tag (str, optional): The tag to checkout. Defaults to None. + force (bool, optional): If set to True, forces the checkout operation. Defaults to False. + optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False. + + Returns: + None + """ + # function implementation... + git = GitInterface(root, logger) + repodir = os.path.join(root, path) + logger.info("Checkout {} into {}/{}".format(name, root, path)) + # if url is provided update to the new url + tmpurl = None + repo_exists = False + if os.path.exists(os.path.join(repodir, ".git")): + logger.info("Submodule {} already checked out".format(name)) + repo_exists = True + # Look for a .gitmodules file in the newly checkedout repo + if not repo_exists and url: + # ssh urls cause problems for those who dont have git accounts with ssh keys defined + # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was + # opened with a GitModules object we don't need to worry about restoring the file here + # it will be done by the GitModules class + if url.startswith("git@"): + tmpurl = url + url = url.replace("git@github.com:", "https://github.com/") + git.git_operation("clone", url, path) + smgit = GitInterface(repodir, logger) + if not tag: + tag = smgit.git_operation("describe", "--tags", "--always").rstrip() + smgit.git_operation("checkout", tag) + # Now need to move the .git dir to the submodule location + rootdotgit = os.path.join(root, ".git") + if os.path.isfile(rootdotgit): + with open(rootdotgit) as f: + line = f.readline() + if line.startswith("gitdir: "): + rootdotgit = line[8:].rstrip() + + newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name)) + if os.path.exists(newpath): + shutil.rmtree(os.path.join(repodir, ".git")) + else: + shutil.move(os.path.join(repodir, ".git"), newpath) + + with open(os.path.join(repodir, ".git"), "w") as f: + f.write("gitdir: " + os.path.relpath(newpath, start=repodir)) + + if not os.path.exists(repodir): + parent = os.path.dirname(repodir) + if not os.path.isdir(parent): + os.makedirs(parent) + git.git_operation("submodule", "add", "--name", name, "--", url, path) + + if not repo_exists or not tmpurl: + git.git_operation("submodule", "update", "--init", "--", path) + + if os.path.exists(os.path.join(repodir, ".gitmodules")): + # recursively handle this checkout + print(f"Recursively checking out submodules of {name}") + gitmodules = GitModules(logger, confpath=repodir) + requiredlist = ["AlwaysRequired"] + if optional: + requiredlist.append("AlwaysOptional") + submodules_checkout(gitmodules, repodir, requiredlist, force=force) + if not os.path.exists(os.path.join(repodir, ".git")): + utils.fatal_error( + f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}" + ) + + if tmpurl: + print(git.git_operation("restore", ".gitmodules")) + + return + + +def submodules_status(gitmodules, root_dir, toplevel=False): + testfails = 0 + localmods = 0 + needsupdate = 0 + for name in gitmodules.sections(): + path = gitmodules.get(name, "path") + tag = gitmodules.get(name, "fxtag") + required = gitmodules.get(name, "fxrequired") + level = required and "Toplevel" in required + if not path: + utils.fatal_error("No path found in .gitmodules for {}".format(name)) + newpath = os.path.join(root_dir, path) + logger.debug("newpath is {}".format(newpath)) + if not os.path.exists(os.path.join(newpath, ".git")): + rootgit = GitInterface(root_dir, logger) + # submodule commands use path, not name + url = gitmodules.get(name, "url") + url = url.replace("git@github.com:", "https://github.com/") + tags = rootgit.git_operation("ls-remote", "--tags", url) + atag = None + needsupdate += 1 + if not toplevel and level: + continue + for htag in tags.split("\n"): + if tag and tag in htag: + atag = (htag.split()[1])[10:] + break + if tag and tag == atag: + print(f"e {name:>20} not checked out, aligned at tag {tag}") + elif tag: + ahash = rootgit.git_operation( + "submodule", "status", "{}".format(path) + ).rstrip() + ahash = ahash[1 : len(tag) + 1] + if tag == ahash: + print(f"e {name:>20} not checked out, aligned at hash {ahash}") + else: + print( + f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}" + ) + testfails += 1 + else: + print(f"e {name:>20} has no fxtag defined in .gitmodules") + testfails += 1 + else: + with utils.pushd(newpath): + git = GitInterface(newpath, logger) + atag = git.git_operation("describe", "--tags", "--always").rstrip() + ahash = git.git_operation("status").partition("\n")[0].split()[-1] + if tag and atag == tag: + print(f" {name:>20} at tag {tag}") + elif tag and ahash[: len(tag)] == tag: + print(f" {name:>20} at hash {ahash}") + elif atag == ahash: + print(f" {name:>20} at hash {ahash}") + elif tag: + print( + f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}" + ) + testfails += 1 + needsupdate += 1 + else: + print( + f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}" + ) + testfails += 1 + + status = git.git_operation("status", "--ignore-submodules") + if "nothing to commit" not in status: + localmods = localmods + 1 + print("M" + textwrap.indent(status, " ")) + + return testfails, localmods, needsupdate + + +def submodules_update(gitmodules, root_dir, requiredlist, force): + _, localmods, needsupdate = submodules_status(gitmodules, root_dir) + + if localmods and not force: + local_mods_output() + return + if needsupdate == 0: + return + + for name in gitmodules.sections(): + fxtag = gitmodules.get(name, "fxtag") + path = gitmodules.get(name, "path") + url = gitmodules.get(name, "url") + logger.info( + "name={} path={} url={} fxtag={} requiredlist={}".format( + name, os.path.join(root_dir, path), url, fxtag, requiredlist + ) + ) + # if not os.path.exists(os.path.join(root_dir,path, ".git")): + fxrequired = gitmodules.get(name, "fxrequired") + assert fxrequired in fxrequired_allowed_values() + rgit = GitInterface(root_dir, logger) + superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree") + + fxsparse = gitmodules.get(name, "fxsparse") + + if ( + fxrequired + and (superroot and "Toplevel" in fxrequired) + or fxrequired not in requiredlist + ): + if "ToplevelOptional" == fxrequired: + print("Skipping optional component {}".format(name)) + continue + if fxsparse: + logger.debug( + "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format( + root_dir, name, url, path, fxsparse, fxtag + ) + ) + submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag) + else: + logger.info( + "Calling submodule_checkout({},{},{},{})".format( + root_dir, name, path, url + ) + ) + + single_submodule_checkout( + root_dir, + name, + path, + url=url, + tag=fxtag, + force=force, + optional=("AlwaysOptional" in requiredlist), + ) + + if os.path.exists(os.path.join(path, ".git")): + submoddir = os.path.join(root_dir, path) + with utils.pushd(submoddir): + git = GitInterface(submoddir, logger) + # first make sure the url is correct + upstream = git.git_operation("ls-remote", "--get-url").rstrip() + newremote = "origin" + if upstream != url: + # TODO - this needs to be a unique name + remotes = git.git_operation("remote", "-v") + if url in remotes: + for line in remotes: + if url in line and "fetch" in line: + newremote = line.split()[0] + break + else: + i = 0 + while newremote in remotes: + i = i + 1 + newremote = f"newremote.{i:02d}" + git.git_operation("remote", "add", newremote, url) + + tags = git.git_operation("tag", "-l") + if fxtag and fxtag not in tags: + git.git_operation("fetch", newremote, "--tags") + atag = git.git_operation("describe", "--tags", "--always").rstrip() + if fxtag and fxtag != atag: + try: + git.git_operation("checkout", fxtag) + print(f"{name:>20} updated to {fxtag}") + except Exception as error: + print(error) + elif not fxtag: + print(f"No fxtag found for submodule {name:>20}") + else: + print(f"{name:>20} up to date.") + + +def local_mods_output(): + text = """\ + The submodules labeled with 'M' above are not in a clean state. + The following are options for how to proceed: + (1) Go into each submodule which is not in a clean state and issue a 'git status' + Either revert or commit your changes so that the submodule is in a clean state. + (2) use the --force option to git-fleximod + (3) you can name the particular submodules to update using the git-fleximod command line + (4) As a last resort you can remove the submodule (via 'rm -fr [directory]') + then rerun git-fleximod update. +""" + print(text) + + +# checkout is done by update if required so this function may be depricated +def submodules_checkout(gitmodules, root_dir, requiredlist, force=False): + """ + This function checks out all git submodules based on the provided parameters. + + Parameters: + gitmodules (ConfigParser): The gitmodules configuration. + root_dir (str): The root directory for the git operation. + requiredlist (list): The list of required modules. + force (bool, optional): If set to True, forces the checkout operation. Defaults to False. + + Returns: + None + """ + # function implementation... + print("") + _, localmods, needsupdate = submodules_status(gitmodules, root_dir) + if localmods and not force: + local_mods_output() + return + if not needsupdate: + return + for name in gitmodules.sections(): + fxrequired = gitmodules.get(name, "fxrequired") + fxsparse = gitmodules.get(name, "fxsparse") + fxtag = gitmodules.get(name, "fxtag") + path = gitmodules.get(name, "path") + url = gitmodules.get(name, "url") + if fxrequired and fxrequired not in requiredlist: + if "Optional" in fxrequired: + print("Skipping optional component {}".format(name)) + continue + + if fxsparse: + logger.debug( + "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format( + root_dir, name, url, path, fxsparse, fxtag + ) + ) + submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag) + else: + logger.debug( + "Calling submodule_checkout({},{},{})".format(root_dir, name, path) + ) + single_submodule_checkout( + root_dir, + name, + path, + url=url, + tag=fxtag, + force=force, + optional="AlwaysOptional" in requiredlist, + ) + + +def submodules_test(gitmodules, root_dir): + """ + This function tests the git submodules based on the provided parameters. + + It first checks that fxtags are present and in sync with submodule hashes. + Then it ensures that urls are consistent with fxurls (not forks and not ssh) + and that sparse checkout files exist. + + Parameters: + gitmodules (ConfigParser): The gitmodules configuration. + root_dir (str): The root directory for the git operation. + + Returns: + int: The number of test failures. + """ + # First check that fxtags are present and in sync with submodule hashes + testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir) + print("") + # Then make sure that urls are consistant with fxurls (not forks and not ssh) + # and that sparse checkout files exist + for name in gitmodules.sections(): + url = gitmodules.get(name, "url") + fxurl = gitmodules.get(name, "fxDONOTMODIFYurl") + fxsparse = gitmodules.get(name, "fxsparse") + path = gitmodules.get(name, "path") + fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl + url = url[:-4] if url.endswith(".git") else url + if not fxurl or url.lower() != fxurl.lower(): + print(f"{name:>20} url {url} not in sync with required {fxurl}") + testfails += 1 + if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)): + print(f"{name:>20} sparse checkout file {fxsparse} not found") + testfails += 1 + return testfails + localmods + needsupdate + + +def main(): + ( + root_dir, + file_name, + fxrequired, + includelist, + excludelist, + force, + action, + ) = commandline_arguments() + # Get a logger for the package + global logger + logger = logging.getLogger(__name__) + + logger.info("action is {}".format(action)) + + if not os.path.isfile(os.path.join(root_dir, file_name)): + file_path = utils.find_upwards(root_dir, file_name) + + if file_path is None: + utils.fatal_error( + "No {} found in {} or any of it's parents".format(file_name, root_dir) + ) + + root_dir = os.path.dirname(file_path) + logger.info( + "root_dir is {} includelist={} excludelist={}".format( + root_dir, includelist, excludelist + ) + ) + gitmodules = GitModules( + logger, + confpath=root_dir, + conffile=file_name, + includelist=includelist, + excludelist=excludelist, + ) + if not gitmodules.sections(): + sys.exit("No submodule components found") + retval = 0 + if action == "update": + submodules_update(gitmodules, root_dir, fxrequired, force) + elif action == "status": + tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True) + if tfails + lmods + updates > 0: + print( + f" testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n" + ) + if lmods > 0: + local_mods_output() + elif action == "test": + retval = submodules_test(gitmodules, root_dir) + else: + utils.fatal_error(f"unrecognized action request {action}") + return retval + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py new file mode 100644 index 0000000000..93ae38ecde --- /dev/null +++ b/.lib/git-fleximod/git_fleximod/gitinterface.py @@ -0,0 +1,79 @@ +import os +import sys +from . import utils +from pathlib import Path + +class GitInterface: + def __init__(self, repo_path, logger): + logger.debug("Initialize GitInterface for {}".format(repo_path)) + if isinstance(repo_path, str): + self.repo_path = Path(repo_path).resolve() + elif isinstance(repo_path, Path): + self.repo_path = repo_path.resolve() + else: + raise TypeError("repo_path must be a str or Path object") + self.logger = logger + try: + import git + + self._use_module = True + try: + self.repo = git.Repo(str(self.repo_path)) # Initialize GitPython repo + except git.exc.InvalidGitRepositoryError: + self.git = git + self._init_git_repo() + msg = "Using GitPython interface to git" + except ImportError: + self._use_module = False + if not (self.repo_path / ".git").exists(): + self._init_git_repo() + msg = "Using shell interface to git" + self.logger.info(msg) + + def _git_command(self, operation, *args): + self.logger.info(operation) + if self._use_module and operation != "submodule": + try: + return getattr(self.repo.git, operation)(*args) + except Exception as e: + sys.exit(e) + else: + return ["git", "-C", str(self.repo_path), operation] + list(args) + + def _init_git_repo(self): + if self._use_module: + self.repo = self.git.Repo.init(str(self.repo_path)) + else: + command = ("git", "-C", str(self.repo_path), "init") + utils.execute_subprocess(command) + + # pylint: disable=unused-argument + def git_operation(self, operation, *args, **kwargs): + command = self._git_command(operation, *args) + self.logger.info(command) + if isinstance(command, list): + try: + return utils.execute_subprocess(command, output_to_caller=True) + except Exception as e: + sys.exit(e) + else: + return command + + def config_get_value(self, section, name): + if self._use_module: + config = self.repo.config_reader() + return config.get_value(section, name) + else: + cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}") + output = utils.execute_subprocess(cmd, output_to_caller=True) + return output.strip() + + def config_set_value(self, section, name, value): + if self._use_module: + with self.repo.config_writer() as writer: + writer.set_value(section, name, value) + writer.release() # Ensure changes are saved + else: + cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value) + self.logger.info(cmd) + utils.execute_subprocess(cmd, output_to_caller=True) diff --git a/.lib/git-fleximod/git_fleximod/gitmodules.py b/.lib/git-fleximod/git_fleximod/gitmodules.py new file mode 100644 index 0000000000..68c82d066f --- /dev/null +++ b/.lib/git-fleximod/git_fleximod/gitmodules.py @@ -0,0 +1,97 @@ +import shutil +from pathlib import Path +from configparser import RawConfigParser, ConfigParser +from .lstripreader import LstripReader + + +class GitModules(RawConfigParser): + def __init__( + self, + logger, + confpath=Path.cwd(), + conffile=".gitmodules", + includelist=None, + excludelist=None, + ): + """ + confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory). + conffile: Name of the configuration file (defaults to .gitmodules). + includelist: Optional list of submodules to include. + excludelist: Optional list of submodules to exclude. + """ + self.logger = logger + self.logger.debug( + "Creating a GitModules object {} {} {} {}".format( + confpath, conffile, includelist, excludelist + ) + ) + super().__init__() + self.conf_file = (Path(confpath) / Path(conffile)) + if self.conf_file.exists(): + self.read_file(LstripReader(str(self.conf_file)), source=conffile) + self.includelist = includelist + self.excludelist = excludelist + self.isdirty = False + + def reload(self): + self.clear() + if self.conf_file.exists(): + self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file) + + + def set(self, name, option, value): + """ + Sets a configuration value for a specific submodule: + Ensures the appropriate section exists for the submodule. + Calls the parent class's set method to store the value. + """ + self.isdirty = True + self.logger.debug("set called {} {} {}".format(name, option, value)) + section = f'submodule "{name}"' + if not self.has_section(section): + self.add_section(section) + super().set(section, option, str(value)) + + # pylint: disable=redefined-builtin, arguments-differ + def get(self, name, option, raw=False, vars=None, fallback=None): + """ + Retrieves a configuration value for a specific submodule: + Uses the parent class's get method to access the value. + Handles potential errors if the section or option doesn't exist. + """ + self.logger.debug("get called {} {}".format(name, option)) + section = f'submodule "{name}"' + try: + return ConfigParser.get( + self, section, option, raw=raw, vars=vars, fallback=fallback + ) + except ConfigParser.NoOptionError: + return None + + def save(self): + if self.isdirty: + self.logger.info("Writing {}".format(self.conf_file)) + with open(self.conf_file, "w") as fd: + self.write(fd) + self.isdirty = False + + def __del__(self): + self.save() + + def sections(self): + """Strip the submodule part out of section and just use the name""" + self.logger.debug("calling GitModules sections iterator") + names = [] + for section in ConfigParser.sections(self): + name = section[11:-1] + if self.includelist and name not in self.includelist: + continue + if self.excludelist and name in self.excludelist: + continue + names.append(name) + return names + + def items(self, name, raw=False, vars=None): + self.logger.debug("calling GitModules items for {}".format(name)) + section = f'submodule "{name}"' + return ConfigParser.items(section, raw=raw, vars=vars) diff --git a/.lib/git-fleximod/git_fleximod/lstripreader.py b/.lib/git-fleximod/git_fleximod/lstripreader.py new file mode 100644 index 0000000000..01d5580ee8 --- /dev/null +++ b/.lib/git-fleximod/git_fleximod/lstripreader.py @@ -0,0 +1,43 @@ +class LstripReader(object): + "LstripReader formats .gitmodules files to be acceptable for configparser" + + def __init__(self, filename): + with open(filename, "r") as infile: + lines = infile.readlines() + self._lines = list() + self._num_lines = len(lines) + self._index = 0 + for line in lines: + self._lines.append(line.lstrip()) + + def readlines(self): + """Return all the lines from this object's file""" + return self._lines + + def readline(self, size=-1): + """Format and return the next line or raise StopIteration""" + try: + line = self.next() + except StopIteration: + line = "" + + if (size > 0) and (len(line) < size): + return line[0:size] + + return line + + def __iter__(self): + """Begin an iteration""" + self._index = 0 + return self + + def next(self): + """Return the next line or raise StopIteration""" + if self._index >= self._num_lines: + raise StopIteration + + self._index = self._index + 1 + return self._lines[self._index - 1] + + def __next__(self): + return self.next() diff --git a/.lib/git-fleximod/git_fleximod/metoflexi.py b/.lib/git-fleximod/git_fleximod/metoflexi.py new file mode 100755 index 0000000000..cc347db2dd --- /dev/null +++ b/.lib/git-fleximod/git_fleximod/metoflexi.py @@ -0,0 +1,236 @@ +#!/usr/bin/env python +from configparser import ConfigParser +import sys +import shutil +from pathlib import Path +import argparse +import logging +from git_fleximod.gitinterface import GitInterface +from git_fleximod.gitmodules import GitModules +from git_fleximod import utils + +logger = None + +def find_root_dir(filename=".git"): + d = Path.cwd() + root = Path(d.root) + while d != root: + attempt = d / filename + if attempt.is_dir(): + return d + d = d.parent + return None + + +def get_parser(): + description = """ + %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models + """ + parser = argparse.ArgumentParser( + description=description, formatter_class=argparse.RawDescriptionHelpFormatter + ) + + parser.add_argument('-e', '--externals', nargs='?', + default='Externals.cfg', + help='The externals description filename. ' + 'Default: %(default)s.') + + parser.add_argument( + "-C", + "--path", + default=find_root_dir(), + help="Toplevel repository directory. Defaults to top git directory relative to current.", + ) + + parser.add_argument( + "-g", + "--gitmodules", + nargs="?", + default=".gitmodules", + help="The submodule description filename. " "Default: %(default)s.", + ) + parser.add_argument( + "-v", + "--verbose", + action="count", + default=0, + help="Output additional information to " + "the screen and log file. This flag can be " + "used up to two times, increasing the " + "verbosity level each time.", + ) + parser.add_argument( + "-d", + "--debug", + action="store_true", + default=False, + help="DEVELOPER: output additional debugging " + "information to the screen and log file.", + ) + + return parser + +def commandline_arguments(args=None): + parser = get_parser() + + options = parser.parse_args(args) + handlers = [logging.StreamHandler()] + + if options.debug: + try: + open("fleximod.log", "w") + except PermissionError: + sys.exit("ABORT: Could not write file fleximod.log") + level = logging.DEBUG + handlers.append(logging.FileHandler("fleximod.log")) + elif options.verbose: + level = logging.INFO + else: + level = logging.WARNING + # Configure the root logger + logging.basicConfig( + level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers + ) + + return( + options.path, + options.gitmodules, + options.externals + ) + +class ExternalRepoTranslator: + """ + Translates external repositories configured in an INI-style externals file. + """ + + def __init__(self, rootpath, gitmodules, externals): + self.rootpath = rootpath + if gitmodules: + self.gitmodules = GitModules(logger, confpath=rootpath) + self.externals = (rootpath / Path(externals)).resolve() + print(f"Translating {self.externals}") + self.git = GitInterface(rootpath, logger) + +# def __del__(self): +# if (self.rootpath / "save.gitignore"): + + + def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol): + """ + Translates a single repository based on configuration details. + + Args: + rootpath (str): Root path of the main repository. + gitmodules (str): Path to the .gitmodules file. + tag (str): The tag to use for the external repository. + url (str): The URL of the external repository. + path (str): The relative path within the main repository for the external repository. + efile (str): The external file or file containing submodules. + hash_ (str): The commit hash to checkout (if applicable). + sparse (str): Boolean indicating whether to use sparse checkout (if applicable). + protocol (str): The protocol to use (e.g., 'git', 'http'). + """ + assert protocol != "svn", "SVN protocol is not currently supported" + print(f"Translating repository {section}") + if efile: + file_path = Path(path) / Path(efile) + newroot = (self.rootpath / file_path).parent.resolve() + if not newroot.exists(): + newroot.mkdir(parents=True) + logger.info("Newroot is {}".format(newroot)) + newt = ExternalRepoTranslator(newroot, ".gitmodules", efile) + newt.translate_repo() + if protocol == "externals_only": + if tag: + self.gitmodules.set(section, "fxtag", tag) + if hash_: + self.gitmodules.set(section, "fxtag", hash_) + + self.gitmodules.set(section, "fxDONOTUSEurl", url) + if sparse: + self.gitmodules.set(section, "fxsparse", sparse) + self.gitmodules.set(section, "fxrequired", "ToplevelRequired") + else: + newpath = (self.rootpath / Path(path)) + if newpath.exists(): + shutil.rmtree(newpath) + logger.info("Creating directory {}".format(newpath)) + newpath.mkdir(parents=True) + if tag: + logger.info("cloning {}".format(section)) + try: + self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path) + except: + self.git.git_operation("clone", url, path) + with utils.pushd(newpath): + ngit = GitInterface(newpath, logger) + ngit.git_operation("checkout", tag) + if hash_: + self.git.git_operation("clone", url, path) + git = GitInterface(newpath, logger) + git.git_operation("fetch", "origin") + git.git_operation("checkout", hash_) + if sparse: + print("setting as sparse submodule {}".format(section)) + sparsefile = (newpath / Path(sparse)) + newfile = (newpath / ".git" / "info" / "sparse-checkout") + print(f"sparsefile {sparsefile} newfile {newfile}") + shutil.copy(sparsefile, newfile) + + logger.info("adding submodule {}".format(section)) + self.gitmodules.save() + self.git.git_operation("submodule", "add", "-f", "--name", section, url, path) + self.git.git_operation("submodule","absorbgitdirs") + self.gitmodules.reload() + if tag: + self.gitmodules.set(section, "fxtag", tag) + if hash_: + self.gitmodules.set(section, "fxtag", hash_) + + self.gitmodules.set(section, "fxDONOTUSEurl", url) + if sparse: + self.gitmodules.set(section, "fxsparse", sparse) + self.gitmodules.set(section, "fxrequired", "ToplevelRequired") + + + def translate_repo(self): + """ + Translates external repositories defined within an external file. + + Args: + rootpath (str): Root path of the main repository. + gitmodules (str): Path to the .gitmodules file. + external_file (str): The path to the external file containing repository definitions. + """ + econfig = ConfigParser() + econfig.read((self.rootpath / Path(self.externals))) + + for section in econfig.sections(): + if section == "externals_description": + logger.info("skipping section {}".format(section)) + return + logger.info("Translating section {}".format(section)) + tag = econfig.get(section, "tag", raw=False, fallback=None) + url = econfig.get(section, "repo_url", raw=False, fallback=None) + path = econfig.get(section, "local_path", raw=False, fallback=None) + efile = econfig.get(section, "externals", raw=False, fallback=None) + hash_ = econfig.get(section, "hash", raw=False, fallback=None) + sparse = econfig.get(section, "sparse", raw=False, fallback=None) + protocol = econfig.get(section, "protocol", raw=False, fallback=None) + + self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol) + + + +def _main(): + rootpath, gitmodules, externals = commandline_arguments() + global logger + logger = logging.getLogger(__name__) + with utils.pushd(rootpath): + t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals) + logger.info("Translating {}".format(rootpath)) + t.translate_repo() + + +if __name__ == "__main__": + sys.exit(_main()) diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py new file mode 100644 index 0000000000..7cc1de38cc --- /dev/null +++ b/.lib/git-fleximod/git_fleximod/utils.py @@ -0,0 +1,365 @@ +#!/usr/bin/env python3 +""" +Common public utilities for manic package + +""" + +import logging +import os +import subprocess +import sys +from threading import Timer +from pathlib import Path + +LOCAL_PATH_INDICATOR = "." +# --------------------------------------------------------------------- +# +# functions to massage text for output and other useful utilities +# +# --------------------------------------------------------------------- +from contextlib import contextmanager + + +@contextmanager +def pushd(new_dir): + """context for chdir. usage: with pushd(new_dir)""" + previous_dir = os.getcwd() + os.chdir(new_dir) + try: + yield + finally: + os.chdir(previous_dir) + + +def log_process_output(output): + """Log each line of process output at debug level so it can be + filtered if necessary. By default, output is a single string, and + logging.debug(output) will only put log info heading on the first + line. This makes it hard to filter with grep. + + """ + output = output.split("\n") + for line in output: + logging.debug(line) + + +def printlog(msg, **kwargs): + """Wrapper script around print to ensure that everything printed to + the screen also gets logged. + + """ + logging.info(msg) + if kwargs: + print(msg, **kwargs) + else: + print(msg) + sys.stdout.flush() + + +def find_upwards(root_dir, filename): + """Find a file in root dir or any of it's parents""" + d = Path(root_dir) + root = Path(d.root) + while d != root: + attempt = d / filename + if attempt.exists(): + return attempt + d = d.parent + return None + + +def last_n_lines(the_string, n_lines, truncation_message=None): + """Returns the last n lines of the given string + + Args: + the_string: str + n_lines: int + truncation_message: str, optional + + Returns a string containing the last n lines of the_string + + If truncation_message is provided, the returned string begins with + the given message if and only if the string is greater than n lines + to begin with. + """ + + lines = the_string.splitlines(True) + if len(lines) <= n_lines: + return_val = the_string + else: + lines_subset = lines[-n_lines:] + str_truncated = "".join(lines_subset) + if truncation_message: + str_truncated = truncation_message + "\n" + str_truncated + return_val = str_truncated + + return return_val + + +def indent_string(the_string, indent_level): + """Indents the given string by a given number of spaces + + Args: + the_string: str + indent_level: int + + Returns a new string that is the same as the_string, except that + each line is indented by 'indent_level' spaces. + + In python3, this can be done with textwrap.indent. + """ + + lines = the_string.splitlines(True) + padding = " " * indent_level + lines_indented = [padding + line for line in lines] + return "".join(lines_indented) + + +# --------------------------------------------------------------------- +# +# error handling +# +# --------------------------------------------------------------------- + + +def fatal_error(message): + """ + Error output function + """ + logging.error(message) + raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message)) + + +# --------------------------------------------------------------------- +# +# Data conversion / manipulation +# +# --------------------------------------------------------------------- +def str_to_bool(bool_str): + """Convert a sting representation of as boolean into a true boolean. + + Conversion should be case insensitive. + """ + value = None + str_lower = bool_str.lower() + if str_lower in ("true", "t"): + value = True + elif str_lower in ("false", "f"): + value = False + if value is None: + msg = ( + 'ERROR: invalid boolean string value "{0}". ' + 'Must be "true" or "false"'.format(bool_str) + ) + fatal_error(msg) + return value + + +REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"] + + +def is_remote_url(url): + """check if the user provided a local file path instead of a + remote. If so, it must be expanded to an absolute + path. + + """ + remote_url = False + for prefix in REMOTE_PREFIXES: + if url.startswith(prefix): + remote_url = True + return remote_url + + +def split_remote_url(url): + """check if the user provided a local file path or a + remote. If remote, try to strip off protocol info. + + """ + remote_url = is_remote_url(url) + if not remote_url: + return url + + for prefix in REMOTE_PREFIXES: + url = url.replace(prefix, "") + + if "@" in url: + url = url.split("@")[1] + + if ":" in url: + url = url.split(":")[1] + + return url + + +def expand_local_url(url, field): + """check if the user provided a local file path instead of a + remote. If so, it must be expanded to an absolute + path. + + Note: local paths of LOCAL_PATH_INDICATOR have special meaning and + represent local copy only, don't work with the remotes. + + """ + remote_url = is_remote_url(url) + if not remote_url: + if url.strip() == LOCAL_PATH_INDICATOR: + pass + else: + url = os.path.expandvars(url) + url = os.path.expanduser(url) + if not os.path.isabs(url): + msg = ( + 'WARNING: Externals description for "{0}" contains a ' + "url that is not remote and does not expand to an " + "absolute path. Version control operations may " + "fail.\n\nurl={1}".format(field, url) + ) + printlog(msg) + else: + url = os.path.normpath(url) + return url + + +# --------------------------------------------------------------------- +# +# subprocess +# +# --------------------------------------------------------------------- + +# Give the user a helpful message if we detect that a command seems to +# be hanging. +_HANGING_SEC = 300 + + +def _hanging_msg(working_directory, command): + print( + """ + +Command '{command}' +from directory {working_directory} +has taken {hanging_sec} seconds. It may be hanging. + +The command will continue to run, but you may want to abort +manage_externals with ^C and investigate. A possible cause of hangs is +when svn or git require authentication to access a private +repository. On some systems, svn and git requests for authentication +information will not be displayed to the user. In this case, the program +will appear to hang. Ensure you can run svn and git manually and access +all repositories without entering your authentication information. + +""".format( + command=command, + working_directory=working_directory, + hanging_sec=_HANGING_SEC, + ) + ) + + +def execute_subprocess(commands, status_to_caller=False, output_to_caller=False): + """Wrapper around subprocess.check_output to handle common + exceptions. + + check_output runs a command with arguments and waits + for it to complete. + + check_output raises an exception on a nonzero return code. if + status_to_caller is true, execute_subprocess returns the subprocess + return code, otherwise execute_subprocess treats non-zero return + status as an error and raises an exception. + + """ + cwd = os.getcwd() + msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd) + logging.info(msg) + commands_str = " ".join(str(element) for element in commands) + logging.info(commands_str) + return_to_caller = status_to_caller or output_to_caller + status = -1 + output = "" + hanging_timer = Timer( + _HANGING_SEC, + _hanging_msg, + kwargs={"working_directory": cwd, "command": commands_str}, + ) + hanging_timer.start() + try: + output = subprocess.check_output( + commands, stderr=subprocess.STDOUT, universal_newlines=True + ) + log_process_output(output) + status = 0 + except OSError as error: + msg = failed_command_msg( + "Command execution failed. Does the executable exist?", commands + ) + logging.error(error) + fatal_error(msg) + except ValueError as error: + msg = failed_command_msg( + "DEV_ERROR: Invalid arguments trying to run subprocess", commands + ) + logging.error(error) + fatal_error(msg) + except subprocess.CalledProcessError as error: + # Only report the error if we are NOT returning to the + # caller. If we are returning to the caller, then it may be a + # simple status check. If returning, it is the callers + # responsibility determine if an error occurred and handle it + # appropriately. + if not return_to_caller: + msg_context = ( + "Process did not run successfully; " + "returned status {0}".format(error.returncode) + ) + msg = failed_command_msg(msg_context, commands, output=error.output) + logging.error(error) + logging.error(msg) + log_process_output(error.output) + fatal_error(msg) + status = error.returncode + finally: + hanging_timer.cancel() + + if status_to_caller and output_to_caller: + ret_value = (status, output) + elif status_to_caller: + ret_value = status + elif output_to_caller: + ret_value = output + else: + ret_value = None + + return ret_value + + +def failed_command_msg(msg_context, command, output=None): + """Template for consistent error messages from subprocess calls. + + If 'output' is given, it should provide the output from the failed + command + """ + + if output: + output_truncated = last_n_lines( + output, 20, truncation_message="[... Output truncated for brevity ...]" + ) + errmsg = ( + "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: " + ) + else: + errmsg = "" + + command_str = " ".join(command) + errmsg += """In directory + {cwd} +{context}: + {command} +""".format( + cwd=os.getcwd(), context=msg_context, command=command_str + ) + + if output: + errmsg += "See above for output from failed command.\n" + + return errmsg diff --git a/.lib/git-fleximod/poetry.lock b/.lib/git-fleximod/poetry.lock new file mode 100644 index 0000000000..b59ed3942c --- /dev/null +++ b/.lib/git-fleximod/poetry.lock @@ -0,0 +1,693 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "alabaster" +version = "0.7.13" +description = "A configurable sidebar-enabled Sphinx theme" +optional = false +python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] + +[[package]] +name = "babel" +version = "2.14.0" +description = "Internationalization utilities" +optional = false +python-versions = ">=3.7" +files = [ + {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, + {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, +] + +[package.dependencies] +pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} + +[package.extras] +dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] + +[[package]] +name = "certifi" +version = "2024.2.2" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"}, + {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.3.2" +description = "The Real First Universal Charset Detector. 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"] +maintainers = ["Jim Edwards "] +license = "MIT" +readme = "README.md" +homepage = "https://github.com/jedwards4b/git-fleximod" +keywords = ["git", "submodule", "sparse-checkout"] +packages = [ +{ include = "git_fleximod"}, +{ include = "doc"}, +] + +[tool.poetry.scripts] +git-fleximod = "git_fleximod.git_fleximod:main" +me2flexi = "git_fleximod.metoflexi:_main" +fsspec = "fsspec.fuse:main" + +[tool.poetry.dependencies] +python = "^3.8" +GitPython = "^3.1.0" +sphinx = "^5.0.0" +fsspec = "^2023.12.2" +wheel = "^0.42.0" +pytest = "^8.0.0" +pyfakefs = "^5.3.5" + +[tool.poetry.urls] +"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues" + +[tool.pytest.ini_options] +markers = [ + "skip_after_first: only run on first iteration" +] + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml new file mode 100644 index 0000000000..d4b8eaee11 --- /dev/null +++ b/.lib/git-fleximod/tbump.toml @@ -0,0 +1,43 @@ +# Uncomment this if your project is hosted on GitHub: +github_url = "https://github.com/jedwards4b/git-fleximod/" + +[version] +current = "0.7.4" + +# Example of a semver regexp. +# Make sure this matches current_version before +# using tbump +regex = ''' + (?P\d+) + \. + (?P\d+) + \. + (?P\d+) + ''' + +[git] +message_template = "Bump to {new_version}" +tag_template = "v{new_version}" + +# For each file to patch, add a [[file]] config +# section containing the path of the file, relative to the +# tbump.toml location. +[[file]] +src = "git_fleximod/cli.py" + +[[file]] +src = "pyproject.toml" + +# You can specify a list of commands to +# run after the files have been patched +# and before the git commit is made + +# [[before_commit]] +# name = "check changelog" +# cmd = "grep -q {new_version} Changelog.rst" + +# Or run some commands after the git tag and the branch +# have been pushed: +# [[after_push]] +# name = "publish" +# cmd = "./publish.sh" diff --git a/.lib/git-fleximod/tests/__init__.py b/.lib/git-fleximod/tests/__init__.py new file mode 100644 index 0000000000..4d4c66c78e --- /dev/null +++ b/.lib/git-fleximod/tests/__init__.py @@ -0,0 +1,3 @@ +import sys, os + +sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src")) diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py new file mode 100644 index 0000000000..942a0efb97 --- /dev/null +++ b/.lib/git-fleximod/tests/conftest.py @@ -0,0 +1,138 @@ +import pytest +from git_fleximod.gitinterface import GitInterface +import os +import subprocess +import logging +from pathlib import Path + +@pytest.fixture(scope='session') +def logger(): + logging.basicConfig( + level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()] + ) + logger = logging.getLogger(__name__) + return logger + +all_repos=[ + {"subrepo_path": "modules/test", + "submodule_name": "test_submodule", + "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", + "status2" : "test_submodule at tag MPIserial_2.4.0", + "status3" : "test_submodule at tag MPIserial_2.4.0", + "status4" : "test_submodule at tag MPIserial_2.4.0", + "gitmodules_content" : """ + [submodule "test_submodule"] + path = modules/test + url = https://github.com/ESMCI/mpi-serial.git + fxtag = MPIserial_2.4.0 + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = ToplevelRequired +"""}, + {"subrepo_path": "modules/test_optional", + "submodule_name": "test_optional", + "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", + "status2" : "test_optional at tag MPIserial_2.4.0", + "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0", + "status4" : "test_optional at tag MPIserial_2.4.0", + "gitmodules_content": """ + [submodule "test_optional"] + path = modules/test_optional + url = https://github.com/ESMCI/mpi-serial.git + fxtag = MPIserial_2.4.0 + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = ToplevelOptional +"""}, + {"subrepo_path": "modules/test_alwaysoptional", + "submodule_name": "test_alwaysoptional", + "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c", + "status2" : "test_alwaysoptional at hash e5cf35c", + "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0", + "status4" : "test_alwaysoptional at hash e5cf35c", + "gitmodules_content": """ + [submodule "test_alwaysoptional"] + path = modules/test_alwaysoptional + url = https://github.com/ESMCI/mpi-serial.git + fxtag = e5cf35c + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = AlwaysOptional +"""}, + {"subrepo_path": "modules/test_sparse", + "submodule_name": "test_sparse", + "status1" : "test_sparse at tag MPIserial_2.5.0", + "status2" : "test_sparse at tag MPIserial_2.5.0", + "status3" : "test_sparse at tag MPIserial_2.5.0", + "status4" : "test_sparse at tag MPIserial_2.5.0", + "gitmodules_content": """ + [submodule "test_sparse"] + path = modules/test_sparse + url = https://github.com/ESMCI/mpi-serial.git + fxtag = MPIserial_2.5.0 + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = AlwaysRequired + fxsparse = ../.sparse_file_list +"""}, +] +@pytest.fixture(params=all_repos) + +def shared_repos(request): + return request.param + +@pytest.fixture +def get_all_repos(): + return all_repos + +def write_sparse_checkout_file(fp): + sparse_content = """m4 +""" + fp.write_text(sparse_content) + +@pytest.fixture +def test_repo(shared_repos, tmp_path, logger): + subrepo_path = shared_repos["subrepo_path"] + submodule_name = shared_repos["submodule_name"] + test_dir = tmp_path / "testrepo" + test_dir.mkdir() + str_path = str(test_dir) + gitp = GitInterface(str_path, logger) + assert test_dir.joinpath(".git").is_dir() + (test_dir / "modules").mkdir() + if "sparse" in submodule_name: + (test_dir / subrepo_path).mkdir() + # Add the sparse checkout file + write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list") + gitp.git_operation("add","modules/.sparse_file_list") + else: + gitp = GitInterface(str(test_dir), logger) + gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path) + assert test_dir.joinpath(".gitmodules").is_file() + gitp.git_operation("add",subrepo_path) + gitp.git_operation("commit","-a","-m","\"add submod\"") + test_dir2 = tmp_path / "testrepo2" + gitp.git_operation("clone",test_dir,test_dir2) + return test_dir2 + + +@pytest.fixture +def complex_repo(tmp_path, logger): + test_dir = tmp_path / "testcomplex" + test_dir.mkdir() + str_path = str(test_dir) + gitp = GitInterface(str_path, logger) + gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2") + gitp.git_operation("fetch", "origin", "main") + gitp.git_operation("checkout", "main") + return test_dir + +@pytest.fixture +def git_fleximod(): + def _run_fleximod(path, args, input=None): + cmd = ["git", "fleximod"] + args.split() + result = subprocess.run(cmd, cwd=path, input=input, + stdout=subprocess.PIPE, stderr=subprocess.PIPE, + text=True) + if result.returncode: + print(result.stdout) + print(result.stderr) + return result + return _run_fleximod + diff --git a/.lib/git-fleximod/tests/test_a_import.py b/.lib/git-fleximod/tests/test_a_import.py new file mode 100644 index 0000000000..d5ca878de5 --- /dev/null +++ b/.lib/git-fleximod/tests/test_a_import.py @@ -0,0 +1,8 @@ +# pylint: disable=unused-import +from git_fleximod import cli +from git_fleximod import utils +from git_fleximod.gitinterface import GitInterface +from git_fleximod.gitmodules import GitModules + +def test_import(): + print("here") diff --git a/.lib/git-fleximod/tests/test_b_update.py b/.lib/git-fleximod/tests/test_b_update.py new file mode 100644 index 0000000000..159f1cfae0 --- /dev/null +++ b/.lib/git-fleximod/tests/test_b_update.py @@ -0,0 +1,26 @@ +import pytest +from pathlib import Path + +def test_basic_checkout(git_fleximod, test_repo, shared_repos): + # Prepare a simple .gitmodules + gm = shared_repos['gitmodules_content'] + file_path = (test_repo / ".gitmodules") + repo_name = shared_repos["submodule_name"] + repo_path = shared_repos["subrepo_path"] + + file_path.write_text(gm) + + # Run the command + result = git_fleximod(test_repo, f"update {repo_name}") + + # Assertions + assert result.returncode == 0 + assert Path(test_repo / repo_path).exists() # Did the submodule directory get created? + if "sparse" in repo_name: + assert Path(test_repo / f"{repo_path}/m4").exists() # Did the submodule sparse directory get created? + assert not Path(test_repo / f"{repo_path}/README").exists() # Did only the submodule sparse directory get created? + + status = git_fleximod(test_repo, f"status {repo_name}") + + assert shared_repos["status2"] in status.stdout + diff --git a/.lib/git-fleximod/tests/test_c_required.py b/.lib/git-fleximod/tests/test_c_required.py new file mode 100644 index 0000000000..89ab8d294d --- /dev/null +++ b/.lib/git-fleximod/tests/test_c_required.py @@ -0,0 +1,30 @@ +import pytest +from pathlib import Path + +def test_required(git_fleximod, test_repo, shared_repos): + file_path = (test_repo / ".gitmodules") + gm = shared_repos["gitmodules_content"] + repo_name = shared_repos["submodule_name"] + if file_path.exists(): + with file_path.open("r") as f: + gitmodules_content = f.read() + # add the entry if it does not exist + if repo_name not in gitmodules_content: + file_path.write_text(gitmodules_content+gm) + # or if it is incomplete + elif gm not in gitmodules_content: + file_path.write_text(gm) + else: + file_path.write_text(gm) + result = git_fleximod(test_repo, "update") + assert result.returncode == 0 + status = git_fleximod(test_repo, f"status {repo_name}") + assert shared_repos["status3"] in status.stdout + status = git_fleximod(test_repo, f"update --optional") + assert result.returncode == 0 + status = git_fleximod(test_repo, f"status {repo_name}") + assert shared_repos["status4"] in status.stdout + status = git_fleximod(test_repo, f"update {repo_name}") + assert result.returncode == 0 + status = git_fleximod(test_repo, f"status {repo_name}") + assert shared_repos["status4"] in status.stdout diff --git a/.lib/git-fleximod/tests/test_d_complex.py b/.lib/git-fleximod/tests/test_d_complex.py new file mode 100644 index 0000000000..fdce516274 --- /dev/null +++ b/.lib/git-fleximod/tests/test_d_complex.py @@ -0,0 +1,67 @@ +import pytest +from pathlib import Path +from git_fleximod.gitinterface import GitInterface + +def test_complex_checkout(git_fleximod, complex_repo, logger): + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) + assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout) + assert("Complex not checked out, aligned at tag testtag01" in status.stdout) + assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) + + # This should checkout and update test_submodule and complex_sub + result = git_fleximod(complex_repo, "update") + assert result.returncode == 0 + + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) + assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) + assert("Complex at tag testtag01" in status.stdout) + + # now check the complex_sub + root = (complex_repo / "modules" / "complex") + assert(not (root / "libraries" / "gptl" / ".git").exists()) + assert(not (root / "libraries" / "mpi-serial" / ".git").exists()) + assert((root / "modules" / "mpi-serial" / ".git").exists()) + assert(not (root / "modules" / "mpi-serial2" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / "m4").exists()) + assert(not (root / "modules" / "mpi-sparse" / "README").exists()) + + # update a single optional submodule + + result = git_fleximod(complex_repo, "update ToplevelOptional") + assert result.returncode == 0 + + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional at tag v5.3.2" in status.stdout) + assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) + assert("Complex at tag testtag01" in status.stdout) + assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) + + + # Finally update optional + result = git_fleximod(complex_repo, "update --optional") + assert result.returncode == 0 + + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional at tag v5.3.2" in status.stdout) + assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) + assert("Complex at tag testtag01" in status.stdout) + assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout) + + # now check the complex_sub + root = (complex_repo / "modules" / "complex" ) + assert(not (root / "libraries" / "gptl" / ".git").exists()) + assert(not (root / "libraries" / "mpi-serial" / ".git").exists()) + assert((root / "modules" / "mpi-serial" / ".git").exists()) + assert((root / "modules" / "mpi-serial2" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / "m4").exists()) + assert(not (root / "modules" / "mpi-sparse" / "README").exists()) + + diff --git a/bin/git-fleximod b/bin/git-fleximod new file mode 100755 index 0000000000..f69ede1c22 --- /dev/null +++ b/bin/git-fleximod @@ -0,0 +1,8 @@ +#!/usr/bin/env python3 +import sys +import os +sys.path.insert(0,os.path.abspath(os.path.join(os.path.dirname(__file__),"..",".lib","git-fleximod"))) +from git_fleximod.git_fleximod import main + +if __name__ == '__main__': + sys.exit(main()) diff --git a/ccs_config b/ccs_config index f90e10502c..2ff978f92a 160000 --- a/ccs_config +++ b/ccs_config @@ -1 +1 @@ -Subproject commit f90e10502c7246c2b45e373b7dd5e0da6cba0828 +Subproject commit 2ff978f92a5ac9a6ab243e5c14d06a7e2d2f5799 diff --git a/components/cdeps b/components/cdeps index 7a522c828c..7476950699 160000 --- a/components/cdeps +++ b/components/cdeps @@ -1 +1 @@ -Subproject commit 7a522c828c32dc35777992653f281ec525509c4a +Subproject commit 7476950699909813d1938a34bd8d71bf5bfbf1e9 diff --git a/components/mizuRoute b/components/mizuRoute index 0a62ee6185..81c720c7ee 160000 --- a/components/mizuRoute +++ b/components/mizuRoute @@ -1 +1 @@ -Subproject commit 0a62ee6185bdc9b99cd88ed5f15ea850602c43a2 +Subproject commit 81c720c7ee51f9c69f2934f696078c42f4493565 diff --git a/components/mosart b/components/mosart index 1c22a8c547..8c682b1b7f 160000 --- a/components/mosart +++ b/components/mosart @@ -1 +1 @@ -Subproject commit 1c22a8c5478b714cf5b7c54b3e5cf7bad09fd9b2 +Subproject commit 8c682b1b7f15d146816de302e0d359da3e957056 diff --git a/libraries/mct b/libraries/mct index e36024c5dd..82b0071e69 160000 --- a/libraries/mct +++ b/libraries/mct @@ -1 +1 @@ -Subproject commit e36024c5ddf482625ae6bd9474eff7d8f393f87c +Subproject commit 82b0071e69d14330b75d23b0bc68543ebea9aadc diff --git a/libraries/parallelio b/libraries/parallelio index 6539ef05ae..f52ade0756 160000 --- a/libraries/parallelio +++ b/libraries/parallelio @@ -1 +1 @@ -Subproject commit 6539ef05ae7584ec570a56fdab9f7dfb336c2b80 +Subproject commit f52ade075619b32fa141993b5665b0fe099befc2 diff --git a/src/fates b/src/fates index f0185f7c70..adfa664806 160000 --- a/src/fates +++ b/src/fates @@ -1 +1 @@ -Subproject commit f0185f7c7033fa69c80d1ddb07cbcbf1f8be1adc +Subproject commit adfa6648063408d443f5cae671bd37f713d3e3e8 From 798d43c0fe673557b98dd7fd1eb614b205641db0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 28 May 2024 08:39:13 -0600 Subject: [PATCH 203/408] Add comment in lilacsmoke.py as per code review --- cime_config/SystemTests/lilacsmoke.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cime_config/SystemTests/lilacsmoke.py b/cime_config/SystemTests/lilacsmoke.py index 366d5d1176..1287301ba2 100644 --- a/cime_config/SystemTests/lilacsmoke.py +++ b/cime_config/SystemTests/lilacsmoke.py @@ -407,6 +407,10 @@ def run_phase(self): # case.get_mpirun_cmd creates a command that runs the executable given by # case.run_exe. So it's important that (elsewhere in this test script) we create a # link pointing from that to the atm_driver.exe executable. + # + # 2024/5/28 slevis: We added the load_env here to replace the + # behavior of the PBS -V directive that was removed from + # /ccs_config/machines/config_batch.xml self._case.load_env(reset=True) lid = new_lid() os.environ["OMP_NUM_THREADS"] = str(self._case.thread_count) From aaeae950ca98d3292e3a02eb95862e69e7783c40 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 28 May 2024 08:54:58 -0600 Subject: [PATCH 204/408] Updated ChangeLog and ChangeSum --- doc/ChangeLog | 26 +++----------------------- doc/ChangeSum | 2 +- 2 files changed, 4 insertions(+), 24 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index d68ef323ac..e15c554f8f 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.006 Originator(s): slevis (Samuel Levis) -Date: Tue 21 May 2024 02:59:05 PM MDT +Date: Tue 28 May 2024 08:45:50 AM MDT One-line Summary: Update externals to cesm2_3_beta17, remove mct, retire /test/tools Purpose and description of changes @@ -48,12 +48,6 @@ Changes to documentation: Substantial timing or memory changes: Not considered -Notes of particular relevance for developers: ---------------------------------------------- -Changes to tests or testing: - I added a long list of izumi nag debug tests to ExpectedFailures as per - https://github.com/ESCOMP/CMEPS/pull/460 - Testing summary: ---------------- [PASS means all tests PASS; OK means tests PASS other than expected fails.] @@ -68,7 +62,7 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- + derecho ----- OK izumi ------- OK any other testing (give details below): @@ -82,21 +76,7 @@ If the tag used for baseline comparisons was NOT the previous tag, note that her Answer changes -------------- -Changes answers relative to baseline: - - [ If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section). - And always remove these three lines and parts that don't apply. ] - - Summarize any changes to answers, i.e., - - what code configurations: - - what platforms/compilers: - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - If bitwise differences were observed, how did you show they were no worse - than roundoff? Roundoff differences means one or more lines of code change results - only by roundoff level (because order of operation changes for example). Roundoff - changes to state fields usually grow to greater than roundoff as the simulation progresses. +Changes answers relative to baseline: NO Other details ------------- diff --git a/doc/ChangeSum b/doc/ChangeSum index 7f8cdaeead..77bc8a426d 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.006 slevis 05/21/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools + ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes ctsm5.2.003 samrabin 05/02/2024 Merge b4b-dev From 62d8ad004e896037f04a626ac7c4fceee9ecf6b0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 28 May 2024 09:03:35 -0600 Subject: [PATCH 205/408] Update share in Externals.cfg --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 70d103a94b..dac119c47c 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -63,7 +63,7 @@ externals = Externals_CDEPS.cfg required = True [share] -tag = share1.0.18 +tag = share1.0.19 protocol = git repo_url = https://github.com/ESCOMP/CESM_share local_path = share From 26c1222668be7b2be11936d666be76916be1b751 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 28 May 2024 15:18:22 -0600 Subject: [PATCH 206/408] Update ChangeLog with latest info about tests --- doc/ChangeLog | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index e15c554f8f..b2f14a2c01 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.006 Originator(s): slevis (Samuel Levis) -Date: Tue 28 May 2024 08:45:50 AM MDT +Date: Tue 28 May 2024 03:14:18 PM MDT One-line Summary: Update externals to cesm2_3_beta17, remove mct, retire /test/tools Purpose and description of changes @@ -68,15 +68,15 @@ Testing summary: any other testing (give details below): ctsm_sci - derecho ---- - -If the tag used for baseline comparisons was NOT the previous tag, note that here: + derecho ---- OK Answer changes -------------- Changes answers relative to baseline: NO + Except two derecho_nvhpc tests due to an update to the nvhpc compiler + as documented in the Pull Request listed a few lines down. Other details ------------- From 51079bfb92ca2d75a71cfee5679bbce40314eaae Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Wed, 29 May 2024 10:17:10 -0600 Subject: [PATCH 207/408] update run_sys_tests.py for fleximod --- python/ctsm/run_sys_tests.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index de93081504..ecea2342a7 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -576,12 +576,12 @@ def _record_git_status(testroot, retry, dry_run): if git_status.count("\n") == 1: # Only line in git status is the branch info output += "(clean sandbox)\n" - manic = os.path.join("manage_externals", "checkout_externals") - manage_externals_status = subprocess.check_output( - [manic, "--status", "--verbose"], cwd=ctsm_root, universal_newlines=True + fleximod = os.path.join("bin", "git-fleximod") + fleximod_status = subprocess.check_output( + [fleximod, "status"], cwd=ctsm_root, universal_newlines=True ) - output += 72 * "-" + "\n" + "manage_externals status:" + "\n" - output += manage_externals_status + output += 72 * "-" + "\n" + "git-fleximod status:" + "\n" + output += fleximod_status output += 72 * "-" + "\n" print(output) From 0537a6a32d586e62c237b6e2a6d645b7895bf76a Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 29 May 2024 11:23:15 -0600 Subject: [PATCH 208/408] add potential veg check to avoid accessing timeseries file --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 88 ++++++++++---------- src/dyn_subgrid/dynSubgridDriverMod.F90 | 4 +- 2 files changed, 48 insertions(+), 44 deletions(-) diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index f330ee2b78..d7c1063494 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -107,6 +107,7 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) ! !USES: use clm_varctl , only : use_cn, use_fates_luh, fates_harvest_mode + use clm_varctl , only : use_fates_potentialveg use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type use dynTimeInfoMod , only : YEAR_POSITION_START_OF_TIMESTEP use dynTimeInfoMod , only : YEAR_POSITION_END_OF_TIMESTEP @@ -148,55 +149,58 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) landuse_transitions = 0._r8 landuse_harvest = 0._r8 - if (use_fates_luh) then + ! Avoid initializing the landuse timeseries file if in fates potential vegetation mode + if (.not. use_fates_potentialveg) then + if (use_fates_luh) then - ! Generate the dyn_file_type object. - ! Start calls get_prev_date, whereas end calls get_curr_date - dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP) + ! Generate the dyn_file_type object. + ! Start calls get_prev_date, whereas end calls get_curr_date + dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP) - ! Get initial land use data from the fates luh2 timeseries dataset - num_points = (bounds%endg - bounds%begg + 1) - landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor? - do varnum = 1, num_landuse_transition_vars - landuse_transition_vars(varnum) = dyn_var_time_uninterp_type( & - dyn_file=dynFatesLandUse_file, varname=landuse_transition_varnames(varnum), & - dim1name=grlnd, conversion_factor=1.0_r8, & - do_check_sums_equal_1=.false., data_shape=landuse_shape) - end do - do varnum = 1, num_landuse_state_vars - landuse_state_vars(varnum) = dyn_var_time_uninterp_type( & - dyn_file=dynFatesLandUse_file, varname=landuse_state_varnames(varnum), & - dim1name=grlnd, conversion_factor=1.0_r8, & - do_check_sums_equal_1=.false., data_shape=landuse_shape) - end do - - ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled - if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. & - trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then - - ! change the harvest varnames being used depending on the mode selected - if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area ) then - landuse_harvest_varnames => landuse_harvest_area_varnames - landuse_harvest_units = landuse_harvest_area_units - elseif (trim(fates_harvest_mode) .eq. fates_harvest_luh_mass ) then - landuse_harvest_varnames => landuse_harvest_mass_varnames - landuse_harvest_units = landuse_harvest_mass_units - else - call endrun(msg=' undefined fates harvest mode selected'//errMsg(__FILE__, __LINE__)) - end if - - do varnum = 1, num_landuse_harvest_vars - landuse_harvest_vars(varnum) = dyn_var_time_uninterp_type( & - dyn_file=dynFatesLandUse_file, varname=landuse_harvest_varnames(varnum), & + ! Get initial land use data from the fates luh2 timeseries dataset + num_points = (bounds%endg - bounds%begg + 1) + landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor? + do varnum = 1, num_landuse_transition_vars + landuse_transition_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_transition_varnames(varnum), & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=landuse_shape) + end do + do varnum = 1, num_landuse_state_vars + landuse_state_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_state_varnames(varnum), & dim1name=grlnd, conversion_factor=1.0_r8, & do_check_sums_equal_1=.false., data_shape=landuse_shape) end do + + ! Get the harvest rate data from the fates luh2 timeseries dataset if enabled + if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area .or. & + trim(fates_harvest_mode) .eq. fates_harvest_luh_mass) then + + ! change the harvest varnames being used depending on the mode selected + if (trim(fates_harvest_mode) .eq. fates_harvest_luh_area ) then + landuse_harvest_varnames => landuse_harvest_area_varnames + landuse_harvest_units = landuse_harvest_area_units + elseif (trim(fates_harvest_mode) .eq. fates_harvest_luh_mass ) then + landuse_harvest_varnames => landuse_harvest_mass_varnames + landuse_harvest_units = landuse_harvest_mass_units + else + call endrun(msg=' undefined fates harvest mode selected'//errMsg(__FILE__, __LINE__)) + end if + + do varnum = 1, num_landuse_harvest_vars + landuse_harvest_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_harvest_varnames(varnum), & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=landuse_shape) + end do + end if end if - end if - ! Since fates needs state data during initialization, make sure to call - ! the interpolation routine at the start - call dynFatesLandUseInterp(bounds,init_state=.true.) + ! Since fates needs state data during initialization, make sure to call + ! the interpolation routine at the start + call dynFatesLandUseInterp(bounds,init_state=.true.) + end if end subroutine dynFatesLandUseInit diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90 index faef029b40..ea1210521d 100644 --- a/src/dyn_subgrid/dynSubgridDriverMod.F90 +++ b/src/dyn_subgrid/dynSubgridDriverMod.F90 @@ -206,7 +206,7 @@ subroutine dynSubgrid_driver(bounds_proc, ! OUTSIDE any loops over clumps in the driver. ! ! !USES: - use clm_varctl , only : use_cn, use_fates, use_fates_luh + use clm_varctl , only : use_cn, use_fates, use_fates_luh, use_fates_potentialveg use dynInitColumnsMod , only : initialize_new_columns use dynConsBiogeophysMod , only : dyn_hwcontent_init, dyn_hwcontent_final use dynEDMod , only : dyn_ED @@ -295,7 +295,7 @@ subroutine dynSubgrid_driver(bounds_proc, call dynurban_interp(bounds_proc) end if - if (use_fates_luh) then + if (use_fates_luh .and. .not. use_fates_potentialveg) then call dynFatesLandUseInterp(bounds_proc) end if From dbbd7954a9b5e9a38d0afe45648b19dd5597c4fe Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 29 May 2024 12:17:31 -0600 Subject: [PATCH 209/408] change fluh_timeseries to use an file with wider time range --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index fe34e9f4b8..37aff979f9 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1557,7 +1557,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc + >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1650-2015_c240216.nc .false. From 2848873409be7eddecb0f62326116afaf9a2e319 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 29 May 2024 12:18:24 -0600 Subject: [PATCH 210/408] fix pvt system test --- cime_config/SystemTests/pvt.py | 34 +++++++++++++++++++++++++++++++--- 1 file changed, 31 insertions(+), 3 deletions(-) diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py index 6b2a958eaa..05da935a0e 100644 --- a/cime_config/SystemTests/pvt.py +++ b/cime_config/SystemTests/pvt.py @@ -51,6 +51,11 @@ def run_phase(self): orig_casevar = self._case.get_value("CASE") caseroot = self._case.get_value("CASEROOT") + # Set the run start date based on the desired starting reference case year + refcase_year = 1700 + stop_n_pveg = 5 + startyear_pveg = refcase_year - stop_n_pveg + # clone the main case to create spinup case logger.info("PVT log: cloning setup") clone_path = "{}.potveg".format(caseroot) @@ -65,10 +70,11 @@ def run_phase(self): self._set_active_case(clone) # set the clone case values - stop_n_pveg = 1 with clone: - # clone.set_value("CLM_ACCELERATED_SPINUP", "on") + clone.set_value("CLM_ACCELERATED_SPINUP", "off") clone.set_value("STOP_N", stop_n_pveg) + clone.set_value("STOP_OPTION", "nyears") + clone.set_value("RUN_STARTDATE", "{}-01-01".format(startyear_pveg)) # Modify the spin up case to use the potential vegetation mode. # Checks for incompatible cases and necessary mapping files are @@ -93,11 +99,33 @@ def run_phase(self): os.chdir(caseroot) self._set_active_case(orig_case) + # Copy restart files from spin up to the transient case run directory + # obtain rpointer files and necessary restart files from short term archiving directory + rundir = self._case.get_value("RUNDIR") + + refdate = str(refcase_year) + '-01-01-00000' + rest_path = os.path.join(dout_sr, "rest", "{}".format(refdate)) + + for item in glob.glob("{}/*{}*".format(rest_path, refdate)): + link_name = os.path.join(rundir, os.path.basename(item)) + if os.path.islink(link_name) and os.readlink(link_name) == item: + # Link is already set up correctly: do nothing + # (os.symlink raises an exception if you try to replace an + # existing file) + pass + else: + os.symlink(item, link_name) + + for item in glob.glob("{}/*rpointer*".format(rest_path)): + shutil.copy(item, rundir) + + # Update run case settings self._case.set_value("CLM_ACCELERATED_SPINUP", "off") self._case.set_value("RUN_TYPE", "hybrid") self._case.set_value("GET_REFCASE", False) self._case.set_value("RUN_REFCASE", "{}.potveg".format(orig_casevar)) - self._case.set_value("RUN_REFDATE", "1700-01-01") + self._case.set_value("RUN_REFDATE", "{}-01-01".format(refcase_year)) + self._case.set_value("RUN_STARTDATE", "{}-01-01".format(refcase_year)) self._case.set_value("DOUT_S", False) self._case.flush() From 6b550b1aa536fed46d197580614226e16691d1f8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 29 May 2024 14:03:29 -0600 Subject: [PATCH 211/408] Replace checkout_externals with git-fleximod in documentation --- .gitignore | 6 ++-- README | 4 +-- README_EXTERNALS.rst | 32 +++++++++---------- bld/CLMBuildNamelist.pm | 2 +- doc/README.CHECKLIST.master_tags | 6 ++-- doc/build_docs | 2 +- doc/design/python_script_user_interface.rst | 2 +- .../obtaining-and-building-ctsm.rst | 6 ++-- doc/source/lilac/specific-atm-models/wrf.rst | 2 +- python/ctsm/site_and_regional/run_neon.py | 2 +- tools/mksurfdata_esmf/README.md | 2 +- 11 files changed, 33 insertions(+), 33 deletions(-) diff --git a/.gitignore b/.gitignore index 1da8072fed..6c8111525a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ -# directories checked out by manage_externals, and other files created -# by manage_externals -manage_externals.log +# directories checked out by git-fleximod, and other files created +# by git-fleximod +git-fleximod.log ccs_config /src/fates/ /cime/ diff --git a/README b/README index 18cc2b1458..97daae2d5a 100644 --- a/README +++ b/README @@ -50,7 +50,7 @@ lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for test -------------- CTSM Testing scripts for CTSM offline tools (deprecated) tools ------------- CTSM Offline tools to prepare input datasets and process output. cime_config ------- Configuration files of cime for compsets and CTSM settings -manage_externals -- Script to manage the external source directories (deprecated) +git-fleximod ------ Script to manage the external source directories py_env_create ----- Script to setup the python environment for CTSM python tools using conda python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts @@ -75,7 +75,7 @@ Top level documentation ($CTSMROOT): README ------------------- This file README.md ---------------- File that displays on github under https::/github.com/ESCOMP/CTSM.git README.rst --------------- File that displays under the project in github -README_EXTERNALS.rst ----- Information on how to work with manage_externals for CTSM (deprecated) +README_EXTERNALS.rst ----- Information on how to work with git-fleximod for CTSM CODE_OF_CONDUCT.md ------- Code of Conduct for how to work with each other on the CTSM project Copyright ---------------- CESM Copyright file doc/UpdateChangeLog.pl --- Script to add documentation on a tag to the diff --git a/README_EXTERNALS.rst b/README_EXTERNALS.rst index ed7a068991..22c56ee6f6 100644 --- a/README_EXTERNALS.rst +++ b/README_EXTERNALS.rst @@ -18,11 +18,11 @@ To obtain the CTSM code you need to do the following: This will create a directory ``my_ctsm_sandbox/`` in your current working directory. -#. Run the script **manage_externals/checkout_externals**. :: +#. Run **./bin/git-fleximod update**. :: - ./manage_externals/checkout_externals + ./bin/git-fleximod update - The **checkout_externals** script is a package manager that will + **git-fleximod** is a package manager that will populate the ctsm directory with the relevant versions of each of the components along with the CIME infrastructure code. @@ -30,21 +30,21 @@ At this point you have a working version of CTSM. To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ . -More details on checkout_externals ----------------------------------- +More details on git-fleximod +---------------------------- The file **Externals.cfg** in your top-level CTSM directory tells -**checkout_externals** which tag/branch of each component should be +**git-fleximod** which tag/branch of each component should be brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**. -NOTE: checkout_externals will always attempt +NOTE: git-fleximod will always attempt to make the working copy exactly match the externals description. If you manually modify an external without updating Externals.cfg, e.g. switch -to a different tag, then rerunning checkout_externals will switch you +to a different tag, then rerunning git-fleximod will switch you back to the external described in Externals.cfg. See below documentation `Customizing your CTSM sandbox`_ for more details. -**You need to rerun checkout_externals whenever Externals.cfg has +**You need to rerun git-fleximod whenever Externals.cfg has changed** (unless you have already manually updated the relevant external(s) to have the correct branch/tag checked out). Common times when this is needed are: @@ -54,17 +54,17 @@ when this is needed are: * After merging some other CTSM branch/tag into your currently checked-out branch -**checkout_externals** must be run from the root of the source +**git-fleximod** must be run from the root of the source tree. For example, if you cloned CTSM with:: git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox -then you must run **checkout_externals** from +then you must run **git-fleximod** from ``/path/to/my_ctsm_sandbox``. -To see more details of **checkout_externals**, issue :: +To see more details of **git-fleximod**, issue :: - ./manage_externals/checkout_externals --help + ./bin/git-fleximod --help Customizing your CTSM sandbox ============================= @@ -80,7 +80,7 @@ checked out ctsm1.0.0 but really wanted to have ctsm1.1.0; you would simply do the following:: git checkout ctsm1.1.0 - ./manage_externals/checkout_externals + ./bin/git-fleximod update You should **not** use this method if you have made any source code changes, or if you have any ongoing CTSM cases that were created from @@ -107,11 +107,11 @@ Each entry specifies either a tag, a hash or a branch. To point to a new tag: #. Checkout the new component(s):: - ./manage_externals/checkout_externals + ./bin/git-fleximod update To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``. -To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``manage_externals/checkout_externals`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.) +To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod update`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.) Keep in mind that changing individual components from a tag may result in an invalid model (won't compile, won't run, not scientifically diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index fb44023cd5..1371ea5c06 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -366,7 +366,7 @@ sub check_for_perl_utils { } else { die <<"EOF"; ** Cannot find the root of the cime directory enter it using the -cimeroot option - Did you run the checkout_externals scripts? + Did you run ./bin/git-fleximod update? EOF } } diff --git a/doc/README.CHECKLIST.master_tags b/doc/README.CHECKLIST.master_tags index ed7794130b..0da52acaaa 100644 --- a/doc/README.CHECKLIST.master_tags +++ b/doc/README.CHECKLIST.master_tags @@ -14,9 +14,9 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow 2a -- run 'git pull' to pull in the latest version from GitHub 2b -- run 'git status' and/or 'git diff' to make sure you don't have any uncommitted local changes - 2c -- run './manage_externals/checkout_externals -S' to make sure all externals are - updated and don't have any uncommitted changes. (If any are marked with 's' in - the first column, run ./manage_externals/checkout_externals to update them.) + 2c -- run './bin/git-fleximod status' to make sure all externals are + updated and don't have any uncommitted changes. If any are marked with 's' in + the first column, run './bin/git-fleximod update'. (3) Do all testing on your fork/feature-branch diff --git a/doc/build_docs b/doc/build_docs index a8e8099b60..45c7099ec5 100755 --- a/doc/build_docs +++ b/doc/build_docs @@ -6,5 +6,5 @@ if [ -f doc-builder/build_docs ]; then echo "Running: ./doc-builder/build_docs $@" ./doc-builder/build_docs "$@" else - echo "Obtain doc-builder by running ./manage_externals/checkout_externals -o from the top-level" + echo "Obtain doc-builder by running './bin/git-fleximod update --optional' from the top-level" fi diff --git a/doc/design/python_script_user_interface.rst b/doc/design/python_script_user_interface.rst index 87c1b3e8fc..d639117810 100644 --- a/doc/design/python_script_user_interface.rst +++ b/doc/design/python_script_user_interface.rst @@ -66,7 +66,7 @@ For logical flags, use a flag without an argument -- ``--feature`` for the case We try to follow the guide at the top of `Python's logging howto `_. In particular, print statements should be used for "console output for ordinary usage of a command line script or program"; ``logger.info`` or ``logger.debug`` should be used to "report events that occur during normal operation of a program (e.g. for status monitoring or fault investigation)", etc. -The distinction between when to use print and when to use logging can admittedly be a bit subjective, as it comes down to the question of whether the given output is part of the fundamental operation of the script – i.e., part of what the script is designed to do is to give this output. For example, ``run_sys_tests`` prints a variety of information when it starts, particularly concerning the git and manage_externals status of the current repository. The rationale for using ``print`` statements for this is that we designed ``run_sys_tests`` to replace some of the repetitive items that we did whenever running the system tests. One of these items was running ``git status`` and ``./manage_externals/checkout_externals -S -v`` to check that the repository is in a clean state. Thus, in this case, our view is that the output from these commands is part of the fundamental purpose of ``run_sys_tests``: it is something we always want to see, and we feel that it is important for anyone running the system tests to review, and thus ``print`` statements are appropriate here. +The distinction between when to use print and when to use logging can admittedly be a bit subjective, as it comes down to the question of whether the given output is part of the fundamental operation of the script – i.e., part of what the script is designed to do is to give this output. For example, ``run_sys_tests`` prints a variety of information when it starts, particularly concerning the git and git-fleximod status of the current repository. The rationale for using ``print`` statements for this is that we designed ``run_sys_tests`` to replace some of the repetitive items that we did whenever running the system tests. One of these items was running ``git status`` and ``./bin/git-fleximod status --verbose`` to check that the repository is in a clean state. Thus, in this case, our view is that the output from these commands is part of the fundamental purpose of ``run_sys_tests``: it is something we always want to see, and we feel that it is important for anyone running the system tests to review, and thus ``print`` statements are appropriate here. In general, ``print`` statements should be used sparingly, just for output that is important for the user to see. That said, users of CTSM scripts often expect more output than you would see from a typical Unix tool (where the philosophy is that there should be no output if everything worked correctly). Some examples of things that users of CTSM scripts typically want to see are: diff --git a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst index c0e510c017..ef24e695b9 100644 --- a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst +++ b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst @@ -26,7 +26,7 @@ Obtain CTSM by running:: git clone https://github.com/ESCOMP/CTSM.git cd CTSM - ./manage_externals/checkout_externals + ./bin/git-fleximod update Then build CTSM and its dependencies. On a machine that has been ported to CIME, the command will look like this (example given for NCAR's ``cheyenne`` machine):: @@ -101,11 +101,11 @@ above`) can be obtained with:: git clone https://github.com/ESCOMP/CTSM.git cd CTSM - ./manage_externals/checkout_externals + ./bin/git-fleximod update By default, this will put you on the ``master`` branch of CTSM, which is the main development branch. You can checkout a different branch or tag using ``git checkout``; -**be sure to rerun** ``./manage_externals/checkout_externals`` **after doing so.** +**be sure to rerun** ``./bin/git-fleximod update`` **after doing so.** For more details, see https://github.com/ESCOMP/CTSM/wiki/Quick-start-to-CTSM-development-with-git diff --git a/doc/source/lilac/specific-atm-models/wrf.rst b/doc/source/lilac/specific-atm-models/wrf.rst index 5d104778ec..ad85fee777 100644 --- a/doc/source/lilac/specific-atm-models/wrf.rst +++ b/doc/source/lilac/specific-atm-models/wrf.rst @@ -44,7 +44,7 @@ Clone the CTSM repository:: git clone https://github.com/ESCOMP/CTSM.git cd CTSM - ./manage_externals/checkout_externals + ./bin/git-fleximod update .. _build-CTSM-and-dependencies: diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 4b0df2722d..3acbf435b1 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -41,7 +41,7 @@ # - [ ] Case dependency and the ability to check case status # - [ ] If Case dependency works we don't need finidat given explicilty for post-ad and transient. -# - [ ] checkout_externals instead of using env varaiable +# - [ ] "./bin/git-fleximod update" instead of using env variable # - [ ] wget the fields available and run for those available # - [ ] Matrix spin-up if (SASU) Eric merged it in diff --git a/tools/mksurfdata_esmf/README.md b/tools/mksurfdata_esmf/README.md index 11cb69c681..3d19c88ff0 100644 --- a/tools/mksurfdata_esmf/README.md +++ b/tools/mksurfdata_esmf/README.md @@ -93,7 +93,7 @@ https://github.com/ESCOMP/CTSM/issues/2341 ``` shell # Assuming pwd is the tools/mksurfdata_esmf directory - ./manage_externals/checkout_externals # Assuming at the top level of the CTSM/CESM checkout + ./bin/git-fleximod update # Assuming at the top level of the CTSM/CESM checkout ``` This will bring in CIME and ccs_config which are required for building. From 612962280d766d86497ae5747c10d8af33623121 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 29 May 2024 14:32:40 -0600 Subject: [PATCH 212/408] Restore .gitignore as it was --- .gitignore | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 6c8111525a..1da8072fed 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ -# directories checked out by git-fleximod, and other files created -# by git-fleximod -git-fleximod.log +# directories checked out by manage_externals, and other files created +# by manage_externals +manage_externals.log ccs_config /src/fates/ /cime/ From 5a577cdf701d028393bacc12bfde1749c9a9a2d8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 29 May 2024 14:34:26 -0600 Subject: [PATCH 213/408] Delete README_EXTERNALS.rst to be like #2559 --- README_EXTERNALS.rst | 132 ------------------------------------------- 1 file changed, 132 deletions(-) delete mode 100644 README_EXTERNALS.rst diff --git a/README_EXTERNALS.rst b/README_EXTERNALS.rst deleted file mode 100644 index 22c56ee6f6..0000000000 --- a/README_EXTERNALS.rst +++ /dev/null @@ -1,132 +0,0 @@ -Obtaining the full model code and associated scripting infrastructure -===================================================================== - -[!CAUTION] -This is deprecated and will be replaced with git submodules. See -https://github.com/ESCOMP/CTSM/pull/2443 - - -CTSM is released via GitHub. You will need some familiarity with git in order -to modify the code and commit these changes. However, to simply checkout and run the -code, no git knowledge is required other than what is documented in the following steps. - -To obtain the CTSM code you need to do the following: - -#. Clone the repository. :: - - git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox - - This will create a directory ``my_ctsm_sandbox/`` in your current working directory. - -#. Run **./bin/git-fleximod update**. :: - - ./bin/git-fleximod update - - **git-fleximod** is a package manager that will - populate the ctsm directory with the relevant versions of each of the - components along with the CIME infrastructure code. - -At this point you have a working version of CTSM. - -To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ . - -More details on git-fleximod ----------------------------- - -The file **Externals.cfg** in your top-level CTSM directory tells -**git-fleximod** which tag/branch of each component should be -brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**. - -NOTE: git-fleximod will always attempt -to make the working copy exactly match the externals description. If -you manually modify an external without updating Externals.cfg, e.g. switch -to a different tag, then rerunning git-fleximod will switch you -back to the external described in Externals.cfg. See below -documentation `Customizing your CTSM sandbox`_ for more details. - -**You need to rerun git-fleximod whenever Externals.cfg has -changed** (unless you have already manually updated the relevant -external(s) to have the correct branch/tag checked out). Common times -when this is needed are: - -* After checking out a new CTSM branch/tag - -* After merging some other CTSM branch/tag into your currently - checked-out branch - -**git-fleximod** must be run from the root of the source -tree. For example, if you cloned CTSM with:: - - git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox - -then you must run **git-fleximod** from -``/path/to/my_ctsm_sandbox``. - -To see more details of **git-fleximod**, issue :: - - ./bin/git-fleximod --help - -Customizing your CTSM sandbox -============================= - -There are several use cases to consider when you want to customize or modify your CTSM sandbox. - -Switching to a different CTSM branch or tag -------------------------------------------- - -If you have already checked out a branch or tag and **HAVE NOT MADE ANY -MODIFICATIONS** it is simple to change your sandbox. Say that you -checked out ctsm1.0.0 but really wanted to have ctsm1.1.0; -you would simply do the following:: - - git checkout ctsm1.1.0 - ./bin/git-fleximod update - -You should **not** use this method if you have made any source code -changes, or if you have any ongoing CTSM cases that were created from -this sandbox. In these cases, it is often easiest to do a second **git -clone**. - -Pointing to a different version of a component ----------------------------------------------- - -Each entry in **Externals.cfg** has the following form (we use CIME as an -example below):: - - [cime] - local_path = cime - protocol = git - repo_url = https://github.com/CESM-Development/cime - tag = cime5.4.0-alpha.20 - required = True - -Each entry specifies either a tag, a hash or a branch. To point to a new tag: - -#. Modify the relevant entry/entries in **Externals.cfg** (e.g., changing - ``cime5.4.0-alpha.20`` to ``cime5.4.0-alpha.21`` above) - -#. Checkout the new component(s):: - - ./bin/git-fleximod update - -To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``. - -To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod update`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.) - -Keep in mind that changing individual components from a tag may result -in an invalid model (won't compile, won't run, not scientifically -meaningful) and is unsupported. - -Committing your change to Externals.cfg -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -After making this change, it's a good idea to commit the change in your -local CTSM git repository. First create a branch in your local -repository, then commit it. (Unlike with subversion, branches are stored -locally unless you explicitly push them up to GitHub. Feel free to -create whatever local branches you'd like.) For example:: - - git checkout -b my_ctsm_branch - git add Externals.cfg - git commit -m "Update CIME to cime5.4.0-alpha.20" - From 61c97a13ebf81bb28f4bbac7aa1072c9f544c85b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 29 May 2024 15:27:22 -0600 Subject: [PATCH 214/408] Add dummy ./manage_externals/checkout_externals with ERROR message --- manage_externals/checkout_externals | 3 +++ 1 file changed, 3 insertions(+) create mode 100755 manage_externals/checkout_externals diff --git a/manage_externals/checkout_externals b/manage_externals/checkout_externals new file mode 100755 index 0000000000..5f848f5da9 --- /dev/null +++ b/manage_externals/checkout_externals @@ -0,0 +1,3 @@ +echo "ERROR: Instead of ./manage_externals/checkout_externals" +echo "please type './bin/git-fleximod update'" +echo "For additional information, please type './bin/git-fleximod --help'" From 709c3da94d1816b42268bf98a4b3d947bdc29a9d Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 29 May 2024 16:30:06 -0600 Subject: [PATCH 215/408] remove unnecessary import call --- cime_config/SystemTests/pvt.py | 2 -- cime_config/SystemTests/systemtest_utils.py | 5 ++--- 2 files changed, 2 insertions(+), 5 deletions(-) diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py index 05da935a0e..feef6cb04c 100644 --- a/cime_config/SystemTests/pvt.py +++ b/cime_config/SystemTests/pvt.py @@ -8,12 +8,10 @@ - use CLM_ACCELERATED_SPINUP? 2) run a transient landuse case with use_fates_lupft - start from the restart file generated in (1) - """ from CIME.XML.standard_module_setup import * from CIME.SystemTests.system_tests_common import SystemTestsCommon from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files -from systemtest_utils import find_user_nl_option import shutil, glob, os logger = logging.getLogger(__name__) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 2591ac4223..c39f5171ba 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -85,9 +85,8 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): except: print(f"ERROR trying to run {tool_name}.") raise -""" -Read a user_nl file and return the namelist option if found -""" + +# Read a user_nl file and return the namelist option if found def find_user_nl_option(caseroot, component, namelist_option): # This is a copy of the CIME _get_list_of_user_nl_files From 1ed3f1967ed4564e2809841ca8a99b09a479299f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 29 May 2024 16:46:46 -0600 Subject: [PATCH 216/408] Replace cheyenne with derecho in a .rst file --- .../obtaining-and-building-ctsm.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst index ef24e695b9..907f63f211 100644 --- a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst +++ b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst @@ -29,9 +29,9 @@ Obtain CTSM by running:: ./bin/git-fleximod update Then build CTSM and its dependencies. On a machine that has been ported to CIME, the -command will look like this (example given for NCAR's ``cheyenne`` machine):: +command will look like this (example given for NCAR's ``derecho`` machine):: - ./lilac/build_ctsm /glade/scratch/$USER/ctsm_build_dir --machine cheyenne --compiler intel + ./lilac/build_ctsm /glade/scratch/$USER/ctsm_build_dir --machine derecho --compiler intel and then, before building the atmosphere model:: @@ -145,13 +145,13 @@ the `CIME documentation`_. Building on a CIME-supported machine ------------------------------------ -If you are using a machine that has been ported to CIME_ (for example, NCAR's ``cheyenne`` +If you are using a machine that has been ported to CIME_ (for example, NCAR's ``derecho`` machine), then you do not need to specify much information to ``build_ctsm``. In addition, in this case, CIME will load the appropriate modules and set the appropriate environment variables at build time, so you do not need to do anything to set up your environment ahead of time. **Building CTSM with LILAC requires ESMF. ESMF is currently an optional CIME dependency, so many CIME-ported machines do not provide information on an ESMF -installation. NCAR's cheyenne machine DOES provide ESMF, but for other machines, you may +installation. NCAR's derecho machine DOES provide ESMF, but for other machines, you may need to add this to your CIME port.** To build CTSM and its dependencies in this case, run:: @@ -231,7 +231,7 @@ Example usage for a Mac (a simple case) is:: ./lilac/build_ctsm ~/ctsm_build_dir --os Darwin --compiler gnu --netcdf-path /usr/local --esmf-mkfile-path /Users/sacks/ESMF/esmf8.0.0/lib/libO/Darwin.gfortranclang.64.mpich3.default/esmf.mk --max-mpitasks-per-node 4 --no-pnetcdf -Example usage for NCAR's ``cheyenne`` machine (a more complex case) is:: +Example usage for NCAR's ``derecho`` machine (a more complex case) is:: module purge module load ncarenv/1.3 python/3.7.9 cmake intel/19.1.1 esmf_libs mkl From 4f9db007afa9b3e1705c7bad78c2cc71714d9cd6 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 30 May 2024 11:51:36 -0600 Subject: [PATCH 217/408] Add "bin/" before git-fleximod in README documentation --- README | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README b/README index 97daae2d5a..07d9c7b13d 100644 --- a/README +++ b/README @@ -50,7 +50,7 @@ lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for test -------------- CTSM Testing scripts for CTSM offline tools (deprecated) tools ------------- CTSM Offline tools to prepare input datasets and process output. cime_config ------- Configuration files of cime for compsets and CTSM settings -git-fleximod ------ Script to manage the external source directories +bin/git-fleximod -- Script to manage the external source directories py_env_create ----- Script to setup the python environment for CTSM python tools using conda python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts From 8ac86a1f21704e952b5dbb753f51cb4ddcfd47f4 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 30 May 2024 12:10:04 -0600 Subject: [PATCH 218/408] Replacing README_EXTERNALS.rst with README_GITFLEXIMOD.rst --- README_GITFLEXIMOD.rst | 127 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 127 insertions(+) create mode 100644 README_GITFLEXIMOD.rst diff --git a/README_GITFLEXIMOD.rst b/README_GITFLEXIMOD.rst new file mode 100644 index 0000000000..f91ef30fae --- /dev/null +++ b/README_GITFLEXIMOD.rst @@ -0,0 +1,127 @@ +Obtaining the full model code and associated scripting infrastructure +===================================================================== + +CTSM is released via GitHub. You will need some familiarity with git in order +to modify the code and commit these changes. However, to simply checkout and run the +code, no git knowledge is required other than what is documented in the following steps. + +To obtain the CTSM code you need to do the following: + +#. Clone the repository. :: + + git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox + + This will create a directory ``my_ctsm_sandbox/`` in your current working directory. + +#. Run **./bin/git-fleximod update**. :: + + ./bin/git-fleximod update + + **git-fleximod** is a package manager that will + populate the ctsm directory with the relevant versions of each of the + components along with the CIME infrastructure code. + +At this point you have a working version of CTSM. + +To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ . + +More details on git-fleximod +---------------------------- + +The file **Externals.cfg** in your top-level CTSM directory tells +**git-fleximod** which tag/branch of each component should be +brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**. + +NOTE: git-fleximod will always attempt +to make the working copy exactly match the externals description. If +you manually modify an external without updating Externals.cfg, e.g. switch +to a different tag, then rerunning git-fleximod will switch you +back to the external described in Externals.cfg. See below +documentation `Customizing your CTSM sandbox`_ for more details. + +**You need to rerun git-fleximod whenever Externals.cfg has +changed** (unless you have already manually updated the relevant +external(s) to have the correct branch/tag checked out). Common times +when this is needed are: + +* After checking out a new CTSM branch/tag + +* After merging some other CTSM branch/tag into your currently + checked-out branch + +**./bin/git-fleximod** must be run from the root of the source +tree. For example, if you cloned CTSM with:: + + git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox + +then you must run **./bin/git-fleximod** from +``/path/to/my_ctsm_sandbox``. + +To see more details of **git-fleximod**, issue :: + + ./bin/git-fleximod --help + +Customizing your CTSM sandbox +============================= + +There are several use cases to consider when you want to customize or modify your CTSM sandbox. + +Switching to a different CTSM branch or tag +------------------------------------------- + +If you have already checked out a branch or tag and **HAVE NOT MADE ANY +MODIFICATIONS** it is simple to change your sandbox. Say that you +checked out ctsm1.0.0 but really wanted to have ctsm1.1.0; +you would simply do the following:: + + git checkout ctsm1.1.0 + ./bin/git-fleximod + +You should **not** use this method if you have made any source code +changes, or if you have any ongoing CTSM cases that were created from +this sandbox. In these cases, it is often easiest to do a second **git +clone**. + +Pointing to a different version of a component +---------------------------------------------- + +Each entry in **Externals.cfg** has the following form (we use CIME as an +example below):: + + [cime] + local_path = cime + protocol = git + repo_url = https://github.com/CESM-Development/cime + tag = cime5.4.0-alpha.20 + required = True + +Each entry specifies either a tag, a hash or a branch. To point to a new tag: + +#. Modify the relevant entry/entries in **Externals.cfg** (e.g., changing + ``cime5.4.0-alpha.20`` to ``cime5.4.0-alpha.21`` above) + +#. Checkout the new component(s):: + + ./bin/git-fleximod + +To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``. + +To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.) + +Keep in mind that changing individual components from a tag may result +in an invalid model (won't compile, won't run, not scientifically +meaningful) and is unsupported. + +Committing your change to Externals.cfg +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +After making this change, it's a good idea to commit the change in your +local CTSM git repository. First create a branch in your local +repository, then commit it. (Unlike with subversion, branches are stored +locally unless you explicitly push them up to GitHub. Feel free to +create whatever local branches you'd like.) For example:: + + git checkout -b my_ctsm_branch + git add Externals.cfg + git commit -m "Update CIME to cime5.4.0-alpha.20" + From 03762a081fd3f283c4ff1b9336fe14b7f71a051a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 30 May 2024 16:08:27 -0600 Subject: [PATCH 219/408] Updates to README_GITFLEXIMOD.rst as per Jim's review --- README_GITFLEXIMOD.rst | 68 +++++++++++++++++------------------------- 1 file changed, 28 insertions(+), 40 deletions(-) diff --git a/README_GITFLEXIMOD.rst b/README_GITFLEXIMOD.rst index f91ef30fae..ab8c412cee 100644 --- a/README_GITFLEXIMOD.rst +++ b/README_GITFLEXIMOD.rst @@ -15,11 +15,15 @@ To obtain the CTSM code you need to do the following: #. Run **./bin/git-fleximod update**. :: + cd my_ctsm_sandbox ./bin/git-fleximod update + ./bin/git-fleximod --help # for a user's guide **git-fleximod** is a package manager that will populate the ctsm directory with the relevant versions of each of the components along with the CIME infrastructure code. + Additional documentation for git-fleximod appears here: + https://github.com/ESMCI/git-fleximod?tab=readme-ov-file#git-fleximod At this point you have a working version of CTSM. @@ -28,18 +32,18 @@ To see full details of how to set up a case, compile and run, see the CIME docum More details on git-fleximod ---------------------------- -The file **Externals.cfg** in your top-level CTSM directory tells +The file **.gitmodules** in your top-level CTSM directory tells **git-fleximod** which tag/branch of each component should be -brought in to generate your sandbox. **Externals_CLM.cfg** is used similarly to point to the correct version of FATES (and possibly other CTSM-specific externals in the future); the below instructions referring to **Externals.cfg** also apply to modifying **Externals_CLM.cfg**. +brought in to generate your sandbox. -NOTE: git-fleximod will always attempt -to make the working copy exactly match the externals description. If -you manually modify an external without updating Externals.cfg, e.g. switch -to a different tag, then rerunning git-fleximod will switch you -back to the external described in Externals.cfg. See below -documentation `Customizing your CTSM sandbox`_ for more details. +NOTE: If you manually modify an external without updating .gitmodules, +e.g. switch to a different tag, then rerunning git-fleximod will warn you of +local changes you need to resolve. +git-fleximod will not change a modified external back to what is specified in +.gitmodules without the --force option. +See below documentation `Customizing your CTSM sandbox`_ for more details. -**You need to rerun git-fleximod whenever Externals.cfg has +**You need to rerun git-fleximod whenever .gitmodules has changed** (unless you have already manually updated the relevant external(s) to have the correct branch/tag checked out). Common times when this is needed are: @@ -49,18 +53,6 @@ when this is needed are: * After merging some other CTSM branch/tag into your currently checked-out branch -**./bin/git-fleximod** must be run from the root of the source -tree. For example, if you cloned CTSM with:: - - git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox - -then you must run **./bin/git-fleximod** from -``/path/to/my_ctsm_sandbox``. - -To see more details of **git-fleximod**, issue :: - - ./bin/git-fleximod --help - Customizing your CTSM sandbox ============================= @@ -75,7 +67,7 @@ checked out ctsm1.0.0 but really wanted to have ctsm1.1.0; you would simply do the following:: git checkout ctsm1.1.0 - ./bin/git-fleximod + ./bin/git-fleximod update You should **not** use this method if you have made any source code changes, or if you have any ongoing CTSM cases that were created from @@ -85,35 +77,31 @@ clone**. Pointing to a different version of a component ---------------------------------------------- -Each entry in **Externals.cfg** has the following form (we use CIME as an +Each entry in **.gitmodules** has the following form (we use CIME as an example below):: - [cime] - local_path = cime - protocol = git - repo_url = https://github.com/CESM-Development/cime - tag = cime5.4.0-alpha.20 - required = True + [submodule "cime"] + path = cime + url = https://github.com/ESMCI/cime + fxtag = cime6.0.246 + fxrequired = ToplevelRequired + fxDONOTUSEurl = https://github.com/ESMCI/cime -Each entry specifies either a tag, a hash or a branch. To point to a new tag: +Each entry specifies either a tag or a hash. To point to a new tag or hash: -#. Modify the relevant entry/entries in **Externals.cfg** (e.g., changing - ``cime5.4.0-alpha.20`` to ``cime5.4.0-alpha.21`` above) +#. Modify the relevant entry/entries in **.gitmodules** (e.g., changing + ``cime6.0.246`` to ``cime6.0.247`` above) #. Checkout the new component(s):: - ./bin/git-fleximod - -To point to a hash, the process is the same, except also change ``tag = ...`` to ``hash = ...``. - -To point to a branch, use ``branch = ...``. Pointing to a branch means that, each time you run ``./bin/git-fleximod`` you will get the current latest version of that branch. This can be convenient for in-progress development work, but should not be used when you need a stable version for scientific simulations. There are a number of gotchas with this workflow, so in general you should default to pointing to fixed hashes. (For CTSM master, we require a fixed hash or, usually, a tag.) + ./bin/git-fleximod update Keep in mind that changing individual components from a tag may result in an invalid model (won't compile, won't run, not scientifically meaningful) and is unsupported. -Committing your change to Externals.cfg -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Committing your change to .gitmodules +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ After making this change, it's a good idea to commit the change in your local CTSM git repository. First create a branch in your local @@ -122,6 +110,6 @@ locally unless you explicitly push them up to GitHub. Feel free to create whatever local branches you'd like.) For example:: git checkout -b my_ctsm_branch - git add Externals.cfg + git add .gitmodules git commit -m "Update CIME to cime5.4.0-alpha.20" From 6fa0255660c848b4f49603511b1da79750b686c8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 30 May 2024 16:09:26 -0600 Subject: [PATCH 220/408] Jim's suggestions for doc/.../lilac/.../obtaining-and-building-ctsm.rst --- .../obtaining-and-building-ctsm.rst | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst index 907f63f211..fcd8235b62 100644 --- a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst +++ b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst @@ -91,7 +91,7 @@ Building CTSM requires: - ESMF version 8 or later - - **ESMF is not needed in general for CTSM, but is needed for LILAC** + - **ESMF is needed for LILAC (and for CESM3 and later)** Obtaining CTSM ============== @@ -149,10 +149,11 @@ If you are using a machine that has been ported to CIME_ (for example, NCAR's `` machine), then you do not need to specify much information to ``build_ctsm``. In addition, in this case, CIME will load the appropriate modules and set the appropriate environment variables at build time, so you do not need to do anything to set up your environment -ahead of time. **Building CTSM with LILAC requires ESMF. ESMF is currently an optional -CIME dependency, so many CIME-ported machines do not provide information on an ESMF -installation. NCAR's derecho machine DOES provide ESMF, but for other machines, you may -need to add this to your CIME port.** +ahead of time. **Building CTSM with LILAC requires ESMF. ESMF is an optional +CIME dependency before CESM3 and not optional for CESM3. +NCAR's derecho machine DOES provide ESMF. For other machines, you may +need to add this to your CIME port. Please see esmf.org for download and build +instructions.** To build CTSM and its dependencies in this case, run:: From ae93d22bfee601a9fbe4561cedbd77945ab23bbf Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 30 May 2024 16:42:18 -0600 Subject: [PATCH 221/408] Remove cheyenne from testlis_clm.xml --- cime_config/testdefs/testlist_clm.xml | 651 +------------------------- 1 file changed, 1 insertion(+), 650 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 9cfba6f5b3..1ac2334ba8 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -43,8 +43,6 @@ - - @@ -259,24 +257,14 @@ --> - - - - - - - - - - @@ -360,8 +348,6 @@ - - @@ -422,15 +408,6 @@ - - - - - - - - - @@ -440,14 +417,6 @@ - - - - - - - - @@ -456,14 +425,6 @@ - - - - - - - - @@ -474,7 +435,6 @@ - @@ -483,8 +443,6 @@ - - @@ -494,7 +452,6 @@ - @@ -512,7 +469,6 @@ - @@ -539,8 +495,6 @@ - - @@ -548,15 +502,6 @@ - - - - - - - - - @@ -568,7 +513,6 @@ - @@ -788,7 +732,6 @@ - @@ -798,7 +741,6 @@ - @@ -808,7 +750,6 @@ - @@ -817,8 +758,6 @@ - - @@ -828,7 +767,6 @@ - @@ -838,8 +776,6 @@ - - @@ -857,7 +793,6 @@ - @@ -866,8 +801,6 @@ - - @@ -877,7 +810,6 @@ - @@ -922,15 +854,6 @@ - - - - - - - - - @@ -940,15 +863,6 @@ - - - - - - - - - @@ -960,7 +874,6 @@ - @@ -984,17 +897,6 @@ - - - - - - - - - - - @@ -1006,14 +908,6 @@ - - - - - - - - @@ -1022,15 +916,6 @@ - - - - - - - - - @@ -1058,14 +943,6 @@ - - - - - - - - @@ -1074,14 +951,6 @@ - - - - - - - - @@ -1090,14 +959,6 @@ - - - - - - - - @@ -1106,15 +967,6 @@ - - - - - - - - - @@ -1124,15 +976,6 @@ - - - - - - - - - @@ -1142,15 +985,6 @@ - - - - - - - - - @@ -1160,15 +994,6 @@ - - - - - - - - - @@ -1180,8 +1005,6 @@ - - @@ -1201,7 +1024,6 @@ - @@ -1210,8 +1032,6 @@ - - @@ -1229,7 +1049,6 @@ - @@ -1286,15 +1105,6 @@ - - - - - - - - - @@ -1306,7 +1116,6 @@ - @@ -1314,15 +1123,6 @@ - - - - - - - - - @@ -1333,14 +1133,6 @@ - - - - - - - - @@ -1349,15 +1141,6 @@ - - - - - - - - - @@ -1367,15 +1150,6 @@ - - - - - - - - - @@ -1387,23 +1161,12 @@ - - - - - - - - - - - @@ -1414,16 +1177,6 @@ - - - - - - - - - - @@ -1434,16 +1187,6 @@ - - - - - - - - - - @@ -1454,15 +1197,6 @@ - - - - - - - - - @@ -1472,14 +1206,6 @@ - - - - - - - - @@ -1489,15 +1215,6 @@ - - - - - - - - - @@ -1507,16 +1224,6 @@ - - - - - - - - - - @@ -1527,14 +1234,6 @@ - - - - - - - - @@ -1543,15 +1242,6 @@ - - - - - - - - - @@ -1561,16 +1251,6 @@ - - - - - - - - - - @@ -1581,16 +1261,6 @@ - - - - - - - - - - @@ -1603,22 +1273,12 @@ - - - - - - - - - - @@ -1639,7 +1299,6 @@ - @@ -1649,7 +1308,6 @@ - @@ -1659,7 +1317,6 @@ - @@ -1667,15 +1324,6 @@ - - - - - - - - - @@ -1687,10 +1335,6 @@ - - - - @@ -1702,7 +1346,6 @@ - @@ -1712,7 +1355,6 @@ - @@ -1721,7 +1363,6 @@ - @@ -1730,8 +1371,6 @@ - - @@ -1750,7 +1389,6 @@ - @@ -1805,7 +1443,6 @@ - @@ -1822,15 +1459,6 @@ - - - - - - - - - @@ -1840,15 +1468,6 @@ - - - - - - - - - @@ -1858,15 +1477,6 @@ - - - - - - - - - @@ -1878,7 +1488,6 @@ - @@ -1888,8 +1497,6 @@ - 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@@ -3237,7 +2667,6 @@ - @@ -3248,7 +2677,6 @@ - @@ -3258,7 +2686,6 @@ - @@ -3268,7 +2695,6 @@ - @@ -3278,7 +2704,6 @@ - @@ -3287,7 +2712,6 @@ - @@ -3298,7 +2722,6 @@ - @@ -3308,7 +2731,6 @@ - @@ -3319,7 +2741,6 @@ - @@ -3329,7 +2750,6 @@ - @@ -3339,7 +2759,6 @@ - @@ -3348,16 +2767,6 @@ - - - - - - - - - - @@ -3370,7 +2779,6 @@ - @@ -3380,7 +2788,6 @@ - @@ -3391,7 +2798,6 @@ - @@ -3402,8 +2808,6 @@ - - @@ -3414,7 +2818,6 @@ - @@ -3424,9 +2827,6 @@ - - - @@ -3448,7 +2848,6 @@ - @@ -3458,11 +2857,8 @@ - - - @@ -3471,7 +2867,6 @@ - @@ -3491,7 +2886,6 @@ - @@ -3539,8 +2933,6 @@ - - @@ -3561,16 +2953,6 @@ - - - - - - - - - - @@ -3580,16 +2962,6 @@ - - - - - - - - - - @@ -3599,16 +2971,6 @@ - - - - - - - - - - @@ -3618,15 +2980,6 @@ - - - - - - - - - @@ -3639,7 +2992,6 @@ - @@ -3650,7 +3002,6 @@ - From b25a02d904bf8cd010fb400b4b0181361f077d83 Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Fri, 31 May 2024 10:20:07 -0600 Subject: [PATCH 222/408] fix subtree add --- .../git-fleximod/.github/workflows/pre-commit | 13 - .../.github/workflows/pytest.yaml | 77 -- .lib/git-fleximod/.pre-commit-config.yaml | 18 - .lib/git-fleximod/License | 20 - .lib/git-fleximod/README.md | 110 --- .lib/git-fleximod/doc/Makefile | 20 - .lib/git-fleximod/doc/conf.py | 26 - .lib/git-fleximod/doc/index.rst | 24 - .lib/git-fleximod/doc/make.bat | 35 - .lib/git-fleximod/escomp_install | 25 - .lib/git-fleximod/git_fleximod/__init__.py | 0 .lib/git-fleximod/git_fleximod/cli.py | 119 --- .../git-fleximod/git_fleximod/git_fleximod.py | 601 --------------- .../git-fleximod/git_fleximod/gitinterface.py | 79 -- .lib/git-fleximod/git_fleximod/gitmodules.py | 97 --- .../git-fleximod/git_fleximod/lstripreader.py | 43 -- .lib/git-fleximod/git_fleximod/metoflexi.py | 236 ------ .lib/git-fleximod/git_fleximod/utils.py | 365 --------- .lib/git-fleximod/poetry.lock | 693 ------------------ .lib/git-fleximod/pyproject.toml | 41 -- .lib/git-fleximod/tbump.toml | 43 -- .lib/git-fleximod/tests/__init__.py | 3 - .lib/git-fleximod/tests/conftest.py | 138 ---- .lib/git-fleximod/tests/test_a_import.py | 8 - .lib/git-fleximod/tests/test_b_update.py | 26 - .lib/git-fleximod/tests/test_c_required.py | 30 - .lib/git-fleximod/tests/test_d_complex.py | 67 -- 27 files changed, 2957 deletions(-) delete mode 100644 .lib/git-fleximod/.github/workflows/pre-commit delete mode 100644 .lib/git-fleximod/.github/workflows/pytest.yaml delete mode 100644 .lib/git-fleximod/.pre-commit-config.yaml delete mode 100644 .lib/git-fleximod/License delete mode 100644 .lib/git-fleximod/README.md delete mode 100644 .lib/git-fleximod/doc/Makefile delete mode 100644 .lib/git-fleximod/doc/conf.py delete mode 100644 .lib/git-fleximod/doc/index.rst delete mode 100644 .lib/git-fleximod/doc/make.bat delete mode 100644 .lib/git-fleximod/escomp_install delete mode 100644 .lib/git-fleximod/git_fleximod/__init__.py delete mode 100644 .lib/git-fleximod/git_fleximod/cli.py delete mode 100755 .lib/git-fleximod/git_fleximod/git_fleximod.py delete mode 100644 .lib/git-fleximod/git_fleximod/gitinterface.py delete mode 100644 .lib/git-fleximod/git_fleximod/gitmodules.py delete mode 100644 .lib/git-fleximod/git_fleximod/lstripreader.py delete mode 100755 .lib/git-fleximod/git_fleximod/metoflexi.py delete mode 100644 .lib/git-fleximod/git_fleximod/utils.py delete mode 100644 .lib/git-fleximod/poetry.lock delete mode 100644 .lib/git-fleximod/pyproject.toml delete mode 100644 .lib/git-fleximod/tbump.toml delete mode 100644 .lib/git-fleximod/tests/__init__.py delete mode 100644 .lib/git-fleximod/tests/conftest.py delete mode 100644 .lib/git-fleximod/tests/test_a_import.py delete mode 100644 .lib/git-fleximod/tests/test_b_update.py delete mode 100644 .lib/git-fleximod/tests/test_c_required.py delete mode 100644 .lib/git-fleximod/tests/test_d_complex.py diff --git a/.lib/git-fleximod/.github/workflows/pre-commit b/.lib/git-fleximod/.github/workflows/pre-commit deleted file mode 100644 index 1a6ad0082a..0000000000 --- a/.lib/git-fleximod/.github/workflows/pre-commit +++ /dev/null @@ -1,13 +0,0 @@ -name: pre-commit -on: - pull_request: - push: - branches: [main] - -jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v3 - - uses: pre-commit/action@v3.0.0 diff --git a/.lib/git-fleximod/.github/workflows/pytest.yaml b/.lib/git-fleximod/.github/workflows/pytest.yaml deleted file mode 100644 index 0868dd9a33..0000000000 --- a/.lib/git-fleximod/.github/workflows/pytest.yaml +++ /dev/null @@ -1,77 +0,0 @@ -# Run this job on pushes to `main`, and for pull requests. If you don't specify -# `branches: [main], then this actions runs _twice_ on pull requests, which is -# annoying. - -on: - push: - branches: [main] - pull_request: - branches: [main] - -jobs: - test: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and - # reference the matrixe python version here. - - uses: actions/setup-python@v5 - with: - python-version: '3.9' - - # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow - # from installing Poetry every time, which can be slow. Note the use of the Poetry version - # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache - # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be - # mildly cleaner by using an environment variable, but I don't really care. - - name: cache poetry install - uses: actions/cache@v4 - with: - path: ~/.local - key: poetry-1.7.1 - - # Install Poetry. You could do this manually, or there are several actions that do this. - # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to - # Poetry's default install script, which feels correct. I pin the Poetry version here - # because Poetry does occasionally change APIs between versions and I don't want my - # actions to break if it does. - # - # The key configuration value here is `virtualenvs-in-project: true`: this creates the - # venv as a `.venv` in your testing directory, which allows the next step to easily - # cache it. - - uses: snok/install-poetry@v1 - with: - version: 1.7.1 - virtualenvs-create: true - virtualenvs-in-project: true - - # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache - # key: if you're using multiple Python versions, or multiple OSes, you'd need to include - # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock. - - name: cache deps - id: cache-deps - uses: actions/cache@v4 - with: - path: .venv - key: pydeps-${{ hashFiles('**/poetry.lock') }} - - # Install dependencies. `--no-root` means "install all dependencies but not the project - # itself", which is what you want to avoid caching _your_ code. The `if` statement - # ensures this only runs on a cache miss. - - run: poetry install --no-interaction --no-root - if: steps.cache-deps.outputs.cache-hit != 'true' - - # Now install _your_ project. This isn't necessary for many types of projects -- particularly - # things like Django apps don't need this. But it's a good idea since it fully-exercises the - # pyproject.toml and makes that if you add things like console-scripts at some point that - # they'll be installed and working. - - run: poetry install --no-interaction - - # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml` - # so this line is super-simple. But it could be as complex as you need. - - run: | - git config --global user.name "${GITHUB_ACTOR}" - git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com" - poetry run pytest - diff --git a/.lib/git-fleximod/.pre-commit-config.yaml b/.lib/git-fleximod/.pre-commit-config.yaml deleted file mode 100644 index 2f6089da72..0000000000 --- a/.lib/git-fleximod/.pre-commit-config.yaml +++ /dev/null @@ -1,18 +0,0 @@ -exclude: ^utils/.*$ - -repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.0.1 - hooks: - - id: end-of-file-fixer - - id: trailing-whitespace - - repo: https://github.com/psf/black - rev: 22.3.0 - hooks: - - id: black - - repo: https://github.com/PyCQA/pylint - rev: v2.11.1 - hooks: - - id: pylint - args: - - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member diff --git a/.lib/git-fleximod/License b/.lib/git-fleximod/License deleted file mode 100644 index 2c6fe768c2..0000000000 --- a/.lib/git-fleximod/License +++ /dev/null @@ -1,20 +0,0 @@ -Copyright 2024 National Center for Atmospheric Sciences (NCAR) - -Permission is hereby granted, free of charge, to any person obtaining -a copy of this software and associated documentation files (the -“Softwareâ€), to deal in the Software without restriction, including -without limitation the rights to use, copy, modify, merge, publish, -distribute, sublicense, and/or sell copies of the Software, and to -permit persons to whom the Software is furnished to do so, subject to -the following conditions: - -The above copyright notice and this permission notice shall be -included in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED “AS ISâ€, WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE -LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION -OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION -WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/.lib/git-fleximod/README.md b/.lib/git-fleximod/README.md deleted file mode 100644 index d1ef632f28..0000000000 --- a/.lib/git-fleximod/README.md +++ /dev/null @@ -1,110 +0,0 @@ -# git-fleximod - -Flexible, Enhanced Submodule Management for Git - -## Overview - -Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way. - -## Installation - -#TODO Install using pip: -# pip install git-fleximod - If you choose to locate git-fleximod in your path you can access it via command: git fleximod - -## Usage - - Basic Usage: - git fleximod [options] - Available Commands: - status: Display the status of submodules. - update: Update submodules to the tag indicated in .gitmodules variable fxtag. - test: Make sure that fxtags and submodule hashes are consistant, - make sure that official urls (as defined by fxDONOTUSEurl) are set - make sure that fxtags are defined for all submodules - Additional Options: - See git fleximod --help for more details. - -## Supported .gitmodules Variables - - fxtag: Specify a specific tag or branch to checkout for a submodule. - fxrequired: Mark a submodule's checkout behavior, with allowed values: - - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module). - - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module). - - AlwaysRequired: Always required (always checked out). - - AlwaysOptional: Always optional (checked out with --optional flag). - fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths. - fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks - **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be - changed by users. Use the url variable to change to a fork if desired. - -## Sparse Checkouts - - To enable sparse checkout for a submodule, set the fxsparse variable - in the .gitmodules file to the path of a file containing the desired - sparse checkout paths. Git-fleximod will automatically configure - sparse checkout based on this file when applicable commands are run. - See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set) - for details on the format of this file. - -## Tests - - The git fleximod test action is designed to be used by, for example, github workflows - to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags - -## Examples - -Here are some common usage examples: - -Update all submodules, including optional ones: -```bash - git fleximod update --optional -``` - -Updating a specific submodule to the fxtag indicated in .gitmodules: - -```bash - git fleximod update submodule-name -``` -Example .gitmodules entry: -```ini, toml - [submodule "cosp2"] - path = src/physics/cosp2/src - url = https://github.com/CFMIP/COSPv2.0 - fxsparse = ../.cosp_sparse_checkout - fxrequired = AlwaysRequired - fxtag = v2.1.4cesm -``` -Explanation: - -This entry indicates that the submodule named cosp2 at tag v2.1.4cesm -should be checked out into the directory src/physics/cosp2/src -relative to the .gitmodules directory. It should be checked out from -the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as -described in the file ../.cosp_sparse_checkout relative to the path -directory. It should be checked out anytime this .gitmodules entry is -read. - -Additional example: -```ini, toml - [submodule "cime"] - path = cime - url = https://github.com/jedwards4b/cime - fxrequired = ToplevelRequired - fxtag = cime6.0.198_rme01 -``` - -Explanation: - -This entry indicates that the submodule cime should be checked out -into a directory named cime at tag cime6.0.198_rme01 from the URL -https://github.com/jedwards4b/cime. This should only be done if -the .gitmodules file is at the top level of the repository clone. - -## Contributing - -We welcome contributions! Please see the CONTRIBUTING.md file for guidelines. - -## License - -Git-fleximod is released under the MIT License. diff --git a/.lib/git-fleximod/doc/Makefile b/.lib/git-fleximod/doc/Makefile deleted file mode 100644 index d4bb2cbb9e..0000000000 --- a/.lib/git-fleximod/doc/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/.lib/git-fleximod/doc/conf.py b/.lib/git-fleximod/doc/conf.py deleted file mode 100644 index 423099eec9..0000000000 --- a/.lib/git-fleximod/doc/conf.py +++ /dev/null @@ -1,26 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# For the full list of built-in configuration values, see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - -# -- Project information ----------------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information - -project = "git-fleximod" -author = "Jim Edwards " -release = "0.4.0" - -# -- General configuration --------------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration - -extensions = ["sphinx_argparse_cli"] - -templates_path = ["_templates"] -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] - - -# -- Options for HTML output ------------------------------------------------- -# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output - -html_theme = "alabaster" -html_static_path = ["_static"] diff --git a/.lib/git-fleximod/doc/index.rst b/.lib/git-fleximod/doc/index.rst deleted file mode 100644 index 0f9c1a7f7e..0000000000 --- a/.lib/git-fleximod/doc/index.rst +++ /dev/null @@ -1,24 +0,0 @@ -.. git-fleximod documentation master file, created by - sphinx-quickstart on Sat Feb 3 12:02:22 2024. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to git-fleximod's documentation! -======================================== - -.. toctree:: - :maxdepth: 2 - :caption: Contents: -.. module:: sphinxcontrib.autoprogram -.. sphinx_argparse_cli:: - :module: git_fleximod.cli - :func: get_parser - :prog: git-fleximod - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/.lib/git-fleximod/doc/make.bat b/.lib/git-fleximod/doc/make.bat deleted file mode 100644 index 32bb24529f..0000000000 --- a/.lib/git-fleximod/doc/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -if "%1" == "" goto help - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/.lib/git-fleximod/escomp_install b/.lib/git-fleximod/escomp_install deleted file mode 100644 index ae782e72a4..0000000000 --- a/.lib/git-fleximod/escomp_install +++ /dev/null @@ -1,25 +0,0 @@ -#!/usr/bin/env python -# updates git-fleximod in an ESCOMP model -# this script should be run from the model root directory, it expects -# git-fleximod to already be installed with the script in bin -# and the classes in lib/python/site-packages -import sys -import shutil -import os - -from glob import iglob - -fleximod_root = sys.argv[1] -fleximod_path = os.path.join(fleximod_root,"src","git-fleximod") -if os.path.isfile(fleximod_path): - with open(fleximod_path,"r") as f: - fleximod = f.readlines() - with open(os.path.join(".","bin","git-fleximod"),"w") as f: - for line in fleximod: - f.write(line) - if "import argparse" in line: - f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n') - - for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")): - shutil.copy(file, - os.path.join("lib","python","site-packages","fleximod",os.path.basename(file))) diff --git a/.lib/git-fleximod/git_fleximod/__init__.py b/.lib/git-fleximod/git_fleximod/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/.lib/git-fleximod/git_fleximod/cli.py b/.lib/git-fleximod/git_fleximod/cli.py deleted file mode 100644 index 1fb959dad0..0000000000 --- a/.lib/git-fleximod/git_fleximod/cli.py +++ /dev/null @@ -1,119 +0,0 @@ -from pathlib import Path -import argparse - -__version__ = "0.7.4" - -def find_root_dir(filename=".git"): - d = Path.cwd() - root = Path(d.root) - while d != root: - attempt = d / filename - if attempt.is_dir(): - return attempt - d = d.parent - return None - - -def get_parser(): - description = """ - %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models - """ - parser = argparse.ArgumentParser( - description=description, formatter_class=argparse.RawDescriptionHelpFormatter - ) - - # - # user options - # - choices = ["update", "status", "test"] - parser.add_argument( - "action", - choices=choices, - default="update", - help=f"Subcommand of git-fleximod, choices are {choices[:-1]}", - ) - - parser.add_argument( - "components", - nargs="*", - help="Specific component(s) to checkout. By default, " - "all required submodules are checked out.", - ) - - parser.add_argument( - "-C", - "--path", - default=find_root_dir(), - help="Toplevel repository directory. Defaults to top git directory relative to current.", - ) - - parser.add_argument( - "-g", - "--gitmodules", - nargs="?", - default=".gitmodules", - help="The submodule description filename. " "Default: %(default)s.", - ) - - parser.add_argument( - "-x", - "--exclude", - nargs="*", - help="Component(s) listed in the gitmodules file which should be ignored.", - ) - parser.add_argument( - "-f", - "--force", - action="store_true", - default=False, - help="Override cautions and update or checkout over locally modified repository.", - ) - - parser.add_argument( - "-o", - "--optional", - action="store_true", - default=False, - help="By default only the required submodules " - "are checked out. This flag will also checkout the " - "optional submodules relative to the toplevel directory.", - ) - - parser.add_argument( - "-v", - "--verbose", - action="count", - default=0, - help="Output additional information to " - "the screen and log file. This flag can be " - "used up to two times, increasing the " - "verbosity level each time.", - ) - - parser.add_argument( - "-V", - "--version", - action="version", - version=f"%(prog)s {__version__}", - help="Print version and exit.", - ) - - # - # developer options - # - parser.add_argument( - "--backtrace", - action="store_true", - help="DEVELOPER: show exception backtraces as extra " "debugging output", - ) - - parser.add_argument( - "-d", - "--debug", - action="store_true", - default=False, - help="DEVELOPER: output additional debugging " - "information to the screen and log file.", - ) - - return parser diff --git a/.lib/git-fleximod/git_fleximod/git_fleximod.py b/.lib/git-fleximod/git_fleximod/git_fleximod.py deleted file mode 100755 index 103cc82a50..0000000000 --- a/.lib/git-fleximod/git_fleximod/git_fleximod.py +++ /dev/null @@ -1,601 +0,0 @@ -#!/usr/bin/env python -import sys - -MIN_PYTHON = (3, 7) -if sys.version_info < MIN_PYTHON: - sys.exit("Python %s.%s or later is required." % MIN_PYTHON) - -import os -import shutil -import logging -import textwrap -from git_fleximod import utils -from git_fleximod import cli -from git_fleximod.gitinterface import GitInterface -from git_fleximod.gitmodules import GitModules -from configparser import NoOptionError - -# logger variable is global -logger = None - - -def fxrequired_allowed_values(): - return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"] - - -def commandline_arguments(args=None): - parser = cli.get_parser() - - if args: - options = parser.parse_args(args) - else: - options = parser.parse_args() - - # explicitly listing a component overrides the optional flag - if options.optional or options.components: - fxrequired = [ - "ToplevelRequired", - "ToplevelOptional", - "AlwaysRequired", - "AlwaysOptional", - ] - else: - fxrequired = ["ToplevelRequired", "AlwaysRequired"] - - action = options.action - if not action: - action = "update" - handlers = [logging.StreamHandler()] - - if options.debug: - try: - open("fleximod.log", "w") - except PermissionError: - sys.exit("ABORT: Could not write file fleximod.log") - level = logging.DEBUG - handlers.append(logging.FileHandler("fleximod.log")) - elif options.verbose: - level = logging.INFO - else: - level = logging.WARNING - # Configure the root logger - logging.basicConfig( - level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers - ) - - if hasattr(options, "version"): - exit() - - return ( - options.path, - options.gitmodules, - fxrequired, - options.components, - options.exclude, - options.force, - action, - ) - - -def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"): - """ - This function performs a sparse checkout of a git submodule. It does so by first creating the .git/info/sparse-checkout fileq - in the submodule and then checking out the desired tag. If the submodule is already checked out, it will not be checked out again. - Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed. This is important - because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time - and disk space consuming. - - Parameters: - root_dir (str): The root directory for the git operation. - name (str): The name of the submodule. - url (str): The URL of the submodule. - path (str): The path to the submodule. - sparsefile (str): The sparse file for the submodule. - tag (str, optional): The tag to checkout. Defaults to "master". - - Returns: - None - """ - logger.info("Called sparse_checkout for {}".format(name)) - rgit = GitInterface(root_dir, logger) - superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree") - if superroot: - gitroot = superroot.strip() - else: - gitroot = root_dir.strip() - assert os.path.isdir(os.path.join(gitroot, ".git")) - # first create the module directory - if not os.path.isdir(os.path.join(root_dir, path)): - os.makedirs(os.path.join(root_dir, path)) - - # initialize a new git repo and set the sparse checkout flag - sprep_repo = os.path.join(root_dir, path) - sprepo_git = GitInterface(sprep_repo, logger) - if os.path.exists(os.path.join(sprep_repo, ".git")): - try: - logger.info("Submodule {} found".format(name)) - chk = sprepo_git.config_get_value("core", "sparseCheckout") - if chk == "true": - logger.info("Sparse submodule {} already checked out".format(name)) - return - except NoOptionError: - logger.debug("Sparse submodule {} not present".format(name)) - except Exception as e: - utils.fatal_error("Unexpected error {} occured.".format(e)) - - sprepo_git.config_set_value("core", "sparseCheckout", "true") - - # set the repository remote - - logger.info("Setting remote origin in {}/{}".format(root_dir, path)) - status = sprepo_git.git_operation("remote", "-v") - if url not in status: - sprepo_git.git_operation("remote", "add", "origin", url) - - topgit = os.path.join(gitroot, ".git") - - if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")): - with open(os.path.join(root_dir, ".git")) as f: - gitpath = os.path.relpath( - os.path.join(root_dir, f.read().split()[1]), - start=os.path.join(root_dir, path), - ) - topgit = os.path.join(gitpath, "modules") - else: - topgit = os.path.relpath( - os.path.join(root_dir, ".git", "modules"), - start=os.path.join(root_dir, path), - ) - - with utils.pushd(sprep_repo): - if not os.path.isdir(topgit): - os.makedirs(topgit) - topgit += os.sep + name - - if os.path.isdir(os.path.join(root_dir, path, ".git")): - with utils.pushd(sprep_repo): - shutil.move(".git", topgit) - with open(".git", "w") as f: - f.write("gitdir: " + os.path.relpath(topgit)) - # assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo))) - gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout")) - if os.path.isfile(gitsparse): - logger.warning( - "submodule {} is already initialized {}".format(name, topgit) - ) - return - - with utils.pushd(sprep_repo): - shutil.copy(sparsefile, gitsparse) - - # Finally checkout the repo - sprepo_git.git_operation("fetch", "origin", "--tags") - sprepo_git.git_operation("checkout", tag) - - print(f"Successfully checked out {name:>20} at {tag}") - rgit.config_set_value(f'submodule "{name}"', "active", "true") - rgit.config_set_value(f'submodule "{name}"', "url", url) - - -def single_submodule_checkout( - root, name, path, url=None, tag=None, force=False, optional=False -): - """ - This function checks out a single git submodule. - - Parameters: - root (str): The root directory for the git operation. - name (str): The name of the submodule. - path (str): The path to the submodule. - url (str, optional): The URL of the submodule. Defaults to None. - tag (str, optional): The tag to checkout. Defaults to None. - force (bool, optional): If set to True, forces the checkout operation. Defaults to False. - optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False. - - Returns: - None - """ - # function implementation... - git = GitInterface(root, logger) - repodir = os.path.join(root, path) - logger.info("Checkout {} into {}/{}".format(name, root, path)) - # if url is provided update to the new url - tmpurl = None - repo_exists = False - if os.path.exists(os.path.join(repodir, ".git")): - logger.info("Submodule {} already checked out".format(name)) - repo_exists = True - # Look for a .gitmodules file in the newly checkedout repo - if not repo_exists and url: - # ssh urls cause problems for those who dont have git accounts with ssh keys defined - # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was - # opened with a GitModules object we don't need to worry about restoring the file here - # it will be done by the GitModules class - if url.startswith("git@"): - tmpurl = url - url = url.replace("git@github.com:", "https://github.com/") - git.git_operation("clone", url, path) - smgit = GitInterface(repodir, logger) - if not tag: - tag = smgit.git_operation("describe", "--tags", "--always").rstrip() - smgit.git_operation("checkout", tag) - # Now need to move the .git dir to the submodule location - rootdotgit = os.path.join(root, ".git") - if os.path.isfile(rootdotgit): - with open(rootdotgit) as f: - line = f.readline() - if line.startswith("gitdir: "): - rootdotgit = line[8:].rstrip() - - newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name)) - if os.path.exists(newpath): - shutil.rmtree(os.path.join(repodir, ".git")) - else: - shutil.move(os.path.join(repodir, ".git"), newpath) - - with open(os.path.join(repodir, ".git"), "w") as f: - f.write("gitdir: " + os.path.relpath(newpath, start=repodir)) - - if not os.path.exists(repodir): - parent = os.path.dirname(repodir) - if not os.path.isdir(parent): - os.makedirs(parent) - git.git_operation("submodule", "add", "--name", name, "--", url, path) - - if not repo_exists or not tmpurl: - git.git_operation("submodule", "update", "--init", "--", path) - - if os.path.exists(os.path.join(repodir, ".gitmodules")): - # recursively handle this checkout - print(f"Recursively checking out submodules of {name}") - gitmodules = GitModules(logger, confpath=repodir) - requiredlist = ["AlwaysRequired"] - if optional: - requiredlist.append("AlwaysOptional") - submodules_checkout(gitmodules, repodir, requiredlist, force=force) - if not os.path.exists(os.path.join(repodir, ".git")): - utils.fatal_error( - f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}" - ) - - if tmpurl: - print(git.git_operation("restore", ".gitmodules")) - - return - - -def submodules_status(gitmodules, root_dir, toplevel=False): - testfails = 0 - localmods = 0 - needsupdate = 0 - for name in gitmodules.sections(): - path = gitmodules.get(name, "path") - tag = gitmodules.get(name, "fxtag") - required = gitmodules.get(name, "fxrequired") - level = required and "Toplevel" in required - if not path: - utils.fatal_error("No path found in .gitmodules for {}".format(name)) - newpath = os.path.join(root_dir, path) - logger.debug("newpath is {}".format(newpath)) - if not os.path.exists(os.path.join(newpath, ".git")): - rootgit = GitInterface(root_dir, logger) - # submodule commands use path, not name - url = gitmodules.get(name, "url") - url = url.replace("git@github.com:", "https://github.com/") - tags = rootgit.git_operation("ls-remote", "--tags", url) - atag = None - needsupdate += 1 - if not toplevel and level: - continue - for htag in tags.split("\n"): - if tag and tag in htag: - atag = (htag.split()[1])[10:] - break - if tag and tag == atag: - print(f"e {name:>20} not checked out, aligned at tag {tag}") - elif tag: - ahash = rootgit.git_operation( - "submodule", "status", "{}".format(path) - ).rstrip() - ahash = ahash[1 : len(tag) + 1] - if tag == ahash: - print(f"e {name:>20} not checked out, aligned at hash {ahash}") - else: - print( - f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}" - ) - testfails += 1 - else: - print(f"e {name:>20} has no fxtag defined in .gitmodules") - testfails += 1 - else: - with utils.pushd(newpath): - git = GitInterface(newpath, logger) - atag = git.git_operation("describe", "--tags", "--always").rstrip() - ahash = git.git_operation("status").partition("\n")[0].split()[-1] - if tag and atag == tag: - print(f" {name:>20} at tag {tag}") - elif tag and ahash[: len(tag)] == tag: - print(f" {name:>20} at hash {ahash}") - elif atag == ahash: - print(f" {name:>20} at hash {ahash}") - elif tag: - print( - f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}" - ) - testfails += 1 - needsupdate += 1 - else: - print( - f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}" - ) - testfails += 1 - - status = git.git_operation("status", "--ignore-submodules") - if "nothing to commit" not in status: - localmods = localmods + 1 - print("M" + textwrap.indent(status, " ")) - - return testfails, localmods, needsupdate - - -def submodules_update(gitmodules, root_dir, requiredlist, force): - _, localmods, needsupdate = submodules_status(gitmodules, root_dir) - - if localmods and not force: - local_mods_output() - return - if needsupdate == 0: - return - - for name in gitmodules.sections(): - fxtag = gitmodules.get(name, "fxtag") - path = gitmodules.get(name, "path") - url = gitmodules.get(name, "url") - logger.info( - "name={} path={} url={} fxtag={} requiredlist={}".format( - name, os.path.join(root_dir, path), url, fxtag, requiredlist - ) - ) - # if not os.path.exists(os.path.join(root_dir,path, ".git")): - fxrequired = gitmodules.get(name, "fxrequired") - assert fxrequired in fxrequired_allowed_values() - rgit = GitInterface(root_dir, logger) - superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree") - - fxsparse = gitmodules.get(name, "fxsparse") - - if ( - fxrequired - and (superroot and "Toplevel" in fxrequired) - or fxrequired not in requiredlist - ): - if "ToplevelOptional" == fxrequired: - print("Skipping optional component {}".format(name)) - continue - if fxsparse: - logger.debug( - "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format( - root_dir, name, url, path, fxsparse, fxtag - ) - ) - submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag) - else: - logger.info( - "Calling submodule_checkout({},{},{},{})".format( - root_dir, name, path, url - ) - ) - - single_submodule_checkout( - root_dir, - name, - path, - url=url, - tag=fxtag, - force=force, - optional=("AlwaysOptional" in requiredlist), - ) - - if os.path.exists(os.path.join(path, ".git")): - submoddir = os.path.join(root_dir, path) - with utils.pushd(submoddir): - git = GitInterface(submoddir, logger) - # first make sure the url is correct - upstream = git.git_operation("ls-remote", "--get-url").rstrip() - newremote = "origin" - if upstream != url: - # TODO - this needs to be a unique name - remotes = git.git_operation("remote", "-v") - if url in remotes: - for line in remotes: - if url in line and "fetch" in line: - newremote = line.split()[0] - break - else: - i = 0 - while newremote in remotes: - i = i + 1 - newremote = f"newremote.{i:02d}" - git.git_operation("remote", "add", newremote, url) - - tags = git.git_operation("tag", "-l") - if fxtag and fxtag not in tags: - git.git_operation("fetch", newremote, "--tags") - atag = git.git_operation("describe", "--tags", "--always").rstrip() - if fxtag and fxtag != atag: - try: - git.git_operation("checkout", fxtag) - print(f"{name:>20} updated to {fxtag}") - except Exception as error: - print(error) - elif not fxtag: - print(f"No fxtag found for submodule {name:>20}") - else: - print(f"{name:>20} up to date.") - - -def local_mods_output(): - text = """\ - The submodules labeled with 'M' above are not in a clean state. - The following are options for how to proceed: - (1) Go into each submodule which is not in a clean state and issue a 'git status' - Either revert or commit your changes so that the submodule is in a clean state. - (2) use the --force option to git-fleximod - (3) you can name the particular submodules to update using the git-fleximod command line - (4) As a last resort you can remove the submodule (via 'rm -fr [directory]') - then rerun git-fleximod update. -""" - print(text) - - -# checkout is done by update if required so this function may be depricated -def submodules_checkout(gitmodules, root_dir, requiredlist, force=False): - """ - This function checks out all git submodules based on the provided parameters. - - Parameters: - gitmodules (ConfigParser): The gitmodules configuration. - root_dir (str): The root directory for the git operation. - requiredlist (list): The list of required modules. - force (bool, optional): If set to True, forces the checkout operation. Defaults to False. - - Returns: - None - """ - # function implementation... - print("") - _, localmods, needsupdate = submodules_status(gitmodules, root_dir) - if localmods and not force: - local_mods_output() - return - if not needsupdate: - return - for name in gitmodules.sections(): - fxrequired = gitmodules.get(name, "fxrequired") - fxsparse = gitmodules.get(name, "fxsparse") - fxtag = gitmodules.get(name, "fxtag") - path = gitmodules.get(name, "path") - url = gitmodules.get(name, "url") - if fxrequired and fxrequired not in requiredlist: - if "Optional" in fxrequired: - print("Skipping optional component {}".format(name)) - continue - - if fxsparse: - logger.debug( - "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format( - root_dir, name, url, path, fxsparse, fxtag - ) - ) - submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag) - else: - logger.debug( - "Calling submodule_checkout({},{},{})".format(root_dir, name, path) - ) - single_submodule_checkout( - root_dir, - name, - path, - url=url, - tag=fxtag, - force=force, - optional="AlwaysOptional" in requiredlist, - ) - - -def submodules_test(gitmodules, root_dir): - """ - This function tests the git submodules based on the provided parameters. - - It first checks that fxtags are present and in sync with submodule hashes. - Then it ensures that urls are consistent with fxurls (not forks and not ssh) - and that sparse checkout files exist. - - Parameters: - gitmodules (ConfigParser): The gitmodules configuration. - root_dir (str): The root directory for the git operation. - - Returns: - int: The number of test failures. - """ - # First check that fxtags are present and in sync with submodule hashes - testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir) - print("") - # Then make sure that urls are consistant with fxurls (not forks and not ssh) - # and that sparse checkout files exist - for name in gitmodules.sections(): - url = gitmodules.get(name, "url") - fxurl = gitmodules.get(name, "fxDONOTMODIFYurl") - fxsparse = gitmodules.get(name, "fxsparse") - path = gitmodules.get(name, "path") - fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl - url = url[:-4] if url.endswith(".git") else url - if not fxurl or url.lower() != fxurl.lower(): - print(f"{name:>20} url {url} not in sync with required {fxurl}") - testfails += 1 - if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)): - print(f"{name:>20} sparse checkout file {fxsparse} not found") - testfails += 1 - return testfails + localmods + needsupdate - - -def main(): - ( - root_dir, - file_name, - fxrequired, - includelist, - excludelist, - force, - action, - ) = commandline_arguments() - # Get a logger for the package - global logger - logger = logging.getLogger(__name__) - - logger.info("action is {}".format(action)) - - if not os.path.isfile(os.path.join(root_dir, file_name)): - file_path = utils.find_upwards(root_dir, file_name) - - if file_path is None: - utils.fatal_error( - "No {} found in {} or any of it's parents".format(file_name, root_dir) - ) - - root_dir = os.path.dirname(file_path) - logger.info( - "root_dir is {} includelist={} excludelist={}".format( - root_dir, includelist, excludelist - ) - ) - gitmodules = GitModules( - logger, - confpath=root_dir, - conffile=file_name, - includelist=includelist, - excludelist=excludelist, - ) - if not gitmodules.sections(): - sys.exit("No submodule components found") - retval = 0 - if action == "update": - submodules_update(gitmodules, root_dir, fxrequired, force) - elif action == "status": - tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True) - if tfails + lmods + updates > 0: - print( - f" testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n" - ) - if lmods > 0: - local_mods_output() - elif action == "test": - retval = submodules_test(gitmodules, root_dir) - else: - utils.fatal_error(f"unrecognized action request {action}") - return retval - - -if __name__ == "__main__": - sys.exit(main()) diff --git a/.lib/git-fleximod/git_fleximod/gitinterface.py b/.lib/git-fleximod/git_fleximod/gitinterface.py deleted file mode 100644 index 93ae38ecde..0000000000 --- a/.lib/git-fleximod/git_fleximod/gitinterface.py +++ /dev/null @@ -1,79 +0,0 @@ -import os -import sys -from . import utils -from pathlib import Path - -class GitInterface: - def __init__(self, repo_path, logger): - logger.debug("Initialize GitInterface for {}".format(repo_path)) - if isinstance(repo_path, str): - self.repo_path = Path(repo_path).resolve() - elif isinstance(repo_path, Path): - self.repo_path = repo_path.resolve() - else: - raise TypeError("repo_path must be a str or Path object") - self.logger = logger - try: - import git - - self._use_module = True - try: - self.repo = git.Repo(str(self.repo_path)) # Initialize GitPython repo - except git.exc.InvalidGitRepositoryError: - self.git = git - self._init_git_repo() - msg = "Using GitPython interface to git" - except ImportError: - self._use_module = False - if not (self.repo_path / ".git").exists(): - self._init_git_repo() - msg = "Using shell interface to git" - self.logger.info(msg) - - def _git_command(self, operation, *args): - self.logger.info(operation) - if self._use_module and operation != "submodule": - try: - return getattr(self.repo.git, operation)(*args) - except Exception as e: - sys.exit(e) - else: - return ["git", "-C", str(self.repo_path), operation] + list(args) - - def _init_git_repo(self): - if self._use_module: - self.repo = self.git.Repo.init(str(self.repo_path)) - else: - command = ("git", "-C", str(self.repo_path), "init") - utils.execute_subprocess(command) - - # pylint: disable=unused-argument - def git_operation(self, operation, *args, **kwargs): - command = self._git_command(operation, *args) - self.logger.info(command) - if isinstance(command, list): - try: - return utils.execute_subprocess(command, output_to_caller=True) - except Exception as e: - sys.exit(e) - else: - return command - - def config_get_value(self, section, name): - if self._use_module: - config = self.repo.config_reader() - return config.get_value(section, name) - else: - cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}") - output = utils.execute_subprocess(cmd, output_to_caller=True) - return output.strip() - - def config_set_value(self, section, name, value): - if self._use_module: - with self.repo.config_writer() as writer: - writer.set_value(section, name, value) - writer.release() # Ensure changes are saved - else: - cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value) - self.logger.info(cmd) - utils.execute_subprocess(cmd, output_to_caller=True) diff --git a/.lib/git-fleximod/git_fleximod/gitmodules.py b/.lib/git-fleximod/git_fleximod/gitmodules.py deleted file mode 100644 index 68c82d066f..0000000000 --- a/.lib/git-fleximod/git_fleximod/gitmodules.py +++ /dev/null @@ -1,97 +0,0 @@ -import shutil -from pathlib import Path -from configparser import RawConfigParser, ConfigParser -from .lstripreader import LstripReader - - -class GitModules(RawConfigParser): - def __init__( - self, - logger, - confpath=Path.cwd(), - conffile=".gitmodules", - includelist=None, - excludelist=None, - ): - """ - confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory). - conffile: Name of the configuration file (defaults to .gitmodules). - includelist: Optional list of submodules to include. - excludelist: Optional list of submodules to exclude. - """ - self.logger = logger - self.logger.debug( - "Creating a GitModules object {} {} {} {}".format( - confpath, conffile, includelist, excludelist - ) - ) - super().__init__() - self.conf_file = (Path(confpath) / Path(conffile)) - if self.conf_file.exists(): - self.read_file(LstripReader(str(self.conf_file)), source=conffile) - self.includelist = includelist - self.excludelist = excludelist - self.isdirty = False - - def reload(self): - self.clear() - if self.conf_file.exists(): - self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file) - - - def set(self, name, option, value): - """ - Sets a configuration value for a specific submodule: - Ensures the appropriate section exists for the submodule. - Calls the parent class's set method to store the value. - """ - self.isdirty = True - self.logger.debug("set called {} {} {}".format(name, option, value)) - section = f'submodule "{name}"' - if not self.has_section(section): - self.add_section(section) - super().set(section, option, str(value)) - - # pylint: disable=redefined-builtin, arguments-differ - def get(self, name, option, raw=False, vars=None, fallback=None): - """ - Retrieves a configuration value for a specific submodule: - Uses the parent class's get method to access the value. - Handles potential errors if the section or option doesn't exist. - """ - self.logger.debug("get called {} {}".format(name, option)) - section = f'submodule "{name}"' - try: - return ConfigParser.get( - self, section, option, raw=raw, vars=vars, fallback=fallback - ) - except ConfigParser.NoOptionError: - return None - - def save(self): - if self.isdirty: - self.logger.info("Writing {}".format(self.conf_file)) - with open(self.conf_file, "w") as fd: - self.write(fd) - self.isdirty = False - - def __del__(self): - self.save() - - def sections(self): - """Strip the submodule part out of section and just use the name""" - self.logger.debug("calling GitModules sections iterator") - names = [] - for section in ConfigParser.sections(self): - name = section[11:-1] - if self.includelist and name not in self.includelist: - continue - if self.excludelist and name in self.excludelist: - continue - names.append(name) - return names - - def items(self, name, raw=False, vars=None): - self.logger.debug("calling GitModules items for {}".format(name)) - section = f'submodule "{name}"' - return ConfigParser.items(section, raw=raw, vars=vars) diff --git a/.lib/git-fleximod/git_fleximod/lstripreader.py b/.lib/git-fleximod/git_fleximod/lstripreader.py deleted file mode 100644 index 01d5580ee8..0000000000 --- a/.lib/git-fleximod/git_fleximod/lstripreader.py +++ /dev/null @@ -1,43 +0,0 @@ -class LstripReader(object): - "LstripReader formats .gitmodules files to be acceptable for configparser" - - def __init__(self, filename): - with open(filename, "r") as infile: - lines = infile.readlines() - self._lines = list() - self._num_lines = len(lines) - self._index = 0 - for line in lines: - self._lines.append(line.lstrip()) - - def readlines(self): - """Return all the lines from this object's file""" - return self._lines - - def readline(self, size=-1): - """Format and return the next line or raise StopIteration""" - try: - line = self.next() - except StopIteration: - line = "" - - if (size > 0) and (len(line) < size): - return line[0:size] - - return line - - def __iter__(self): - """Begin an iteration""" - self._index = 0 - return self - - def next(self): - """Return the next line or raise StopIteration""" - if self._index >= self._num_lines: - raise StopIteration - - self._index = self._index + 1 - return self._lines[self._index - 1] - - def __next__(self): - return self.next() diff --git a/.lib/git-fleximod/git_fleximod/metoflexi.py b/.lib/git-fleximod/git_fleximod/metoflexi.py deleted file mode 100755 index cc347db2dd..0000000000 --- a/.lib/git-fleximod/git_fleximod/metoflexi.py +++ /dev/null @@ -1,236 +0,0 @@ -#!/usr/bin/env python -from configparser import ConfigParser -import sys -import shutil -from pathlib import Path -import argparse -import logging -from git_fleximod.gitinterface import GitInterface -from git_fleximod.gitmodules import GitModules -from git_fleximod import utils - -logger = None - -def find_root_dir(filename=".git"): - d = Path.cwd() - root = Path(d.root) - while d != root: - attempt = d / filename - if attempt.is_dir(): - return d - d = d.parent - return None - - -def get_parser(): - description = """ - %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models - """ - parser = argparse.ArgumentParser( - description=description, formatter_class=argparse.RawDescriptionHelpFormatter - ) - - parser.add_argument('-e', '--externals', nargs='?', - default='Externals.cfg', - help='The externals description filename. ' - 'Default: %(default)s.') - - parser.add_argument( - "-C", - "--path", - default=find_root_dir(), - help="Toplevel repository directory. Defaults to top git directory relative to current.", - ) - - parser.add_argument( - "-g", - "--gitmodules", - nargs="?", - default=".gitmodules", - help="The submodule description filename. " "Default: %(default)s.", - ) - parser.add_argument( - "-v", - "--verbose", - action="count", - default=0, - help="Output additional information to " - "the screen and log file. This flag can be " - "used up to two times, increasing the " - "verbosity level each time.", - ) - parser.add_argument( - "-d", - "--debug", - action="store_true", - default=False, - help="DEVELOPER: output additional debugging " - "information to the screen and log file.", - ) - - return parser - -def commandline_arguments(args=None): - parser = get_parser() - - options = parser.parse_args(args) - handlers = [logging.StreamHandler()] - - if options.debug: - try: - open("fleximod.log", "w") - except PermissionError: - sys.exit("ABORT: Could not write file fleximod.log") - level = logging.DEBUG - handlers.append(logging.FileHandler("fleximod.log")) - elif options.verbose: - level = logging.INFO - else: - level = logging.WARNING - # Configure the root logger - logging.basicConfig( - level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers - ) - - return( - options.path, - options.gitmodules, - options.externals - ) - -class ExternalRepoTranslator: - """ - Translates external repositories configured in an INI-style externals file. - """ - - def __init__(self, rootpath, gitmodules, externals): - self.rootpath = rootpath - if gitmodules: - self.gitmodules = GitModules(logger, confpath=rootpath) - self.externals = (rootpath / Path(externals)).resolve() - print(f"Translating {self.externals}") - self.git = GitInterface(rootpath, logger) - -# def __del__(self): -# if (self.rootpath / "save.gitignore"): - - - def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol): - """ - Translates a single repository based on configuration details. - - Args: - rootpath (str): Root path of the main repository. - gitmodules (str): Path to the .gitmodules file. - tag (str): The tag to use for the external repository. - url (str): The URL of the external repository. - path (str): The relative path within the main repository for the external repository. - efile (str): The external file or file containing submodules. - hash_ (str): The commit hash to checkout (if applicable). - sparse (str): Boolean indicating whether to use sparse checkout (if applicable). - protocol (str): The protocol to use (e.g., 'git', 'http'). - """ - assert protocol != "svn", "SVN protocol is not currently supported" - print(f"Translating repository {section}") - if efile: - file_path = Path(path) / Path(efile) - newroot = (self.rootpath / file_path).parent.resolve() - if not newroot.exists(): - newroot.mkdir(parents=True) - logger.info("Newroot is {}".format(newroot)) - newt = ExternalRepoTranslator(newroot, ".gitmodules", efile) - newt.translate_repo() - if protocol == "externals_only": - if tag: - self.gitmodules.set(section, "fxtag", tag) - if hash_: - self.gitmodules.set(section, "fxtag", hash_) - - self.gitmodules.set(section, "fxDONOTUSEurl", url) - if sparse: - self.gitmodules.set(section, "fxsparse", sparse) - self.gitmodules.set(section, "fxrequired", "ToplevelRequired") - else: - newpath = (self.rootpath / Path(path)) - if newpath.exists(): - shutil.rmtree(newpath) - logger.info("Creating directory {}".format(newpath)) - newpath.mkdir(parents=True) - if tag: - logger.info("cloning {}".format(section)) - try: - self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path) - except: - self.git.git_operation("clone", url, path) - with utils.pushd(newpath): - ngit = GitInterface(newpath, logger) - ngit.git_operation("checkout", tag) - if hash_: - self.git.git_operation("clone", url, path) - git = GitInterface(newpath, logger) - git.git_operation("fetch", "origin") - git.git_operation("checkout", hash_) - if sparse: - print("setting as sparse submodule {}".format(section)) - sparsefile = (newpath / Path(sparse)) - newfile = (newpath / ".git" / "info" / "sparse-checkout") - print(f"sparsefile {sparsefile} newfile {newfile}") - shutil.copy(sparsefile, newfile) - - logger.info("adding submodule {}".format(section)) - self.gitmodules.save() - self.git.git_operation("submodule", "add", "-f", "--name", section, url, path) - self.git.git_operation("submodule","absorbgitdirs") - self.gitmodules.reload() - if tag: - self.gitmodules.set(section, "fxtag", tag) - if hash_: - self.gitmodules.set(section, "fxtag", hash_) - - self.gitmodules.set(section, "fxDONOTUSEurl", url) - if sparse: - self.gitmodules.set(section, "fxsparse", sparse) - self.gitmodules.set(section, "fxrequired", "ToplevelRequired") - - - def translate_repo(self): - """ - Translates external repositories defined within an external file. - - Args: - rootpath (str): Root path of the main repository. - gitmodules (str): Path to the .gitmodules file. - external_file (str): The path to the external file containing repository definitions. - """ - econfig = ConfigParser() - econfig.read((self.rootpath / Path(self.externals))) - - for section in econfig.sections(): - if section == "externals_description": - logger.info("skipping section {}".format(section)) - return - logger.info("Translating section {}".format(section)) - tag = econfig.get(section, "tag", raw=False, fallback=None) - url = econfig.get(section, "repo_url", raw=False, fallback=None) - path = econfig.get(section, "local_path", raw=False, fallback=None) - efile = econfig.get(section, "externals", raw=False, fallback=None) - hash_ = econfig.get(section, "hash", raw=False, fallback=None) - sparse = econfig.get(section, "sparse", raw=False, fallback=None) - protocol = econfig.get(section, "protocol", raw=False, fallback=None) - - self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol) - - - -def _main(): - rootpath, gitmodules, externals = commandline_arguments() - global logger - logger = logging.getLogger(__name__) - with utils.pushd(rootpath): - t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals) - logger.info("Translating {}".format(rootpath)) - t.translate_repo() - - -if __name__ == "__main__": - sys.exit(_main()) diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py deleted file mode 100644 index 7cc1de38cc..0000000000 --- a/.lib/git-fleximod/git_fleximod/utils.py +++ /dev/null @@ -1,365 +0,0 @@ -#!/usr/bin/env python3 -""" -Common public utilities for manic package - -""" - -import logging -import os -import subprocess -import sys -from threading import Timer -from pathlib import Path - -LOCAL_PATH_INDICATOR = "." -# --------------------------------------------------------------------- -# -# functions to massage text for output and other useful utilities -# -# --------------------------------------------------------------------- -from contextlib import contextmanager - - -@contextmanager -def pushd(new_dir): - """context for chdir. usage: with pushd(new_dir)""" - previous_dir = os.getcwd() - os.chdir(new_dir) - try: - yield - finally: - os.chdir(previous_dir) - - -def log_process_output(output): - """Log each line of process output at debug level so it can be - filtered if necessary. By default, output is a single string, and - logging.debug(output) will only put log info heading on the first - line. This makes it hard to filter with grep. - - """ - output = output.split("\n") - for line in output: - logging.debug(line) - - -def printlog(msg, **kwargs): - """Wrapper script around print to ensure that everything printed to - the screen also gets logged. - - """ - logging.info(msg) - if kwargs: - print(msg, **kwargs) - else: - print(msg) - sys.stdout.flush() - - -def find_upwards(root_dir, filename): - """Find a file in root dir or any of it's parents""" - d = Path(root_dir) - root = Path(d.root) - while d != root: - attempt = d / filename - if attempt.exists(): - return attempt - d = d.parent - return None - - -def last_n_lines(the_string, n_lines, truncation_message=None): - """Returns the last n lines of the given string - - Args: - the_string: str - n_lines: int - truncation_message: str, optional - - Returns a string containing the last n lines of the_string - - If truncation_message is provided, the returned string begins with - the given message if and only if the string is greater than n lines - to begin with. - """ - - lines = the_string.splitlines(True) - if len(lines) <= n_lines: - return_val = the_string - else: - lines_subset = lines[-n_lines:] - str_truncated = "".join(lines_subset) - if truncation_message: - str_truncated = truncation_message + "\n" + str_truncated - return_val = str_truncated - - return return_val - - -def indent_string(the_string, indent_level): - """Indents the given string by a given number of spaces - - Args: - the_string: str - indent_level: int - - Returns a new string that is the same as the_string, except that - each line is indented by 'indent_level' spaces. - - In python3, this can be done with textwrap.indent. - """ - - lines = the_string.splitlines(True) - padding = " " * indent_level - lines_indented = [padding + line for line in lines] - return "".join(lines_indented) - - -# --------------------------------------------------------------------- -# -# error handling -# -# --------------------------------------------------------------------- - - -def fatal_error(message): - """ - Error output function - """ - logging.error(message) - raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message)) - - -# --------------------------------------------------------------------- -# -# Data conversion / manipulation -# -# --------------------------------------------------------------------- -def str_to_bool(bool_str): - """Convert a sting representation of as boolean into a true boolean. - - Conversion should be case insensitive. - """ - value = None - str_lower = bool_str.lower() - if str_lower in ("true", "t"): - value = True - elif str_lower in ("false", "f"): - value = False - if value is None: - msg = ( - 'ERROR: invalid boolean string value "{0}". ' - 'Must be "true" or "false"'.format(bool_str) - ) - fatal_error(msg) - return value - - -REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"] - - -def is_remote_url(url): - """check if the user provided a local file path instead of a - remote. If so, it must be expanded to an absolute - path. - - """ - remote_url = False - for prefix in REMOTE_PREFIXES: - if url.startswith(prefix): - remote_url = True - return remote_url - - -def split_remote_url(url): - """check if the user provided a local file path or a - remote. If remote, try to strip off protocol info. - - """ - remote_url = is_remote_url(url) - if not remote_url: - return url - - for prefix in REMOTE_PREFIXES: - url = url.replace(prefix, "") - - if "@" in url: - url = url.split("@")[1] - - if ":" in url: - url = url.split(":")[1] - - return url - - -def expand_local_url(url, field): - """check if the user provided a local file path instead of a - remote. If so, it must be expanded to an absolute - path. - - Note: local paths of LOCAL_PATH_INDICATOR have special meaning and - represent local copy only, don't work with the remotes. - - """ - remote_url = is_remote_url(url) - if not remote_url: - if url.strip() == LOCAL_PATH_INDICATOR: - pass - else: - url = os.path.expandvars(url) - url = os.path.expanduser(url) - if not os.path.isabs(url): - msg = ( - 'WARNING: Externals description for "{0}" contains a ' - "url that is not remote and does not expand to an " - "absolute path. Version control operations may " - "fail.\n\nurl={1}".format(field, url) - ) - printlog(msg) - else: - url = os.path.normpath(url) - return url - - -# --------------------------------------------------------------------- -# -# subprocess -# -# --------------------------------------------------------------------- - -# Give the user a helpful message if we detect that a command seems to -# be hanging. -_HANGING_SEC = 300 - - -def _hanging_msg(working_directory, command): - print( - """ - -Command '{command}' -from directory {working_directory} -has taken {hanging_sec} seconds. It may be hanging. - -The command will continue to run, but you may want to abort -manage_externals with ^C and investigate. A possible cause of hangs is -when svn or git require authentication to access a private -repository. On some systems, svn and git requests for authentication -information will not be displayed to the user. In this case, the program -will appear to hang. Ensure you can run svn and git manually and access -all repositories without entering your authentication information. - -""".format( - command=command, - working_directory=working_directory, - hanging_sec=_HANGING_SEC, - ) - ) - - -def execute_subprocess(commands, status_to_caller=False, output_to_caller=False): - """Wrapper around subprocess.check_output to handle common - exceptions. - - check_output runs a command with arguments and waits - for it to complete. - - check_output raises an exception on a nonzero return code. if - status_to_caller is true, execute_subprocess returns the subprocess - return code, otherwise execute_subprocess treats non-zero return - status as an error and raises an exception. - - """ - cwd = os.getcwd() - msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd) - logging.info(msg) - commands_str = " ".join(str(element) for element in commands) - logging.info(commands_str) - return_to_caller = status_to_caller or output_to_caller - status = -1 - output = "" - hanging_timer = Timer( - _HANGING_SEC, - _hanging_msg, - kwargs={"working_directory": cwd, "command": commands_str}, - ) - hanging_timer.start() - try: - output = subprocess.check_output( - commands, stderr=subprocess.STDOUT, universal_newlines=True - ) - log_process_output(output) - status = 0 - except OSError as error: - msg = failed_command_msg( - "Command execution failed. Does the executable exist?", commands - ) - logging.error(error) - fatal_error(msg) - except ValueError as error: - msg = failed_command_msg( - "DEV_ERROR: Invalid arguments trying to run subprocess", commands - ) - logging.error(error) - fatal_error(msg) - except subprocess.CalledProcessError as error: - # Only report the error if we are NOT returning to the - # caller. If we are returning to the caller, then it may be a - # simple status check. If returning, it is the callers - # responsibility determine if an error occurred and handle it - # appropriately. - if not return_to_caller: - msg_context = ( - "Process did not run successfully; " - "returned status {0}".format(error.returncode) - ) - msg = failed_command_msg(msg_context, commands, output=error.output) - logging.error(error) - logging.error(msg) - log_process_output(error.output) - fatal_error(msg) - status = error.returncode - finally: - hanging_timer.cancel() - - if status_to_caller and output_to_caller: - ret_value = (status, output) - elif status_to_caller: - ret_value = status - elif output_to_caller: - ret_value = output - else: - ret_value = None - - return ret_value - - -def failed_command_msg(msg_context, command, output=None): - """Template for consistent error messages from subprocess calls. - - If 'output' is given, it should provide the output from the failed - command - """ - - if output: - output_truncated = last_n_lines( - output, 20, truncation_message="[... 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-[metadata] -lock-version = "2.0" -python-versions = "^3.8" -content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d" diff --git a/.lib/git-fleximod/pyproject.toml b/.lib/git-fleximod/pyproject.toml deleted file mode 100644 index 2484552e4f..0000000000 --- a/.lib/git-fleximod/pyproject.toml +++ /dev/null @@ -1,41 +0,0 @@ -[tool.poetry] -name = "git-fleximod" -version = "0.7.4" -description = "Extended support for git-submodule and git-sparse-checkout" -authors = ["Jim Edwards "] -maintainers = ["Jim Edwards "] -license = "MIT" -readme = "README.md" -homepage = "https://github.com/jedwards4b/git-fleximod" -keywords = ["git", "submodule", "sparse-checkout"] -packages = [ -{ include = "git_fleximod"}, -{ include = "doc"}, -] - -[tool.poetry.scripts] -git-fleximod = "git_fleximod.git_fleximod:main" -me2flexi = "git_fleximod.metoflexi:_main" -fsspec = "fsspec.fuse:main" - -[tool.poetry.dependencies] -python = "^3.8" -GitPython = "^3.1.0" -sphinx = "^5.0.0" -fsspec = "^2023.12.2" -wheel = "^0.42.0" -pytest = "^8.0.0" -pyfakefs = "^5.3.5" - -[tool.poetry.urls] -"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues" - -[tool.pytest.ini_options] -markers = [ - "skip_after_first: only run on first iteration" -] - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" - diff --git a/.lib/git-fleximod/tbump.toml b/.lib/git-fleximod/tbump.toml deleted file mode 100644 index d4b8eaee11..0000000000 --- a/.lib/git-fleximod/tbump.toml +++ /dev/null @@ -1,43 +0,0 @@ -# Uncomment this if your project is hosted on GitHub: -github_url = "https://github.com/jedwards4b/git-fleximod/" - -[version] -current = "0.7.4" - -# Example of a semver regexp. -# Make sure this matches current_version before -# using tbump -regex = ''' - (?P\d+) - \. - (?P\d+) - \. - (?P\d+) - ''' - -[git] -message_template = "Bump to {new_version}" -tag_template = "v{new_version}" - -# For each file to patch, add a [[file]] config -# section containing the path of the file, relative to the -# tbump.toml location. -[[file]] -src = "git_fleximod/cli.py" - -[[file]] -src = "pyproject.toml" - -# You can specify a list of commands to -# run after the files have been patched -# and before the git commit is made - -# [[before_commit]] -# name = "check changelog" -# cmd = "grep -q {new_version} Changelog.rst" - -# Or run some commands after the git tag and the branch -# have been pushed: -# [[after_push]] -# name = "publish" -# cmd = "./publish.sh" diff --git a/.lib/git-fleximod/tests/__init__.py b/.lib/git-fleximod/tests/__init__.py deleted file mode 100644 index 4d4c66c78e..0000000000 --- a/.lib/git-fleximod/tests/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -import sys, os - -sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src")) diff --git a/.lib/git-fleximod/tests/conftest.py b/.lib/git-fleximod/tests/conftest.py deleted file mode 100644 index 942a0efb97..0000000000 --- a/.lib/git-fleximod/tests/conftest.py +++ /dev/null @@ -1,138 +0,0 @@ -import pytest -from git_fleximod.gitinterface import GitInterface -import os -import subprocess -import logging -from pathlib import Path - -@pytest.fixture(scope='session') -def logger(): - logging.basicConfig( - level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()] - ) - logger = logging.getLogger(__name__) - return logger - -all_repos=[ - {"subrepo_path": "modules/test", - "submodule_name": "test_submodule", - "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", - "status2" : "test_submodule at tag MPIserial_2.4.0", - "status3" : "test_submodule at tag MPIserial_2.4.0", - "status4" : "test_submodule at tag MPIserial_2.4.0", - "gitmodules_content" : """ - [submodule "test_submodule"] - path = modules/test - url = https://github.com/ESMCI/mpi-serial.git - fxtag = MPIserial_2.4.0 - fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git - fxrequired = ToplevelRequired -"""}, - {"subrepo_path": "modules/test_optional", - "submodule_name": "test_optional", - "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", - "status2" : "test_optional at tag MPIserial_2.4.0", - "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0", - "status4" : "test_optional at tag MPIserial_2.4.0", - "gitmodules_content": """ - [submodule "test_optional"] - path = modules/test_optional - url = https://github.com/ESMCI/mpi-serial.git - fxtag = MPIserial_2.4.0 - fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git - fxrequired = ToplevelOptional -"""}, - {"subrepo_path": "modules/test_alwaysoptional", - "submodule_name": "test_alwaysoptional", - "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c", - "status2" : "test_alwaysoptional at hash e5cf35c", - "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0", - "status4" : "test_alwaysoptional at hash e5cf35c", - "gitmodules_content": """ - [submodule "test_alwaysoptional"] - path = modules/test_alwaysoptional - url = https://github.com/ESMCI/mpi-serial.git - fxtag = e5cf35c - fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git - fxrequired = AlwaysOptional -"""}, - {"subrepo_path": "modules/test_sparse", - "submodule_name": "test_sparse", - "status1" : "test_sparse at tag MPIserial_2.5.0", - "status2" : "test_sparse at tag MPIserial_2.5.0", - "status3" : "test_sparse at tag MPIserial_2.5.0", - "status4" : "test_sparse at tag MPIserial_2.5.0", - "gitmodules_content": """ - [submodule "test_sparse"] - path = modules/test_sparse - url = https://github.com/ESMCI/mpi-serial.git - fxtag = MPIserial_2.5.0 - fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git - fxrequired = AlwaysRequired - fxsparse = ../.sparse_file_list -"""}, -] -@pytest.fixture(params=all_repos) - -def shared_repos(request): - return request.param - -@pytest.fixture -def get_all_repos(): - return all_repos - -def write_sparse_checkout_file(fp): - sparse_content = """m4 -""" - fp.write_text(sparse_content) - -@pytest.fixture -def test_repo(shared_repos, tmp_path, logger): - subrepo_path = shared_repos["subrepo_path"] - submodule_name = shared_repos["submodule_name"] - test_dir = tmp_path / "testrepo" - test_dir.mkdir() - str_path = str(test_dir) - gitp = GitInterface(str_path, logger) - assert test_dir.joinpath(".git").is_dir() - (test_dir / "modules").mkdir() - if "sparse" in submodule_name: - (test_dir / subrepo_path).mkdir() - # Add the sparse checkout file - write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list") - gitp.git_operation("add","modules/.sparse_file_list") - else: - gitp = GitInterface(str(test_dir), logger) - gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path) - assert test_dir.joinpath(".gitmodules").is_file() - gitp.git_operation("add",subrepo_path) - gitp.git_operation("commit","-a","-m","\"add submod\"") - test_dir2 = tmp_path / "testrepo2" - gitp.git_operation("clone",test_dir,test_dir2) - return test_dir2 - - -@pytest.fixture -def complex_repo(tmp_path, logger): - test_dir = tmp_path / "testcomplex" - test_dir.mkdir() - str_path = str(test_dir) - gitp = GitInterface(str_path, logger) - gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2") - gitp.git_operation("fetch", "origin", "main") - gitp.git_operation("checkout", "main") - return test_dir - -@pytest.fixture -def git_fleximod(): - def _run_fleximod(path, args, input=None): - cmd = ["git", "fleximod"] + args.split() - result = subprocess.run(cmd, cwd=path, input=input, - stdout=subprocess.PIPE, stderr=subprocess.PIPE, - text=True) - if result.returncode: - print(result.stdout) - print(result.stderr) - return result - return _run_fleximod - diff --git a/.lib/git-fleximod/tests/test_a_import.py b/.lib/git-fleximod/tests/test_a_import.py deleted file mode 100644 index d5ca878de5..0000000000 --- a/.lib/git-fleximod/tests/test_a_import.py +++ /dev/null @@ -1,8 +0,0 @@ -# pylint: disable=unused-import -from git_fleximod import cli -from git_fleximod import utils -from git_fleximod.gitinterface import GitInterface -from git_fleximod.gitmodules import GitModules - -def test_import(): - print("here") diff --git a/.lib/git-fleximod/tests/test_b_update.py b/.lib/git-fleximod/tests/test_b_update.py deleted file mode 100644 index 159f1cfae0..0000000000 --- a/.lib/git-fleximod/tests/test_b_update.py +++ /dev/null @@ -1,26 +0,0 @@ -import pytest -from pathlib import Path - -def test_basic_checkout(git_fleximod, test_repo, shared_repos): - # Prepare a simple .gitmodules - gm = shared_repos['gitmodules_content'] - file_path = (test_repo / ".gitmodules") - repo_name = shared_repos["submodule_name"] - repo_path = shared_repos["subrepo_path"] - - file_path.write_text(gm) - - # Run the command - result = git_fleximod(test_repo, f"update {repo_name}") - - # Assertions - assert result.returncode == 0 - assert Path(test_repo / repo_path).exists() # Did the submodule directory get created? - if "sparse" in repo_name: - assert Path(test_repo / f"{repo_path}/m4").exists() # Did the submodule sparse directory get created? - assert not Path(test_repo / f"{repo_path}/README").exists() # Did only the submodule sparse directory get created? - - status = git_fleximod(test_repo, f"status {repo_name}") - - assert shared_repos["status2"] in status.stdout - diff --git a/.lib/git-fleximod/tests/test_c_required.py b/.lib/git-fleximod/tests/test_c_required.py deleted file mode 100644 index 89ab8d294d..0000000000 --- a/.lib/git-fleximod/tests/test_c_required.py +++ /dev/null @@ -1,30 +0,0 @@ -import pytest -from pathlib import Path - -def test_required(git_fleximod, test_repo, shared_repos): - file_path = (test_repo / ".gitmodules") - gm = shared_repos["gitmodules_content"] - repo_name = shared_repos["submodule_name"] - if file_path.exists(): - with file_path.open("r") as f: - gitmodules_content = f.read() - # add the entry if it does not exist - if repo_name not in gitmodules_content: - file_path.write_text(gitmodules_content+gm) - # or if it is incomplete - elif gm not in gitmodules_content: - file_path.write_text(gm) - else: - file_path.write_text(gm) - result = git_fleximod(test_repo, "update") - assert result.returncode == 0 - status = git_fleximod(test_repo, f"status {repo_name}") - assert shared_repos["status3"] in status.stdout - status = git_fleximod(test_repo, f"update --optional") - assert result.returncode == 0 - status = git_fleximod(test_repo, f"status {repo_name}") - assert shared_repos["status4"] in status.stdout - status = git_fleximod(test_repo, f"update {repo_name}") - assert result.returncode == 0 - status = git_fleximod(test_repo, f"status {repo_name}") - assert shared_repos["status4"] in status.stdout diff --git a/.lib/git-fleximod/tests/test_d_complex.py b/.lib/git-fleximod/tests/test_d_complex.py deleted file mode 100644 index fdce516274..0000000000 --- a/.lib/git-fleximod/tests/test_d_complex.py +++ /dev/null @@ -1,67 +0,0 @@ -import pytest -from pathlib import Path -from git_fleximod.gitinterface import GitInterface - -def test_complex_checkout(git_fleximod, complex_repo, logger): - status = git_fleximod(complex_repo, "status") - assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) - assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout) - assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout) - assert("Complex not checked out, aligned at tag testtag01" in status.stdout) - assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) - - # This should checkout and update test_submodule and complex_sub - result = git_fleximod(complex_repo, "update") - assert result.returncode == 0 - - status = git_fleximod(complex_repo, "status") - assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) - assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) - assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) - assert("Complex at tag testtag01" in status.stdout) - - # now check the complex_sub - root = (complex_repo / "modules" / "complex") - assert(not (root / "libraries" / "gptl" / ".git").exists()) - assert(not (root / "libraries" / "mpi-serial" / ".git").exists()) - assert((root / "modules" / "mpi-serial" / ".git").exists()) - assert(not (root / "modules" / "mpi-serial2" / ".git").exists()) - assert((root / "modules" / "mpi-sparse" / ".git").exists()) - assert((root / "modules" / "mpi-sparse" / "m4").exists()) - assert(not (root / "modules" / "mpi-sparse" / "README").exists()) - - # update a single optional submodule - - result = git_fleximod(complex_repo, "update ToplevelOptional") - assert result.returncode == 0 - - status = git_fleximod(complex_repo, "status") - assert("ToplevelOptional at tag v5.3.2" in status.stdout) - assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) - assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) - assert("Complex at tag testtag01" in status.stdout) - assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) - - - # Finally update optional - result = git_fleximod(complex_repo, "update --optional") - assert result.returncode == 0 - - status = git_fleximod(complex_repo, "status") - assert("ToplevelOptional at tag v5.3.2" in status.stdout) - assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) - assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) - assert("Complex at tag testtag01" in status.stdout) - assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout) - - # now check the complex_sub - root = (complex_repo / "modules" / "complex" ) - assert(not (root / "libraries" / "gptl" / ".git").exists()) - assert(not (root / "libraries" / "mpi-serial" / ".git").exists()) - assert((root / "modules" / "mpi-serial" / ".git").exists()) - assert((root / "modules" / "mpi-serial2" / ".git").exists()) - assert((root / "modules" / "mpi-sparse" / ".git").exists()) - assert((root / "modules" / "mpi-sparse" / "m4").exists()) - assert(not (root / "modules" / "mpi-sparse" / "README").exists()) - - From eb94e4d298564d52197d9cf632d73ffad74c5f61 Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Fri, 31 May 2024 10:20:12 -0600 Subject: [PATCH 223/408] Squashed '.lib/git-fleximod/' content from commit a354b0528 git-subtree-dir: .lib/git-fleximod git-subtree-split: a354b0528228ac89ce103b3b42b2a203fe495ba5 --- .github/workflows/pre-commit | 13 + .github/workflows/pytest.yaml | 77 ++++ .pre-commit-config.yaml | 18 + License | 20 + README.md | 108 ++++++ doc/Makefile | 20 + doc/conf.py | 26 ++ doc/index.rst | 24 ++ doc/make.bat | 35 ++ escomp_install | 25 ++ git_fleximod/__init__.py | 0 git_fleximod/cli.py | 129 +++++++ git_fleximod/git_fleximod.py | 605 +++++++++++++++++++++++++++++ git_fleximod/gitinterface.py | 79 ++++ git_fleximod/gitmodules.py | 97 +++++ git_fleximod/lstripreader.py | 43 +++ git_fleximod/metoflexi.py | 236 ++++++++++++ git_fleximod/utils.py | 365 ++++++++++++++++++ poetry.lock | 693 ++++++++++++++++++++++++++++++++++ pyproject.toml | 41 ++ tbump.toml | 43 +++ tests/__init__.py | 3 + tests/conftest.py | 138 +++++++ tests/test_a_import.py | 8 + tests/test_b_update.py | 26 ++ tests/test_c_required.py | 30 ++ tests/test_d_complex.py | 67 ++++ 27 files changed, 2969 insertions(+) create mode 100644 .github/workflows/pre-commit create mode 100644 .github/workflows/pytest.yaml create mode 100644 .pre-commit-config.yaml create mode 100644 License create mode 100644 README.md create mode 100644 doc/Makefile create mode 100644 doc/conf.py create mode 100644 doc/index.rst create mode 100644 doc/make.bat create mode 100644 escomp_install create mode 100644 git_fleximod/__init__.py create mode 100644 git_fleximod/cli.py create mode 100755 git_fleximod/git_fleximod.py create mode 100644 git_fleximod/gitinterface.py create mode 100644 git_fleximod/gitmodules.py create mode 100644 git_fleximod/lstripreader.py create mode 100755 git_fleximod/metoflexi.py create mode 100644 git_fleximod/utils.py create mode 100644 poetry.lock create mode 100644 pyproject.toml create mode 100644 tbump.toml create mode 100644 tests/__init__.py create mode 100644 tests/conftest.py create mode 100644 tests/test_a_import.py create mode 100644 tests/test_b_update.py create mode 100644 tests/test_c_required.py create mode 100644 tests/test_d_complex.py diff --git a/.github/workflows/pre-commit b/.github/workflows/pre-commit new file mode 100644 index 0000000000..1a6ad0082a --- /dev/null +++ b/.github/workflows/pre-commit @@ -0,0 +1,13 @@ +name: pre-commit +on: + pull_request: + push: + branches: [main] + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - uses: actions/setup-python@v3 + - uses: pre-commit/action@v3.0.0 diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml new file mode 100644 index 0000000000..0868dd9a33 --- /dev/null +++ b/.github/workflows/pytest.yaml @@ -0,0 +1,77 @@ +# Run this job on pushes to `main`, and for pull requests. If you don't specify +# `branches: [main], then this actions runs _twice_ on pull requests, which is +# annoying. + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + # If you wanted to use multiple Python versions, you'd have specify a matrix in the job and + # reference the matrixe python version here. + - uses: actions/setup-python@v5 + with: + python-version: '3.9' + + # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow + # from installing Poetry every time, which can be slow. Note the use of the Poetry version + # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache + # manually if/when you want to upgrade Poetry, or if something goes wrong. This could be + # mildly cleaner by using an environment variable, but I don't really care. + - name: cache poetry install + uses: actions/cache@v4 + with: + path: ~/.local + key: poetry-1.7.1 + + # Install Poetry. You could do this manually, or there are several actions that do this. + # `snok/install-poetry` seems to be minimal yet complete, and really just calls out to + # Poetry's default install script, which feels correct. I pin the Poetry version here + # because Poetry does occasionally change APIs between versions and I don't want my + # actions to break if it does. + # + # The key configuration value here is `virtualenvs-in-project: true`: this creates the + # venv as a `.venv` in your testing directory, which allows the next step to easily + # cache it. + - uses: snok/install-poetry@v1 + with: + version: 1.7.1 + virtualenvs-create: true + virtualenvs-in-project: true + + # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache + # key: if you're using multiple Python versions, or multiple OSes, you'd need to include + # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock. + - name: cache deps + id: cache-deps + uses: actions/cache@v4 + with: + path: .venv + key: pydeps-${{ hashFiles('**/poetry.lock') }} + + # Install dependencies. `--no-root` means "install all dependencies but not the project + # itself", which is what you want to avoid caching _your_ code. The `if` statement + # ensures this only runs on a cache miss. + - run: poetry install --no-interaction --no-root + if: steps.cache-deps.outputs.cache-hit != 'true' + + # Now install _your_ project. This isn't necessary for many types of projects -- particularly + # things like Django apps don't need this. But it's a good idea since it fully-exercises the + # pyproject.toml and makes that if you add things like console-scripts at some point that + # they'll be installed and working. + - run: poetry install --no-interaction + + # And finally run tests. I'm using pytest and all my pytest config is in my `pyproject.toml` + # so this line is super-simple. But it could be as complex as you need. + - run: | + git config --global user.name "${GITHUB_ACTOR}" + git config --global user.email "${GITHUB_ACTOR_ID}+${GITHUB_ACTOR}@users.noreply.github.com" + poetry run pytest + diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000000..2f6089da72 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,18 @@ +exclude: ^utils/.*$ + +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.0.1 + hooks: + - id: end-of-file-fixer + - id: trailing-whitespace + - repo: https://github.com/psf/black + rev: 22.3.0 + hooks: + - id: black + - repo: https://github.com/PyCQA/pylint + rev: v2.11.1 + hooks: + - id: pylint + args: + - --disable=I,C,R,logging-not-lazy,wildcard-import,unused-wildcard-import,fixme,broad-except,bare-except,eval-used,exec-used,global-statement,logging-format-interpolation,no-name-in-module,arguments-renamed,unspecified-encoding,protected-access,import-error,no-member diff --git a/License b/License new file mode 100644 index 0000000000..88bc22515e --- /dev/null +++ b/License @@ -0,0 +1,20 @@ +Copyright 2024 NSF National Center for Atmospheric Sciences (NCAR) + +Permission is hereby granted, free of charge, to any person obtaining +a copy of this software and associated documentation files (the +“Softwareâ€), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED “AS ISâ€, WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE +LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000000..53917da400 --- /dev/null +++ b/README.md @@ -0,0 +1,108 @@ +# git-fleximod + +Flexible, Enhanced Submodule Management for Git + +## Overview + +Git-fleximod is a Python-based tool that extends Git's submodule and sparse checkout capabilities, offering additional features for managing submodules in a more flexible and efficient way. + +## Installation + + If you choose to locate git-fleximod in your path you can access it via command: git fleximod + +## Usage + + Basic Usage: + git fleximod [options] + Available Commands: + status: Display the status of submodules. + update: Update submodules to the tag indicated in .gitmodules variable fxtag. + test: Make sure that fxtags and submodule hashes are consistant, + make sure that official urls (as defined by fxDONOTUSEurl) are set + make sure that fxtags are defined for all submodules + Additional Options: + See git fleximod --help for more details. + +## Supported .gitmodules Variables + + fxtag: Specify a specific tag or branch to checkout for a submodule. + fxrequired: Mark a submodule's checkout behavior, with allowed values: + - ToplevelRequired: Top-level and required (checked out only when this is the Toplevel module). + - ToplevelOptional: Top-level and optional (checked out with --optional flag if this is the Toplevel module). + - AlwaysRequired: Always required (always checked out). + - AlwaysOptional: Always optional (checked out with --optional flag). + fxsparse: Enable sparse checkout for a submodule, pointing to a file containing sparse checkout paths. + fxDONOTUSEurl: This is the url used in the test subcommand to assure that protected branches do not point to forks + **NOTE** the fxDONOTUSEurl variable is only used to identify the official project repository and should not be + changed by users. Use the url variable to change to a fork if desired. + +## Sparse Checkouts + + To enable sparse checkout for a submodule, set the fxsparse variable + in the .gitmodules file to the path of a file containing the desired + sparse checkout paths. Git-fleximod will automatically configure + sparse checkout based on this file when applicable commands are run. + See [git-sparse-checkout](https://git-scm.com/docs/git-sparse-checkout#_internalsfull_pattern_set) + for details on the format of this file. + +## Tests + + The git fleximod test action is designed to be used by, for example, github workflows + to assure that protected branches are consistant with respect to submodule hashes and fleximod fxtags + +## Examples + +Here are some common usage examples: + +Update all submodules, including optional ones: +```bash + git fleximod update --optional +``` + +Updating a specific submodule to the fxtag indicated in .gitmodules: + +```bash + git fleximod update submodule-name +``` +Example .gitmodules entry: +```ini, toml + [submodule "cosp2"] + path = src/physics/cosp2/src + url = https://github.com/CFMIP/COSPv2.0 + fxsparse = ../.cosp_sparse_checkout + fxrequired = AlwaysRequired + fxtag = v2.1.4cesm +``` +Explanation: + +This entry indicates that the submodule named cosp2 at tag v2.1.4cesm +should be checked out into the directory src/physics/cosp2/src +relative to the .gitmodules directory. It should be checked out from +the URL https://github.com/CFMIP/COSPv2.0 and use sparse checkout as +described in the file ../.cosp_sparse_checkout relative to the path +directory. It should be checked out anytime this .gitmodules entry is +read. + +Additional example: +```ini, toml + [submodule "cime"] + path = cime + url = https://github.com/jedwards4b/cime + fxrequired = ToplevelRequired + fxtag = cime6.0.198_rme01 +``` + +Explanation: + +This entry indicates that the submodule cime should be checked out +into a directory named cime at tag cime6.0.198_rme01 from the URL +https://github.com/jedwards4b/cime. This should only be done if +the .gitmodules file is at the top level of the repository clone. + +## Contributing + +We welcome contributions! Please see the CONTRIBUTING.md file for guidelines. + +## License + +Git-fleximod is released under the MIT License. diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 0000000000..d4bb2cbb9e --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 0000000000..423099eec9 --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,26 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = "git-fleximod" +author = "Jim Edwards " +release = "0.4.0" + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = ["sphinx_argparse_cli"] + +templates_path = ["_templates"] +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = "alabaster" +html_static_path = ["_static"] diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 0000000000..0f9c1a7f7e --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,24 @@ +.. git-fleximod documentation master file, created by + sphinx-quickstart on Sat Feb 3 12:02:22 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to git-fleximod's documentation! +======================================== + +.. toctree:: + :maxdepth: 2 + :caption: Contents: +.. module:: sphinxcontrib.autoprogram +.. sphinx_argparse_cli:: + :module: git_fleximod.cli + :func: get_parser + :prog: git-fleximod + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/doc/make.bat b/doc/make.bat new file mode 100644 index 0000000000..32bb24529f --- /dev/null +++ b/doc/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/escomp_install b/escomp_install new file mode 100644 index 0000000000..ae782e72a4 --- /dev/null +++ b/escomp_install @@ -0,0 +1,25 @@ +#!/usr/bin/env python +# updates git-fleximod in an ESCOMP model +# this script should be run from the model root directory, it expects +# git-fleximod to already be installed with the script in bin +# and the classes in lib/python/site-packages +import sys +import shutil +import os + +from glob import iglob + +fleximod_root = sys.argv[1] +fleximod_path = os.path.join(fleximod_root,"src","git-fleximod") +if os.path.isfile(fleximod_path): + with open(fleximod_path,"r") as f: + fleximod = f.readlines() + with open(os.path.join(".","bin","git-fleximod"),"w") as f: + for line in fleximod: + f.write(line) + if "import argparse" in line: + f.write('\nsys.path.append(os.path.join(os.path.dirname(__file__),"..","lib","python","site-packages"))\n\n') + + for file in iglob(os.path.join(fleximod_root, "src", "fleximod", "*.py")): + shutil.copy(file, + os.path.join("lib","python","site-packages","fleximod",os.path.basename(file))) diff --git a/git_fleximod/__init__.py b/git_fleximod/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py new file mode 100644 index 0000000000..4c3fb1a8f9 --- /dev/null +++ b/git_fleximod/cli.py @@ -0,0 +1,129 @@ +from pathlib import Path +import argparse +from git_fleximod import utils + +__version__ = "0.7.5" + +def find_root_dir(filename=".gitmodules"): + """ finds the highest directory in tree + which contains a file called filename """ + d = Path.cwd() + root = Path(d.root) + dirlist = [] + dl = d + while dl != root: + dirlist.append(dl) + dl = dl.parent + dirlist.append(root) + dirlist.reverse() + + for dl in dirlist: + attempt = dl / filename + if attempt.is_file(): + return str(dl) + utils.fatal_error("No .gitmodules found in directory tree") + + +def get_parser(): + description = """ + %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models + """ + parser = argparse.ArgumentParser( + description=description, formatter_class=argparse.RawDescriptionHelpFormatter + ) + + # + # user options + # + choices = ["update", "status", "test"] + parser.add_argument( + "action", + choices=choices, + default="update", + help=f"Subcommand of git-fleximod, choices are {choices[:-1]}", + ) + + parser.add_argument( + "components", + nargs="*", + help="Specific component(s) to checkout. By default, " + "all required submodules are checked out.", + ) + + parser.add_argument( + "-C", + "--path", + default=find_root_dir(), + help="Toplevel repository directory. Defaults to top git directory relative to current.", + ) + + parser.add_argument( + "-g", + "--gitmodules", + nargs="?", + default=".gitmodules", + help="The submodule description filename. " "Default: %(default)s.", + ) + + parser.add_argument( + "-x", + "--exclude", + nargs="*", + help="Component(s) listed in the gitmodules file which should be ignored.", + ) + parser.add_argument( + "-f", + "--force", + action="store_true", + default=False, + help="Override cautions and update or checkout over locally modified repository.", + ) + + parser.add_argument( + "-o", + "--optional", + action="store_true", + default=False, + help="By default only the required submodules " + "are checked out. This flag will also checkout the " + "optional submodules relative to the toplevel directory.", + ) + + parser.add_argument( + "-v", + "--verbose", + action="count", + default=0, + help="Output additional information to " + "the screen and log file. This flag can be " + "used up to two times, increasing the " + "verbosity level each time.", + ) + + parser.add_argument( + "-V", + "--version", + action="version", + version=f"%(prog)s {__version__}", + help="Print version and exit.", + ) + + # + # developer options + # + parser.add_argument( + "--backtrace", + action="store_true", + help="DEVELOPER: show exception backtraces as extra " "debugging output", + ) + + parser.add_argument( + "-d", + "--debug", + action="store_true", + default=False, + help="DEVELOPER: output additional debugging " + "information to the screen and log file.", + ) + + return parser diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py new file mode 100755 index 0000000000..f080513a52 --- /dev/null +++ b/git_fleximod/git_fleximod.py @@ -0,0 +1,605 @@ +#!/usr/bin/env python +import sys + +MIN_PYTHON = (3, 7) +if sys.version_info < MIN_PYTHON: + sys.exit("Python %s.%s or later is required." % MIN_PYTHON) + +import os +import shutil +import logging +import textwrap +from git_fleximod import utils +from git_fleximod import cli +from git_fleximod.gitinterface import GitInterface +from git_fleximod.gitmodules import GitModules +from configparser import NoOptionError + +# logger variable is global +logger = None + + +def fxrequired_allowed_values(): + return ["ToplevelRequired", "ToplevelOptional", "AlwaysRequired", "AlwaysOptional"] + + +def commandline_arguments(args=None): + parser = cli.get_parser() + + if args: + options = parser.parse_args(args) + else: + options = parser.parse_args() + + # explicitly listing a component overrides the optional flag + if options.optional or options.components: + fxrequired = [ + "ToplevelRequired", + "ToplevelOptional", + "AlwaysRequired", + "AlwaysOptional", + ] + else: + fxrequired = ["ToplevelRequired", "AlwaysRequired"] + + action = options.action + if not action: + action = "update" + handlers = [logging.StreamHandler()] + + if options.debug: + try: + open("fleximod.log", "w") + except PermissionError: + sys.exit("ABORT: Could not write file fleximod.log") + level = logging.DEBUG + handlers.append(logging.FileHandler("fleximod.log")) + elif options.verbose: + level = logging.INFO + else: + level = logging.WARNING + # Configure the root logger + logging.basicConfig( + level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers + ) + + if hasattr(options, "version"): + exit() + + return ( + options.path, + options.gitmodules, + fxrequired, + options.components, + options.exclude, + options.force, + action, + ) + + +def submodule_sparse_checkout(root_dir, name, url, path, sparsefile, tag="master"): + """ + This function performs a sparse checkout of a git submodule. It does so by first creating the .git/info/sparse-checkout fileq + in the submodule and then checking out the desired tag. If the submodule is already checked out, it will not be checked out again. + Creating the sparse-checkout file first prevents the entire submodule from being checked out and then removed. This is important + because the submodule may have a large number of files and checking out the entire submodule and then removing it would be time + and disk space consuming. + + Parameters: + root_dir (str): The root directory for the git operation. + name (str): The name of the submodule. + url (str): The URL of the submodule. + path (str): The path to the submodule. + sparsefile (str): The sparse file for the submodule. + tag (str, optional): The tag to checkout. Defaults to "master". + + Returns: + None + """ + logger.info("Called sparse_checkout for {}".format(name)) + rgit = GitInterface(root_dir, logger) + superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree") + if superroot: + gitroot = superroot.strip() + else: + gitroot = root_dir.strip() + assert os.path.isdir(os.path.join(gitroot, ".git")) + # first create the module directory + if not os.path.isdir(os.path.join(root_dir, path)): + os.makedirs(os.path.join(root_dir, path)) + + # initialize a new git repo and set the sparse checkout flag + sprep_repo = os.path.join(root_dir, path) + sprepo_git = GitInterface(sprep_repo, logger) + if os.path.exists(os.path.join(sprep_repo, ".git")): + try: + logger.info("Submodule {} found".format(name)) + chk = sprepo_git.config_get_value("core", "sparseCheckout") + if chk == "true": + logger.info("Sparse submodule {} already checked out".format(name)) + return + except NoOptionError: + logger.debug("Sparse submodule {} not present".format(name)) + except Exception as e: + utils.fatal_error("Unexpected error {} occured.".format(e)) + + sprepo_git.config_set_value("core", "sparseCheckout", "true") + + # set the repository remote + + logger.info("Setting remote origin in {}/{}".format(root_dir, path)) + status = sprepo_git.git_operation("remote", "-v") + if url not in status: + sprepo_git.git_operation("remote", "add", "origin", url) + + topgit = os.path.join(gitroot, ".git") + + if gitroot != root_dir and os.path.isfile(os.path.join(root_dir, ".git")): + with open(os.path.join(root_dir, ".git")) as f: + gitpath = os.path.relpath( + os.path.join(root_dir, f.read().split()[1]), + start=os.path.join(root_dir, path), + ) + topgit = os.path.join(gitpath, "modules") + else: + topgit = os.path.relpath( + os.path.join(root_dir, ".git", "modules"), + start=os.path.join(root_dir, path), + ) + + with utils.pushd(sprep_repo): + if not os.path.isdir(topgit): + os.makedirs(topgit) + topgit += os.sep + name + + if os.path.isdir(os.path.join(root_dir, path, ".git")): + with utils.pushd(sprep_repo): + shutil.move(".git", topgit) + with open(".git", "w") as f: + f.write("gitdir: " + os.path.relpath(topgit)) + # assert(os.path.isdir(os.path.relpath(topgit, start=sprep_repo))) + gitsparse = os.path.abspath(os.path.join(topgit, "info", "sparse-checkout")) + if os.path.isfile(gitsparse): + logger.warning( + "submodule {} is already initialized {}".format(name, topgit) + ) + return + + with utils.pushd(sprep_repo): + shutil.copy(sparsefile, gitsparse) + + # Finally checkout the repo + sprepo_git.git_operation("fetch", "origin", "--tags") + sprepo_git.git_operation("checkout", tag) + + print(f"Successfully checked out {name:>20} at {tag}") + rgit.config_set_value(f'submodule "{name}"', "active", "true") + rgit.config_set_value(f'submodule "{name}"', "url", url) + + +def single_submodule_checkout( + root, name, path, url=None, tag=None, force=False, optional=False +): + """ + This function checks out a single git submodule. + + Parameters: + root (str): The root directory for the git operation. + name (str): The name of the submodule. + path (str): The path to the submodule. + url (str, optional): The URL of the submodule. Defaults to None. + tag (str, optional): The tag to checkout. Defaults to None. + force (bool, optional): If set to True, forces the checkout operation. Defaults to False. + optional (bool, optional): If set to True, the submodule is considered optional. Defaults to False. + + Returns: + None + """ + # function implementation... + git = GitInterface(root, logger) + repodir = os.path.join(root, path) + logger.info("Checkout {} into {}/{}".format(name, root, path)) + # if url is provided update to the new url + tmpurl = None + repo_exists = False + if os.path.exists(os.path.join(repodir, ".git")): + logger.info("Submodule {} already checked out".format(name)) + repo_exists = True + # Look for a .gitmodules file in the newly checkedout repo + if not repo_exists and url: + # ssh urls cause problems for those who dont have git accounts with ssh keys defined + # but cime has one since e3sm prefers ssh to https, because the .gitmodules file was + # opened with a GitModules object we don't need to worry about restoring the file here + # it will be done by the GitModules class + if url.startswith("git@"): + tmpurl = url + url = url.replace("git@github.com:", "https://github.com/") + git.git_operation("clone", url, path) + smgit = GitInterface(repodir, logger) + if not tag: + tag = smgit.git_operation("describe", "--tags", "--always").rstrip() + smgit.git_operation("checkout", tag) + # Now need to move the .git dir to the submodule location + rootdotgit = os.path.join(root, ".git") + if os.path.isfile(rootdotgit): + with open(rootdotgit) as f: + line = f.readline() + if line.startswith("gitdir: "): + rootdotgit = line[8:].rstrip() + + newpath = os.path.abspath(os.path.join(root, rootdotgit, "modules", name)) + if os.path.exists(newpath): + shutil.rmtree(os.path.join(repodir, ".git")) + else: + shutil.move(os.path.join(repodir, ".git"), newpath) + + with open(os.path.join(repodir, ".git"), "w") as f: + f.write("gitdir: " + os.path.relpath(newpath, start=repodir)) + + if not os.path.exists(repodir): + parent = os.path.dirname(repodir) + if not os.path.isdir(parent): + os.makedirs(parent) + git.git_operation("submodule", "add", "--name", name, "--", url, path) + + if not repo_exists or not tmpurl: + git.git_operation("submodule", "update", "--init", "--", path) + + if os.path.exists(os.path.join(repodir, ".gitmodules")): + # recursively handle this checkout + print(f"Recursively checking out submodules of {name}") + gitmodules = GitModules(logger, confpath=repodir) + requiredlist = ["AlwaysRequired"] + if optional: + requiredlist.append("AlwaysOptional") + submodules_checkout(gitmodules, repodir, requiredlist, force=force) + if not os.path.exists(os.path.join(repodir, ".git")): + utils.fatal_error( + f"Failed to checkout {name} {repo_exists} {tmpurl} {repodir} {path}" + ) + + if tmpurl: + print(git.git_operation("restore", ".gitmodules")) + + return + + +def submodules_status(gitmodules, root_dir, toplevel=False): + testfails = 0 + localmods = 0 + needsupdate = 0 + for name in gitmodules.sections(): + path = gitmodules.get(name, "path") + tag = gitmodules.get(name, "fxtag") + required = gitmodules.get(name, "fxrequired") + level = required and "Toplevel" in required + if not path: + utils.fatal_error("No path found in .gitmodules for {}".format(name)) + newpath = os.path.join(root_dir, path) + logger.debug("newpath is {}".format(newpath)) + if not os.path.exists(os.path.join(newpath, ".git")): + rootgit = GitInterface(root_dir, logger) + # submodule commands use path, not name + url = gitmodules.get(name, "url") + url = url.replace("git@github.com:", "https://github.com/") + tags = rootgit.git_operation("ls-remote", "--tags", url) + atag = None + needsupdate += 1 + if not toplevel and level: + continue + for htag in tags.split("\n"): + if tag and tag in htag: + atag = (htag.split()[1])[10:] + break + if tag and tag == atag: + print(f"e {name:>20} not checked out, aligned at tag {tag}") + elif tag: + ahash = rootgit.git_operation( + "submodule", "status", "{}".format(path) + ).rstrip() + ahash = ahash[1 : len(tag) + 1] + if tag == ahash: + print(f"e {name:>20} not checked out, aligned at hash {ahash}") + else: + print( + f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}" + ) + testfails += 1 + else: + print(f"e {name:>20} has no fxtag defined in .gitmodules") + testfails += 1 + else: + with utils.pushd(newpath): + git = GitInterface(newpath, logger) + atag = git.git_operation("describe", "--tags", "--always").rstrip() + part = git.git_operation("status").partition("\n")[0] + # fake hash to initialize + ahash = "xxxx" + if part: + ahash = part.split()[-1] + if tag and atag == tag: + print(f" {name:>20} at tag {tag}") + elif tag and ahash[: len(tag)] == tag: + print(f" {name:>20} at hash {ahash}") + elif atag == ahash: + print(f" {name:>20} at hash {ahash}") + elif tag: + print( + f"s {name:>20} {atag} {ahash} is out of sync with .gitmodules {tag}" + ) + testfails += 1 + needsupdate += 1 + else: + print( + f"e {name:>20} has no fxtag defined in .gitmodules, module at {atag}" + ) + testfails += 1 + + status = git.git_operation("status", "--ignore-submodules") + if "nothing to commit" not in status: + localmods = localmods + 1 + print("M" + textwrap.indent(status, " ")) + + return testfails, localmods, needsupdate + + +def submodules_update(gitmodules, root_dir, requiredlist, force): + _, localmods, needsupdate = submodules_status(gitmodules, root_dir) + + if localmods and not force: + local_mods_output() + return + if needsupdate == 0: + return + + for name in gitmodules.sections(): + fxtag = gitmodules.get(name, "fxtag") + path = gitmodules.get(name, "path") + url = gitmodules.get(name, "url") + logger.info( + "name={} path={} url={} fxtag={} requiredlist={}".format( + name, os.path.join(root_dir, path), url, fxtag, requiredlist + ) + ) + # if not os.path.exists(os.path.join(root_dir,path, ".git")): + fxrequired = gitmodules.get(name, "fxrequired") + assert fxrequired in fxrequired_allowed_values() + rgit = GitInterface(root_dir, logger) + superroot = rgit.git_operation("rev-parse", "--show-superproject-working-tree") + + fxsparse = gitmodules.get(name, "fxsparse") + + if ( + fxrequired + and (superroot and "Toplevel" in fxrequired) + or fxrequired not in requiredlist + ): + if "ToplevelOptional" == fxrequired: + print("Skipping optional component {}".format(name)) + continue + if fxsparse: + logger.debug( + "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format( + root_dir, name, url, path, fxsparse, fxtag + ) + ) + submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag) + else: + logger.info( + "Calling submodule_checkout({},{},{},{})".format( + root_dir, name, path, url + ) + ) + + single_submodule_checkout( + root_dir, + name, + path, + url=url, + tag=fxtag, + force=force, + optional=("AlwaysOptional" in requiredlist), + ) + + if os.path.exists(os.path.join(path, ".git")): + submoddir = os.path.join(root_dir, path) + with utils.pushd(submoddir): + git = GitInterface(submoddir, logger) + # first make sure the url is correct + upstream = git.git_operation("ls-remote", "--get-url").rstrip() + newremote = "origin" + if upstream != url: + # TODO - this needs to be a unique name + remotes = git.git_operation("remote", "-v") + if url in remotes: + for line in remotes: + if url in line and "fetch" in line: + newremote = line.split()[0] + break + else: + i = 0 + while newremote in remotes: + i = i + 1 + newremote = f"newremote.{i:02d}" + git.git_operation("remote", "add", newremote, url) + + tags = git.git_operation("tag", "-l") + if fxtag and fxtag not in tags: + git.git_operation("fetch", newremote, "--tags") + atag = git.git_operation("describe", "--tags", "--always").rstrip() + if fxtag and fxtag != atag: + try: + git.git_operation("checkout", fxtag) + print(f"{name:>20} updated to {fxtag}") + except Exception as error: + print(error) + elif not fxtag: + print(f"No fxtag found for submodule {name:>20}") + else: + print(f"{name:>20} up to date.") + + +def local_mods_output(): + text = """\ + The submodules labeled with 'M' above are not in a clean state. + The following are options for how to proceed: + (1) Go into each submodule which is not in a clean state and issue a 'git status' + Either revert or commit your changes so that the submodule is in a clean state. + (2) use the --force option to git-fleximod + (3) you can name the particular submodules to update using the git-fleximod command line + (4) As a last resort you can remove the submodule (via 'rm -fr [directory]') + then rerun git-fleximod update. +""" + print(text) + + +# checkout is done by update if required so this function may be depricated +def submodules_checkout(gitmodules, root_dir, requiredlist, force=False): + """ + This function checks out all git submodules based on the provided parameters. + + Parameters: + gitmodules (ConfigParser): The gitmodules configuration. + root_dir (str): The root directory for the git operation. + requiredlist (list): The list of required modules. + force (bool, optional): If set to True, forces the checkout operation. Defaults to False. + + Returns: + None + """ + # function implementation... + print("") + _, localmods, needsupdate = submodules_status(gitmodules, root_dir) + if localmods and not force: + local_mods_output() + return + if not needsupdate: + return + for name in gitmodules.sections(): + fxrequired = gitmodules.get(name, "fxrequired") + fxsparse = gitmodules.get(name, "fxsparse") + fxtag = gitmodules.get(name, "fxtag") + path = gitmodules.get(name, "path") + url = gitmodules.get(name, "url") + if fxrequired and fxrequired not in requiredlist: + if "Optional" in fxrequired: + print("Skipping optional component {}".format(name)) + continue + + if fxsparse: + logger.debug( + "Callng submodule_sparse_checkout({}, {}, {}, {}, {}, {}".format( + root_dir, name, url, path, fxsparse, fxtag + ) + ) + submodule_sparse_checkout(root_dir, name, url, path, fxsparse, tag=fxtag) + else: + logger.debug( + "Calling submodule_checkout({},{},{})".format(root_dir, name, path) + ) + single_submodule_checkout( + root_dir, + name, + path, + url=url, + tag=fxtag, + force=force, + optional="AlwaysOptional" in requiredlist, + ) + + +def submodules_test(gitmodules, root_dir): + """ + This function tests the git submodules based on the provided parameters. + + It first checks that fxtags are present and in sync with submodule hashes. + Then it ensures that urls are consistent with fxurls (not forks and not ssh) + and that sparse checkout files exist. + + Parameters: + gitmodules (ConfigParser): The gitmodules configuration. + root_dir (str): The root directory for the git operation. + + Returns: + int: The number of test failures. + """ + # First check that fxtags are present and in sync with submodule hashes + testfails, localmods, needsupdate = submodules_status(gitmodules, root_dir) + print("") + # Then make sure that urls are consistant with fxurls (not forks and not ssh) + # and that sparse checkout files exist + for name in gitmodules.sections(): + url = gitmodules.get(name, "url") + fxurl = gitmodules.get(name, "fxDONOTMODIFYurl") + fxsparse = gitmodules.get(name, "fxsparse") + path = gitmodules.get(name, "path") + fxurl = fxurl[:-4] if fxurl.endswith(".git") else fxurl + url = url[:-4] if url.endswith(".git") else url + if not fxurl or url.lower() != fxurl.lower(): + print(f"{name:>20} url {url} not in sync with required {fxurl}") + testfails += 1 + if fxsparse and not os.path.isfile(os.path.join(root_dir, path, fxsparse)): + print(f"{name:>20} sparse checkout file {fxsparse} not found") + testfails += 1 + return testfails + localmods + needsupdate + + +def main(): + ( + root_dir, + file_name, + fxrequired, + includelist, + excludelist, + force, + action, + ) = commandline_arguments() + # Get a logger for the package + global logger + logger = logging.getLogger(__name__) + + logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name)) + + if not os.path.isfile(os.path.join(root_dir, file_name)): + file_path = utils.find_upwards(root_dir, file_name) + + if file_path is None: + utils.fatal_error( + "No {} found in {} or any of it's parents".format(file_name, root_dir) + ) + + root_dir = os.path.dirname(file_path) + logger.info( + "root_dir is {} includelist={} excludelist={}".format( + root_dir, includelist, excludelist + ) + ) + gitmodules = GitModules( + logger, + confpath=root_dir, + conffile=file_name, + includelist=includelist, + excludelist=excludelist, + ) + if not gitmodules.sections(): + sys.exit("No submodule components found") + retval = 0 + if action == "update": + submodules_update(gitmodules, root_dir, fxrequired, force) + elif action == "status": + tfails, lmods, updates = submodules_status(gitmodules, root_dir, toplevel=True) + if tfails + lmods + updates > 0: + print( + f" testfails = {tfails}, local mods = {lmods}, needs updates {updates}\n" + ) + if lmods > 0: + local_mods_output() + elif action == "test": + retval = submodules_test(gitmodules, root_dir) + else: + utils.fatal_error(f"unrecognized action request {action}") + return retval + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/git_fleximod/gitinterface.py b/git_fleximod/gitinterface.py new file mode 100644 index 0000000000..93ae38ecde --- /dev/null +++ b/git_fleximod/gitinterface.py @@ -0,0 +1,79 @@ +import os +import sys +from . import utils +from pathlib import Path + +class GitInterface: + def __init__(self, repo_path, logger): + logger.debug("Initialize GitInterface for {}".format(repo_path)) + if isinstance(repo_path, str): + self.repo_path = Path(repo_path).resolve() + elif isinstance(repo_path, Path): + self.repo_path = repo_path.resolve() + else: + raise TypeError("repo_path must be a str or Path object") + self.logger = logger + try: + import git + + self._use_module = True + try: + self.repo = git.Repo(str(self.repo_path)) # Initialize GitPython repo + except git.exc.InvalidGitRepositoryError: + self.git = git + self._init_git_repo() + msg = "Using GitPython interface to git" + except ImportError: + self._use_module = False + if not (self.repo_path / ".git").exists(): + self._init_git_repo() + msg = "Using shell interface to git" + self.logger.info(msg) + + def _git_command(self, operation, *args): + self.logger.info(operation) + if self._use_module and operation != "submodule": + try: + return getattr(self.repo.git, operation)(*args) + except Exception as e: + sys.exit(e) + else: + return ["git", "-C", str(self.repo_path), operation] + list(args) + + def _init_git_repo(self): + if self._use_module: + self.repo = self.git.Repo.init(str(self.repo_path)) + else: + command = ("git", "-C", str(self.repo_path), "init") + utils.execute_subprocess(command) + + # pylint: disable=unused-argument + def git_operation(self, operation, *args, **kwargs): + command = self._git_command(operation, *args) + self.logger.info(command) + if isinstance(command, list): + try: + return utils.execute_subprocess(command, output_to_caller=True) + except Exception as e: + sys.exit(e) + else: + return command + + def config_get_value(self, section, name): + if self._use_module: + config = self.repo.config_reader() + return config.get_value(section, name) + else: + cmd = ("git", "-C", str(self.repo_path), "config", "--get", f"{section}.{name}") + output = utils.execute_subprocess(cmd, output_to_caller=True) + return output.strip() + + def config_set_value(self, section, name, value): + if self._use_module: + with self.repo.config_writer() as writer: + writer.set_value(section, name, value) + writer.release() # Ensure changes are saved + else: + cmd = ("git", "-C", str(self.repo_path), "config", f"{section}.{name}", value) + self.logger.info(cmd) + utils.execute_subprocess(cmd, output_to_caller=True) diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py new file mode 100644 index 0000000000..68c82d066f --- /dev/null +++ b/git_fleximod/gitmodules.py @@ -0,0 +1,97 @@ +import shutil +from pathlib import Path +from configparser import RawConfigParser, ConfigParser +from .lstripreader import LstripReader + + +class GitModules(RawConfigParser): + def __init__( + self, + logger, + confpath=Path.cwd(), + conffile=".gitmodules", + includelist=None, + excludelist=None, + ): + """ + confpath: Path to the directory containing the .gitmodules file (defaults to the current working directory). + conffile: Name of the configuration file (defaults to .gitmodules). + includelist: Optional list of submodules to include. + excludelist: Optional list of submodules to exclude. + """ + self.logger = logger + self.logger.debug( + "Creating a GitModules object {} {} {} {}".format( + confpath, conffile, includelist, excludelist + ) + ) + super().__init__() + self.conf_file = (Path(confpath) / Path(conffile)) + if self.conf_file.exists(): + self.read_file(LstripReader(str(self.conf_file)), source=conffile) + self.includelist = includelist + self.excludelist = excludelist + self.isdirty = False + + def reload(self): + self.clear() + if self.conf_file.exists(): + self.read_file(LstripReader(str(self.conf_file)), source=self.conf_file) + + + def set(self, name, option, value): + """ + Sets a configuration value for a specific submodule: + Ensures the appropriate section exists for the submodule. + Calls the parent class's set method to store the value. + """ + self.isdirty = True + self.logger.debug("set called {} {} {}".format(name, option, value)) + section = f'submodule "{name}"' + if not self.has_section(section): + self.add_section(section) + super().set(section, option, str(value)) + + # pylint: disable=redefined-builtin, arguments-differ + def get(self, name, option, raw=False, vars=None, fallback=None): + """ + Retrieves a configuration value for a specific submodule: + Uses the parent class's get method to access the value. + Handles potential errors if the section or option doesn't exist. + """ + self.logger.debug("get called {} {}".format(name, option)) + section = f'submodule "{name}"' + try: + return ConfigParser.get( + self, section, option, raw=raw, vars=vars, fallback=fallback + ) + except ConfigParser.NoOptionError: + return None + + def save(self): + if self.isdirty: + self.logger.info("Writing {}".format(self.conf_file)) + with open(self.conf_file, "w") as fd: + self.write(fd) + self.isdirty = False + + def __del__(self): + self.save() + + def sections(self): + """Strip the submodule part out of section and just use the name""" + self.logger.debug("calling GitModules sections iterator") + names = [] + for section in ConfigParser.sections(self): + name = section[11:-1] + if self.includelist and name not in self.includelist: + continue + if self.excludelist and name in self.excludelist: + continue + names.append(name) + return names + + def items(self, name, raw=False, vars=None): + self.logger.debug("calling GitModules items for {}".format(name)) + section = f'submodule "{name}"' + return ConfigParser.items(section, raw=raw, vars=vars) diff --git a/git_fleximod/lstripreader.py b/git_fleximod/lstripreader.py new file mode 100644 index 0000000000..01d5580ee8 --- /dev/null +++ b/git_fleximod/lstripreader.py @@ -0,0 +1,43 @@ +class LstripReader(object): + "LstripReader formats .gitmodules files to be acceptable for configparser" + + def __init__(self, filename): + with open(filename, "r") as infile: + lines = infile.readlines() + self._lines = list() + self._num_lines = len(lines) + self._index = 0 + for line in lines: + self._lines.append(line.lstrip()) + + def readlines(self): + """Return all the lines from this object's file""" + return self._lines + + def readline(self, size=-1): + """Format and return the next line or raise StopIteration""" + try: + line = self.next() + except StopIteration: + line = "" + + if (size > 0) and (len(line) < size): + return line[0:size] + + return line + + def __iter__(self): + """Begin an iteration""" + self._index = 0 + return self + + def next(self): + """Return the next line or raise StopIteration""" + if self._index >= self._num_lines: + raise StopIteration + + self._index = self._index + 1 + return self._lines[self._index - 1] + + def __next__(self): + return self.next() diff --git a/git_fleximod/metoflexi.py b/git_fleximod/metoflexi.py new file mode 100755 index 0000000000..cc347db2dd --- /dev/null +++ b/git_fleximod/metoflexi.py @@ -0,0 +1,236 @@ +#!/usr/bin/env python +from configparser import ConfigParser +import sys +import shutil +from pathlib import Path +import argparse +import logging +from git_fleximod.gitinterface import GitInterface +from git_fleximod.gitmodules import GitModules +from git_fleximod import utils + +logger = None + +def find_root_dir(filename=".git"): + d = Path.cwd() + root = Path(d.root) + while d != root: + attempt = d / filename + if attempt.is_dir(): + return d + d = d.parent + return None + + +def get_parser(): + description = """ + %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models + """ + parser = argparse.ArgumentParser( + description=description, formatter_class=argparse.RawDescriptionHelpFormatter + ) + + parser.add_argument('-e', '--externals', nargs='?', + default='Externals.cfg', + help='The externals description filename. ' + 'Default: %(default)s.') + + parser.add_argument( + "-C", + "--path", + default=find_root_dir(), + help="Toplevel repository directory. Defaults to top git directory relative to current.", + ) + + parser.add_argument( + "-g", + "--gitmodules", + nargs="?", + default=".gitmodules", + help="The submodule description filename. " "Default: %(default)s.", + ) + parser.add_argument( + "-v", + "--verbose", + action="count", + default=0, + help="Output additional information to " + "the screen and log file. This flag can be " + "used up to two times, increasing the " + "verbosity level each time.", + ) + parser.add_argument( + "-d", + "--debug", + action="store_true", + default=False, + help="DEVELOPER: output additional debugging " + "information to the screen and log file.", + ) + + return parser + +def commandline_arguments(args=None): + parser = get_parser() + + options = parser.parse_args(args) + handlers = [logging.StreamHandler()] + + if options.debug: + try: + open("fleximod.log", "w") + except PermissionError: + sys.exit("ABORT: Could not write file fleximod.log") + level = logging.DEBUG + handlers.append(logging.FileHandler("fleximod.log")) + elif options.verbose: + level = logging.INFO + else: + level = logging.WARNING + # Configure the root logger + logging.basicConfig( + level=level, format="%(name)s - %(levelname)s - %(message)s", handlers=handlers + ) + + return( + options.path, + options.gitmodules, + options.externals + ) + +class ExternalRepoTranslator: + """ + Translates external repositories configured in an INI-style externals file. + """ + + def __init__(self, rootpath, gitmodules, externals): + self.rootpath = rootpath + if gitmodules: + self.gitmodules = GitModules(logger, confpath=rootpath) + self.externals = (rootpath / Path(externals)).resolve() + print(f"Translating {self.externals}") + self.git = GitInterface(rootpath, logger) + +# def __del__(self): +# if (self.rootpath / "save.gitignore"): + + + def translate_single_repo(self, section, tag, url, path, efile, hash_, sparse, protocol): + """ + Translates a single repository based on configuration details. + + Args: + rootpath (str): Root path of the main repository. + gitmodules (str): Path to the .gitmodules file. + tag (str): The tag to use for the external repository. + url (str): The URL of the external repository. + path (str): The relative path within the main repository for the external repository. + efile (str): The external file or file containing submodules. + hash_ (str): The commit hash to checkout (if applicable). + sparse (str): Boolean indicating whether to use sparse checkout (if applicable). + protocol (str): The protocol to use (e.g., 'git', 'http'). + """ + assert protocol != "svn", "SVN protocol is not currently supported" + print(f"Translating repository {section}") + if efile: + file_path = Path(path) / Path(efile) + newroot = (self.rootpath / file_path).parent.resolve() + if not newroot.exists(): + newroot.mkdir(parents=True) + logger.info("Newroot is {}".format(newroot)) + newt = ExternalRepoTranslator(newroot, ".gitmodules", efile) + newt.translate_repo() + if protocol == "externals_only": + if tag: + self.gitmodules.set(section, "fxtag", tag) + if hash_: + self.gitmodules.set(section, "fxtag", hash_) + + self.gitmodules.set(section, "fxDONOTUSEurl", url) + if sparse: + self.gitmodules.set(section, "fxsparse", sparse) + self.gitmodules.set(section, "fxrequired", "ToplevelRequired") + else: + newpath = (self.rootpath / Path(path)) + if newpath.exists(): + shutil.rmtree(newpath) + logger.info("Creating directory {}".format(newpath)) + newpath.mkdir(parents=True) + if tag: + logger.info("cloning {}".format(section)) + try: + self.git.git_operation("clone", "-b", tag, "--depth", "1", url, path) + except: + self.git.git_operation("clone", url, path) + with utils.pushd(newpath): + ngit = GitInterface(newpath, logger) + ngit.git_operation("checkout", tag) + if hash_: + self.git.git_operation("clone", url, path) + git = GitInterface(newpath, logger) + git.git_operation("fetch", "origin") + git.git_operation("checkout", hash_) + if sparse: + print("setting as sparse submodule {}".format(section)) + sparsefile = (newpath / Path(sparse)) + newfile = (newpath / ".git" / "info" / "sparse-checkout") + print(f"sparsefile {sparsefile} newfile {newfile}") + shutil.copy(sparsefile, newfile) + + logger.info("adding submodule {}".format(section)) + self.gitmodules.save() + self.git.git_operation("submodule", "add", "-f", "--name", section, url, path) + self.git.git_operation("submodule","absorbgitdirs") + self.gitmodules.reload() + if tag: + self.gitmodules.set(section, "fxtag", tag) + if hash_: + self.gitmodules.set(section, "fxtag", hash_) + + self.gitmodules.set(section, "fxDONOTUSEurl", url) + if sparse: + self.gitmodules.set(section, "fxsparse", sparse) + self.gitmodules.set(section, "fxrequired", "ToplevelRequired") + + + def translate_repo(self): + """ + Translates external repositories defined within an external file. + + Args: + rootpath (str): Root path of the main repository. + gitmodules (str): Path to the .gitmodules file. + external_file (str): The path to the external file containing repository definitions. + """ + econfig = ConfigParser() + econfig.read((self.rootpath / Path(self.externals))) + + for section in econfig.sections(): + if section == "externals_description": + logger.info("skipping section {}".format(section)) + return + logger.info("Translating section {}".format(section)) + tag = econfig.get(section, "tag", raw=False, fallback=None) + url = econfig.get(section, "repo_url", raw=False, fallback=None) + path = econfig.get(section, "local_path", raw=False, fallback=None) + efile = econfig.get(section, "externals", raw=False, fallback=None) + hash_ = econfig.get(section, "hash", raw=False, fallback=None) + sparse = econfig.get(section, "sparse", raw=False, fallback=None) + protocol = econfig.get(section, "protocol", raw=False, fallback=None) + + self.translate_single_repo(section, tag, url, path, efile, hash_, sparse, protocol) + + + +def _main(): + rootpath, gitmodules, externals = commandline_arguments() + global logger + logger = logging.getLogger(__name__) + with utils.pushd(rootpath): + t = ExternalRepoTranslator(Path(rootpath), gitmodules, externals) + logger.info("Translating {}".format(rootpath)) + t.translate_repo() + + +if __name__ == "__main__": + sys.exit(_main()) diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py new file mode 100644 index 0000000000..7cc1de38cc --- /dev/null +++ b/git_fleximod/utils.py @@ -0,0 +1,365 @@ +#!/usr/bin/env python3 +""" +Common public utilities for manic package + +""" + +import logging +import os +import subprocess +import sys +from threading import Timer +from pathlib import Path + +LOCAL_PATH_INDICATOR = "." +# --------------------------------------------------------------------- +# +# functions to massage text for output and other useful utilities +# +# --------------------------------------------------------------------- +from contextlib import contextmanager + + +@contextmanager +def pushd(new_dir): + """context for chdir. usage: with pushd(new_dir)""" + previous_dir = os.getcwd() + os.chdir(new_dir) + try: + yield + finally: + os.chdir(previous_dir) + + +def log_process_output(output): + """Log each line of process output at debug level so it can be + filtered if necessary. By default, output is a single string, and + logging.debug(output) will only put log info heading on the first + line. This makes it hard to filter with grep. + + """ + output = output.split("\n") + for line in output: + logging.debug(line) + + +def printlog(msg, **kwargs): + """Wrapper script around print to ensure that everything printed to + the screen also gets logged. + + """ + logging.info(msg) + if kwargs: + print(msg, **kwargs) + else: + print(msg) + sys.stdout.flush() + + +def find_upwards(root_dir, filename): + """Find a file in root dir or any of it's parents""" + d = Path(root_dir) + root = Path(d.root) + while d != root: + attempt = d / filename + if attempt.exists(): + return attempt + d = d.parent + return None + + +def last_n_lines(the_string, n_lines, truncation_message=None): + """Returns the last n lines of the given string + + Args: + the_string: str + n_lines: int + truncation_message: str, optional + + Returns a string containing the last n lines of the_string + + If truncation_message is provided, the returned string begins with + the given message if and only if the string is greater than n lines + to begin with. + """ + + lines = the_string.splitlines(True) + if len(lines) <= n_lines: + return_val = the_string + else: + lines_subset = lines[-n_lines:] + str_truncated = "".join(lines_subset) + if truncation_message: + str_truncated = truncation_message + "\n" + str_truncated + return_val = str_truncated + + return return_val + + +def indent_string(the_string, indent_level): + """Indents the given string by a given number of spaces + + Args: + the_string: str + indent_level: int + + Returns a new string that is the same as the_string, except that + each line is indented by 'indent_level' spaces. + + In python3, this can be done with textwrap.indent. + """ + + lines = the_string.splitlines(True) + padding = " " * indent_level + lines_indented = [padding + line for line in lines] + return "".join(lines_indented) + + +# --------------------------------------------------------------------- +# +# error handling +# +# --------------------------------------------------------------------- + + +def fatal_error(message): + """ + Error output function + """ + logging.error(message) + raise RuntimeError("{0}ERROR: {1}".format(os.linesep, message)) + + +# --------------------------------------------------------------------- +# +# Data conversion / manipulation +# +# --------------------------------------------------------------------- +def str_to_bool(bool_str): + """Convert a sting representation of as boolean into a true boolean. + + Conversion should be case insensitive. + """ + value = None + str_lower = bool_str.lower() + if str_lower in ("true", "t"): + value = True + elif str_lower in ("false", "f"): + value = False + if value is None: + msg = ( + 'ERROR: invalid boolean string value "{0}". ' + 'Must be "true" or "false"'.format(bool_str) + ) + fatal_error(msg) + return value + + +REMOTE_PREFIXES = ["http://", "https://", "ssh://", "git@"] + + +def is_remote_url(url): + """check if the user provided a local file path instead of a + remote. If so, it must be expanded to an absolute + path. + + """ + remote_url = False + for prefix in REMOTE_PREFIXES: + if url.startswith(prefix): + remote_url = True + return remote_url + + +def split_remote_url(url): + """check if the user provided a local file path or a + remote. If remote, try to strip off protocol info. + + """ + remote_url = is_remote_url(url) + if not remote_url: + return url + + for prefix in REMOTE_PREFIXES: + url = url.replace(prefix, "") + + if "@" in url: + url = url.split("@")[1] + + if ":" in url: + url = url.split(":")[1] + + return url + + +def expand_local_url(url, field): + """check if the user provided a local file path instead of a + remote. If so, it must be expanded to an absolute + path. + + Note: local paths of LOCAL_PATH_INDICATOR have special meaning and + represent local copy only, don't work with the remotes. + + """ + remote_url = is_remote_url(url) + if not remote_url: + if url.strip() == LOCAL_PATH_INDICATOR: + pass + else: + url = os.path.expandvars(url) + url = os.path.expanduser(url) + if not os.path.isabs(url): + msg = ( + 'WARNING: Externals description for "{0}" contains a ' + "url that is not remote and does not expand to an " + "absolute path. Version control operations may " + "fail.\n\nurl={1}".format(field, url) + ) + printlog(msg) + else: + url = os.path.normpath(url) + return url + + +# --------------------------------------------------------------------- +# +# subprocess +# +# --------------------------------------------------------------------- + +# Give the user a helpful message if we detect that a command seems to +# be hanging. +_HANGING_SEC = 300 + + +def _hanging_msg(working_directory, command): + print( + """ + +Command '{command}' +from directory {working_directory} +has taken {hanging_sec} seconds. It may be hanging. + +The command will continue to run, but you may want to abort +manage_externals with ^C and investigate. A possible cause of hangs is +when svn or git require authentication to access a private +repository. On some systems, svn and git requests for authentication +information will not be displayed to the user. In this case, the program +will appear to hang. Ensure you can run svn and git manually and access +all repositories without entering your authentication information. + +""".format( + command=command, + working_directory=working_directory, + hanging_sec=_HANGING_SEC, + ) + ) + + +def execute_subprocess(commands, status_to_caller=False, output_to_caller=False): + """Wrapper around subprocess.check_output to handle common + exceptions. + + check_output runs a command with arguments and waits + for it to complete. + + check_output raises an exception on a nonzero return code. if + status_to_caller is true, execute_subprocess returns the subprocess + return code, otherwise execute_subprocess treats non-zero return + status as an error and raises an exception. + + """ + cwd = os.getcwd() + msg = "In directory: {0}\nexecute_subprocess running command:".format(cwd) + logging.info(msg) + commands_str = " ".join(str(element) for element in commands) + logging.info(commands_str) + return_to_caller = status_to_caller or output_to_caller + status = -1 + output = "" + hanging_timer = Timer( + _HANGING_SEC, + _hanging_msg, + kwargs={"working_directory": cwd, "command": commands_str}, + ) + hanging_timer.start() + try: + output = subprocess.check_output( + commands, stderr=subprocess.STDOUT, universal_newlines=True + ) + log_process_output(output) + status = 0 + except OSError as error: + msg = failed_command_msg( + "Command execution failed. Does the executable exist?", commands + ) + logging.error(error) + fatal_error(msg) + except ValueError as error: + msg = failed_command_msg( + "DEV_ERROR: Invalid arguments trying to run subprocess", commands + ) + logging.error(error) + fatal_error(msg) + except subprocess.CalledProcessError as error: + # Only report the error if we are NOT returning to the + # caller. If we are returning to the caller, then it may be a + # simple status check. If returning, it is the callers + # responsibility determine if an error occurred and handle it + # appropriately. + if not return_to_caller: + msg_context = ( + "Process did not run successfully; " + "returned status {0}".format(error.returncode) + ) + msg = failed_command_msg(msg_context, commands, output=error.output) + logging.error(error) + logging.error(msg) + log_process_output(error.output) + fatal_error(msg) + status = error.returncode + finally: + hanging_timer.cancel() + + if status_to_caller and output_to_caller: + ret_value = (status, output) + elif status_to_caller: + ret_value = status + elif output_to_caller: + ret_value = output + else: + ret_value = None + + return ret_value + + +def failed_command_msg(msg_context, command, output=None): + """Template for consistent error messages from subprocess calls. + + If 'output' is given, it should provide the output from the failed + command + """ + + if output: + output_truncated = last_n_lines( + output, 20, truncation_message="[... Output truncated for brevity ...]" + ) + errmsg = ( + "Failed with output:\n" + indent_string(output_truncated, 4) + "\nERROR: " + ) + else: + errmsg = "" + + command_str = " ".join(command) + errmsg += """In directory + {cwd} +{context}: + {command} +""".format( + cwd=os.getcwd(), context=msg_context, command=command_str + ) + + if output: + errmsg += "See above for output from failed command.\n" + + return errmsg diff --git a/poetry.lock b/poetry.lock new file mode 100644 index 0000000000..b59ed3942c --- /dev/null +++ b/poetry.lock @@ -0,0 +1,693 @@ +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. + +[[package]] +name = "alabaster" +version = "0.7.13" +description = "A configurable sidebar-enabled Sphinx theme" +optional = false +python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] + +[[package]] +name = "babel" +version = "2.14.0" +description = "Internationalization utilities" +optional = false +python-versions = ">=3.7" +files = [ + {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"}, + {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"}, +] + +[package.dependencies] +pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""} + +[package.extras] +dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] + +[[package]] +name = "certifi" +version = "2024.2.2" +description = "Python package for providing Mozilla's CA Bundle." +optional = false +python-versions = ">=3.6" +files = [ + {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"}, + {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"}, +] + +[[package]] +name = "charset-normalizer" +version = "3.3.2" +description = "The Real First Universal Charset Detector. 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"sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, +] + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.8" +content-hash = "25ee2ae1d74abedde3a6637a60d4a3095ea5cf9731960875741bbc2ba84a475d" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000000..ac1684ea0f --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,41 @@ +[tool.poetry] +name = "git-fleximod" +version = "0.7.5" +description = "Extended support for git-submodule and git-sparse-checkout" +authors = ["Jim Edwards "] +maintainers = ["Jim Edwards "] +license = "MIT" +readme = "README.md" +homepage = "https://github.com/jedwards4b/git-fleximod" +keywords = ["git", "submodule", "sparse-checkout"] +packages = [ +{ include = "git_fleximod"}, +{ include = "doc"}, +] + +[tool.poetry.scripts] +git-fleximod = "git_fleximod.git_fleximod:main" +me2flexi = "git_fleximod.metoflexi:_main" +fsspec = "fsspec.fuse:main" + +[tool.poetry.dependencies] +python = "^3.8" +GitPython = "^3.1.0" +sphinx = "^5.0.0" +fsspec = "^2023.12.2" +wheel = "^0.42.0" +pytest = "^8.0.0" +pyfakefs = "^5.3.5" + +[tool.poetry.urls] +"Bug Tracker" = "https://github.com/jedwards4b/git-fleximod/issues" + +[tool.pytest.ini_options] +markers = [ + "skip_after_first: only run on first iteration" +] + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + diff --git a/tbump.toml b/tbump.toml new file mode 100644 index 0000000000..e644fc4d24 --- /dev/null +++ b/tbump.toml @@ -0,0 +1,43 @@ +# Uncomment this if your project is hosted on GitHub: +github_url = "https://github.com/jedwards4b/git-fleximod/" + +[version] +current = "0.7.5" + +# Example of a semver regexp. +# Make sure this matches current_version before +# using tbump +regex = ''' + (?P\d+) + \. + (?P\d+) + \. + (?P\d+) + ''' + +[git] +message_template = "Bump to {new_version}" +tag_template = "v{new_version}" + +# For each file to patch, add a [[file]] config +# section containing the path of the file, relative to the +# tbump.toml location. +[[file]] +src = "git_fleximod/cli.py" + +[[file]] +src = "pyproject.toml" + +# You can specify a list of commands to +# run after the files have been patched +# and before the git commit is made + +# [[before_commit]] +# name = "check changelog" +# cmd = "grep -q {new_version} Changelog.rst" + +# Or run some commands after the git tag and the branch +# have been pushed: +# [[after_push]] +# name = "publish" +# cmd = "./publish.sh" diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000000..4d4c66c78e --- /dev/null +++ b/tests/__init__.py @@ -0,0 +1,3 @@ +import sys, os + +sys.path.append(os.path.join(os.path.dirname(__file__), os.path.pardir, "src")) diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000000..942a0efb97 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,138 @@ +import pytest +from git_fleximod.gitinterface import GitInterface +import os +import subprocess +import logging +from pathlib import Path + +@pytest.fixture(scope='session') +def logger(): + logging.basicConfig( + level=logging.INFO, format="%(name)s - %(levelname)s - %(message)s", handlers=[logging.StreamHandler()] + ) + logger = logging.getLogger(__name__) + return logger + +all_repos=[ + {"subrepo_path": "modules/test", + "submodule_name": "test_submodule", + "status1" : "test_submodule MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", + "status2" : "test_submodule at tag MPIserial_2.4.0", + "status3" : "test_submodule at tag MPIserial_2.4.0", + "status4" : "test_submodule at tag MPIserial_2.4.0", + "gitmodules_content" : """ + [submodule "test_submodule"] + path = modules/test + url = https://github.com/ESMCI/mpi-serial.git + fxtag = MPIserial_2.4.0 + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = ToplevelRequired +"""}, + {"subrepo_path": "modules/test_optional", + "submodule_name": "test_optional", + "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", + "status2" : "test_optional at tag MPIserial_2.4.0", + "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0", + "status4" : "test_optional at tag MPIserial_2.4.0", + "gitmodules_content": """ + [submodule "test_optional"] + path = modules/test_optional + url = https://github.com/ESMCI/mpi-serial.git + fxtag = MPIserial_2.4.0 + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = ToplevelOptional +"""}, + {"subrepo_path": "modules/test_alwaysoptional", + "submodule_name": "test_alwaysoptional", + "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c", + "status2" : "test_alwaysoptional at hash e5cf35c", + "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0", + "status4" : "test_alwaysoptional at hash e5cf35c", + "gitmodules_content": """ + [submodule "test_alwaysoptional"] + path = modules/test_alwaysoptional + url = https://github.com/ESMCI/mpi-serial.git + fxtag = e5cf35c + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = AlwaysOptional +"""}, + {"subrepo_path": "modules/test_sparse", + "submodule_name": "test_sparse", + "status1" : "test_sparse at tag MPIserial_2.5.0", + "status2" : "test_sparse at tag MPIserial_2.5.0", + "status3" : "test_sparse at tag MPIserial_2.5.0", + "status4" : "test_sparse at tag MPIserial_2.5.0", + "gitmodules_content": """ + [submodule "test_sparse"] + path = modules/test_sparse + url = https://github.com/ESMCI/mpi-serial.git + fxtag = MPIserial_2.5.0 + fxDONOTUSEurl = https://github.com/ESMCI/mpi-serial.git + fxrequired = AlwaysRequired + fxsparse = ../.sparse_file_list +"""}, +] +@pytest.fixture(params=all_repos) + +def shared_repos(request): + return request.param + +@pytest.fixture +def get_all_repos(): + return all_repos + +def write_sparse_checkout_file(fp): + sparse_content = """m4 +""" + fp.write_text(sparse_content) + +@pytest.fixture +def test_repo(shared_repos, tmp_path, logger): + subrepo_path = shared_repos["subrepo_path"] + submodule_name = shared_repos["submodule_name"] + test_dir = tmp_path / "testrepo" + test_dir.mkdir() + str_path = str(test_dir) + gitp = GitInterface(str_path, logger) + assert test_dir.joinpath(".git").is_dir() + (test_dir / "modules").mkdir() + if "sparse" in submodule_name: + (test_dir / subrepo_path).mkdir() + # Add the sparse checkout file + write_sparse_checkout_file(test_dir / "modules" / ".sparse_file_list") + gitp.git_operation("add","modules/.sparse_file_list") + else: + gitp = GitInterface(str(test_dir), logger) + gitp.git_operation("submodule", "add", "--depth","1","--name", submodule_name, "https://github.com/ESMCI/mpi-serial.git", subrepo_path) + assert test_dir.joinpath(".gitmodules").is_file() + gitp.git_operation("add",subrepo_path) + gitp.git_operation("commit","-a","-m","\"add submod\"") + test_dir2 = tmp_path / "testrepo2" + gitp.git_operation("clone",test_dir,test_dir2) + return test_dir2 + + +@pytest.fixture +def complex_repo(tmp_path, logger): + test_dir = tmp_path / "testcomplex" + test_dir.mkdir() + str_path = str(test_dir) + gitp = GitInterface(str_path, logger) + gitp.git_operation("remote", "add", "origin", "https://github.com/jedwards4b/fleximod-test2") + gitp.git_operation("fetch", "origin", "main") + gitp.git_operation("checkout", "main") + return test_dir + +@pytest.fixture +def git_fleximod(): + def _run_fleximod(path, args, input=None): + cmd = ["git", "fleximod"] + args.split() + result = subprocess.run(cmd, cwd=path, input=input, + stdout=subprocess.PIPE, stderr=subprocess.PIPE, + text=True) + if result.returncode: + print(result.stdout) + print(result.stderr) + return result + return _run_fleximod + diff --git a/tests/test_a_import.py b/tests/test_a_import.py new file mode 100644 index 0000000000..d5ca878de5 --- /dev/null +++ b/tests/test_a_import.py @@ -0,0 +1,8 @@ +# pylint: disable=unused-import +from git_fleximod import cli +from git_fleximod import utils +from git_fleximod.gitinterface import GitInterface +from git_fleximod.gitmodules import GitModules + +def test_import(): + print("here") diff --git a/tests/test_b_update.py b/tests/test_b_update.py new file mode 100644 index 0000000000..159f1cfae0 --- /dev/null +++ b/tests/test_b_update.py @@ -0,0 +1,26 @@ +import pytest +from pathlib import Path + +def test_basic_checkout(git_fleximod, test_repo, shared_repos): + # Prepare a simple .gitmodules + gm = shared_repos['gitmodules_content'] + file_path = (test_repo / ".gitmodules") + repo_name = shared_repos["submodule_name"] + repo_path = shared_repos["subrepo_path"] + + file_path.write_text(gm) + + # Run the command + result = git_fleximod(test_repo, f"update {repo_name}") + + # Assertions + assert result.returncode == 0 + assert Path(test_repo / repo_path).exists() # Did the submodule directory get created? + if "sparse" in repo_name: + assert Path(test_repo / f"{repo_path}/m4").exists() # Did the submodule sparse directory get created? + assert not Path(test_repo / f"{repo_path}/README").exists() # Did only the submodule sparse directory get created? + + status = git_fleximod(test_repo, f"status {repo_name}") + + assert shared_repos["status2"] in status.stdout + diff --git a/tests/test_c_required.py b/tests/test_c_required.py new file mode 100644 index 0000000000..89ab8d294d --- /dev/null +++ b/tests/test_c_required.py @@ -0,0 +1,30 @@ +import pytest +from pathlib import Path + +def test_required(git_fleximod, test_repo, shared_repos): + file_path = (test_repo / ".gitmodules") + gm = shared_repos["gitmodules_content"] + repo_name = shared_repos["submodule_name"] + if file_path.exists(): + with file_path.open("r") as f: + gitmodules_content = f.read() + # add the entry if it does not exist + if repo_name not in gitmodules_content: + file_path.write_text(gitmodules_content+gm) + # or if it is incomplete + elif gm not in gitmodules_content: + file_path.write_text(gm) + else: + file_path.write_text(gm) + result = git_fleximod(test_repo, "update") + assert result.returncode == 0 + status = git_fleximod(test_repo, f"status {repo_name}") + assert shared_repos["status3"] in status.stdout + status = git_fleximod(test_repo, f"update --optional") + assert result.returncode == 0 + status = git_fleximod(test_repo, f"status {repo_name}") + assert shared_repos["status4"] in status.stdout + status = git_fleximod(test_repo, f"update {repo_name}") + assert result.returncode == 0 + status = git_fleximod(test_repo, f"status {repo_name}") + assert shared_repos["status4"] in status.stdout diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py new file mode 100644 index 0000000000..fdce516274 --- /dev/null +++ b/tests/test_d_complex.py @@ -0,0 +1,67 @@ +import pytest +from pathlib import Path +from git_fleximod.gitinterface import GitInterface + +def test_complex_checkout(git_fleximod, complex_repo, logger): + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) + assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout) + assert("Complex not checked out, aligned at tag testtag01" in status.stdout) + assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) + + # This should checkout and update test_submodule and complex_sub + result = git_fleximod(complex_repo, "update") + assert result.returncode == 0 + + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) + assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) + assert("Complex at tag testtag01" in status.stdout) + + # now check the complex_sub + root = (complex_repo / "modules" / "complex") + assert(not (root / "libraries" / "gptl" / ".git").exists()) + assert(not (root / "libraries" / "mpi-serial" / ".git").exists()) + assert((root / "modules" / "mpi-serial" / ".git").exists()) + assert(not (root / "modules" / "mpi-serial2" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / "m4").exists()) + assert(not (root / "modules" / "mpi-sparse" / "README").exists()) + + # update a single optional submodule + + result = git_fleximod(complex_repo, "update ToplevelOptional") + assert result.returncode == 0 + + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional at tag v5.3.2" in status.stdout) + assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) + assert("Complex at tag testtag01" in status.stdout) + assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) + + + # Finally update optional + result = git_fleximod(complex_repo, "update --optional") + assert result.returncode == 0 + + status = git_fleximod(complex_repo, "status") + assert("ToplevelOptional at tag v5.3.2" in status.stdout) + assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) + assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) + assert("Complex at tag testtag01" in status.stdout) + assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout) + + # now check the complex_sub + root = (complex_repo / "modules" / "complex" ) + assert(not (root / "libraries" / "gptl" / ".git").exists()) + assert(not (root / "libraries" / "mpi-serial" / ".git").exists()) + assert((root / "modules" / "mpi-serial" / ".git").exists()) + assert((root / "modules" / "mpi-serial2" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / ".git").exists()) + assert((root / "modules" / "mpi-sparse" / "m4").exists()) + assert(not (root / "modules" / "mpi-sparse" / "README").exists()) + + From c834c30292c96bf27b63a78c0ce01be66c14f64d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 31 May 2024 11:28:29 -0600 Subject: [PATCH 224/408] Draft of ChangeLog/ChageSum --- doc/ChangeLog | 96 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 97 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index b2f14a2c01..ee2e861be7 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,100 @@ =============================================================== +Tag name: ctsm5.2.007 +Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD) +Date: Fri 31 May 2024 11:24:29 AM MDT +One-line Summary: Rm manage_externals and update documentation accordingly + +Purpose and description of changes +---------------------------------- +#2443 Jim replaced this PR with the next one +#2559 Remove manage externals +#2564 Replace checkout_externals with git-fleximod in documentation + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: +Fixes #2537 Remove manage_externals stuff from run_sys_tests +Fixes #2536 Update documentation for git-fleximod +Fixes #2467 Remove references to cheyenne from the testlist + +Notes of particular relevance for users +--------------------------------------- +Caveats for users (e.g., need to interpolate initial conditions): + ./manage_externals/checkout_externals + is replaced with + ./bin/git-fleximod + +Changes to documentation: + Accordingly + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python + code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system + tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in + either model output or namelists, is: create sym links pointing to the last tag's baseline directory, + named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT + doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to + separately run the clm_pymods test suite, and you can remove the following line.] + + clm_pymods test suite on derecho - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- OK + + any other testing (give details below): + + ctsm_sci + derecho ---- OK + +Answer changes +-------------- +Changes answers relative to baseline: No + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + JIM: What's the answer here? + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2443 + https://github.com/ESCOMP/ctsm/pull/2559 + https://github.com/ESCOMP/ctsm/pull/2564 + +=============================================================== +=============================================================== Tag name: ctsm5.2.006 Originator(s): slevis (Samuel Levis) Date: Tue 28 May 2024 03:14:18 PM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index 77bc8a426d..b3f1632571 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems ctsm5.2.004 multiple 05/09/2024 CTSM5.2 1979 fsurdat and 1979-2026 landuse ne0np4 files + two fixes From 9a82a3fb531de7f1d31578f51091b700bccc3651 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 31 May 2024 13:54:53 -0600 Subject: [PATCH 225/408] Replace manage_externals with git-fleximod in an error message --- .lib/git-fleximod/git_fleximod/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.lib/git-fleximod/git_fleximod/utils.py b/.lib/git-fleximod/git_fleximod/utils.py index 7cc1de38cc..64a2e70d98 100644 --- a/.lib/git-fleximod/git_fleximod/utils.py +++ b/.lib/git-fleximod/git_fleximod/utils.py @@ -241,7 +241,7 @@ def _hanging_msg(working_directory, command): has taken {hanging_sec} seconds. It may be hanging. The command will continue to run, but you may want to abort -manage_externals with ^C and investigate. A possible cause of hangs is +git-fleximod with ^C and investigate. A possible cause of hangs is when svn or git require authentication to access a private repository. On some systems, svn and git requests for authentication information will not be displayed to the user. In this case, the program From c9020ec5320013121b84e4abc03bc0cf5bab2133 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 31 May 2024 13:57:53 -0600 Subject: [PATCH 226/408] Replace "externals directories" with "git submodules" in ChangeLogs --- doc/.ChangeLog_template | 2 +- doc/ChangeLog | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index f6a6dbd2f8..60a7f49288 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -157,7 +157,7 @@ Other details ------------- [Remove any lines that don't apply. Remove entire section if nothing applies.] -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): Pull Requests that document the changes (include PR ids): (https://github.com/ESCOMP/ctsm/pull) diff --git a/doc/ChangeLog b/doc/ChangeLog index ee2e861be7..8b6bb8f0d2 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.007 Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD) -Date: Fri 31 May 2024 11:24:29 AM MDT +Date: Fri 31 May 2024 13:49:29 AM MDT One-line Summary: Rm manage_externals and update documentation accordingly Purpose and description of changes @@ -85,8 +85,11 @@ Changes answers relative to baseline: No Other details ------------- -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): - JIM: What's the answer here? +List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): + Comparing .gitmodules against Externals.cfg and Externals_CLM_cfg: + - cismwrap_2_2_001 from cismwrap_2_1_100 + - cime6.0.246 from cime6.0.238_httpsbranch01 + - cdeps1.0.34 from cdeps1.0.33 Pull Requests that document the changes (include PR ids): https://github.com/ESCOMP/ctsm/pull/2443 From 34f2dd45ea32ea9e4a8d4e2c7d81f07806ca1710 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 31 May 2024 15:16:08 -0600 Subject: [PATCH 227/408] Make dns_aer a global constant --- src/biogeochem/DustEmisZender2003.F90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index 22bbbe0742..d17ebc8f1c 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -43,7 +43,7 @@ module DustEmisZender2003 real(r8) , allocatable :: dmt_vwr(:) ![m] Mass-weighted mean diameter resolved real(r8) , allocatable :: stk_crc(:) ![frc] Correction to Stokes settling velocity real(r8) tmp1 !Factor in saltation computation (named as in Charlie's code) - real(r8) dns_aer ![kg m-3] Aerosol density + real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density ! ! !PUBLIC DATA TYPES: ! @@ -880,7 +880,6 @@ subroutine InitDustVars(this, bounds) gsd_anl = 2.0_r8 ! [frc] Geometric std dev PaG77 p. 2080 Table1 ln_gsd = log(gsd_anl) - dns_aer = 2.5e+3_r8 ! [kg m-3] Aerosol density ! Set a fundamental statistic for each bin From 6fbb432e97389e4c0bde8aad7d8da77646c98936 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 1 Jun 2024 15:52:19 -0600 Subject: [PATCH 228/408] Move tmp1 to inside the dustemis type --- src/biogeochem/DustEmisZender2003.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index d17ebc8f1c..a2d4ed2d26 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -37,18 +37,18 @@ module DustEmisZender2003 implicit none private ! - ! !PUBLIC DATA: + ! !PRIVATE DATA: ! - real(r8) , allocatable :: ovr_src_snk_mss(:,:) + real(r8) , allocatable :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin real(r8) , allocatable :: dmt_vwr(:) ![m] Mass-weighted mean diameter resolved real(r8) , allocatable :: stk_crc(:) ![frc] Correction to Stokes settling velocity - real(r8) tmp1 !Factor in saltation computation (named as in Charlie's code) real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density ! ! !PUBLIC DATA TYPES: ! type, public :: dust_type + real(r8), private :: tmp1 ! Factor in saltation computation (named as in Charlie's code) real(r8), pointer, PUBLIC :: flx_mss_vrt_dst_patch (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:) ! total dust flux into atmosphere real(r8), pointer, private :: vlc_trb_patch (:,:) ! turbulent deposition velocity (m/s) (ndst) @@ -293,7 +293,7 @@ subroutine GetConstVars(this, SaltationFactor ) class(dust_type) , intent(in) :: this real(r8) , intent(out) :: SaltationFactor - SaltationFactor = tmp1 + SaltationFactor = this%tmp1 end subroutine GetConstVars !------------------------------------------------------------------------ @@ -505,7 +505,7 @@ subroutine DustEmission (this, bounds, & ! subr. wnd_frc_thr_slt_get which computes dry threshold ! friction velocity for saltation - wnd_frc_thr_slt = tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct + wnd_frc_thr_slt = this%tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct ! reset these variables which will be updated in the following if-block @@ -846,7 +846,7 @@ subroutine InitDustVars(this, bounds) icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8)) dns_fct = dns_slt * grav * dmt_slt_opt - tmp1 = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc) + this%tmp1 = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc) ! Introducing particle diameter. Needed by atm model and by dry dep model. ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl, From 1cf137bf57ed63aa9f9716f6425917268e13e4e4 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 1 Jun 2024 16:05:33 -0600 Subject: [PATCH 229/408] Move three module variables to inside the data type --- src/biogeochem/DustEmisZender2003.F90 | 54 +++++++++++++-------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index a2d4ed2d26..6adbac8521 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -39,15 +39,15 @@ module DustEmisZender2003 ! ! !PRIVATE DATA: ! - real(r8) , allocatable :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin - real(r8) , allocatable :: dmt_vwr(:) ![m] Mass-weighted mean diameter resolved - real(r8) , allocatable :: stk_crc(:) ![frc] Correction to Stokes settling velocity real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density ! ! !PUBLIC DATA TYPES: ! type, public :: dust_type + real(r8) , allocatable, private :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin + real(r8) , allocatable, private :: dmt_vwr(:) ! [m] Mass-weighted mean diameter resolved + real(r8) , allocatable, private :: stk_crc(:) ! [frc] Correction to Stokes settling velocity real(r8), private :: tmp1 ! Factor in saltation computation (named as in Charlie's code) real(r8), pointer, PUBLIC :: flx_mss_vrt_dst_patch (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:) ! total dust flux into atmosphere @@ -116,9 +116,9 @@ subroutine Clean(this) deallocate(this%vlc_trb_4_patch) deallocate(this%mbl_bsn_fct_col) - deallocate (ovr_src_snk_mss) - deallocate (dmt_vwr) - deallocate (stk_crc) + deallocate (this%ovr_src_snk_mss) + deallocate (this%dmt_vwr) + deallocate (this%stk_crc) end subroutine Clean @@ -146,6 +146,11 @@ subroutine InitAllocate(this, bounds) allocate(this%vlc_trb_4_patch (begp:endp)) ; this%vlc_trb_4_patch (:) = nan allocate(this%mbl_bsn_fct_col (begc:endc)) ; this%mbl_bsn_fct_col (:) = nan + allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst)) ; this%ovr_src_snk_mss (:,:) = nan + allocate (this%dmt_vwr(ndst)) ; this%dmt_vwr (:) = nan + allocate (this%stk_crc(ndst)) ; this%stk_crc (:) = nan + + end subroutine InitAllocate !------------------------------------------------------------------------ @@ -564,7 +569,7 @@ subroutine DustEmission (this, bounds, & do fp = 1,num_nolakep p = filter_nolakep(fp) if (lnd_frc_mbl(p) > 0.0_r8) then - flx_mss_vrt_dst(p,n) = flx_mss_vrt_dst(p,n) + ovr_src_snk_mss(m,n) * flx_mss_vrt_dst_ttl(p) + flx_mss_vrt_dst(p,n) = flx_mss_vrt_dst(p,n) + this%ovr_src_snk_mss(m,n) * flx_mss_vrt_dst_ttl(p) end if end do end do @@ -663,11 +668,11 @@ subroutine DustDryDep (this, bounds, & do m = 1, ndst slp_crc(p,m) = 1.0_r8 + 2.0_r8 * mfp_atm * & - (1.257_r8+0.4_r8*exp(-1.1_r8*dmt_vwr(m)/(2.0_r8*mfp_atm))) / & - dmt_vwr(m) ![frc] Slip correction factor SeP97 p. 464 - vlc_grv(p,m) = (1.0_r8/18.0_r8) * dmt_vwr(m) * dmt_vwr(m) * dns_aer * & + (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / & + this%dmt_vwr(m) ![frc] Slip correction factor SeP97 p. 464 + vlc_grv(p,m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * & grav * slp_crc(p,m) / vsc_dyn_atm(p) ![m s-1] Stokes' settling velocity SeP97 p. 466 - vlc_grv(p,m) = vlc_grv(p,m) * stk_crc(m) ![m s-1] Correction to Stokes settling velocity + vlc_grv(p,m) = vlc_grv(p,m) * this%stk_crc(m) ![m s-1] Correction to Stokes settling velocity end do end if end do @@ -680,7 +685,7 @@ subroutine DustDryDep (this, bounds, & stk_nbr = vlc_grv(p,m) * fv(p) * fv(p) / (grav * vsc_knm_atm(p)) ![frc] SeP97 p.965 dff_aer = SHR_CONST_BOLTZ * forc_t(c) * slp_crc(p,m) / & ![m2 s-1] - (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * dmt_vwr(m)) !SeP97 p.474 + (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * this%dmt_vwr(m)) !SeP97 p.474 shm_nbr = vsc_knm_atm(p) / dff_aer ![frc] SeP97 p.972 shm_nbr_xpn = shm_nbr_xpn_lnd ![frc] @@ -796,11 +801,6 @@ subroutine InitDustVars(this, bounds) real(r8), parameter :: dns_slt = 2650.0_r8 ! [kg m-3] Density of optimal saltation particles !------------------------------------------------------------------------ - ! allocate module variable - allocate (ovr_src_snk_mss(dst_src_nbr,ndst)) - allocate (dmt_vwr(ndst)) - allocate (stk_crc(ndst)) - ! allocate local variable allocate (dmt_vma_src(dst_src_nbr)) allocate (gsd_anl_src(dst_src_nbr)) @@ -824,7 +824,7 @@ subroutine InitDustVars(this, bounds) lndminjovrdmdni = log(dmt_grd(n )/dmt_vma_src(m)) ovr_src_snk_frc = 0.5_r8 * (erf(lndmaxjovrdmdni/sqrt2lngsdi) - & erf(lndminjovrdmdni/sqrt2lngsdi)) - ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m) + this%ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m) end do end do @@ -914,7 +914,7 @@ subroutine InitDustVars(this, bounds) end do lngsdsqrttwopi_rcp = 1.0_r8 / (ln_gsd*sqrt(2.0_r8*SHR_CONST_PI)) - dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved + this%dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved vlm_rsl(n) = 0.0_r8 ! [m3 m-3] Volume concentration resolved do m = 1, sz_nbr @@ -924,7 +924,7 @@ subroutine InitDustVars(this, bounds) lgn_dst = lngsdsqrttwopi_rcp * exp(-0.5_r8*tmp*tmp) / sz_ctr(m) ! Integrate moments of size distribution - dmt_vwr(n) = dmt_vwr(n) + sz_ctr(m) * & + this%dmt_vwr(n) = this%dmt_vwr(n) + sz_ctr(m) * & SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume lgn_dst * sz_dlt(m) ![# m-3] Number concentrn vlm_rsl(n) = vlm_rsl(n) + & @@ -933,7 +933,7 @@ subroutine InitDustVars(this, bounds) end do - dmt_vwr(n) = dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved + this%dmt_vwr(n) = this%dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved end do @@ -952,9 +952,9 @@ subroutine InitDustVars(this, bounds) do m = 1, ndst slp_crc(m) = 1.0_r8 + 2.0_r8 * mfp_atm * & - (1.257_r8+0.4_r8*exp(-1.1_r8*dmt_vwr(m)/(2.0_r8*mfp_atm))) / & - dmt_vwr(m) ! [frc] Slip correction factor SeP97 p.464 - vlc_stk(m) = (1.0_r8/18.0_r8) * dmt_vwr(m) * dmt_vwr(m) * dns_aer * & + (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / & + this%dmt_vwr(m) ! [frc] Slip correction factor SeP97 p.464 + vlc_stk(m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * & grav * slp_crc(m) / vsc_dyn_atm ! [m s-1] SeP97 p.466 end do @@ -979,7 +979,7 @@ subroutine InitDustVars(this, bounds) ! Save terminal velocity for convergence test vlc_grv_old = vlc_grv(m) ![m s-1] - ryn_nbr_grv(m) = vlc_grv(m) * dmt_vwr(m) / vsc_knm_atm !SeP97 p.460 + ryn_nbr_grv(m) = vlc_grv(m) * this%dmt_vwr(m) / vsc_knm_atm !SeP97 p.460 ! Update drag coefficient based on new Reynolds number if (ryn_nbr_grv(m) < 0.1_r8) then @@ -1003,7 +1003,7 @@ subroutine InitDustVars(this, bounds) ! Update terminal velocity based on new Reynolds number and drag coeff ! [m s-1] Terminal veloc SeP97 p.467 (8.44) - vlc_grv(m) = sqrt(4.0_r8 * grav * dmt_vwr(m) * slp_crc(m) * dns_aer / & + vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / & (3.0_r8*cff_drg_grv(m)*dns_mdp)) eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence if (itr_idx == 12) then @@ -1027,7 +1027,7 @@ subroutine InitDustVars(this, bounds) ! actual settling velocities do m = 1, ndst - stk_crc(m) = vlc_grv(m) / vlc_stk(m) + this%stk_crc(m) = vlc_grv(m) / vlc_stk(m) end do end subroutine InitDustVars From 17864ceae227f9a42dd724b58dacc5987bcef27f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 1 Jun 2024 16:13:08 -0600 Subject: [PATCH 230/408] Change name of tmp1 to saltation_factor --- src/biogeochem/DustEmisZender2003.F90 | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index 6adbac8521..db6f93581a 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -39,7 +39,7 @@ module DustEmisZender2003 ! ! !PRIVATE DATA: ! - real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density + real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density ! ! !PUBLIC DATA TYPES: ! @@ -48,7 +48,7 @@ module DustEmisZender2003 real(r8) , allocatable, private :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin real(r8) , allocatable, private :: dmt_vwr(:) ! [m] Mass-weighted mean diameter resolved real(r8) , allocatable, private :: stk_crc(:) ! [frc] Correction to Stokes settling velocity - real(r8), private :: tmp1 ! Factor in saltation computation (named as in Charlie's code) + real(r8), private :: saltation_factor ! Factor in saltation computation (named as in Charlie's code) real(r8), pointer, PUBLIC :: flx_mss_vrt_dst_patch (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:) ! total dust flux into atmosphere real(r8), pointer, private :: vlc_trb_patch (:,:) ! turbulent deposition velocity (m/s) (ndst) @@ -298,7 +298,7 @@ subroutine GetConstVars(this, SaltationFactor ) class(dust_type) , intent(in) :: this real(r8) , intent(out) :: SaltationFactor - SaltationFactor = this%tmp1 + SaltationFactor = this%saltation_factor end subroutine GetConstVars !------------------------------------------------------------------------ @@ -506,11 +506,11 @@ subroutine DustEmission (this, bounds, & ! the following lines come from subr. dst_mbl ! purpose: adjust threshold friction velocity to acct for moisture and - ! roughness. The ratio tmp1 / sqrt(forc_rho) comes from + ! roughness. The ratio saltation_factor / sqrt(forc_rho) comes from ! subr. wnd_frc_thr_slt_get which computes dry threshold ! friction velocity for saltation - wnd_frc_thr_slt = this%tmp1 / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct + wnd_frc_thr_slt = this%saltation_factor / sqrt(forc_rho(c)) * frc_thr_wet_fct * frc_thr_rgh_fct ! reset these variables which will be updated in the following if-block @@ -733,7 +733,7 @@ subroutine InitDustVars(this, bounds) ! ! Compute source efficiency factor from topography ! Initialize other variables used in subroutine Dust: - ! ovr_src_snk_mss(m,n) and tmp1. + ! ovr_src_snk_mss(m,n) and saltation_factor. ! Define particle diameter and density needed by atm model ! as well as by dry dep model ! Source: Paul Ginoux (for source efficiency factor) @@ -829,7 +829,7 @@ subroutine InitDustVars(this, bounds) end do ! The following code from subroutine wnd_frc_thr_slt_get was placed - ! here because tmp1 needs to be defined just once + ! here because saltation_factor needs to be defined just once ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8 @@ -846,7 +846,7 @@ subroutine InitDustVars(this, bounds) icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8)) dns_fct = dns_slt * grav * dmt_slt_opt - this%tmp1 = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc) + this%saltation_factor = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc) ! Introducing particle diameter. Needed by atm model and by dry dep model. ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl, From b3b8e08acdcad393844207ac9e556bdee8b3ef08 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 3 Jun 2024 15:42:23 -0600 Subject: [PATCH 231/408] Add reference for ThresholdSoilMoist and add extended comments from Danny Leung from the Leung PR, actually use it in the code and make sure the unit test uses the new name --- .../DustEmis_test/test_DustEmisZender2003.pf | 4 +- src/biogeophys/SoilStateInitTimeConstMod.F90 | 49 ++++++++++++++++--- 2 files changed, 45 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index c99f4bd97d..a7fea904c9 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -19,7 +19,7 @@ module test_DustEmisZender2003 use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type - use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay + use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay implicit none @@ -156,7 +156,7 @@ contains ! considered bedrock col%nbedrock(c) = nlevsoi - this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay ) + this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay ) this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) end do diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90 index 3b71efe103..0be54571e5 100644 --- a/src/biogeophys/SoilStateInitTimeConstMod.F90 +++ b/src/biogeophys/SoilStateInitTimeConstMod.F90 @@ -19,7 +19,7 @@ module SoilStateInitTimeConstMod public :: readParams ! PRIVATE FUNCTIONS MADE PUBLIC Just for unit-testing: - public :: ThresholdSoilMoist + public :: ThresholdSoilMoistZender2003 public :: ThresholdSoilMoistKok2014 public :: MassFracClay ! @@ -707,8 +707,8 @@ subroutine SoilStateInitTimeConst(bounds, soilstate_inst, nlfilename) do c = begc,endc g = col%gridcell(c) - soilstate_inst%gwc_thr_col(c) = 0.17_r8 + 0.14_r8 * clay3d(g,1) * 0.01_r8 - soilstate_inst%mss_frc_cly_vld_col(c) = min(clay3d(g,1) * 0.01_r8, 0.20_r8) + soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay3d(g,1) ) + soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay3d(g,1) ) end do ! -------------------------------------------------------------------- @@ -722,9 +722,31 @@ end subroutine SoilStateInitTimeConst !------------------------------------------------------------------------------ - real(r8) function ThresholdSoilMoist( clay ) + real(r8) function ThresholdSoilMoistZender2003( clay ) + !------------------------------------------------------------------------------ + ! ! Calculate the threshold soil moisture needed for dust emission, based on clay content - use abortUtils , only : endrun + ! This was the original equation with a = 1 / (%clay) being the tuning factor for soil + ! moisture effect in Zender's 2003 dust emission scheme. + ! + ! 0.17 and 0.14 are fitting coefficients in Fecan et al. (1999), and 0.01 is used to + ! convert surface clay fraction from percentage to fraction. + ! + !------------------------------------------------------------------------------ + ! For future developments Danny M. Leung decided (Dec, 2023) that the Leung et al. (2023) o + ! dust emission scheme in the CESM will use Zender's tuning as well, which overall + ! encourages more dust emissions from seriamid and more marginal dust sources. + ! Another advantage of using this tuning factor instead of a = 1 is that the dust emission + ! threshold is linearly dependent on the clay fraction instead of parabolically dependent + ! on clay fraction as in the above line. This means that dust emission becomes a little + ! less sensitive to clay content (soil texture). + ! + ! Also see the notes below for ThresholdSoilMoistKok2014. + ! + ! Notes from: dmleung 19 Feb 2024. + ! + !------------------------------------------------------------------------------ + use abortUtils , only : endrun use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=) real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%) @@ -734,12 +756,27 @@ real(r8) function ThresholdSoilMoist( clay ) return end if ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 - end function ThresholdSoilMoist + end function ThresholdSoilMoistZender2003 !------------------------------------------------------------------------------ real(r8) function ThresholdSoilMoistKok2014( clay ) + !------------------------------------------------------------------------------ ! Calculate the threshold soil moisture needed for dust emission, based on clay content + ! + ! The below calculates the threshold gravimetric water content for the dust emission + ! calculation in DustEmis. The equation comes from Eq. 14 of Fecan et al. + ! (1999; https://doi.org/10.1007/s00585-999-0149-7). + ! gwc_thr_col = 0.17*clay3d + 0.0014*(clay3d**2), and we only concern the topmost + ! soil layer. Charlie Zender later on added a tuning factor (a) such that the + ! equation becomes gwc_thr_col = a*[0.17*clay3d + 0.0014*(clay3d**2)]. + ! (Zender et al., 2003a; https://doi.org/10.1029/2002JD002775) + ! Kok et al. (2014a, b) chose to use a = 1. Resulting in this function + ! Charlie Zender (2003a) chose: a = 1/clay3d, which gives the ThresholdSoilMoistZender2003 + ! function above. + ! + ! Notes from: dmleung 24 May 2024. + !------------------------------------------------------------------------------ real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%) ThresholdSoilMoistKok2014 = 0.01_r8*(0.17_r8*clay + 0.0014_r8*clay*clay) From afbdcbfd8517fbe951772c39bcb1f57da2abd24d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 3 Jun 2024 17:16:08 -0600 Subject: [PATCH 232/408] Squashed '.lib/git-fleximod/' changes from a354b0528..a34070be0 a34070be0 Bump to 0.7.6 9e5d5f72b Merge pull request #40 from ESMCI/fix/change_url 00b7b3817 some fixes when modifying url git-subtree-dir: .lib/git-fleximod git-subtree-split: a34070be02d10071b544be3839f6c9ed79662665 --- git_fleximod/cli.py | 2 +- git_fleximod/git_fleximod.py | 49 ++++++++++++++++++++---------------- git_fleximod/gitmodules.py | 2 +- pyproject.toml | 2 +- tbump.toml | 2 +- 5 files changed, 31 insertions(+), 26 deletions(-) diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py index 4c3fb1a8f9..7d09abd83b 100644 --- a/git_fleximod/cli.py +++ b/git_fleximod/cli.py @@ -2,7 +2,7 @@ import argparse from git_fleximod import utils -__version__ = "0.7.5" +__version__ = "0.7.6" def find_root_dir(filename=".gitmodules"): """ finds the highest directory in tree diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py index f080513a52..a003c0da8c 100755 --- a/git_fleximod/git_fleximod.py +++ b/git_fleximod/git_fleximod.py @@ -263,6 +263,21 @@ def single_submodule_checkout( return +def add_remote(git, url): + remotes = git.git_operation("remote", "-v") + newremote = "newremote.00" + if url in remotes: + for line in remotes: + if url in line and "fetch" in line: + newremote = line.split()[0] + break + else: + i = 0 + while "newremote" in remotes: + i = i + 1 + newremote = f"newremote.{i:02d}" + git.git_operation("remote", "add", newremote, url) + return newremote def submodules_status(gitmodules, root_dir, toplevel=False): testfails = 0 @@ -271,6 +286,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False): for name in gitmodules.sections(): path = gitmodules.get(name, "path") tag = gitmodules.get(name, "fxtag") + url = gitmodules.get(name, "url") required = gitmodules.get(name, "fxrequired") level = required and "Toplevel" in required if not path: @@ -280,7 +296,6 @@ def submodules_status(gitmodules, root_dir, toplevel=False): if not os.path.exists(os.path.join(newpath, ".git")): rootgit = GitInterface(root_dir, logger) # submodule commands use path, not name - url = gitmodules.get(name, "url") url = url.replace("git@github.com:", "https://github.com/") tags = rootgit.git_operation("ls-remote", "--tags", url) atag = None @@ -312,11 +327,11 @@ def submodules_status(gitmodules, root_dir, toplevel=False): with utils.pushd(newpath): git = GitInterface(newpath, logger) atag = git.git_operation("describe", "--tags", "--always").rstrip() - part = git.git_operation("status").partition("\n")[0] - # fake hash to initialize - ahash = "xxxx" - if part: - ahash = part.split()[-1] + ahash = git.git_operation("rev-list", "HEAD").partition("\n")[0] + rurl = git.git_operation("ls-remote","--get-url").rstrip() + if rurl != url: + remote = add_remote(git, url) + git.git_operation("fetch", remote) if tag and atag == tag: print(f" {name:>20} at tag {tag}") elif tag and ahash[: len(tag)] == tag: @@ -335,7 +350,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False): ) testfails += 1 - status = git.git_operation("status", "--ignore-submodules") + status = git.git_operation("status", "--ignore-submodules", "-uno") if "nothing to commit" not in status: localmods = localmods + 1 print("M" + textwrap.indent(status, " ")) @@ -357,11 +372,11 @@ def submodules_update(gitmodules, root_dir, requiredlist, force): path = gitmodules.get(name, "path") url = gitmodules.get(name, "url") logger.info( - "name={} path={} url={} fxtag={} requiredlist={}".format( + "name={} path={} url={} fxtag={} requiredlist={} ".format( name, os.path.join(root_dir, path), url, fxtag, requiredlist ) ) - # if not os.path.exists(os.path.join(root_dir,path, ".git")): + fxrequired = gitmodules.get(name, "fxrequired") assert fxrequired in fxrequired_allowed_values() rgit = GitInterface(root_dir, logger) @@ -409,19 +424,7 @@ def submodules_update(gitmodules, root_dir, requiredlist, force): upstream = git.git_operation("ls-remote", "--get-url").rstrip() newremote = "origin" if upstream != url: - # TODO - this needs to be a unique name - remotes = git.git_operation("remote", "-v") - if url in remotes: - for line in remotes: - if url in line and "fetch" in line: - newremote = line.split()[0] - break - else: - i = 0 - while newremote in remotes: - i = i + 1 - newremote = f"newremote.{i:02d}" - git.git_operation("remote", "add", newremote, url) + add_remote(git, url) tags = git.git_operation("tag", "-l") if fxtag and fxtag not in tags: @@ -439,6 +442,8 @@ def submodules_update(gitmodules, root_dir, requiredlist, force): print(f"{name:>20} up to date.") + + def local_mods_output(): text = """\ The submodules labeled with 'M' above are not in a clean state. diff --git a/git_fleximod/gitmodules.py b/git_fleximod/gitmodules.py index 68c82d066f..7e4e05394a 100644 --- a/git_fleximod/gitmodules.py +++ b/git_fleximod/gitmodules.py @@ -59,7 +59,7 @@ def get(self, name, option, raw=False, vars=None, fallback=None): Uses the parent class's get method to access the value. Handles potential errors if the section or option doesn't exist. """ - self.logger.debug("get called {} {}".format(name, option)) + self.logger.debug("git get called {} {}".format(name, option)) section = f'submodule "{name}"' try: return ConfigParser.get( diff --git a/pyproject.toml b/pyproject.toml index ac1684ea0f..3c70c6c9c7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "git-fleximod" -version = "0.7.5" +version = "0.7.6" description = "Extended support for git-submodule and git-sparse-checkout" authors = ["Jim Edwards "] maintainers = ["Jim Edwards "] diff --git a/tbump.toml b/tbump.toml index e644fc4d24..3854682df4 100644 --- a/tbump.toml +++ b/tbump.toml @@ -2,7 +2,7 @@ github_url = "https://github.com/jedwards4b/git-fleximod/" [version] -current = "0.7.5" +current = "0.7.6" # Example of a semver regexp. # Make sure this matches current_version before From 4a06a23d1b2bcab8e177f6ad57bb64e8bb4db1d6 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 3 Jun 2024 22:55:25 -0600 Subject: [PATCH 233/408] Get unit tests to work again --- src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf | 4 ++-- src/biogeophys/SoilStateInitTimeConstMod.F90 | 4 ++-- .../test_dust_soil_clay_functions.pf | 8 ++++---- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf index b25ad5c44c..e60ec2cc7f 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf @@ -19,7 +19,7 @@ module test_DustEmisBase use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type - use SoilStateInitTimeConstMod, only : ThresholdSoilMoist, ThresholdSoilMoistKok2014, MassFracClay + use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay implicit none @@ -156,7 +156,7 @@ contains ! considered bedrock col%nbedrock(c) = nlevsoi - this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoist( clay ) + this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay ) this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) end do diff --git a/src/biogeophys/SoilStateInitTimeConstMod.F90 b/src/biogeophys/SoilStateInitTimeConstMod.F90 index 0be54571e5..e47577c9b9 100644 --- a/src/biogeophys/SoilStateInitTimeConstMod.F90 +++ b/src/biogeophys/SoilStateInitTimeConstMod.F90 @@ -751,11 +751,11 @@ real(r8) function ThresholdSoilMoistZender2003( clay ) real(r8), intent(IN) :: clay ! Fraction of clay in the soil (%) if ( clay < 0.0_r8 .or. clay > 100.0_r8 )then - ThresholdSoilMoist = nan + ThresholdSoilMoistZender2003 = nan call endrun( 'Clay fraction is out of bounds (0 to 100)') return end if - ThresholdSoilMoist = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 + ThresholdSoilMoistZender2003 = 0.17_r8 + 0.14_r8 * clay * 0.01_r8 end function ThresholdSoilMoistZender2003 !------------------------------------------------------------------------------ diff --git a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf index 0e4ac8b3db..5a8f858286 100644 --- a/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf +++ b/src/biogeophys/test/SoilStateInitTimeConst_test/test_dust_soil_clay_functions.pf @@ -33,10 +33,10 @@ contains real(r8) :: value character(len=100) :: expected_msg - value = ThresholdSoilMoist( -1.e-15_r8 ) + value = ThresholdSoilMoistZender2003( -1.e-15_r8 ) expected_msg = "ABORTED: Clay fraction is out of bounds (0 to 100)" @assertExceptionRaised(expected_msg) - value = ThresholdSoilMoist( 1._r8 + 1.-15_r8 ) + value = ThresholdSoilMoistZender2003( 1._r8 + 1.-15_r8 ) @assertExceptionRaised(expected_msg) end subroutine TestClayOutOfRangeThreshold @@ -45,9 +45,9 @@ contains class(TestDustEmisSoilFunctions), intent(inout) :: this real(r8) :: value - value = ThresholdSoilMoist( 0.0_r8 ) + value = ThresholdSoilMoistZender2003( 0.0_r8 ) @assertEqual( value, 0.17_r8, tolerance=tol ) - value = ThresholdSoilMoist( 100.0_r8 ) + value = ThresholdSoilMoistZender2003( 100.0_r8 ) @assertEqual( value, 0.31_r8, tolerance=tol ) end subroutine TestThresholdValues From 7ff7d6a2a272297f4b3d4ae8cb0765ada163e33e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 4 Jun 2024 09:49:03 -0600 Subject: [PATCH 234/408] Spin off a base class and have the Zender2003 class extend it, unit tests working and passes --- src/biogeochem/CMakeLists.txt | 1 + src/biogeochem/DustEmisBase.F90 | 740 ++++++++++++++++++++++++++ src/biogeochem/DustEmisZender2003.F90 | 629 +--------------------- 3 files changed, 770 insertions(+), 600 deletions(-) create mode 100644 src/biogeochem/DustEmisBase.F90 diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt index 0dd06ac09e..9824bcb072 100644 --- a/src/biogeochem/CMakeLists.txt +++ b/src/biogeochem/CMakeLists.txt @@ -6,6 +6,7 @@ list(APPEND clm_sources CNPhenologyMod.F90 CNSpeciesMod.F90 CNDVType.F90 + DustEmisBase.F90 DustEmisZender2003.F90 CropReprPoolsMod.F90 CropType.F90 diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90 new file mode 100644 index 0000000000..11912096fd --- /dev/null +++ b/src/biogeochem/DustEmisBase.F90 @@ -0,0 +1,740 @@ +module DustEmisBase + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Routines in this module calculate Dust mobilization and dry deposition for dust. + ! Simulates dust mobilization due to wind from the surface into the + ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust + ! emission (kg/m**2/s) [ + = to atm]. + ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition + ! velocity through the lowest atmospheric layer). CAM will calculate the settling + ! velocity through the whole atmospheric column. The two calculations will determine + ! the dust dry deposition flux to the surface. + ! + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg + use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + use clm_varpar , only : dst_src_nbr, ndst, sz_nbr + use clm_varcon , only : grav, spval + use landunit_varcon , only : istcrop, istsoil + use clm_varctl , only : iulog + use abortutils , only : endrun + use decompMod , only : bounds_type, subgrid_level_landunit, subgrid_level_patch + use atm2lndType , only : atm2lnd_type + use SoilStateType , only : soilstate_type + use CanopyStateType , only : canopystate_type + use WaterStateBulkType , only : waterstatebulk_type + use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type + use FrictionVelocityMod , only : frictionvel_type + use LandunitType , only : lun + use ColumnType , only : col + use PatchType , only : patch + use clm_varctl , only : dust_emis_method + ! + ! !PUBLIC TYPES + implicit none + private + ! + ! !PRIVATE DATA: + ! + real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density + ! + ! !PUBLIC DATA TYPES: + ! + type, abstract, public :: dust_base_type + + real(r8) , allocatable, public :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin + real(r8) , allocatable, private :: dmt_vwr(:) ! [m] Mass-weighted mean diameter resolved + real(r8) , allocatable, private :: stk_crc(:) ! [frc] Correction to Stokes settling velocity + real(r8), public :: saltation_factor ! Factor in saltation computation (named as in Charlie's code) + real(r8), pointer, PUBLIC :: flx_mss_vrt_dst_patch (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) + real(r8), pointer, public :: flx_mss_vrt_dst_tot_patch (:) ! total dust flux into atmosphere + real(r8), pointer, private :: vlc_trb_patch (:,:) ! turbulent deposition velocity (m/s) (ndst) + real(r8), pointer, private :: vlc_trb_1_patch (:) ! turbulent deposition velocity 1(m/s) + real(r8), pointer, private :: vlc_trb_2_patch (:) ! turbulent deposition velocity 2(m/s) + real(r8), pointer, private :: vlc_trb_3_patch (:) ! turbulent deposition velocity 3(m/s) + real(r8), pointer, private :: vlc_trb_4_patch (:) ! turbulent deposition velocity 4(m/s) + + contains + + procedure , public :: InitBase ! Base object initiatlization (allows it to be extended) + procedure , public :: Init => InitBase ! Initialization name used by callers + procedure(DustEmission_interface) , public, deferred :: DustEmission ! Dust mobilization + procedure , public :: DustDryDep ! Turbulent dry deposition for dust + procedure , public :: WritePatchToLog ! Write information on the given patch to the log file + procedure , public :: GetPatchVars ! Get important variables on a given patch + procedure , public :: GetConstVars ! Get important constant variables + procedure , public :: CleanBase ! Base object deallocation (allows extension) + procedure , public :: Clean => CleanBase ! Deallocation used by callers + procedure , private :: InitAllocate + procedure , private :: InitHistory + procedure , private :: InitDustVars ! Initialize variables used in DustEmission method + + end type dust_base_type + !------------------------------------------------------------------------ + + abstract interface + !------------------------------------------------------------------------ + + subroutine DustEmission_interface (this, bounds, & + num_nolakep, filter_nolakep, & + atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, & + frictionvel_inst) + ! + ! !DESCRIPTION: + ! Dust mobilization. This code simulates dust mobilization due to wind + ! from the surface into the lowest atmospheric layer + ! On output flx_mss_vrt_dst(ndst) is the surface dust emission + ! (kg/m**2/s) [ + = to atm] + ! + ! !USES + use decompMod , only : bounds_type + use atm2lndType , only : atm2lnd_type + use SoilStateType , only : soilstate_type + use CanopyStateType , only : canopystate_type + use WaterStateBulkType , only : waterstatebulk_type + use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type + use FrictionVelocityMod , only : frictionvel_type + + import :: dust_base_type + ! + ! !ARGUMENTS: + class (dust_base_type) :: this + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter + integer , intent(in) :: filter_nolakep(num_nolakep) ! patch filter for non-lake points + type(atm2lnd_type) , intent(in) :: atm2lnd_inst + type(soilstate_type) , intent(in) :: soilstate_inst + type(canopystate_type) , intent(in) :: canopystate_inst + type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst + type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst + type(frictionvel_type) , intent(in) :: frictionvel_inst + + end subroutine DustEmission_interface + + end interface + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +contains + + !------------------------------------------------------------------------ + subroutine InitBase(this, bounds, NLFilename) + + ! Base level initialization of this base object, this allows classes that extend + ! this base class to use this one and extend it with additional initialization + class(dust_base_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename + + call this%InitAllocate (bounds) + call this%InitHistory (bounds) + call this%InitDustVars (bounds) + + end subroutine InitBase + + !------------------------------------------------------------------------ + subroutine CleanBase(this) + ! + ! Base level deallocation of this base object, this allows classes that extend + ! this base class to use this one and extend it with additional deallocation. + ! !ARGUMENTS: + class (dust_base_type) :: this + ! + ! !LOCAL VARIABLES: + !------------------------------------------------------------------------ + + deallocate(this%flx_mss_vrt_dst_patch) + deallocate(this%flx_mss_vrt_dst_tot_patch) + deallocate(this%vlc_trb_patch) + deallocate(this%vlc_trb_1_patch) + deallocate(this%vlc_trb_2_patch) + deallocate(this%vlc_trb_3_patch) + deallocate(this%vlc_trb_4_patch) + + deallocate (this%ovr_src_snk_mss) + deallocate (this%dmt_vwr) + deallocate (this%stk_crc) + + end subroutine CleanBase + + !------------------------------------------------------------------------ + subroutine InitAllocate(this, bounds) + ! + ! !ARGUMENTS: + class (dust_base_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: begp,endp + integer :: begc,endc + !------------------------------------------------------------------------ + + begp = bounds%begp ; endp = bounds%endp + begc = bounds%begc ; endc = bounds%endc + + allocate(this%flx_mss_vrt_dst_patch (begp:endp,1:ndst)) ; this%flx_mss_vrt_dst_patch (:,:) = nan + allocate(this%flx_mss_vrt_dst_tot_patch (begp:endp)) ; this%flx_mss_vrt_dst_tot_patch (:) = nan + allocate(this%vlc_trb_patch (begp:endp,1:ndst)) ; this%vlc_trb_patch (:,:) = nan + allocate(this%vlc_trb_1_patch (begp:endp)) ; this%vlc_trb_1_patch (:) = nan + allocate(this%vlc_trb_2_patch (begp:endp)) ; this%vlc_trb_2_patch (:) = nan + allocate(this%vlc_trb_3_patch (begp:endp)) ; this%vlc_trb_3_patch (:) = nan + allocate(this%vlc_trb_4_patch (begp:endp)) ; this%vlc_trb_4_patch (:) = nan + + allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst)) ; this%ovr_src_snk_mss (:,:) = nan + allocate (this%dmt_vwr(ndst)) ; this%dmt_vwr (:) = nan + allocate (this%stk_crc(ndst)) ; this%stk_crc (:) = nan + + + end subroutine InitAllocate + + !------------------------------------------------------------------------ + subroutine InitHistory(this, bounds) + ! + ! !USES: + use histFileMod, only : hist_addfld1d + ! + ! + ! !ARGUMENTS: + class (dust_base_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: begp,endp + integer :: begc,endc + !------------------------------------------------------------------------ + + begp = bounds%begp; endp = bounds%endp + begc = bounds%begc; endc = bounds%endc + + this%flx_mss_vrt_dst_tot_patch(begp:endp) = spval + call hist_addfld1d (fname='DSTFLXT', units='kg/m2/s', & + avgflag='A', long_name='total surface dust emission', & + ptr_patch=this%flx_mss_vrt_dst_tot_patch, set_lake=0._r8, set_urb=0._r8) + + this%vlc_trb_1_patch(begp:endp) = spval + call hist_addfld1d (fname='DPVLTRB1', units='m/s', & + avgflag='A', long_name='turbulent deposition velocity 1', & + ptr_patch=this%vlc_trb_1_patch, default='inactive') + + this%vlc_trb_2_patch(begp:endp) = spval + call hist_addfld1d (fname='DPVLTRB2', units='m/s', & + avgflag='A', long_name='turbulent deposition velocity 2', & + ptr_patch=this%vlc_trb_2_patch, default='inactive') + + this%vlc_trb_3_patch(begp:endp) = spval + call hist_addfld1d (fname='DPVLTRB3', units='m/s', & + avgflag='A', long_name='turbulent deposition velocity 3', & + ptr_patch=this%vlc_trb_3_patch, default='inactive') + + this%vlc_trb_4_patch(begp:endp) = spval + call hist_addfld1d (fname='DPVLTRB4', units='m/s', & + avgflag='A', long_name='turbulent deposition velocity 4', & + ptr_patch=this%vlc_trb_4_patch, default='inactive') + + end subroutine InitHistory + + !----------------------------------------------------------------------- + + subroutine WritePatchToLog(this, p) + ! + ! !DESCRIPTION: + ! Write out information on dust emisisons for this patch to the log file + ! !ARGUMENTS: + class(dust_base_type), intent(in) :: this + integer , intent(in) :: p ! Patch to display + + write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p) + write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p) + write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p) + write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p) + write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p) + end subroutine WritePatchToLog + + !----------------------------------------------------------------------- + + subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, & + vlc_trb_2, vlc_trb_3, vlc_trb_4) + ! + ! !DESCRIPTION: + ! Get important variables on the given patch + ! !ARGUMENTS: + class(dust_base_type) , intent(in) :: this + integer , intent(in) :: p ! Patch to get + real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst) + real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot + real(r8), optional, intent(out) :: vlc_trb(ndst) + real(r8), optional, intent(out) :: vlc_trb_1 + real(r8), optional, intent(out) :: vlc_trb_2 + real(r8), optional, intent(out) :: vlc_trb_3 + real(r8), optional, intent(out) :: vlc_trb_4 + + if ( present(flx_mss_vrt_dst ) ) flx_mss_vrt_dst = this%flx_mss_vrt_dst_patch(p,:) + if ( present(flx_mss_vrt_dst_tot) ) flx_mss_vrt_dst_tot = this%flx_mss_vrt_dst_tot_patch(p) + if ( present(vlc_trb ) ) vlc_trb = this%vlc_trb_patch(p,:) + if ( present(vlc_trb_1) ) vlc_trb_1 = this%vlc_trb_1_patch(p) + if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p) + if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p) + if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p) + end subroutine GetPatchVars + + !----------------------------------------------------------------------- + + subroutine GetConstVars(this, SaltationFactor ) + ! + ! !DESCRIPTION: + ! Get important constant variables + ! !ARGUMENTS: + class(dust_base_type) , intent(in) :: this + real(r8) , intent(out) :: SaltationFactor + + SaltationFactor = this%saltation_factor + end subroutine GetConstVars + + !------------------------------------------------------------------------ + subroutine DustDryDep (this, bounds, & + atm2lnd_inst, frictionvel_inst) + ! + ! !DESCRIPTION: + ! + ! Determine Turbulent dry deposition for dust. Calculate the turbulent + ! component of dust dry deposition, (the turbulent deposition velocity + ! through the lowest atmospheric layer. CAM will calculate the settling + ! velocity through the whole atmospheric column. The two calculations + ! will determine the dust dry deposition flux to the surface. + ! Note: Same process should occur over oceans. For the coupled CESM, + ! we may find it more efficient to let CAM calculate the turbulent dep + ! velocity over all surfaces. This would require passing the + ! aerodynamic resistance, ram(1), and the friction velocity, fv, from + ! the land to the atmosphere component. In that case, dustini need not + ! calculate particle diamter (dmt_vwr) and particle density (dns_aer). + ! Source: C. Zender's dry deposition code + ! + ! !USES + use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ + ! + ! !ARGUMENTS: + class (dust_base_type) :: this + type(bounds_type) , intent(in) :: bounds + type(atm2lnd_type) , intent(in) :: atm2lnd_inst + type(frictionvel_type) , intent(in) :: frictionvel_inst + ! + ! !LOCAL VARIABLES + integer :: p,c,g,m,n ! indices + real(r8) :: vsc_dyn_atm(bounds%begp:bounds%endp) ! [kg m-1 s-1] Dynamic viscosity of air + real(r8) :: vsc_knm_atm(bounds%begp:bounds%endp) ! [m2 s-1] Kinematic viscosity of atmosphere + real(r8) :: shm_nbr_xpn ! [frc] Sfc-dep exponent for aerosol-diffusion dependence on Schmidt number + real(r8) :: shm_nbr ! [frc] Schmidt number + real(r8) :: stk_nbr ! [frc] Stokes number + real(r8) :: mfp_atm ! [m] Mean free path of air + real(r8) :: dff_aer ! [m2 s-1] Brownian diffusivity of particle + real(r8) :: rss_trb ! [s m-1] Resistance to turbulent deposition + real(r8) :: slp_crc(bounds%begp:bounds%endp,ndst) ! [frc] Slip correction factor + real(r8) :: vlc_grv(bounds%begp:bounds%endp,ndst) ! [m s-1] Settling velocity + real(r8) :: rss_lmn(bounds%begp:bounds%endp,ndst) ! [s m-1] Quasi-laminar layer resistance + real(r8) :: tmp ! temporary + real(r8), parameter::shm_nbr_xpn_lnd=-2._r8/3._r8 ![frc] shm_nbr_xpn over land + !------------------------------------------------------------------------ + + associate( & + forc_pbot => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input: [real(r8) (:) ] atm pressure (Pa) + forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] atm density (kg/m**3) + forc_t => atm2lnd_inst%forc_t_downscaled_col , & ! Input: [real(r8) (:) ] atm temperature (K) + + ram1 => frictionvel_inst%ram1_patch , & ! Input: [real(r8) (:) ] aerodynamical resistance (s/m) + fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) + + vlc_trb => this%vlc_trb_patch , & ! Output: [real(r8) (:,:) ] Turbulent deposn velocity (m/s) + vlc_trb_1 => this%vlc_trb_1_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 1 + vlc_trb_2 => this%vlc_trb_2_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 2 + vlc_trb_3 => this%vlc_trb_3_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 3 + vlc_trb_4 => this%vlc_trb_4_patch & ! Output: [real(r8) (:) ] Turbulent deposition velocity 4 + ) + + do p = bounds%begp,bounds%endp + if (patch%active(p)) then + g = patch%gridcell(p) + c = patch%column(p) + + ! from subroutine dst_dps_dry (consider adding sanity checks from line 212) + ! when code asks to use midlayer density, pressure, temperature, + ! I use the data coming in from the atmosphere, ie forc_t, forc_pbot, forc_rho + + ! Quasi-laminar layer resistance: call rss_lmn_get + ! Size-independent thermokinetic properties + + vsc_dyn_atm(p) = 1.72e-5_r8 * ((forc_t(c)/273.0_r8)**1.5_r8) * 393.0_r8 / & + (forc_t(c)+120.0_r8) ![kg m-1 s-1] RoY94 p. 102 + mfp_atm = 2.0_r8 * vsc_dyn_atm(p) / & ![m] SeP97 p. 455 + (forc_pbot(c)*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*forc_t(c)))) + vsc_knm_atm(p) = vsc_dyn_atm(p) / forc_rho(c) ![m2 s-1] Kinematic viscosity of air + + do m = 1, ndst + slp_crc(p,m) = 1.0_r8 + 2.0_r8 * mfp_atm * & + (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / & + this%dmt_vwr(m) ![frc] Slip correction factor SeP97 p. 464 + vlc_grv(p,m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * & + grav * slp_crc(p,m) / vsc_dyn_atm(p) ![m s-1] Stokes' settling velocity SeP97 p. 466 + vlc_grv(p,m) = vlc_grv(p,m) * this%stk_crc(m) ![m s-1] Correction to Stokes settling velocity + end do + end if + end do + + do m = 1, ndst + do p = bounds%begp,bounds%endp + if (patch%active(p)) then + g = patch%gridcell(p) + c = patch%column(p) + + stk_nbr = vlc_grv(p,m) * fv(p) * fv(p) / (grav * vsc_knm_atm(p)) ![frc] SeP97 p.965 + dff_aer = SHR_CONST_BOLTZ * forc_t(c) * slp_crc(p,m) / & ![m2 s-1] + (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * this%dmt_vwr(m)) !SeP97 p.474 + shm_nbr = vsc_knm_atm(p) / dff_aer ![frc] SeP97 p.972 + shm_nbr_xpn = shm_nbr_xpn_lnd ![frc] + + ! fxm: Turning this on dramatically reduces + ! deposition velocity in low wind regimes + ! Schmidt number exponent is -2/3 over solid surfaces and + ! -1/2 over liquid surfaces SlS80 p. 1014 + ! if (oro(i)==0.0) shm_nbr_xpn=shm_nbr_xpn_ocn else shm_nbr_xpn=shm_nbr_xpn_lnd + ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # + + tmp = shm_nbr**shm_nbr_xpn + 10.0_r8**(-3.0_r8/stk_nbr) + rss_lmn(p,m) = 1.0_r8 / (tmp * fv(p)) ![s m-1] SeP97 p.972,965 + end if + end do + end do + + ! Lowest layer: Turbulent deposition (CAM will calc. gravitational dep) + + do m = 1, ndst + do p = bounds%begp,bounds%endp + if (patch%active(p)) then + rss_trb = ram1(p) + rss_lmn(p,m) + ram1(p) * rss_lmn(p,m) * vlc_grv(p,m) ![s m-1] + vlc_trb(p,m) = 1.0_r8 / rss_trb ![m s-1] + end if + end do + end do + + do p = bounds%begp,bounds%endp + if (patch%active(p)) then + vlc_trb_1(p) = vlc_trb(p,1) + vlc_trb_2(p) = vlc_trb(p,2) + vlc_trb_3(p) = vlc_trb(p,3) + vlc_trb_4(p) = vlc_trb(p,4) + end if + end do + + end associate + + end subroutine DustDryDep + + !------------------------------------------------------------------------ + subroutine InitDustVars(this, bounds) + ! + ! !DESCRIPTION: + ! + ! Compute source efficiency factor from topography + ! Initialize other variables used in subroutine Dust: + ! ovr_src_snk_mss(m,n) and saltation_factor. + ! Define particle diameter and density needed by atm model + ! as well as by dry dep model + ! Source: Paul Ginoux (for source efficiency factor) + ! Modifications by C. Zender and later by S. Levis + ! Rest of subroutine from C. Zender's dust model + ! + ! !USES + use shr_const_mod , only: SHR_CONST_PI, SHR_CONST_RDAIR + use shr_spfn_mod , only: erf => shr_spfn_erf + use decompMod , only : get_proc_bounds + ! + ! !ARGUMENTS: + class(dust_base_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES + integer :: fc,c,l,m,n ! indices + real(r8) :: ovr_src_snk_frc + real(r8) :: sqrt2lngsdi ! [frc] Factor in erf argument + real(r8) :: lndmaxjovrdmdni ! [frc] Factor in erf argument + real(r8) :: lndminjovrdmdni ! [frc] Factor in erf argument + real(r8) :: ryn_nbr_frc_thr_prx_opt ! [frc] Threshold friction Reynolds number approximation for optimal size + real(r8) :: ryn_nbr_frc_thr_opt_fnc ! [frc] Threshold friction Reynolds factor for saltation calculation + real(r8) :: icf_fct ! Interpartical cohesive forces factor for saltation calc + real(r8) :: dns_fct ! Density ratio factor for saltation calculation + real(r8) :: dmt_min(ndst) ! [m] Size grid minimum + real(r8) :: dmt_max(ndst) ! [m] Size grid maximum + real(r8) :: dmt_ctr(ndst) ! [m] Diameter at bin center + real(r8) :: dmt_dlt(ndst) ! [m] Width of size bin + real(r8) :: slp_crc(ndst) ! [frc] Slip correction factor + real(r8) :: vlm_rsl(ndst) ! [m3 m-3] Volume concentration resolved + real(r8) :: vlc_stk(ndst) ! [m s-1] Stokes settling velocity + real(r8) :: vlc_grv(ndst) ! [m s-1] Settling velocity + real(r8) :: ryn_nbr_grv(ndst) ! [frc] Reynolds number at terminal velocity + real(r8) :: cff_drg_grv(ndst) ! [frc] Drag coefficient at terminal velocity + real(r8) :: tmp ! temporary + real(r8) :: ln_gsd ! [frc] ln(gsd) + real(r8) :: gsd_anl ! [frc] Geometric standard deviation + real(r8) :: dmt_vma ! [m] Mass median diameter analytic She84 p.75 Tabl.1 + real(r8) :: dmt_nma ! [m] Number median particle diameter + real(r8) :: lgn_dst ! Lognormal distribution at sz_ctr + real(r8) :: eps_max ! [frc] Relative accuracy for convergence + real(r8) :: eps_crr ! [frc] Current relative accuracy + real(r8) :: itr_idx ! [idx] Counting index + real(r8) :: dns_mdp ! [kg m-3] Midlayer density + real(r8) :: mfp_atm ! [m] Mean free path of air + real(r8) :: vsc_dyn_atm ! [kg m-1 s-1] Dynamic viscosity of air + real(r8) :: vsc_knm_atm ! [kg m-1 s-1] Kinematic viscosity of air + real(r8) :: vlc_grv_old ! [m s-1] Previous gravitational settling velocity + real(r8) :: series_ratio ! Factor for logarithmic grid + real(r8) :: lngsdsqrttwopi_rcp ! Factor in lognormal distribution + real(r8) :: sz_min(sz_nbr) ! [m] Size Bin minima + real(r8) :: sz_max(sz_nbr) ! [m] Size Bin maxima + real(r8) :: sz_ctr(sz_nbr) ! [m] Size Bin centers + real(r8) :: sz_dlt(sz_nbr) ! [m] Size Bin widths + + ! constants + real(r8), allocatable :: dmt_vma_src(:) ! [m] Mass median diameter BSM96 p. 73 Table 2 + real(r8), allocatable :: gsd_anl_src(:) ! [frc] Geometric std deviation BSM96 p. 73 Table 2 + real(r8), allocatable :: mss_frc_src(:) ! [frc] Mass fraction BSM96 p. 73 Table 2 + + real(r8) :: dmt_grd(5) = & ! [m] Particle diameter grid + (/ 0.1e-6_r8, 1.0e-6_r8, 2.5e-6_r8, 5.0e-6_r8, 10.0e-6_r8 /) + real(r8), parameter :: dmt_slt_opt = 75.0e-6_r8 ! [m] Optim diam for saltation + real(r8), parameter :: dns_slt = 2650.0_r8 ! [kg m-3] Density of optimal saltation particles + !------------------------------------------------------------------------ + + ! allocate local variable + allocate (dmt_vma_src(dst_src_nbr)) + allocate (gsd_anl_src(dst_src_nbr)) + allocate (mss_frc_src(dst_src_nbr)) + + dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /) + gsd_anl_src(:) = (/ 2.10_r8 , 1.90_r8 , 1.60_r8 /) + mss_frc_src(:) = (/ 0.036_r8 , 0.957_r8 , 0.007_r8 /) + + ! the following comes from (1) szdstlgn.F subroutine ovr_src_snk_frc_get + ! and (2) dstszdst.F subroutine dst_szdst_ini + ! purpose(1): given one set (the "source") of lognormal distributions, + ! and one set of bin boundaries (the "sink"), compute and return + ! the overlap factors between the source and sink distributions + ! purpose(2): set important statistics of size distributions + + do m = 1, dst_src_nbr + sqrt2lngsdi = sqrt(2.0_r8) * log(gsd_anl_src(m)) + do n = 1, ndst + lndmaxjovrdmdni = log(dmt_grd(n+1)/dmt_vma_src(m)) + lndminjovrdmdni = log(dmt_grd(n )/dmt_vma_src(m)) + ovr_src_snk_frc = 0.5_r8 * (erf(lndmaxjovrdmdni/sqrt2lngsdi) - & + erf(lndminjovrdmdni/sqrt2lngsdi)) + this%ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m) + end do + end do + + ! The following code from subroutine wnd_frc_thr_slt_get was placed + ! here because saltation_factor needs to be defined just once + + ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8 + + if (ryn_nbr_frc_thr_prx_opt < 0.03_r8) then + write(iulog,*) 'dstmbl: ryn_nbr_frc_thr_prx_opt < 0.03' + call endrun(msg=errMsg(sourcefile, __LINE__)) + else if (ryn_nbr_frc_thr_prx_opt < 10.0_r8) then + ryn_nbr_frc_thr_opt_fnc = -1.0_r8 + 1.928_r8 * (ryn_nbr_frc_thr_prx_opt**0.0922_r8) + ryn_nbr_frc_thr_opt_fnc = 0.1291_r8 * 0.1291_r8 / ryn_nbr_frc_thr_opt_fnc + else + ryn_nbr_frc_thr_opt_fnc = 1.0_r8 - 0.0858_r8 * exp(-0.0617_r8*(ryn_nbr_frc_thr_prx_opt-10.0_r8)) + ryn_nbr_frc_thr_opt_fnc = 0.120_r8 * 0.120_r8 * ryn_nbr_frc_thr_opt_fnc * ryn_nbr_frc_thr_opt_fnc + end if + + icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8)) + dns_fct = dns_slt * grav * dmt_slt_opt + this%saltation_factor = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc) + + ! Introducing particle diameter. Needed by atm model and by dry dep model. + ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl, + ! grd_mk (dstpsd.F90) and subroutine lgn_evl (psdlgn.F90) + + ! Charlie allows logarithmic or linear option for size distribution + ! however, he hardwires the distribution to logarithmic in his code + ! therefore, I take his logarithmic code only + ! furthermore, if dst_nbr == 4, he overrides the automatic grid calculation + ! he currently works with dst_nbr = 4, so I only take the relevant code + ! if ndst ever becomes different from 4, must add call grd_mk (dstpsd.F90) + ! as done in subroutine dst_psd_ini + ! note that here ndst = dst_nbr + + ! Override automatic grid with preset grid if available + + if (ndst == 4) then + do n = 1, ndst + dmt_min(n) = dmt_grd(n) ![m] Max diameter in bin + dmt_max(n) = dmt_grd(n+1) ![m] Min diameter in bin + dmt_ctr(n) = 0.5_r8 * (dmt_min(n)+dmt_max(n)) ![m] Diameter at bin ctr + dmt_dlt(n) = dmt_max(n)-dmt_min(n) ![m] Width of size bin + end do + else + write(iulog,*) 'Dustini error: ndst must equal to 4 with current code' + call endrun(msg=errMsg(sourcefile, __LINE__)) + !see more comments above end if ndst == 4 + end if + + ! Bin physical properties + + gsd_anl = 2.0_r8 ! [frc] Geometric std dev PaG77 p. 2080 Table1 + ln_gsd = log(gsd_anl) + + ! Set a fundamental statistic for each bin + + dmt_vma = 3.5000e-6_r8 ! [m] Mass median diameter analytic She84 p.75 Table1 + + ! Compute analytic size statistics + ! Convert mass median diameter to number median diameter (call vma2nma) + + dmt_nma = dmt_vma * exp(-3.0_r8*ln_gsd*ln_gsd) ! [m] + + ! Compute resolved size statistics for each size distribution + ! In C. Zender's code call dst_sz_rsl + + do n = 1, ndst + + series_ratio = (dmt_max(n)/dmt_min(n))**(1.0_r8/sz_nbr) + sz_min(1) = dmt_min(n) + do m = 2, sz_nbr ! Loop starts at 2 + sz_min(m) = sz_min(m-1) * series_ratio + end do + + ! Derived grid values + do m = 1, sz_nbr-1 ! Loop ends at sz_nbr-1 + sz_max(m) = sz_min(m+1) ! [m] + end do + sz_max(sz_nbr) = dmt_max(n) ! [m] + + ! Final derived grid values + do m = 1, sz_nbr + sz_ctr(m) = 0.5_r8 * (sz_min(m)+sz_max(m)) + sz_dlt(m) = sz_max(m)-sz_min(m) + end do + + lngsdsqrttwopi_rcp = 1.0_r8 / (ln_gsd*sqrt(2.0_r8*SHR_CONST_PI)) + this%dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved + vlm_rsl(n) = 0.0_r8 ! [m3 m-3] Volume concentration resolved + + do m = 1, sz_nbr + + ! Evaluate lognormal distribution for these sizes (call lgn_evl) + tmp = log(sz_ctr(m)/dmt_nma) / ln_gsd + lgn_dst = lngsdsqrttwopi_rcp * exp(-0.5_r8*tmp*tmp) / sz_ctr(m) + + ! Integrate moments of size distribution + this%dmt_vwr(n) = this%dmt_vwr(n) + sz_ctr(m) * & + SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume + lgn_dst * sz_dlt(m) ![# m-3] Number concentrn + vlm_rsl(n) = vlm_rsl(n) + & + SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume + lgn_dst * sz_dlt(m) ![# m-3] Number concentrn + + end do + + this%dmt_vwr(n) = this%dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved + + end do + + ! calculate correction to Stokes' settling velocity (subroutine stk_crc_get) + + eps_max = 1.0e-4_r8 + dns_mdp = 100000._r8 / (295.0_r8*SHR_CONST_RDAIR) ![kg m-3] const prs_mdp & tpt_vrt + + ! Size-independent thermokinetic properties + + vsc_dyn_atm = 1.72e-5_r8 * ((295.0_r8/273.0_r8)**1.5_r8) * 393.0_r8 / & + (295.0_r8+120.0_r8) ![kg m-1 s-1] RoY94 p.102 tpt_mdp=295.0 + mfp_atm = 2.0_r8 * vsc_dyn_atm / & !SeP97 p. 455 constant prs_mdp, tpt_mdp + (100000._r8*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*295.0_r8))) + vsc_knm_atm = vsc_dyn_atm / dns_mdp ![m2 s-1] Kinematic viscosity of air + + do m = 1, ndst + slp_crc(m) = 1.0_r8 + 2.0_r8 * mfp_atm * & + (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / & + this%dmt_vwr(m) ! [frc] Slip correction factor SeP97 p.464 + vlc_stk(m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * & + grav * slp_crc(m) / vsc_dyn_atm ! [m s-1] SeP97 p.466 + end do + + ! For Reynolds number flows Re < 0.1 Stokes' velocity is valid for + ! vlc_grv SeP97 p. 466 (8.42). For larger Re, inertial effects become + ! important and empirical drag coefficients must be employed + ! Implicit equation for Re, Cd, and Vt is SeP97 p. 467 (8.44) + ! Using Stokes' velocity rather than iterative solution with empirical + ! drag coefficient causes 60% errors for D = 200 um SeP97 p. 468 + + ! Iterative solution for drag coefficient, Reynolds number, and terminal veloc + do m = 1, ndst + + ! Initialize accuracy and counter + eps_crr = eps_max + 1.0_r8 ![frc] Current relative accuracy + itr_idx = 0 ![idx] Counting index + + ! Initial guess for vlc_grv is exact for Re < 0.1 + vlc_grv(m) = vlc_stk(m) ![m s-1] + + do while(eps_crr > eps_max) + + ! Save terminal velocity for convergence test + vlc_grv_old = vlc_grv(m) ![m s-1] + ryn_nbr_grv(m) = vlc_grv(m) * this%dmt_vwr(m) / vsc_knm_atm !SeP97 p.460 + + ! Update drag coefficient based on new Reynolds number + if (ryn_nbr_grv(m) < 0.1_r8) then + cff_drg_grv(m) = 24.0_r8 / ryn_nbr_grv(m) !Stokes' law Sep97 p.463 (8.32) + else if (ryn_nbr_grv(m) < 2.0_r8) then + cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) * & + (1.0_r8 + 3.0_r8*ryn_nbr_grv(m)/16.0_r8 + & + 9.0_r8*ryn_nbr_grv(m)*ryn_nbr_grv(m)* & + log(2.0_r8*ryn_nbr_grv(m))/160.0_r8) !Sep97 p.463 (8.32) + else if (ryn_nbr_grv(m) < 500.0_r8) then + cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) * & + (1.0_r8 + 0.15_r8*ryn_nbr_grv(m)**0.687_r8) !Sep97 p.463 (8.32) + else if (ryn_nbr_grv(m) < 2.0e5_r8) then + cff_drg_grv(m) = 0.44_r8 !Sep97 p.463 (8.32) + else + write(iulog,'(a,es9.2)') "ryn_nbr_grv(m) = ",ryn_nbr_grv(m) + write(iulog,*)'Dustini error: Reynolds number too large in stk_crc_get()' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + + ! Update terminal velocity based on new Reynolds number and drag coeff + ! [m s-1] Terminal veloc SeP97 p.467 (8.44) + + vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / & + (3.0_r8*cff_drg_grv(m)*dns_mdp)) + eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence + if (itr_idx == 12) then + ! Numerical pingpong may occur when Re = 0.1, 2.0, or 500.0 + ! due to discontinuities in derivative of drag coefficient + vlc_grv(m) = 0.5_r8 * (vlc_grv(m)+vlc_grv_old) ! [m s-1] + end if + if (itr_idx > 20) then + write(iulog,*) 'Dustini error: Terminal velocity not converging ',& + ' in stk_crc_get(), breaking loop...' + goto 100 !to next iteration + end if + itr_idx = itr_idx + 1 + + end do !end while + +100 continue !Label to jump to when iteration does not converge + end do !end loop over size + + ! Compute factors to convert Stokes' settling velocities to + ! actual settling velocities + + do m = 1, ndst + this%stk_crc(m) = vlc_grv(m) / vlc_stk(m) + end do + + end subroutine InitDustVars + +end module DustEmisBase diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index db6f93581a..442fddbedf 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -15,12 +15,12 @@ module DustEmisZender2003 use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) - use clm_varpar , only : dst_src_nbr, ndst, sz_nbr + use clm_varpar , only : dst_src_nbr, ndst use clm_varcon , only : grav, spval use landunit_varcon , only : istcrop, istsoil use clm_varctl , only : iulog use abortutils , only : endrun - use decompMod , only : bounds_type, subgrid_level_landunit, subgrid_level_patch + use decompMod , only : bounds_type, subgrid_level_landunit use atm2lndType , only : atm2lnd_type use SoilStateType , only : soilstate_type use CanopyStateType , only : canopystate_type @@ -28,9 +28,9 @@ module DustEmisZender2003 use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type use FrictionVelocityMod , only : frictionvel_type use LandunitType , only : lun - use ColumnType , only : col use PatchType , only : patch use ZenderSoilErodStreamType, only : soil_erod_stream_type + use DustEmisBase , only : dust_base_type use clm_varctl , only : dust_emis_method ! ! !PUBLIC TYPES @@ -39,39 +39,22 @@ module DustEmisZender2003 ! ! !PRIVATE DATA: ! - real(r8), parameter :: dns_aer = 2.5e+3_r8 ![kg m-3] Aerosol density ! ! !PUBLIC DATA TYPES: ! - type, public :: dust_type - - real(r8) , allocatable, private :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin - real(r8) , allocatable, private :: dmt_vwr(:) ! [m] Mass-weighted mean diameter resolved - real(r8) , allocatable, private :: stk_crc(:) ! [frc] Correction to Stokes settling velocity - real(r8), private :: saltation_factor ! Factor in saltation computation (named as in Charlie's code) - real(r8), pointer, PUBLIC :: flx_mss_vrt_dst_patch (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) - real(r8), pointer, private :: flx_mss_vrt_dst_tot_patch (:) ! total dust flux into atmosphere - real(r8), pointer, private :: vlc_trb_patch (:,:) ! turbulent deposition velocity (m/s) (ndst) - real(r8), pointer, private :: vlc_trb_1_patch (:) ! turbulent deposition velocity 1(m/s) - real(r8), pointer, private :: vlc_trb_2_patch (:) ! turbulent deposition velocity 2(m/s) - real(r8), pointer, private :: vlc_trb_3_patch (:) ! turbulent deposition velocity 3(m/s) - real(r8), pointer, private :: vlc_trb_4_patch (:) ! turbulent deposition velocity 4(m/s) + type, public, extends(dust_base_type) :: dust_type + + real(r8), pointer, private :: mbl_bsn_fct_col (:) ! [dimensionless] basin factor, or soil rodibility, time-constant type(soil_erod_stream_type), private :: soil_erod_stream ! Zender soil erodibility stream data - real(r8), pointer, private :: mbl_bsn_fct_col (:) ! [dimensionless] basin factor, or soil erodibility, time-constant contains - procedure , public :: Init + procedure , public :: Init => InitZender2003 procedure , public :: DustEmission ! Dust mobilization - procedure , public :: DustDryDep ! Turbulent dry deposition for dust - procedure , public :: WritePatchToLog ! Write information on the given patch to the log file - procedure , public :: GetPatchVars ! Get important variables on a given patch - procedure , public :: GetConstVars ! Get important constant variables - procedure , public :: Clean ! Deallocate data - procedure , private :: InitAllocate - procedure , private :: InitHistory + procedure , public :: Clean => CleanZender2003 + procedure , private :: InitAllocate ! Allocate data + procedure , private :: InitHistory ! History initialization procedure , private :: InitCold - procedure , private :: InitDustVars ! Initialize variables used in DustEmission method end type dust_type !------------------------------------------------------------------------ @@ -82,76 +65,52 @@ module DustEmisZender2003 contains !------------------------------------------------------------------------ - subroutine Init(this, bounds, NLFilename) + subroutine InitZender2003(this, bounds, NLFilename) + ! Initialization for this extended class, calling base level initiation and adding to it class(dust_type) :: this type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename call this%soil_erod_stream%Init( bounds, NLFilename ) + call this%InitBase(bounds, NLFilename) call this%InitAllocate (bounds) call this%InitHistory (bounds) call this%InitCold (bounds) - call this%InitDustVars (bounds) - - end subroutine Init - + end subroutine InitZender2003 !------------------------------------------------------------------------ - subroutine Clean(this) + subroutine InitAllocate(this, bounds) ! ! !ARGUMENTS: class (dust_type) :: this + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: + integer :: begc,endc !------------------------------------------------------------------------ - deallocate(this%flx_mss_vrt_dst_patch) - deallocate(this%flx_mss_vrt_dst_tot_patch) - deallocate(this%vlc_trb_patch) - deallocate(this%vlc_trb_1_patch) - deallocate(this%vlc_trb_2_patch) - deallocate(this%vlc_trb_3_patch) - deallocate(this%vlc_trb_4_patch) - deallocate(this%mbl_bsn_fct_col) + begc = bounds%begc ; endc = bounds%endc - deallocate (this%ovr_src_snk_mss) - deallocate (this%dmt_vwr) - deallocate (this%stk_crc) + allocate(this%mbl_bsn_fct_col (begc:endc)) ; this%mbl_bsn_fct_col (:) = nan - end subroutine Clean + end subroutine InitAllocate - !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds) + !------------------------------------------------------------------------ + subroutine CleanZender2003(this) ! + ! Deallocation for this extended class, calling base level deallocation and adding to it ! !ARGUMENTS: class (dust_type) :: this - type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: - integer :: begp,endp - integer :: begc,endc !------------------------------------------------------------------------ - begp = bounds%begp ; endp = bounds%endp - begc = bounds%begc ; endc = bounds%endc + call this%CleanBase() + deallocate(this%mbl_bsn_fct_col) - allocate(this%flx_mss_vrt_dst_patch (begp:endp,1:ndst)) ; this%flx_mss_vrt_dst_patch (:,:) = nan - allocate(this%flx_mss_vrt_dst_tot_patch (begp:endp)) ; this%flx_mss_vrt_dst_tot_patch (:) = nan - allocate(this%vlc_trb_patch (begp:endp,1:ndst)) ; this%vlc_trb_patch (:,:) = nan - allocate(this%vlc_trb_1_patch (begp:endp)) ; this%vlc_trb_1_patch (:) = nan - allocate(this%vlc_trb_2_patch (begp:endp)) ; this%vlc_trb_2_patch (:) = nan - allocate(this%vlc_trb_3_patch (begp:endp)) ; this%vlc_trb_3_patch (:) = nan - allocate(this%vlc_trb_4_patch (begp:endp)) ; this%vlc_trb_4_patch (:) = nan - allocate(this%mbl_bsn_fct_col (begc:endc)) ; this%mbl_bsn_fct_col (:) = nan - - allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst)) ; this%ovr_src_snk_mss (:,:) = nan - allocate (this%dmt_vwr(ndst)) ; this%dmt_vwr (:) = nan - allocate (this%stk_crc(ndst)) ; this%stk_crc (:) = nan - - - end subroutine InitAllocate + end subroutine CleanZender2003 !------------------------------------------------------------------------ subroutine InitHistory(this, bounds) @@ -165,45 +124,16 @@ subroutine InitHistory(this, bounds) type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: - integer :: begp,endp integer :: begc,endc !------------------------------------------------------------------------ - begp = bounds%begp; endp = bounds%endp begc = bounds%begc; endc = bounds%endc - this%flx_mss_vrt_dst_tot_patch(begp:endp) = spval - call hist_addfld1d (fname='DSTFLXT', units='kg/m2/s', & - avgflag='A', long_name='total surface dust emission', & - ptr_patch=this%flx_mss_vrt_dst_tot_patch, set_lake=0._r8, set_urb=0._r8) - - this%vlc_trb_1_patch(begp:endp) = spval - call hist_addfld1d (fname='DPVLTRB1', units='m/s', & - avgflag='A', long_name='turbulent deposition velocity 1', & - ptr_patch=this%vlc_trb_1_patch, default='inactive') - - this%vlc_trb_2_patch(begp:endp) = spval - call hist_addfld1d (fname='DPVLTRB2', units='m/s', & - avgflag='A', long_name='turbulent deposition velocity 2', & - ptr_patch=this%vlc_trb_2_patch, default='inactive') - - this%vlc_trb_3_patch(begp:endp) = spval - call hist_addfld1d (fname='DPVLTRB3', units='m/s', & - avgflag='A', long_name='turbulent deposition velocity 3', & - ptr_patch=this%vlc_trb_3_patch, default='inactive') - - this%vlc_trb_4_patch(begp:endp) = spval - call hist_addfld1d (fname='DPVLTRB4', units='m/s', & - avgflag='A', long_name='turbulent deposition velocity 4', & - ptr_patch=this%vlc_trb_4_patch, default='inactive') - - if (dust_emis_method == 'Zender_2003') then - if ( this%soil_erod_stream%UseStreams() )then - this%mbl_bsn_fct_col(begc:endc) = spval - call hist_addfld1d (fname='LND_MBL', units='fraction', & + if ( this%soil_erod_stream%UseStreams() )then + this%mbl_bsn_fct_col(begc:endc) = spval + call hist_addfld1d (fname='LND_MBL', units='fraction', & avgflag='A', long_name='Soil erodibility factor', & ptr_col=this%mbl_bsn_fct_col, default='inactive') - end if end if end subroutine InitHistory @@ -244,63 +174,6 @@ subroutine InitCold(this, bounds) end subroutine InitCold - !----------------------------------------------------------------------- - - subroutine WritePatchToLog(this, p) - ! - ! !DESCRIPTION: - ! Write out information on dust emisisons for this patch to the log file - ! !ARGUMENTS: - class(dust_type), intent(in) :: this - integer , intent(in) :: p ! Patch to display - - write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p) - write(iulog,*) 'vlc_trb_1', this%vlc_trb_1_patch(p) - write(iulog,*) 'vlc_trb_2', this%vlc_trb_2_patch(p) - write(iulog,*) 'vlc_trb_3', this%vlc_trb_3_patch(p) - write(iulog,*) 'vlc_trb_4', this%vlc_trb_4_patch(p) - end subroutine WritePatchToLog - - !----------------------------------------------------------------------- - - subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, vlc_trb_1, & - vlc_trb_2, vlc_trb_3, vlc_trb_4) - ! - ! !DESCRIPTION: - ! Get important variables on the given patch - ! !ARGUMENTS: - class(dust_type) , intent(in) :: this - integer , intent(in) :: p ! Patch to get - real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst) - real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot - real(r8), optional, intent(out) :: vlc_trb(ndst) - real(r8), optional, intent(out) :: vlc_trb_1 - real(r8), optional, intent(out) :: vlc_trb_2 - real(r8), optional, intent(out) :: vlc_trb_3 - real(r8), optional, intent(out) :: vlc_trb_4 - - if ( present(flx_mss_vrt_dst ) ) flx_mss_vrt_dst = this%flx_mss_vrt_dst_patch(p,:) - if ( present(flx_mss_vrt_dst_tot) ) flx_mss_vrt_dst_tot = this%flx_mss_vrt_dst_tot_patch(p) - if ( present(vlc_trb ) ) vlc_trb = this%vlc_trb_patch(p,:) - if ( present(vlc_trb_1) ) vlc_trb_1 = this%vlc_trb_1_patch(p) - if ( present(vlc_trb_2) ) vlc_trb_2 = this%vlc_trb_2_patch(p) - if ( present(vlc_trb_3) ) vlc_trb_3 = this%vlc_trb_3_patch(p) - if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p) - end subroutine GetPatchVars - - !----------------------------------------------------------------------- - - subroutine GetConstVars(this, SaltationFactor ) - ! - ! !DESCRIPTION: - ! Get important constant variables - ! !ARGUMENTS: - class(dust_type) , intent(in) :: this - real(r8) , intent(out) :: SaltationFactor - - SaltationFactor = this%saltation_factor - end subroutine GetConstVars - !------------------------------------------------------------------------ subroutine DustEmission (this, bounds, & num_nolakep, filter_nolakep, & @@ -588,448 +461,4 @@ subroutine DustEmission (this, bounds, & end subroutine DustEmission - !------------------------------------------------------------------------ - subroutine DustDryDep (this, bounds, & - atm2lnd_inst, frictionvel_inst) - ! - ! !DESCRIPTION: - ! - ! Determine Turbulent dry deposition for dust. Calculate the turbulent - ! component of dust dry deposition, (the turbulent deposition velocity - ! through the lowest atmospheric layer. CAM will calculate the settling - ! velocity through the whole atmospheric column. The two calculations - ! will determine the dust dry deposition flux to the surface. - ! Note: Same process should occur over oceans. For the coupled CESM, - ! we may find it more efficient to let CAM calculate the turbulent dep - ! velocity over all surfaces. This would require passing the - ! aerodynamic resistance, ram(1), and the friction velocity, fv, from - ! the land to the atmosphere component. In that case, dustini need not - ! calculate particle diamter (dmt_vwr) and particle density (dns_aer). - ! Source: C. Zender's dry deposition code - ! - ! !USES - use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ - ! - ! !ARGUMENTS: - class (dust_type) :: this - type(bounds_type) , intent(in) :: bounds - type(atm2lnd_type) , intent(in) :: atm2lnd_inst - type(frictionvel_type) , intent(in) :: frictionvel_inst - ! - ! !LOCAL VARIABLES - integer :: p,c,g,m,n ! indices - real(r8) :: vsc_dyn_atm(bounds%begp:bounds%endp) ! [kg m-1 s-1] Dynamic viscosity of air - real(r8) :: vsc_knm_atm(bounds%begp:bounds%endp) ! [m2 s-1] Kinematic viscosity of atmosphere - real(r8) :: shm_nbr_xpn ! [frc] Sfc-dep exponent for aerosol-diffusion dependence on Schmidt number - real(r8) :: shm_nbr ! [frc] Schmidt number - real(r8) :: stk_nbr ! [frc] Stokes number - real(r8) :: mfp_atm ! [m] Mean free path of air - real(r8) :: dff_aer ! [m2 s-1] Brownian diffusivity of particle - real(r8) :: rss_trb ! [s m-1] Resistance to turbulent deposition - real(r8) :: slp_crc(bounds%begp:bounds%endp,ndst) ! [frc] Slip correction factor - real(r8) :: vlc_grv(bounds%begp:bounds%endp,ndst) ! [m s-1] Settling velocity - real(r8) :: rss_lmn(bounds%begp:bounds%endp,ndst) ! [s m-1] Quasi-laminar layer resistance - real(r8) :: tmp ! temporary - real(r8), parameter::shm_nbr_xpn_lnd=-2._r8/3._r8 ![frc] shm_nbr_xpn over land - !------------------------------------------------------------------------ - - associate( & - forc_pbot => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input: [real(r8) (:) ] atm pressure (Pa) - forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] atm density (kg/m**3) - forc_t => atm2lnd_inst%forc_t_downscaled_col , & ! Input: [real(r8) (:) ] atm temperature (K) - - ram1 => frictionvel_inst%ram1_patch , & ! Input: [real(r8) (:) ] aerodynamical resistance (s/m) - fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) - - vlc_trb => this%vlc_trb_patch , & ! Output: [real(r8) (:,:) ] Turbulent deposn velocity (m/s) - vlc_trb_1 => this%vlc_trb_1_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 1 - vlc_trb_2 => this%vlc_trb_2_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 2 - vlc_trb_3 => this%vlc_trb_3_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 3 - vlc_trb_4 => this%vlc_trb_4_patch & ! Output: [real(r8) (:) ] Turbulent deposition velocity 4 - ) - - do p = bounds%begp,bounds%endp - if (patch%active(p)) then - g = patch%gridcell(p) - c = patch%column(p) - - ! from subroutine dst_dps_dry (consider adding sanity checks from line 212) - ! when code asks to use midlayer density, pressure, temperature, - ! I use the data coming in from the atmosphere, ie forc_t, forc_pbot, forc_rho - - ! Quasi-laminar layer resistance: call rss_lmn_get - ! Size-independent thermokinetic properties - - vsc_dyn_atm(p) = 1.72e-5_r8 * ((forc_t(c)/273.0_r8)**1.5_r8) * 393.0_r8 / & - (forc_t(c)+120.0_r8) ![kg m-1 s-1] RoY94 p. 102 - mfp_atm = 2.0_r8 * vsc_dyn_atm(p) / & ![m] SeP97 p. 455 - (forc_pbot(c)*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*forc_t(c)))) - vsc_knm_atm(p) = vsc_dyn_atm(p) / forc_rho(c) ![m2 s-1] Kinematic viscosity of air - - do m = 1, ndst - slp_crc(p,m) = 1.0_r8 + 2.0_r8 * mfp_atm * & - (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / & - this%dmt_vwr(m) ![frc] Slip correction factor SeP97 p. 464 - vlc_grv(p,m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * & - grav * slp_crc(p,m) / vsc_dyn_atm(p) ![m s-1] Stokes' settling velocity SeP97 p. 466 - vlc_grv(p,m) = vlc_grv(p,m) * this%stk_crc(m) ![m s-1] Correction to Stokes settling velocity - end do - end if - end do - - do m = 1, ndst - do p = bounds%begp,bounds%endp - if (patch%active(p)) then - g = patch%gridcell(p) - c = patch%column(p) - - stk_nbr = vlc_grv(p,m) * fv(p) * fv(p) / (grav * vsc_knm_atm(p)) ![frc] SeP97 p.965 - dff_aer = SHR_CONST_BOLTZ * forc_t(c) * slp_crc(p,m) / & ![m2 s-1] - (3.0_r8*SHR_CONST_PI * vsc_dyn_atm(p) * this%dmt_vwr(m)) !SeP97 p.474 - shm_nbr = vsc_knm_atm(p) / dff_aer ![frc] SeP97 p.972 - shm_nbr_xpn = shm_nbr_xpn_lnd ![frc] - - ! fxm: Turning this on dramatically reduces - ! deposition velocity in low wind regimes - ! Schmidt number exponent is -2/3 over solid surfaces and - ! -1/2 over liquid surfaces SlS80 p. 1014 - ! if (oro(i)==0.0) shm_nbr_xpn=shm_nbr_xpn_ocn else shm_nbr_xpn=shm_nbr_xpn_lnd - ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # - - tmp = shm_nbr**shm_nbr_xpn + 10.0_r8**(-3.0_r8/stk_nbr) - rss_lmn(p,m) = 1.0_r8 / (tmp * fv(p)) ![s m-1] SeP97 p.972,965 - end if - end do - end do - - ! Lowest layer: Turbulent deposition (CAM will calc. gravitational dep) - - do m = 1, ndst - do p = bounds%begp,bounds%endp - if (patch%active(p)) then - rss_trb = ram1(p) + rss_lmn(p,m) + ram1(p) * rss_lmn(p,m) * vlc_grv(p,m) ![s m-1] - vlc_trb(p,m) = 1.0_r8 / rss_trb ![m s-1] - end if - end do - end do - - do p = bounds%begp,bounds%endp - if (patch%active(p)) then - vlc_trb_1(p) = vlc_trb(p,1) - vlc_trb_2(p) = vlc_trb(p,2) - vlc_trb_3(p) = vlc_trb(p,3) - vlc_trb_4(p) = vlc_trb(p,4) - end if - end do - - end associate - - end subroutine DustDryDep - - !------------------------------------------------------------------------ - subroutine InitDustVars(this, bounds) - ! - ! !DESCRIPTION: - ! - ! Compute source efficiency factor from topography - ! Initialize other variables used in subroutine Dust: - ! ovr_src_snk_mss(m,n) and saltation_factor. - ! Define particle diameter and density needed by atm model - ! as well as by dry dep model - ! Source: Paul Ginoux (for source efficiency factor) - ! Modifications by C. Zender and later by S. Levis - ! Rest of subroutine from C. Zender's dust model - ! - ! !USES - use shr_const_mod , only: SHR_CONST_PI, SHR_CONST_RDAIR - use shr_spfn_mod , only: erf => shr_spfn_erf - use decompMod , only : get_proc_bounds - ! - ! !ARGUMENTS: - class(dust_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES - integer :: fc,c,l,m,n ! indices - real(r8) :: ovr_src_snk_frc - real(r8) :: sqrt2lngsdi ! [frc] Factor in erf argument - real(r8) :: lndmaxjovrdmdni ! [frc] Factor in erf argument - real(r8) :: lndminjovrdmdni ! [frc] Factor in erf argument - real(r8) :: ryn_nbr_frc_thr_prx_opt ! [frc] Threshold friction Reynolds number approximation for optimal size - real(r8) :: ryn_nbr_frc_thr_opt_fnc ! [frc] Threshold friction Reynolds factor for saltation calculation - real(r8) :: icf_fct ! Interpartical cohesive forces factor for saltation calc - real(r8) :: dns_fct ! Density ratio factor for saltation calculation - real(r8) :: dmt_min(ndst) ! [m] Size grid minimum - real(r8) :: dmt_max(ndst) ! [m] Size grid maximum - real(r8) :: dmt_ctr(ndst) ! [m] Diameter at bin center - real(r8) :: dmt_dlt(ndst) ! [m] Width of size bin - real(r8) :: slp_crc(ndst) ! [frc] Slip correction factor - real(r8) :: vlm_rsl(ndst) ! [m3 m-3] Volume concentration resolved - real(r8) :: vlc_stk(ndst) ! [m s-1] Stokes settling velocity - real(r8) :: vlc_grv(ndst) ! [m s-1] Settling velocity - real(r8) :: ryn_nbr_grv(ndst) ! [frc] Reynolds number at terminal velocity - real(r8) :: cff_drg_grv(ndst) ! [frc] Drag coefficient at terminal velocity - real(r8) :: tmp ! temporary - real(r8) :: ln_gsd ! [frc] ln(gsd) - real(r8) :: gsd_anl ! [frc] Geometric standard deviation - real(r8) :: dmt_vma ! [m] Mass median diameter analytic She84 p.75 Tabl.1 - real(r8) :: dmt_nma ! [m] Number median particle diameter - real(r8) :: lgn_dst ! Lognormal distribution at sz_ctr - real(r8) :: eps_max ! [frc] Relative accuracy for convergence - real(r8) :: eps_crr ! [frc] Current relative accuracy - real(r8) :: itr_idx ! [idx] Counting index - real(r8) :: dns_mdp ! [kg m-3] Midlayer density - real(r8) :: mfp_atm ! [m] Mean free path of air - real(r8) :: vsc_dyn_atm ! [kg m-1 s-1] Dynamic viscosity of air - real(r8) :: vsc_knm_atm ! [kg m-1 s-1] Kinematic viscosity of air - real(r8) :: vlc_grv_old ! [m s-1] Previous gravitational settling velocity - real(r8) :: series_ratio ! Factor for logarithmic grid - real(r8) :: lngsdsqrttwopi_rcp ! Factor in lognormal distribution - real(r8) :: sz_min(sz_nbr) ! [m] Size Bin minima - real(r8) :: sz_max(sz_nbr) ! [m] Size Bin maxima - real(r8) :: sz_ctr(sz_nbr) ! [m] Size Bin centers - real(r8) :: sz_dlt(sz_nbr) ! [m] Size Bin widths - - ! constants - real(r8), allocatable :: dmt_vma_src(:) ! [m] Mass median diameter BSM96 p. 73 Table 2 - real(r8), allocatable :: gsd_anl_src(:) ! [frc] Geometric std deviation BSM96 p. 73 Table 2 - real(r8), allocatable :: mss_frc_src(:) ! [frc] Mass fraction BSM96 p. 73 Table 2 - - real(r8) :: dmt_grd(5) = & ! [m] Particle diameter grid - (/ 0.1e-6_r8, 1.0e-6_r8, 2.5e-6_r8, 5.0e-6_r8, 10.0e-6_r8 /) - real(r8), parameter :: dmt_slt_opt = 75.0e-6_r8 ! [m] Optim diam for saltation - real(r8), parameter :: dns_slt = 2650.0_r8 ! [kg m-3] Density of optimal saltation particles - !------------------------------------------------------------------------ - - ! allocate local variable - allocate (dmt_vma_src(dst_src_nbr)) - allocate (gsd_anl_src(dst_src_nbr)) - allocate (mss_frc_src(dst_src_nbr)) - - dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /) - gsd_anl_src(:) = (/ 2.10_r8 , 1.90_r8 , 1.60_r8 /) - mss_frc_src(:) = (/ 0.036_r8 , 0.957_r8 , 0.007_r8 /) - - ! the following comes from (1) szdstlgn.F subroutine ovr_src_snk_frc_get - ! and (2) dstszdst.F subroutine dst_szdst_ini - ! purpose(1): given one set (the "source") of lognormal distributions, - ! and one set of bin boundaries (the "sink"), compute and return - ! the overlap factors between the source and sink distributions - ! purpose(2): set important statistics of size distributions - - do m = 1, dst_src_nbr - sqrt2lngsdi = sqrt(2.0_r8) * log(gsd_anl_src(m)) - do n = 1, ndst - lndmaxjovrdmdni = log(dmt_grd(n+1)/dmt_vma_src(m)) - lndminjovrdmdni = log(dmt_grd(n )/dmt_vma_src(m)) - ovr_src_snk_frc = 0.5_r8 * (erf(lndmaxjovrdmdni/sqrt2lngsdi) - & - erf(lndminjovrdmdni/sqrt2lngsdi)) - this%ovr_src_snk_mss(m,n) = ovr_src_snk_frc * mss_frc_src(m) - end do - end do - - ! The following code from subroutine wnd_frc_thr_slt_get was placed - ! here because saltation_factor needs to be defined just once - - ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8 - - if (ryn_nbr_frc_thr_prx_opt < 0.03_r8) then - write(iulog,*) 'dstmbl: ryn_nbr_frc_thr_prx_opt < 0.03' - call endrun(msg=errMsg(sourcefile, __LINE__)) - else if (ryn_nbr_frc_thr_prx_opt < 10.0_r8) then - ryn_nbr_frc_thr_opt_fnc = -1.0_r8 + 1.928_r8 * (ryn_nbr_frc_thr_prx_opt**0.0922_r8) - ryn_nbr_frc_thr_opt_fnc = 0.1291_r8 * 0.1291_r8 / ryn_nbr_frc_thr_opt_fnc - else - ryn_nbr_frc_thr_opt_fnc = 1.0_r8 - 0.0858_r8 * exp(-0.0617_r8*(ryn_nbr_frc_thr_prx_opt-10.0_r8)) - ryn_nbr_frc_thr_opt_fnc = 0.120_r8 * 0.120_r8 * ryn_nbr_frc_thr_opt_fnc * ryn_nbr_frc_thr_opt_fnc - end if - - icf_fct = 1.0_r8 + 6.0e-07_r8 / (dns_slt * grav * (dmt_slt_opt**2.5_r8)) - dns_fct = dns_slt * grav * dmt_slt_opt - this%saltation_factor = sqrt(icf_fct * dns_fct * ryn_nbr_frc_thr_opt_fnc) - - ! Introducing particle diameter. Needed by atm model and by dry dep model. - ! Taken from Charlie Zender's subroutines dst_psd_ini, dst_sz_rsl, - ! grd_mk (dstpsd.F90) and subroutine lgn_evl (psdlgn.F90) - - ! Charlie allows logarithmic or linear option for size distribution - ! however, he hardwires the distribution to logarithmic in his code - ! therefore, I take his logarithmic code only - ! furthermore, if dst_nbr == 4, he overrides the automatic grid calculation - ! he currently works with dst_nbr = 4, so I only take the relevant code - ! if ndst ever becomes different from 4, must add call grd_mk (dstpsd.F90) - ! as done in subroutine dst_psd_ini - ! note that here ndst = dst_nbr - - ! Override automatic grid with preset grid if available - - if (ndst == 4) then - do n = 1, ndst - dmt_min(n) = dmt_grd(n) ![m] Max diameter in bin - dmt_max(n) = dmt_grd(n+1) ![m] Min diameter in bin - dmt_ctr(n) = 0.5_r8 * (dmt_min(n)+dmt_max(n)) ![m] Diameter at bin ctr - dmt_dlt(n) = dmt_max(n)-dmt_min(n) ![m] Width of size bin - end do - else - write(iulog,*) 'Dustini error: ndst must equal to 4 with current code' - call endrun(msg=errMsg(sourcefile, __LINE__)) - !see more comments above end if ndst == 4 - end if - - ! Bin physical properties - - gsd_anl = 2.0_r8 ! [frc] Geometric std dev PaG77 p. 2080 Table1 - ln_gsd = log(gsd_anl) - - ! Set a fundamental statistic for each bin - - dmt_vma = 3.5000e-6_r8 ! [m] Mass median diameter analytic She84 p.75 Table1 - - ! Compute analytic size statistics - ! Convert mass median diameter to number median diameter (call vma2nma) - - dmt_nma = dmt_vma * exp(-3.0_r8*ln_gsd*ln_gsd) ! [m] - - ! Compute resolved size statistics for each size distribution - ! In C. Zender's code call dst_sz_rsl - - do n = 1, ndst - - series_ratio = (dmt_max(n)/dmt_min(n))**(1.0_r8/sz_nbr) - sz_min(1) = dmt_min(n) - do m = 2, sz_nbr ! Loop starts at 2 - sz_min(m) = sz_min(m-1) * series_ratio - end do - - ! Derived grid values - do m = 1, sz_nbr-1 ! Loop ends at sz_nbr-1 - sz_max(m) = sz_min(m+1) ! [m] - end do - sz_max(sz_nbr) = dmt_max(n) ! [m] - - ! Final derived grid values - do m = 1, sz_nbr - sz_ctr(m) = 0.5_r8 * (sz_min(m)+sz_max(m)) - sz_dlt(m) = sz_max(m)-sz_min(m) - end do - - lngsdsqrttwopi_rcp = 1.0_r8 / (ln_gsd*sqrt(2.0_r8*SHR_CONST_PI)) - this%dmt_vwr(n) = 0.0_r8 ! [m] Mass wgted diameter resolved - vlm_rsl(n) = 0.0_r8 ! [m3 m-3] Volume concentration resolved - - do m = 1, sz_nbr - - ! Evaluate lognormal distribution for these sizes (call lgn_evl) - tmp = log(sz_ctr(m)/dmt_nma) / ln_gsd - lgn_dst = lngsdsqrttwopi_rcp * exp(-0.5_r8*tmp*tmp) / sz_ctr(m) - - ! Integrate moments of size distribution - this%dmt_vwr(n) = this%dmt_vwr(n) + sz_ctr(m) * & - SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume - lgn_dst * sz_dlt(m) ![# m-3] Number concentrn - vlm_rsl(n) = vlm_rsl(n) + & - SHR_CONST_PI / 6.0_r8 * (sz_ctr(m)**3.0_r8) * & ![m3] Volume - lgn_dst * sz_dlt(m) ![# m-3] Number concentrn - - end do - - this%dmt_vwr(n) = this%dmt_vwr(n) / vlm_rsl(n) ![m] Mass weighted diameter resolved - - end do - - ! calculate correction to Stokes' settling velocity (subroutine stk_crc_get) - - eps_max = 1.0e-4_r8 - dns_mdp = 100000._r8 / (295.0_r8*SHR_CONST_RDAIR) ![kg m-3] const prs_mdp & tpt_vrt - - ! Size-independent thermokinetic properties - - vsc_dyn_atm = 1.72e-5_r8 * ((295.0_r8/273.0_r8)**1.5_r8) * 393.0_r8 / & - (295.0_r8+120.0_r8) ![kg m-1 s-1] RoY94 p.102 tpt_mdp=295.0 - mfp_atm = 2.0_r8 * vsc_dyn_atm / & !SeP97 p. 455 constant prs_mdp, tpt_mdp - (100000._r8*sqrt(8.0_r8/(SHR_CONST_PI*SHR_CONST_RDAIR*295.0_r8))) - vsc_knm_atm = vsc_dyn_atm / dns_mdp ![m2 s-1] Kinematic viscosity of air - - do m = 1, ndst - slp_crc(m) = 1.0_r8 + 2.0_r8 * mfp_atm * & - (1.257_r8+0.4_r8*exp(-1.1_r8*this%dmt_vwr(m)/(2.0_r8*mfp_atm))) / & - this%dmt_vwr(m) ! [frc] Slip correction factor SeP97 p.464 - vlc_stk(m) = (1.0_r8/18.0_r8) * this%dmt_vwr(m) * this%dmt_vwr(m) * dns_aer * & - grav * slp_crc(m) / vsc_dyn_atm ! [m s-1] SeP97 p.466 - end do - - ! For Reynolds number flows Re < 0.1 Stokes' velocity is valid for - ! vlc_grv SeP97 p. 466 (8.42). For larger Re, inertial effects become - ! important and empirical drag coefficients must be employed - ! Implicit equation for Re, Cd, and Vt is SeP97 p. 467 (8.44) - ! Using Stokes' velocity rather than iterative solution with empirical - ! drag coefficient causes 60% errors for D = 200 um SeP97 p. 468 - - ! Iterative solution for drag coefficient, Reynolds number, and terminal veloc - do m = 1, ndst - - ! Initialize accuracy and counter - eps_crr = eps_max + 1.0_r8 ![frc] Current relative accuracy - itr_idx = 0 ![idx] Counting index - - ! Initial guess for vlc_grv is exact for Re < 0.1 - vlc_grv(m) = vlc_stk(m) ![m s-1] - - do while(eps_crr > eps_max) - - ! Save terminal velocity for convergence test - vlc_grv_old = vlc_grv(m) ![m s-1] - ryn_nbr_grv(m) = vlc_grv(m) * this%dmt_vwr(m) / vsc_knm_atm !SeP97 p.460 - - ! Update drag coefficient based on new Reynolds number - if (ryn_nbr_grv(m) < 0.1_r8) then - cff_drg_grv(m) = 24.0_r8 / ryn_nbr_grv(m) !Stokes' law Sep97 p.463 (8.32) - else if (ryn_nbr_grv(m) < 2.0_r8) then - cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) * & - (1.0_r8 + 3.0_r8*ryn_nbr_grv(m)/16.0_r8 + & - 9.0_r8*ryn_nbr_grv(m)*ryn_nbr_grv(m)* & - log(2.0_r8*ryn_nbr_grv(m))/160.0_r8) !Sep97 p.463 (8.32) - else if (ryn_nbr_grv(m) < 500.0_r8) then - cff_drg_grv(m) = (24.0_r8/ryn_nbr_grv(m)) * & - (1.0_r8 + 0.15_r8*ryn_nbr_grv(m)**0.687_r8) !Sep97 p.463 (8.32) - else if (ryn_nbr_grv(m) < 2.0e5_r8) then - cff_drg_grv(m) = 0.44_r8 !Sep97 p.463 (8.32) - else - write(iulog,'(a,es9.2)') "ryn_nbr_grv(m) = ",ryn_nbr_grv(m) - write(iulog,*)'Dustini error: Reynolds number too large in stk_crc_get()' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - - ! Update terminal velocity based on new Reynolds number and drag coeff - ! [m s-1] Terminal veloc SeP97 p.467 (8.44) - - vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / & - (3.0_r8*cff_drg_grv(m)*dns_mdp)) - eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence - if (itr_idx == 12) then - ! Numerical pingpong may occur when Re = 0.1, 2.0, or 500.0 - ! due to discontinuities in derivative of drag coefficient - vlc_grv(m) = 0.5_r8 * (vlc_grv(m)+vlc_grv_old) ! [m s-1] - end if - if (itr_idx > 20) then - write(iulog,*) 'Dustini error: Terminal velocity not converging ',& - ' in stk_crc_get(), breaking loop...' - goto 100 !to next iteration - end if - itr_idx = itr_idx + 1 - - end do !end while - -100 continue !Label to jump to when iteration does not converge - end do !end loop over size - - ! Compute factors to convert Stokes' settling velocities to - ! actual settling velocities - - do m = 1, ndst - this%stk_crc(m) = vlc_grv(m) / vlc_stk(m) - end do - - end subroutine InitDustVars - end module DustEmisZender2003 From aed9d31c060ce247a3c7dd29ccf138552e56a1f4 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 4 Jun 2024 10:40:46 -0700 Subject: [PATCH 235/408] remove hydro tests that are now passing per NGEET/FATES#1164 --- cime_config/testdefs/ExpectedTestFails.xml | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 23e481222b..2d59568602 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -190,20 +190,6 @@ - - - FAIL - #2373 - - - - - - FAIL - FATES#701 - - - FAIL From 5431850c991fbed4a2c7e3ac7d9f321e7d907ed0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 4 Jun 2024 15:57:53 -0600 Subject: [PATCH 236/408] Add cime_config/usermods_dirs/NEON/NIWO/user_nl_clm for tests to pass --- cime_config/usermods_dirs/NEON/NIWO/user_nl_clm | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 cime_config/usermods_dirs/NEON/NIWO/user_nl_clm diff --git a/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm b/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm new file mode 100644 index 0000000000..cf427d738b --- /dev/null +++ b/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm @@ -0,0 +1,8 @@ +! 20240604 slevis introduced this file to bypass test failures in the +! cnmatrix branch (so cnmatrix on by default) with two izumi tests: +! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO--clm-matrixcnOn +! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO +! when the tests point to the default finidat, as documented in this post: +! https://github.com/ESCOMP/CTSM/pull/640#issuecomment-2143101361 +use_init_interp = .true. +finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc' From 0edef8a33450154a60d0d50af5419dc57e5c0996 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 4 Jun 2024 16:00:30 -0600 Subject: [PATCH 237/408] Update ntests in bld/unit_testers/build-namelist_test.pl --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 152430d514..28a2392736 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 3357; +my $ntests = 3283; if ( defined($opts{'compare'}) ) { $ntests += 2045; From 1a49e547ba3c48fa483f9ae81a8f05adcd6b888c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 4 Jun 2024 16:01:28 -0600 Subject: [PATCH 238/408] Reformatting by "make run-black" --- cime_config/SystemTests/sspmatrixcn.py | 20 +++++--------------- cime_config/buildnml | 24 ++++++------------------ 2 files changed, 11 insertions(+), 33 deletions(-) diff --git a/cime_config/SystemTests/sspmatrixcn.py b/cime_config/SystemTests/sspmatrixcn.py index 37d4154121..f4a09a277e 100644 --- a/cime_config/SystemTests/sspmatrixcn.py +++ b/cime_config/SystemTests/sspmatrixcn.py @@ -163,28 +163,18 @@ def append_user_nl(self, caseroot, n=0): self.check_n(n) # For all set output to yearly contents_to_append = "hist_nhtfrq = -8760" - contents_to_append = ( - contents_to_append + ", hist_mfilt = " + str(self.nyr_forcing) - ) + contents_to_append = contents_to_append + ", hist_mfilt = " + str(self.nyr_forcing) # For all but last step turn extra matrix output to off b4last = self.n_steps() - 1 if n < b4last: - contents_to_append = ( - contents_to_append + ", hist_wrt_matrixcn_diag = .False." - ) + contents_to_append = contents_to_append + ", hist_wrt_matrixcn_diag = .False." # For matrix spinup steps, set the matrix spinup and other variables associated with it if self.spin[n] == "sasu": - contents_to_append = ( - contents_to_append + ", nyr_forcing = " + str(self.nyr_forcing) - ) + contents_to_append = contents_to_append + ", nyr_forcing = " + str(self.nyr_forcing) if self.sasu[n] != -999: - contents_to_append = ( - contents_to_append + ", nyr_sasu = " + str(self.sasu[n]) - ) + contents_to_append = contents_to_append + ", nyr_sasu = " + str(self.sasu[n]) if self.iloop[n] != -999: - contents_to_append = ( - contents_to_append + ", iloop_avg = " + str(self.iloop[n]) - ) + contents_to_append = contents_to_append + ", iloop_avg = " + str(self.iloop[n]) # For cold start, run with matrix off if self.cold[n]: diff --git a/cime_config/buildnml b/cime_config/buildnml index 9be7c447fb..3eb45dff31 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -182,9 +182,7 @@ def buildnml(case, caseroot, compname): clm_phys = case.get_value("CLM_PHYSICS_VERSION") config_cache_text = _config_cache_template.format(clm_phys=clm_phys) - config_cache_path = os.path.join( - caseroot, "Buildconf", compname + "conf", "config_cache.xml" - ) + config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml") with open(config_cache_path, "w") as config_cache_file: config_cache_file.write(config_cache_text) @@ -283,17 +281,13 @@ def buildnml(case, caseroot, compname): if (yr_start != None) and (yr_end != None): nyr = yr_end - yr_start + 1 if (yr_end <= 0) or (yr_start <= 0): - logger.error( - "ERROR: Year start and end are both negative and should not be" - ) + logger.error("ERROR: Year start and end are both negative and should not be") clm_namelist_opts = "nyr_forcing={} {}".format(nyr, clm_namelist_opts) else: logger.warning( "WARNING: It does not make sense to do a SASU spinup with a prognostic atmosphere model" ) - logger.warning( - " as it expects regular atmosphere forcing that is cycled over" - ) + logger.warning(" as it expects regular atmosphere forcing that is cycled over") infile = os.path.join(ctsmconf, "namelist") @@ -307,9 +301,7 @@ def buildnml(case, caseroot, compname): lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file) lndfrac_setting = "-lnd_frac " + lndfrac_file - config_cache_file = os.path.join( - caseroot, "Buildconf", compname + "conf", "config_cache.xml" - ) + config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml") # ----------------------------------------------------- # Clear out old data @@ -372,9 +364,7 @@ def buildnml(case, caseroot, compname): break if not os.path.exists(os.path.join(rundir, clm_startfile)): - logger.warning( - "WARNING: Could NOT find a start file to use using" + clm_startfile - ) + logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile) clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile) else: clm_icfile = "" @@ -385,9 +375,7 @@ def buildnml(case, caseroot, compname): user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string) namelist_infile = os.path.join(ctsmconf, "namelist") - create_namelist_infile( - case, user_nl_file, namelist_infile, "\n".join(infile_lines) - ) + create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines)) cmd = os.path.join(lnd_root, "bld", "build-namelist") From dd6a5a434b95e70e85814812089fd78ee0216c2f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 4 Jun 2024 16:04:07 -0600 Subject: [PATCH 239/408] Change occurances of dust_type with dust_emis_zender2003_type with VS code --- src/biogeochem/DustEmisZender2003.F90 | 16 ++++++++-------- .../test/DustEmis_test/test_DustEmisBase.pf | 2 +- .../DustEmis_test/test_DustEmisZender2003.pf | 2 +- src/main/clm_instMod.F90 | 4 ++-- src/main/lnd2atmMod.F90 | 4 ++-- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index 442fddbedf..e67bd43e1b 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -42,7 +42,7 @@ module DustEmisZender2003 ! ! !PUBLIC DATA TYPES: ! - type, public, extends(dust_base_type) :: dust_type + type, public, extends(dust_base_type) :: dust_emis_zender2003_type real(r8), pointer, private :: mbl_bsn_fct_col (:) ! [dimensionless] basin factor, or soil rodibility, time-constant type(soil_erod_stream_type), private :: soil_erod_stream ! Zender soil erodibility stream data @@ -56,7 +56,7 @@ module DustEmisZender2003 procedure , private :: InitHistory ! History initialization procedure , private :: InitCold - end type dust_type + end type dust_emis_zender2003_type !------------------------------------------------------------------------ character(len=*), parameter, private :: sourcefile = & @@ -68,7 +68,7 @@ module DustEmisZender2003 subroutine InitZender2003(this, bounds, NLFilename) ! Initialization for this extended class, calling base level initiation and adding to it - class(dust_type) :: this + class(dust_emis_zender2003_type) :: this type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename @@ -84,7 +84,7 @@ end subroutine InitZender2003 subroutine InitAllocate(this, bounds) ! ! !ARGUMENTS: - class (dust_type) :: this + class (dust_emis_zender2003_type) :: this type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: @@ -102,7 +102,7 @@ subroutine CleanZender2003(this) ! ! Deallocation for this extended class, calling base level deallocation and adding to it ! !ARGUMENTS: - class (dust_type) :: this + class (dust_emis_zender2003_type) :: this ! ! !LOCAL VARIABLES: !------------------------------------------------------------------------ @@ -120,7 +120,7 @@ subroutine InitHistory(this, bounds) ! ! ! !ARGUMENTS: - class (dust_type) :: this + class (dust_emis_zender2003_type) :: this type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: @@ -142,7 +142,7 @@ end subroutine InitHistory subroutine InitCold(this, bounds) ! ! !ARGUMENTS: - class (dust_type) :: this + class (dust_emis_zender2003_type) :: this type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: @@ -192,7 +192,7 @@ subroutine DustEmission (this, bounds, & use subgridaveMod, only : p2g ! ! !ARGUMENTS: - class (dust_type) :: this + class (dust_emis_zender2003_type) :: this type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter integer , intent(in) :: filter_nolakep(num_nolakep) ! patch filter for non-lake points diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf index e60ec2cc7f..cf8df87d64 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf @@ -27,7 +27,7 @@ module test_DustEmisBase @TestCase type, extends(TestCase) :: TestDustEmisBase - type(dust_type) :: dust_emis + type(dust_emis_zender2003_type) :: dust_emis integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) integer :: num_nolakep ! number of patches in non-lake filter type(atm2lnd_type) :: atm2lnd_inst diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index a7fea904c9..1168200cfe 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -27,7 +27,7 @@ module test_DustEmisZender2003 @TestCase type, extends(TestCase) :: TestDustEmisZender2003 - type(dust_type) :: dust_emis + type(dust_emis_zender2003_type) :: dust_emis integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) integer :: num_nolakep ! number of patches in non-lake filter type(atm2lnd_type) :: atm2lnd_inst diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index f11805a755..c3ea8a68b3 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -45,7 +45,7 @@ module clm_instMod use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use CropType , only : crop_type use DryDepVelocity , only : drydepvel_type - use DustEmisZender2003 , only : dust_type + use DustEmisZender2003 , only : dust_emis_zender2003_type use EnergyFluxType , only : energyflux_type use FrictionVelocityMod , only : frictionvel_type use GlacierSurfaceMassBalanceMod , only : glacier_smb_type @@ -151,7 +151,7 @@ module clm_instMod ! General biogeochem types type(ch4_type) , public :: ch4_inst type(crop_type) , public :: crop_inst - type(dust_type) , public :: dust_inst + type(dust_emis_zender2003_type) , public :: dust_inst type(vocemis_type) , public :: vocemis_inst type(fireemis_type) , public :: fireemis_inst type(drydepvel_type), public :: drydepvel_inst diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90 index b91feaabf9..e6b1bb43f0 100644 --- a/src/main/lnd2atmMod.F90 +++ b/src/main/lnd2atmMod.F90 @@ -20,7 +20,7 @@ module lnd2atmMod use lnd2atmType , only : lnd2atm_type use atm2lndType , only : atm2lnd_type use ch4Mod , only : ch4_type - use DustEmisZender2003 , only : dust_type + use DustEmisZender2003 , only : dust_emis_zender2003_type use DryDepVelocity , only : drydepvel_type use VocEmissionMod , only : vocemis_type use CNFireEmissionsMod , only : fireemis_type @@ -173,7 +173,7 @@ subroutine lnd2atm(bounds, & type(drydepvel_type) , intent(in) :: drydepvel_inst type(vocemis_type) , intent(in) :: vocemis_inst type(fireemis_type) , intent(in) :: fireemis_inst - type(dust_type) , intent(in) :: dust_inst + type(dust_emis_zender2003_type) , intent(in) :: dust_inst type(ch4_type) , intent(in) :: ch4_inst type(glc_behavior_type) , intent(in) :: glc_behavior type(lnd2atm_type) , intent(inout) :: lnd2atm_inst From 66e1c3d6dd330accc670b8ea281e43e938d2018d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 4 Jun 2024 16:05:05 -0600 Subject: [PATCH 240/408] Update .git-blame-ignore-revs --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index c62b279ba0..bc3600b925 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -47,3 +47,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b 6c6f57e948bfa31e60b383536cc21663fedb8b70 9660667b1267dcd4150889f5f39db540158be74a 665cf86102e09b4c4c5a140700676dca23bc55a9 +1a49e547ba3c48fa483f9ae81a8f05adcd6b888c From e0cbd401b56a466676beceedd2796abd813a6272 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 4 Jun 2024 16:17:57 -0600 Subject: [PATCH 241/408] Update dust_base_type to dust_emis_base_type --- src/biogeochem/DustEmisBase.F90 | 26 +++++++++++++------------- src/biogeochem/DustEmisZender2003.F90 | 4 ++-- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90 index 11912096fd..adf2716f8a 100644 --- a/src/biogeochem/DustEmisBase.F90 +++ b/src/biogeochem/DustEmisBase.F90 @@ -42,7 +42,7 @@ module DustEmisBase ! ! !PUBLIC DATA TYPES: ! - type, abstract, public :: dust_base_type + type, abstract, public :: dust_emis_base_type real(r8) , allocatable, public :: ovr_src_snk_mss(:,:) ! overlap factors between the source and sin real(r8) , allocatable, private :: dmt_vwr(:) ! [m] Mass-weighted mean diameter resolved @@ -71,7 +71,7 @@ module DustEmisBase procedure , private :: InitHistory procedure , private :: InitDustVars ! Initialize variables used in DustEmission method - end type dust_base_type + end type dust_emis_base_type !------------------------------------------------------------------------ abstract interface @@ -97,10 +97,10 @@ subroutine DustEmission_interface (this, bounds, & use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type use FrictionVelocityMod , only : frictionvel_type - import :: dust_base_type + import :: dust_emis_base_type ! ! !ARGUMENTS: - class (dust_base_type) :: this + class (dust_emis_base_type) :: this type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter integer , intent(in) :: filter_nolakep(num_nolakep) ! patch filter for non-lake points @@ -125,7 +125,7 @@ subroutine InitBase(this, bounds, NLFilename) ! Base level initialization of this base object, this allows classes that extend ! this base class to use this one and extend it with additional initialization - class(dust_base_type) :: this + class(dust_emis_base_type) :: this type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename @@ -141,7 +141,7 @@ subroutine CleanBase(this) ! Base level deallocation of this base object, this allows classes that extend ! this base class to use this one and extend it with additional deallocation. ! !ARGUMENTS: - class (dust_base_type) :: this + class (dust_emis_base_type) :: this ! ! !LOCAL VARIABLES: !------------------------------------------------------------------------ @@ -164,7 +164,7 @@ end subroutine CleanBase subroutine InitAllocate(this, bounds) ! ! !ARGUMENTS: - class (dust_base_type) :: this + class (dust_emis_base_type) :: this type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: @@ -198,7 +198,7 @@ subroutine InitHistory(this, bounds) ! ! ! !ARGUMENTS: - class (dust_base_type) :: this + class (dust_emis_base_type) :: this type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: @@ -243,7 +243,7 @@ subroutine WritePatchToLog(this, p) ! !DESCRIPTION: ! Write out information on dust emisisons for this patch to the log file ! !ARGUMENTS: - class(dust_base_type), intent(in) :: this + class(dust_emis_base_type), intent(in) :: this integer , intent(in) :: p ! Patch to display write(iulog,*) 'flx_mss_vrt_dst_tot', this%flx_mss_vrt_dst_tot_patch(p) @@ -261,7 +261,7 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, ! !DESCRIPTION: ! Get important variables on the given patch ! !ARGUMENTS: - class(dust_base_type) , intent(in) :: this + class(dust_emis_base_type) , intent(in) :: this integer , intent(in) :: p ! Patch to get real(r8), optional, intent(out) :: flx_mss_vrt_dst(ndst) real(r8), optional, intent(out) :: flx_mss_vrt_dst_tot @@ -287,7 +287,7 @@ subroutine GetConstVars(this, SaltationFactor ) ! !DESCRIPTION: ! Get important constant variables ! !ARGUMENTS: - class(dust_base_type) , intent(in) :: this + class(dust_emis_base_type) , intent(in) :: this real(r8) , intent(out) :: SaltationFactor SaltationFactor = this%saltation_factor @@ -316,7 +316,7 @@ subroutine DustDryDep (this, bounds, & use shr_const_mod, only : SHR_CONST_PI, SHR_CONST_RDAIR, SHR_CONST_BOLTZ ! ! !ARGUMENTS: - class (dust_base_type) :: this + class (dust_emis_base_type) :: this type(bounds_type) , intent(in) :: bounds type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(frictionvel_type) , intent(in) :: frictionvel_inst @@ -451,7 +451,7 @@ subroutine InitDustVars(this, bounds) use decompMod , only : get_proc_bounds ! ! !ARGUMENTS: - class(dust_base_type) :: this + class(dust_emis_base_type) :: this type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index e67bd43e1b..fa2a96b7e0 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -30,7 +30,7 @@ module DustEmisZender2003 use LandunitType , only : lun use PatchType , only : patch use ZenderSoilErodStreamType, only : soil_erod_stream_type - use DustEmisBase , only : dust_base_type + use DustEmisBase , only : dust_emis_base_type use clm_varctl , only : dust_emis_method ! ! !PUBLIC TYPES @@ -42,7 +42,7 @@ module DustEmisZender2003 ! ! !PUBLIC DATA TYPES: ! - type, public, extends(dust_base_type) :: dust_emis_zender2003_type + type, public, extends(dust_emis_base_type) :: dust_emis_zender2003_type real(r8), pointer, private :: mbl_bsn_fct_col (:) ! [dimensionless] basin factor, or soil rodibility, time-constant type(soil_erod_stream_type), private :: soil_erod_stream ! Zender soil erodibility stream data From da722568a24220ce5bd128e081a4acc2c46e0e6b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 4 Jun 2024 16:22:39 -0600 Subject: [PATCH 242/408] Update dust emission calls to OO format, now a case passes: SMS_D.f10_f10_mg37.I2000Clm60Bgc.derecho_intel --- src/main/clm_driver.F90 | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index f9db72e0ed..b6dacf3866 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -62,7 +62,6 @@ module clm_driver use ndepStreamMod , only : ndep_interp use cropcalStreamMod , only : cropcal_advance, cropcal_interp use ch4Mod , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check - use DustEmisZender2003 , only : DustDryDep, DustEmission use VOCEmissionMod , only : VOCEmission ! use filterMod , only : setFilters @@ -806,15 +805,15 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_startf('bgc') ! Dust mobilization (C. Zender's modified codes) - call DustEmission(bounds_clump, & + call dust_inst%DustEmission(bounds_clump, & filter(nc)%num_nolakep, filter(nc)%nolakep, & atm2lnd_inst, soilstate_inst, canopystate_inst, & water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, & - frictionvel_inst, dust_inst) + frictionvel_inst) ! Dust dry deposition (C. Zender's modified codes) - call DustDryDep(bounds_clump, & - atm2lnd_inst, frictionvel_inst, dust_inst) + call dust_inst%DustDryDep(bounds_clump, & + atm2lnd_inst, frictionvel_inst) ! VOC emission (A. Guenther's MEGAN (2006) model) call VOCEmission(bounds_clump, & From c6060dba9dd6298f1c274b33e5f4e75b14b53cdd Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 4 Jun 2024 16:46:35 -0600 Subject: [PATCH 243/408] Some whitespace formatting changes --- src/biogeochem/DustEmisBase.F90 | 193 +++++++++++++------------- src/biogeochem/DustEmisZender2003.F90 | 100 +++++++------ 2 files changed, 152 insertions(+), 141 deletions(-) diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90 index adf2716f8a..6fb1066607 100644 --- a/src/biogeochem/DustEmisBase.F90 +++ b/src/biogeochem/DustEmisBase.F90 @@ -1,18 +1,18 @@ module DustEmisBase - !----------------------------------------------------------------------- - ! !DESCRIPTION: + !----------------------------------------------------------------------- + ! !DESCRIPTION: ! Routines in this module calculate Dust mobilization and dry deposition for dust. - ! Simulates dust mobilization due to wind from the surface into the - ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust + ! Simulates dust mobilization due to wind from the surface into the + ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust ! emission (kg/m**2/s) [ + = to atm]. - ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition - ! velocity through the lowest atmospheric layer). CAM will calculate the settling - ! velocity through the whole atmospheric column. The two calculations will determine + ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition + ! velocity through the lowest atmospheric layer). CAM will calculate the settling + ! velocity through the whole atmospheric column. The two calculations will determine ! the dust dry deposition flux to the surface. - ! + ! ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) use clm_varpar , only : dst_src_nbr, ndst, sz_nbr @@ -24,14 +24,14 @@ module DustEmisBase use atm2lndType , only : atm2lnd_type use SoilStateType , only : soilstate_type use CanopyStateType , only : canopystate_type - use WaterStateBulkType , only : waterstatebulk_type - use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type + use WaterStateBulkType , only : waterstatebulk_type + use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type use FrictionVelocityMod , only : frictionvel_type use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch use clm_varctl , only : dust_emis_method - ! + ! ! !PUBLIC TYPES implicit none private @@ -48,9 +48,9 @@ module DustEmisBase real(r8) , allocatable, private :: dmt_vwr(:) ! [m] Mass-weighted mean diameter resolved real(r8) , allocatable, private :: stk_crc(:) ! [frc] Correction to Stokes settling velocity real(r8), public :: saltation_factor ! Factor in saltation computation (named as in Charlie's code) - real(r8), pointer, PUBLIC :: flx_mss_vrt_dst_patch (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) + real(r8), pointer, PUBLIC :: flx_mss_vrt_dst_patch (:,:) ! surface dust emission (kg/m**2/s) [ + = to atm] (ndst) real(r8), pointer, public :: flx_mss_vrt_dst_tot_patch (:) ! total dust flux into atmosphere - real(r8), pointer, private :: vlc_trb_patch (:,:) ! turbulent deposition velocity (m/s) (ndst) + real(r8), pointer, private :: vlc_trb_patch (:,:) ! turbulent deposition velocity (m/s) (ndst) real(r8), pointer, private :: vlc_trb_1_patch (:) ! turbulent deposition velocity 1(m/s) real(r8), pointer, private :: vlc_trb_2_patch (:) ! turbulent deposition velocity 2(m/s) real(r8), pointer, private :: vlc_trb_3_patch (:) ! turbulent deposition velocity 3(m/s) @@ -67,8 +67,8 @@ module DustEmisBase procedure , public :: GetConstVars ! Get important constant variables procedure , public :: CleanBase ! Base object deallocation (allows extension) procedure , public :: Clean => CleanBase ! Deallocation used by callers - procedure , private :: InitAllocate - procedure , private :: InitHistory + procedure , private :: InitAllocate + procedure , private :: InitHistory procedure , private :: InitDustVars ! Initialize variables used in DustEmission method end type dust_emis_base_type @@ -77,41 +77,41 @@ module DustEmisBase abstract interface !------------------------------------------------------------------------ - subroutine DustEmission_interface (this, bounds, & - num_nolakep, filter_nolakep, & - atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, & - frictionvel_inst) - ! - ! !DESCRIPTION: - ! Dust mobilization. This code simulates dust mobilization due to wind - ! from the surface into the lowest atmospheric layer - ! On output flx_mss_vrt_dst(ndst) is the surface dust emission - ! (kg/m**2/s) [ + = to atm] - ! - ! !USES - use decompMod , only : bounds_type - use atm2lndType , only : atm2lnd_type - use SoilStateType , only : soilstate_type - use CanopyStateType , only : canopystate_type - use WaterStateBulkType , only : waterstatebulk_type - use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type - use FrictionVelocityMod , only : frictionvel_type - - import :: dust_emis_base_type - ! - ! !ARGUMENTS: - class (dust_emis_base_type) :: this - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter - integer , intent(in) :: filter_nolakep(num_nolakep) ! patch filter for non-lake points - type(atm2lnd_type) , intent(in) :: atm2lnd_inst - type(soilstate_type) , intent(in) :: soilstate_inst - type(canopystate_type) , intent(in) :: canopystate_inst - type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst - type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst - type(frictionvel_type) , intent(in) :: frictionvel_inst - - end subroutine DustEmission_interface + subroutine DustEmission_interface (this, bounds, & + num_nolakep, filter_nolakep, & + atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, & + frictionvel_inst) + ! + ! !DESCRIPTION: + ! Dust mobilization. This code simulates dust mobilization due to wind + ! from the surface into the lowest atmospheric layer + ! On output flx_mss_vrt_dst(ndst) is the surface dust emission + ! (kg/m**2/s) [ + = to atm] + ! + ! !USES + use decompMod , only : bounds_type + use atm2lndType , only : atm2lnd_type + use SoilStateType , only : soilstate_type + use CanopyStateType , only : canopystate_type + use WaterStateBulkType , only : waterstatebulk_type + use WaterDiagnosticBulkType, only : waterdiagnosticbulk_type + use FrictionVelocityMod , only : frictionvel_type + + import :: dust_emis_base_type + ! + ! !ARGUMENTS: + class (dust_emis_base_type) :: this + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter + integer , intent(in) :: filter_nolakep(num_nolakep) ! patch filter for non-lake points + type(atm2lnd_type) , intent(in) :: atm2lnd_inst + type(soilstate_type) , intent(in) :: soilstate_inst + type(canopystate_type) , intent(in) :: canopystate_inst + type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst + type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst + type(frictionvel_type) , intent(in) :: frictionvel_inst + + end subroutine DustEmission_interface end interface @@ -126,7 +126,7 @@ subroutine InitBase(this, bounds, NLFilename) ! Base level initialization of this base object, this allows classes that extend ! this base class to use this one and extend it with additional initialization class(dust_emis_base_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename call this%InitAllocate (bounds) @@ -158,14 +158,14 @@ subroutine CleanBase(this) deallocate (this%dmt_vwr) deallocate (this%stk_crc) - end subroutine CleanBase + end subroutine CleanBase !------------------------------------------------------------------------ subroutine InitAllocate(this, bounds) ! ! !ARGUMENTS: class (dust_emis_base_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: begp,endp @@ -179,7 +179,7 @@ subroutine InitAllocate(this, bounds) allocate(this%flx_mss_vrt_dst_tot_patch (begp:endp)) ; this%flx_mss_vrt_dst_tot_patch (:) = nan allocate(this%vlc_trb_patch (begp:endp,1:ndst)) ; this%vlc_trb_patch (:,:) = nan allocate(this%vlc_trb_1_patch (begp:endp)) ; this%vlc_trb_1_patch (:) = nan - allocate(this%vlc_trb_2_patch (begp:endp)) ; this%vlc_trb_2_patch (:) = nan + allocate(this%vlc_trb_2_patch (begp:endp)) ; this%vlc_trb_2_patch (:) = nan allocate(this%vlc_trb_3_patch (begp:endp)) ; this%vlc_trb_3_patch (:) = nan allocate(this%vlc_trb_4_patch (begp:endp)) ; this%vlc_trb_4_patch (:) = nan @@ -187,7 +187,6 @@ subroutine InitAllocate(this, bounds) allocate (this%dmt_vwr(ndst)) ; this%dmt_vwr (:) = nan allocate (this%stk_crc(ndst)) ; this%stk_crc (:) = nan - end subroutine InitAllocate !------------------------------------------------------------------------ @@ -199,7 +198,7 @@ subroutine InitHistory(this, bounds) ! ! !ARGUMENTS: class (dust_emis_base_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: begp,endp @@ -236,7 +235,7 @@ subroutine InitHistory(this, bounds) end subroutine InitHistory - !----------------------------------------------------------------------- + !----------------------------------------------------------------------- subroutine WritePatchToLog(this, p) ! @@ -280,7 +279,7 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p) end subroutine GetPatchVars - !----------------------------------------------------------------------- + !----------------------------------------------------------------------- subroutine GetConstVars(this, SaltationFactor ) ! @@ -293,16 +292,17 @@ subroutine GetConstVars(this, SaltationFactor ) SaltationFactor = this%saltation_factor end subroutine GetConstVars - !------------------------------------------------------------------------ + !------------------------------------------------------------------------ + subroutine DustDryDep (this, bounds, & atm2lnd_inst, frictionvel_inst) ! - ! !DESCRIPTION: + ! !DESCRIPTION: ! - ! Determine Turbulent dry deposition for dust. Calculate the turbulent - ! component of dust dry deposition, (the turbulent deposition velocity - ! through the lowest atmospheric layer. CAM will calculate the settling - ! velocity through the whole atmospheric column. The two calculations + ! Determine Turbulent dry deposition for dust. Calculate the turbulent + ! component of dust dry deposition, (the turbulent deposition velocity + ! through the lowest atmospheric layer. CAM will calculate the settling + ! velocity through the whole atmospheric column. The two calculations ! will determine the dust dry deposition flux to the surface. ! Note: Same process should occur over oceans. For the coupled CESM, ! we may find it more efficient to let CAM calculate the turbulent dep @@ -317,7 +317,7 @@ subroutine DustDryDep (this, bounds, & ! ! !ARGUMENTS: class (dust_emis_base_type) :: this - type(bounds_type) , intent(in) :: bounds + type(bounds_type) , intent(in) :: bounds type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(frictionvel_type) , intent(in) :: frictionvel_inst ! @@ -334,23 +334,23 @@ subroutine DustDryDep (this, bounds, & real(r8) :: slp_crc(bounds%begp:bounds%endp,ndst) ! [frc] Slip correction factor real(r8) :: vlc_grv(bounds%begp:bounds%endp,ndst) ! [m s-1] Settling velocity real(r8) :: rss_lmn(bounds%begp:bounds%endp,ndst) ! [s m-1] Quasi-laminar layer resistance - real(r8) :: tmp ! temporary + real(r8) :: tmp ! temporary real(r8), parameter::shm_nbr_xpn_lnd=-2._r8/3._r8 ![frc] shm_nbr_xpn over land !------------------------------------------------------------------------ - associate( & - forc_pbot => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input: [real(r8) (:) ] atm pressure (Pa) - forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] atm density (kg/m**3) - forc_t => atm2lnd_inst%forc_t_downscaled_col , & ! Input: [real(r8) (:) ] atm temperature (K) - - ram1 => frictionvel_inst%ram1_patch , & ! Input: [real(r8) (:) ] aerodynamical resistance (s/m) - fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) - - vlc_trb => this%vlc_trb_patch , & ! Output: [real(r8) (:,:) ] Turbulent deposn velocity (m/s) - vlc_trb_1 => this%vlc_trb_1_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 1 - vlc_trb_2 => this%vlc_trb_2_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 2 - vlc_trb_3 => this%vlc_trb_3_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 3 - vlc_trb_4 => this%vlc_trb_4_patch & ! Output: [real(r8) (:) ] Turbulent deposition velocity 4 + associate( & + forc_pbot => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input: [real(r8) (:) ] atm pressure (Pa) + forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] atm density (kg/m**3) + forc_t => atm2lnd_inst%forc_t_downscaled_col , & ! Input: [real(r8) (:) ] atm temperature (K) + + ram1 => frictionvel_inst%ram1_patch , & ! Input: [real(r8) (:) ] aerodynamical resistance (s/m) + fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) + + vlc_trb => this%vlc_trb_patch , & ! Output: [real(r8) (:,:) ] Turbulent deposn velocity (m/s) + vlc_trb_1 => this%vlc_trb_1_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 1 + vlc_trb_2 => this%vlc_trb_2_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 2 + vlc_trb_3 => this%vlc_trb_3_patch , & ! Output: [real(r8) (:) ] Turbulent deposition velocity 3 + vlc_trb_4 => this%vlc_trb_4_patch & ! Output: [real(r8) (:) ] Turbulent deposition velocity 4 ) do p = bounds%begp,bounds%endp @@ -399,7 +399,7 @@ subroutine DustDryDep (this, bounds, & ! Schmidt number exponent is -2/3 over solid surfaces and ! -1/2 over liquid surfaces SlS80 p. 1014 ! if (oro(i)==0.0) shm_nbr_xpn=shm_nbr_xpn_ocn else shm_nbr_xpn=shm_nbr_xpn_lnd - ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # + ! [frc] Surface-dependent exponent for aerosol-diffusion dependence on Schmidt # tmp = shm_nbr**shm_nbr_xpn + 10.0_r8**(-3.0_r8/stk_nbr) rss_lmn(p,m) = 1.0_r8 / (tmp * fv(p)) ![s m-1] SeP97 p.972,965 @@ -431,10 +431,11 @@ subroutine DustDryDep (this, bounds, & end subroutine DustDryDep - !------------------------------------------------------------------------ - subroutine InitDustVars(this, bounds) + !------------------------------------------------------------------------ + + subroutine InitDustVars(this, bounds) ! - ! !DESCRIPTION: + ! !DESCRIPTION: ! ! Compute source efficiency factor from topography ! Initialize other variables used in subroutine Dust: @@ -452,7 +453,7 @@ subroutine InitDustVars(this, bounds) ! ! !ARGUMENTS: class(dust_emis_base_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES integer :: fc,c,l,m,n ! indices @@ -474,7 +475,7 @@ subroutine InitDustVars(this, bounds) real(r8) :: vlc_grv(ndst) ! [m s-1] Settling velocity real(r8) :: ryn_nbr_grv(ndst) ! [frc] Reynolds number at terminal velocity real(r8) :: cff_drg_grv(ndst) ! [frc] Drag coefficient at terminal velocity - real(r8) :: tmp ! temporary + real(r8) :: tmp ! temporary real(r8) :: ln_gsd ! [frc] ln(gsd) real(r8) :: gsd_anl ! [frc] Geometric standard deviation real(r8) :: dmt_vma ! [m] Mass median diameter analytic She84 p.75 Tabl.1 @@ -494,7 +495,7 @@ subroutine InitDustVars(this, bounds) real(r8) :: sz_max(sz_nbr) ! [m] Size Bin maxima real(r8) :: sz_ctr(sz_nbr) ! [m] Size Bin centers real(r8) :: sz_dlt(sz_nbr) ! [m] Size Bin widths - + ! constants real(r8), allocatable :: dmt_vma_src(:) ! [m] Mass median diameter BSM96 p. 73 Table 2 real(r8), allocatable :: gsd_anl_src(:) ! [frc] Geometric std deviation BSM96 p. 73 Table 2 @@ -507,13 +508,13 @@ subroutine InitDustVars(this, bounds) !------------------------------------------------------------------------ ! allocate local variable - allocate (dmt_vma_src(dst_src_nbr)) - allocate (gsd_anl_src(dst_src_nbr)) - allocate (mss_frc_src(dst_src_nbr)) + allocate (dmt_vma_src(dst_src_nbr)) + allocate (gsd_anl_src(dst_src_nbr)) + allocate (mss_frc_src(dst_src_nbr)) - dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /) - gsd_anl_src(:) = (/ 2.10_r8 , 1.90_r8 , 1.60_r8 /) - mss_frc_src(:) = (/ 0.036_r8 , 0.957_r8 , 0.007_r8 /) + dmt_vma_src(:) = (/ 0.832e-6_r8 , 4.82e-6_r8 , 19.38e-6_r8 /) + gsd_anl_src(:) = (/ 2.10_r8 , 1.90_r8 , 1.60_r8 /) + mss_frc_src(:) = (/ 0.036_r8 , 0.957_r8 , 0.007_r8 /) ! the following comes from (1) szdstlgn.F subroutine ovr_src_snk_frc_get ! and (2) dstszdst.F subroutine dst_szdst_ini @@ -533,7 +534,7 @@ subroutine InitDustVars(this, bounds) end do end do - ! The following code from subroutine wnd_frc_thr_slt_get was placed + ! The following code from subroutine wnd_frc_thr_slt_get was placed ! here because saltation_factor needs to be defined just once ryn_nbr_frc_thr_prx_opt = 0.38_r8 + 1331.0_r8 * (100.0_r8*dmt_slt_opt)**1.56_r8 @@ -709,7 +710,7 @@ subroutine InitDustVars(this, bounds) ! [m s-1] Terminal veloc SeP97 p.467 (8.44) vlc_grv(m) = sqrt(4.0_r8 * grav * this%dmt_vwr(m) * slp_crc(m) * dns_aer / & - (3.0_r8*cff_drg_grv(m)*dns_mdp)) + (3.0_r8*cff_drg_grv(m)*dns_mdp)) eps_crr = abs((vlc_grv(m)-vlc_grv_old)/vlc_grv(m)) !Relative convergence if (itr_idx == 12) then ! Numerical pingpong may occur when Re = 0.1, 2.0, or 500.0 @@ -737,4 +738,6 @@ subroutine InitDustVars(this, bounds) end subroutine InitDustVars + !------------------------------------------------------------------------ + end module DustEmisBase diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index fa2a96b7e0..bebbc7ff30 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -1,18 +1,18 @@ module DustEmisZender2003 - !----------------------------------------------------------------------- - ! !DESCRIPTION: + !----------------------------------------------------------------------- + ! !DESCRIPTION: ! Routines in this module calculate Dust mobilization and dry deposition for dust. - ! Simulates dust mobilization due to wind from the surface into the - ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust + ! Simulates dust mobilization due to wind from the surface into the + ! lowest atmospheric layer. On output flx_mss_vrt_dst(ndst) is the surface dust ! emission (kg/m**2/s) [ + = to atm]. - ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition - ! velocity through the lowest atmospheric layer). CAM will calculate the settling - ! velocity through the whole atmospheric column. The two calculations will determine + ! Calculates the turbulent component of dust dry deposition, (the turbulent deposition + ! velocity through the lowest atmospheric layer). CAM will calculate the settling + ! velocity through the whole atmospheric column. The two calculations will determine ! the dust dry deposition flux to the surface. - ! + ! ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) use clm_varpar , only : dst_src_nbr, ndst @@ -32,7 +32,7 @@ module DustEmisZender2003 use ZenderSoilErodStreamType, only : soil_erod_stream_type use DustEmisBase , only : dust_emis_base_type use clm_varctl , only : dust_emis_method - ! + ! ! !PUBLIC TYPES implicit none private @@ -54,7 +54,7 @@ module DustEmisZender2003 procedure , public :: Clean => CleanZender2003 procedure , private :: InitAllocate ! Allocate data procedure , private :: InitHistory ! History initialization - procedure , private :: InitCold + procedure , private :: InitCold end type dust_emis_zender2003_type !------------------------------------------------------------------------ @@ -65,11 +65,12 @@ module DustEmisZender2003 contains !------------------------------------------------------------------------ + subroutine InitZender2003(this, bounds, NLFilename) ! Initialization for this extended class, calling base level initiation and adding to it class(dust_emis_zender2003_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename call this%soil_erod_stream%Init( bounds, NLFilename ) @@ -81,11 +82,12 @@ subroutine InitZender2003(this, bounds, NLFilename) end subroutine InitZender2003 !------------------------------------------------------------------------ + subroutine InitAllocate(this, bounds) ! ! !ARGUMENTS: class (dust_emis_zender2003_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: begc,endc @@ -95,9 +97,10 @@ subroutine InitAllocate(this, bounds) allocate(this%mbl_bsn_fct_col (begc:endc)) ; this%mbl_bsn_fct_col (:) = nan - end subroutine InitAllocate + end subroutine InitAllocate + + !------------------------------------------------------------------------ - !------------------------------------------------------------------------ subroutine CleanZender2003(this) ! ! Deallocation for this extended class, calling base level deallocation and adding to it @@ -113,6 +116,7 @@ subroutine CleanZender2003(this) end subroutine CleanZender2003 !------------------------------------------------------------------------ + subroutine InitHistory(this, bounds) ! ! !USES: @@ -121,7 +125,7 @@ subroutine InitHistory(this, bounds) ! ! !ARGUMENTS: class (dust_emis_zender2003_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: begc,endc @@ -139,11 +143,12 @@ subroutine InitHistory(this, bounds) end subroutine InitHistory !----------------------------------------------------------------------- + subroutine InitCold(this, bounds) ! ! !ARGUMENTS: class (dust_emis_zender2003_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: c,l @@ -175,15 +180,16 @@ subroutine InitCold(this, bounds) end subroutine InitCold !------------------------------------------------------------------------ + subroutine DustEmission (this, bounds, & num_nolakep, filter_nolakep, & atm2lnd_inst, soilstate_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, & frictionvel_inst) ! - ! !DESCRIPTION: + ! !DESCRIPTION: ! Dust mobilization. This code simulates dust mobilization due to wind ! from the surface into the lowest atmospheric layer - ! On output flx_mss_vrt_dst(ndst) is the surface dust emission + ! On output flx_mss_vrt_dst(ndst) is the surface dust emission ! (kg/m**2/s) [ + = to atm] ! Source: C. Zender's dust model ! @@ -192,8 +198,8 @@ subroutine DustEmission (this, bounds, & use subgridaveMod, only : p2g ! ! !ARGUMENTS: - class (dust_emis_zender2003_type) :: this - type(bounds_type) , intent(in) :: bounds + class (dust_emis_zender2003_type) :: this + type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter integer , intent(in) :: filter_nolakep(num_nolakep) ! patch filter for non-lake points type(atm2lnd_type) , intent(in) :: atm2lnd_inst @@ -226,7 +232,7 @@ subroutine DustEmission (this, bounds, & real(r8) :: sumwt(bounds%begl:bounds%endl) ! sum of weights logical :: found ! temporary for error check integer :: index - ! + ! ! constants ! real(r8), parameter :: cst_slt = 2.61_r8 ! [frc] Saltation constant @@ -235,26 +241,26 @@ subroutine DustEmission (this, bounds, & character(len=*),parameter :: subname = 'DUSTEmission' !------------------------------------------------------------------------ - associate( & - forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] downscaled density (kg/m**3) - + associate( & + forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] downscaled density (kg/m**3) + gwc_thr => soilstate_inst%gwc_thr_col , & ! Input: [real(r8) (:) ] threshold gravimetric soil moisture based on clay content - mss_frc_cly_vld => soilstate_inst%mss_frc_cly_vld_col , & ! Input: [real(r8) (:) ] [frc] Mass fraction clay limited to 0.20 - watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] saturated volumetric soil water - - tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow - tsai => canopystate_inst%tsai_patch , & ! Input: [real(r8) (:) ] one-sided stem area index, no burying by snow - - frac_sno => waterdiagnosticbulk_inst%frac_sno_col , & ! Input: [real(r8) (:) ] fraction of ground covered by snow (0 to 1) - h2osoi_vol => waterstatebulk_inst%h2osoi_vol_col , & ! Input: [real(r8) (:,:) ] volumetric soil water (0<=h2osoi_vol<=watsat) - h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid soil water (kg/m2) - h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] frozen soil water (kg/m2) - - fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) (for dust model) - u10 => frictionvel_inst%u10_patch , & ! Input: [real(r8) (:) ] 10-m wind (m/s) (created for dust model) - + mss_frc_cly_vld => soilstate_inst%mss_frc_cly_vld_col , & ! Input: [real(r8) (:) ] [frc] Mass fraction clay limited to 0.20 + watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] saturated volumetric soil water + + tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow + tsai => canopystate_inst%tsai_patch , & ! Input: [real(r8) (:) ] one-sided stem area index, no burying by snow + + frac_sno => waterdiagnosticbulk_inst%frac_sno_col , & ! Input: [real(r8) (:) ] fraction of ground covered by snow (0 to 1) + h2osoi_vol => waterstatebulk_inst%h2osoi_vol_col , & ! Input: [real(r8) (:,:) ] volumetric soil water (0<=h2osoi_vol<=watsat) + h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid soil water (kg/m2) + h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] frozen soil water (kg/m2) + + fv => frictionvel_inst%fv_patch , & ! Input: [real(r8) (:) ] friction velocity (m/s) (for dust model) + u10 => frictionvel_inst%u10_patch , & ! Input: [real(r8) (:) ] 10-m wind (m/s) (created for dust model) + mbl_bsn_fct => this%mbl_bsn_fct_col , & ! Input: [real(r8) (:) ] basin factor - flx_mss_vrt_dst => this%flx_mss_vrt_dst_patch , & ! Output: [real(r8) (:,:) ] surface dust emission (kg/m**2/s) + flx_mss_vrt_dst => this%flx_mss_vrt_dst_patch , & ! Output: [real(r8) (:,:) ] surface dust emission (kg/m**2/s) flx_mss_vrt_dst_tot => this%flx_mss_vrt_dst_tot_patch & ! Output: [real(r8) (:) ] total dust flux back to atmosphere (pft) ) @@ -315,8 +321,8 @@ subroutine DustEmission (this, bounds, & lnd_frc_mbl(p) = 0.0_r8 endif lnd_frc_mbl(p) = lnd_frc_mbl(p) * (1.0_r8 - frac_sno(c)) - else - lnd_frc_mbl(p) = 0.0_r8 + else + lnd_frc_mbl(p) = 0.0_r8 end if end do @@ -349,7 +355,7 @@ subroutine DustEmission (this, bounds, & l = patch%landunit(p) g = patch%gridcell(p) - ! only perform the following calculations if lnd_frc_mbl is non-zero + ! only perform the following calculations if lnd_frc_mbl is non-zero if (lnd_frc_mbl(p) > 0.0_r8) then @@ -396,7 +402,7 @@ subroutine DustEmission (this, bounds, & wnd_rfr_thr_slt = u10(p) * wnd_frc_thr_slt / fv(p) - ! the following if-block comes from subr. wnd_frc_slt_get + ! the following if-block comes from subr. wnd_frc_slt_get ! purpose: compute the saltating friction velocity ! theory: saltation roughens the boundary layer, AKA "Owen's effect" @@ -416,7 +422,7 @@ subroutine DustEmission (this, bounds, & ! the following loop originates from subr. dst_mbl ! purpose: apply land sfc and veg limitations and global tuning factor - ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect + ! slevis: multiply flx_mss_hrz_slt_ttl by liqfrac to incude the effect ! of frozen soil flx_mss_hrz_slt_ttl = flx_mss_hrz_slt_ttl * lnd_frc_mbl(p) * mbl_bsn_fct(c) * & @@ -461,4 +467,6 @@ subroutine DustEmission (this, bounds, & end subroutine DustEmission -end module DustEmisZender2003 + !------------------------------------------------------------------------ + +end module DustEmisZender2003 \ No newline at end of file From ccb4f1e3b5d80068225512ac188a275f38807970 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 4 Jun 2024 16:59:43 -0600 Subject: [PATCH 244/408] Remove test_DustEmisBase.pf as it wasn't doing anything, I had trouble trying to make it a base class of the Zender Test case and get that to both build and run in the unit testing, so remove for now --- .../test/DustEmis_test/CMakeLists.txt | 1 - .../test/DustEmis_test/test_DustEmisBase.pf | 298 ------------------ 2 files changed, 299 deletions(-) delete mode 100644 src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf diff --git a/src/biogeochem/test/DustEmis_test/CMakeLists.txt b/src/biogeochem/test/DustEmis_test/CMakeLists.txt index 49e3c16391..9239d16e22 100644 --- a/src/biogeochem/test/DustEmis_test/CMakeLists.txt +++ b/src/biogeochem/test/DustEmis_test/CMakeLists.txt @@ -1,5 +1,4 @@ set (pfunit_sources - test_DustEmisBase.pf test_DustEmisZender2003.pf) add_pfunit_ctest(DustEmis diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf deleted file mode 100644 index cf8df87d64..0000000000 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisBase.pf +++ /dev/null @@ -1,298 +0,0 @@ -module test_DustEmisBase - - ! Tests of DustEmisBase - - use funit - use unittestSubgridMod - use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch - use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst - use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit - use clm_varcon, only : clm_varcon_init, clm_varcon_clean - use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean - use DustEmisZender2003 - use shr_kind_mod , only : r8 => shr_kind_r8 - use unittestFilterBuilderMod, only : filter_from_range - use atm2lndType, only : atm2lnd_type, atm2lnd_params_type - use SoilStateType, only : soilstate_type - use CanopyStateType, only : canopystate_type - use TemperatureType, only : temperature_type - use WaterType, only : water_type - use FrictionVelocityMod, only : frictionvel_type - use unittestWaterTypeFactory, only : unittest_water_type_factory_type - use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay - - implicit none - - real(r8), parameter :: tol = 1.e-18_r8 - - @TestCase - type, extends(TestCase) :: TestDustEmisBase - type(dust_emis_zender2003_type) :: dust_emis - integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) - integer :: num_nolakep ! number of patches in non-lake filter - type(atm2lnd_type) :: atm2lnd_inst - type(soilstate_type) :: soilstate_inst - type(canopystate_type) :: canopystate_inst - type(temperature_type) :: temperature_inst - type(unittest_water_type_factory_type) :: water_factory - type(water_type) :: water_inst - type(frictionvel_type) :: frictionvel_inst - contains - procedure :: setUp - procedure :: tearDown - procedure :: setupEnvironment - procedure :: create_atm2lnd - procedure :: create_fv - procedure :: print_values - procedure :: validate_patch - end type TestDustEmisBase - -contains - - !----------------------------------------------------------------------- - - subroutine setUp(this) - use ColumnType, only : col - class(TestDustEmisBase), intent(inout) :: this - - character(len=5) :: NLFilename = 'none' - real(r8), allocatable :: snow_depth_col(:) - real(r8), allocatable :: urb_em(:) - integer :: begl, endl, begc, endc - integer :: c - type(atm2lnd_params_type) :: atm2lnd_params - - soil_layerstruct_predefined = '20SL_8.5m' - create_crop_landunit = .true. - use_crop = .false. - call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) - call clm_varcon_init( is_simple_buildtemp=.true.) - call this%water_factory%init() - call this%water_factory%setup_before_subgrid( & - my_nlevsoi = nlevsoi, & - nlevgrnd_additional = nlevgrnd - nlevsoi, & - my_nlevsno = 3) - call setup_single_veg_patch( pft_type=0 ) - begl = bounds%begl - endl = bounds%endl - begc = bounds%begc - endc = bounds%endc - allocate( urb_em(begl:endl) ) - - call this%dust_emis%Init( bounds, NLFilename ) - call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) - atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & - glcmec_downscale_longwave = .false., & - lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) - ) - allocate (snow_depth_col(begc:endc)) - snow_depth_col(begc:endc) = 0.0_r8 - call SnowHydrologySetControlForTesting() - call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc)) - call this%water_factory%setup_after_subgrid(snl = 3) - call this%soilstate_inst%Init(bounds) - do c = begc, endc - this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1) - end do - call this%setupEnvironment( ) - call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) - call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) - call this%canopystate_inst%SetNMLForTesting() - call this%canopystate_inst%Init(bounds) - call this%frictionvel_inst%InitForTesting(bounds) - urb_em(begl:endl) = 0.99_r8 - call this%temperature_inst%Init(bounds, & - em_roof_lun=urb_em(begl:endl), & - em_wall_lun=urb_em(begl:endl), & - em_improad_lun=urb_em(begl:endl), & - em_perroad_lun=urb_em(begl:endl), & - is_simple_buildtemp=.true., is_prog_buildtemp=.false.) - deallocate (snow_depth_col ) - deallocate( urb_em ) - end subroutine setUp - - !----------------------------------------------------------------------- - - subroutine tearDown(this) - class(TestDustEmisBase), intent(inout) :: this - - call this%dust_emis%Clean() - call this%water_factory%teardown(this%water_inst) - call SnowHydrologyClean() - call unittest_subgrid_teardown() - call this%atm2lnd_inst%Clean() - call clm_varcon_clean() - deallocate( this%filter_nolakep ) - end subroutine tearDown - - !----------------------------------------------------------------------- - - subroutine setupEnvironment(this) - ! - ! !DESCRIPTION: - ! Sets up the external environment used by Dust emissions - i.e., things accessed via - ! 'use' statements. - ! - ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has - ! been completed. - ! - use ColumnType, only : col - use GridcellType, only : grc - class(TestDustEmisBase), intent(in) :: this - ! - integer :: c,j - real(r8), parameter :: clay = 10.0_r8 - - !----------------------------------------------------------------------- - col%dz(:,1:nlevgrnd) = 1.0_r8 - do j = 1, nlevgrnd - do c = bounds%begc, bounds%endc - col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j) - end do - end do - - do c = bounds%begc, bounds%endc - ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are - ! considered bedrock - col%nbedrock(c) = nlevsoi - - this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay ) - this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) - end do - - - ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager) - grc%londeg(:) = 0.0_r8 - - grc%area(:) = 10.0_r8 - - end subroutine setupEnvironment - - !----------------------------------------------------------------------- - - subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho ) - ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets - ! forcing fields based on inputs. Excluded inputs are given a default value - class(TestDustEmisBase), intent(inout) :: this - real(r8), intent(in), optional :: forc_t(:) - real(r8), intent(in), optional :: forc_pbot(:) - real(r8), intent(in), optional :: forc_rho(:) - - real(r8), parameter :: forc_t_default = 301._r8 - real(r8), parameter :: forc_pbot_default = 100000._r8 - real(r8), parameter :: forc_rho_default = 1.1_r8 - ! ------------------------------------------------------------------------ - - if (present(forc_t)) then - this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:) - else - this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default - end if - - if (present(forc_pbot)) then - this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:) - else - this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default - end if - - if (present(forc_rho)) then - this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:) - else - this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default - end if - - end subroutine create_atm2lnd - - !----------------------------------------------------------------------- - - subroutine create_fv(this, fv, u10, ram1) - ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets - ! fields based on inputs. Excluded inputs are given a default value - class(TestDustEmisBase), intent(inout) :: this - real(r8), intent(in), optional :: fv - real(r8), intent(in), optional :: u10 - real(r8), intent(in), optional :: ram1 - - real(r8), parameter :: fv_default = 2.0_r8 - real(r8), parameter :: u10_default = 4._r8 - real(r8), parameter :: ram1_default = 200._r8 - ! ------------------------------------------------------------------------ - - if (present(fv)) then - this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv - else - this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default - end if - - if (present(u10)) then - this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10 - else - this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default - end if - - if (present(ram1)) then - this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1 - else - this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default - end if - - end subroutine create_fv - - subroutine print_values(this) - use LandunitType, only : lun - use PatchType, only : patch - class(TestDustEmisBase), intent(inout) :: this - real(r8) :: SaltationFactor - integer :: p, c, l - - call this%dust_emis%GetConstVars( SaltationFactor ) - do l = bounds%begl, bounds%endl - print *, 'landunit type= ', lun%itype(l) - end do - do c = bounds%begc, bounds%endc - print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1) - print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1) - print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c) - print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c) - print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) - end do - do p = bounds%begp, bounds%endp - print *, 'patch type= ', patch%itype(p) - print *, 'patch weight= ', patch%wtgcell(p) - print *, 'patch active= ', patch%active(p) - print *, 'tlai = ', this%canopystate_inst%tlai_patch(p) - print *, 'tsai = ', this%canopystate_inst%tsai_patch(p) - c = patch%column(p) - print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) & - / this%frictionvel_inst%fv_patch(p) - call this%dust_emis%WritePatchToLog( p ) - end do - end subroutine print_values - - !----------------------------------------------------------------------- - subroutine validate_patch(this, p) - class(TestDustEmisBase), intent(inout) :: this - integer, intent(in) :: p - - real(r8) :: flx_mss_vrt_dst(ndst) - real(r8) :: flx_mss_vrt_dst_tot - real(r8) :: vlc_trb(ndst) - real(r8) :: vlc_trb_1 - real(r8) :: vlc_trb_2 - real(r8) :: vlc_trb_3 - real(r8) :: vlc_trb_4 - - call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, & - flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, & - vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, & - vlc_trb_4=vlc_trb_4 ) - @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot ) - @assertEqual( vlc_trb(1), vlc_trb_1) - @assertEqual( vlc_trb(2), vlc_trb_2) - @assertEqual( vlc_trb(3), vlc_trb_3) - @assertEqual( vlc_trb(4), vlc_trb_4) - end subroutine validate_patch - - !----------------------------------------------------------------------- - -end module test_DustEmisBase From d101b25e174d1bffe43f6f6e97d6efc209a62a03 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 4 Jun 2024 18:17:23 -0600 Subject: [PATCH 245/408] Make a validate function for dust emission part of the dust_emis base class --- src/biogeochem/DustEmisBase.F90 | 47 +++++++++++++++++++ .../DustEmis_test/test_DustEmisZender2003.pf | 18 +------ 2 files changed, 48 insertions(+), 17 deletions(-) diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90 index 6fb1066607..dbc5729403 100644 --- a/src/biogeochem/DustEmisBase.F90 +++ b/src/biogeochem/DustEmisBase.F90 @@ -61,6 +61,7 @@ module DustEmisBase procedure , public :: InitBase ! Base object initiatlization (allows it to be extended) procedure , public :: Init => InitBase ! Initialization name used by callers procedure(DustEmission_interface) , public, deferred :: DustEmission ! Dust mobilization + procedure , public :: CheckDustEmisIsValid ! Check that the dust emission type is valid procedure , public :: DustDryDep ! Turbulent dry deposition for dust procedure , public :: WritePatchToLog ! Write information on the given patch to the log file procedure , public :: GetPatchVars ! Get important variables on a given patch @@ -279,6 +280,52 @@ subroutine GetPatchVars(this, p, flx_mss_vrt_dst, flx_mss_vrt_dst_tot, vlc_trb, if ( present(vlc_trb_4) ) vlc_trb_4 = this%vlc_trb_4_patch(p) end subroutine GetPatchVars + !------------------------------------------------------------------------ + subroutine CheckDustEmisIsValid( this, p ) + ! Check that dust emission state for this patch is valid + ! This means ensuring that total dust is the sum of all the dust bins + ! And that dry deposition for each dust bins agrees with the array of all + class(dust_emis_base_type) :: this + integer , intent(in) :: p ! Patch to display + integer :: i + + if ( abs(sum(this%flx_mss_vrt_dst_patch(p,:)) - this%flx_mss_vrt_dst_tot_patch(p)) > 0.0_r8 )then + write(iulog,*) 'sum(flx_mss_vrt_dst(:)) /=flx_mss_vrt_dst_tot for p = ', p, & + errMsg(sourcefile, __LINE__) + call endrun(msg="Sum over dust bins does NOT equal total dust") + return + end if + i = 1 + if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_1_patch(p) )then + write(iulog,*) 'vlc_trb(i)) /= glc_trb for p = ', p, 'dust bin = ', i, & + errMsg(sourcefile, __LINE__) + call endrun(msg="Dry deposition for dust bin not equal to the array bin for it") + return + end if + i = 2 + if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_2_patch(p) )then + write(iulog,*) 'vlc_trb(i) /= glc_trb for p = ', p, 'dust bin = ', i, & + errMsg(sourcefile, __LINE__) + call endrun(msg="Dry deposition for dust bin not equal to the array bin for it") + return + end if + i = 3 + if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_3_patch(p) )then + write(iulog,*) 'vlc_trb(i)) /= glc_trb for p = ', p, 'dust bin = ', i, & + errMsg(sourcefile, __LINE__) + call endrun(msg="Dry deposition for dust bin not equal to the array bin for it") + return + end if + i = 4 + if ( this%vlc_trb_patch(p,i) /= this%vlc_trb_4_patch(p) )then + write(iulog,*) 'vlc_trb(i)) /= glc_trb for p = ', p, 'dust bin = ', i, & + errMsg(sourcefile, __LINE__) + call endrun(msg="Dry deposition for dust bin not equal to the array bin for it") + return + end if + + end subroutine CheckDustEmisIsValid + !----------------------------------------------------------------------- subroutine GetConstVars(this, SaltationFactor ) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 1168200cfe..7ba4e4b63e 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -274,23 +274,7 @@ contains class(TestDustEmisZender2003), intent(inout) :: this integer, intent(in) :: p - real(r8) :: flx_mss_vrt_dst(ndst) - real(r8) :: flx_mss_vrt_dst_tot - real(r8) :: vlc_trb(ndst) - real(r8) :: vlc_trb_1 - real(r8) :: vlc_trb_2 - real(r8) :: vlc_trb_3 - real(r8) :: vlc_trb_4 - - call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst=flx_mss_vrt_dst, & - flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, vlc_trb=vlc_trb, & - vlc_trb_1=vlc_trb_1, vlc_trb_2=vlc_trb_2, vlc_trb_3=vlc_trb_3, & - vlc_trb_4=vlc_trb_4 ) - @assertEqual( sum(flx_mss_vrt_dst), flx_mss_vrt_dst_tot ) - @assertEqual( vlc_trb(1), vlc_trb_1) - @assertEqual( vlc_trb(2), vlc_trb_2) - @assertEqual( vlc_trb(3), vlc_trb_3) - @assertEqual( vlc_trb(4), vlc_trb_4) + call this%dust_emis%CheckDustEmisIsValid( p ) end subroutine validate_patch !----------------------------------------------------------------------- From 0f511eed129f00561af2611925de6463615ca696 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 5 Jun 2024 19:02:58 -0600 Subject: [PATCH 246/408] Change dust_inst to dust_emis_inst with VS code, unit test and a case works --- src/biogeochem/CNVegetationFacade.F90 | 2 +- src/main/clm_driver.F90 | 6 +++--- src/main/clm_instMod.F90 | 4 ++-- src/main/lnd2atmMod.F90 | 6 +++--- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 61e2e9cf91..f42cf17d68 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -147,7 +147,7 @@ module CNVegetationFacade ! - ch4_inst ! - probably not: really seems to belong in soilbiogeochem ! - crop_inst - ! - dust_inst + ! - dust_emis_inst ! - vocemis_inst ! - fireemis_inst ! - drydepvel_inst diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index b6dacf3866..c1845d0de6 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -805,14 +805,14 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_startf('bgc') ! Dust mobilization (C. Zender's modified codes) - call dust_inst%DustEmission(bounds_clump, & + call dust_emis_inst%DustEmission(bounds_clump, & filter(nc)%num_nolakep, filter(nc)%nolakep, & atm2lnd_inst, soilstate_inst, canopystate_inst, & water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, & frictionvel_inst) ! Dust dry deposition (C. Zender's modified codes) - call dust_inst%DustDryDep(bounds_clump, & + call dust_emis_inst%DustDryDep(bounds_clump, & atm2lnd_inst, frictionvel_inst) ! VOC emission (A. Guenther's MEGAN (2006) model) @@ -1307,7 +1307,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro atm2lnd_inst, surfalb_inst, temperature_inst, frictionvel_inst, & water_inst, & energyflux_inst, solarabs_inst, drydepvel_inst, & - vocemis_inst, fireemis_inst, dust_inst, ch4_inst, glc_behavior, & + vocemis_inst, fireemis_inst, dust_emis_inst, ch4_inst, glc_behavior, & lnd2atm_inst, & net_carbon_exchange_grc = net_carbon_exchange_grc(bounds_proc%begg:bounds_proc%endg)) deallocate(net_carbon_exchange_grc) diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index c3ea8a68b3..9e187f639c 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -151,7 +151,7 @@ module clm_instMod ! General biogeochem types type(ch4_type) , public :: ch4_inst type(crop_type) , public :: crop_inst - type(dust_emis_zender2003_type) , public :: dust_inst + type(dust_emis_zender2003_type) , public :: dust_emis_inst type(vocemis_type) , public :: vocemis_inst type(fireemis_type) , public :: fireemis_inst type(drydepvel_type), public :: drydepvel_inst @@ -350,7 +350,7 @@ subroutine clm_instInit(bounds) call surfrad_inst%Init(bounds) - call dust_inst%Init(bounds, NLFilename) + call dust_emis_inst%Init(bounds, NLFilename) allocate(scf_method, source = CreateAndInitSnowCoverFraction( & snow_cover_fraction_method = snow_cover_fraction_method, & diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90 index e6b1bb43f0..71f55b3b05 100644 --- a/src/main/lnd2atmMod.F90 +++ b/src/main/lnd2atmMod.F90 @@ -150,7 +150,7 @@ subroutine lnd2atm(bounds, & atm2lnd_inst, surfalb_inst, temperature_inst, frictionvel_inst, & water_inst, & energyflux_inst, solarabs_inst, drydepvel_inst, & - vocemis_inst, fireemis_inst, dust_inst, ch4_inst, glc_behavior, & + vocemis_inst, fireemis_inst, dust_emis_inst, ch4_inst, glc_behavior, & lnd2atm_inst, & net_carbon_exchange_grc) ! @@ -173,7 +173,7 @@ subroutine lnd2atm(bounds, & type(drydepvel_type) , intent(in) :: drydepvel_inst type(vocemis_type) , intent(in) :: vocemis_inst type(fireemis_type) , intent(in) :: fireemis_inst - type(dust_emis_zender2003_type) , intent(in) :: dust_inst + type(dust_emis_zender2003_type) , intent(in) :: dust_emis_inst type(ch4_type) , intent(in) :: ch4_inst type(glc_behavior_type) , intent(in) :: glc_behavior type(lnd2atm_type) , intent(inout) :: lnd2atm_inst @@ -332,7 +332,7 @@ subroutine lnd2atm(bounds, & ! dust emission flux call p2g(bounds, ndst, & - dust_inst%flx_mss_vrt_dst_patch(bounds%begp:bounds%endp, :), & + dust_emis_inst%flx_mss_vrt_dst_patch(bounds%begp:bounds%endp, :), & lnd2atm_inst%flxdst_grc (bounds%begg:bounds%endg, :), & p2c_scale_type='unity', c2l_scale_type= 'unity', l2g_scale_type='unity') From 46862cc47510f3b4f4b376ab64f436f668c9d788 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 7 Jun 2024 00:11:41 -0600 Subject: [PATCH 247/408] Add a barebones dust emission factory module to create a dust emission class object to be used depending on the namelist option, need to add documentation to it --- src/biogeochem/CMakeLists.txt | 1 + src/biogeochem/DustEmisFactory.F90 | 51 +++++++++++++++++++ src/biogeochem/DustEmisZender2003.F90 | 14 +++++ .../DustEmis_test/test_DustEmisZender2003.pf | 6 ++- src/main/clm_instMod.F90 | 7 +-- src/main/lnd2atmMod.F90 | 4 +- 6 files changed, 76 insertions(+), 7 deletions(-) create mode 100644 src/biogeochem/DustEmisFactory.F90 diff --git a/src/biogeochem/CMakeLists.txt b/src/biogeochem/CMakeLists.txt index 9824bcb072..50eb64cdb7 100644 --- a/src/biogeochem/CMakeLists.txt +++ b/src/biogeochem/CMakeLists.txt @@ -8,6 +8,7 @@ list(APPEND clm_sources CNDVType.F90 DustEmisBase.F90 DustEmisZender2003.F90 + DustEmisFactory.F90 CropReprPoolsMod.F90 CropType.F90 CNVegStateType.F90 diff --git a/src/biogeochem/DustEmisFactory.F90 b/src/biogeochem/DustEmisFactory.F90 new file mode 100644 index 0000000000..29787c1855 --- /dev/null +++ b/src/biogeochem/DustEmisFactory.F90 @@ -0,0 +1,51 @@ +module DustEmisFactory + + use abortutils , only : endrun + use shr_log_mod , only : errMsg => shr_log_errMsg + use clm_varctl , only : iulog + + implicit none + save + private + ! + public :: create_dust_emissions ! create an object of class dust_emis_base + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +contains + + function create_dust_emissions(bounds, NLFilename) result(dust_emis) + use DustEmisBase , only : dust_emis_base_type + use DustEmisZender2003, only : dust_emis_zender2003_type + use clm_varctl , only : dust_emis_method + use decompMod , only : bounds_type + use shr_kind_mod , only : CL => shr_kind_cl + implicit none + class(dust_emis_base_type), allocatable :: dust_emis + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename + character(len=CL) :: method + + method = dust_emis_method + + select case ( trim(method) ) + + case( "Zender_2003" ) + allocate(dust_emis, source=dust_emis_zender2003_type() ) + + ! This will be added when the Leung2023 comes in + !case( "Leung_2023" ) + ! allocate(dust_emis, source=dust_emis_zender2003_type() ) + case default + write(iulog,*) 'ERROR: unknown dust_emis_method: ', method, & + errMsg(sourcefile, __LINE__) + call endrun( "Unrecognized dust_emis_method" ) + + end select + + call dust_emis%Init(bounds, NLFilename) + + end function create_dust_emissions + +end module DustEmisFactory \ No newline at end of file diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index bebbc7ff30..e3c4d4115e 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -57,6 +57,11 @@ module DustEmisZender2003 procedure , private :: InitCold end type dust_emis_zender2003_type + + interface dust_emis_zender2003_type + ! initialize a new dust emission object + module procedure constructor + end interface dust_emis_zender2003_type !------------------------------------------------------------------------ character(len=*), parameter, private :: sourcefile = & @@ -64,6 +69,15 @@ module DustEmisZender2003 contains + !----------------------------------------------------------------------- + type(dust_emis_zender2003_type) function constructor() + ! + ! Creates a dust emission object for Zender-2003 type + ! For now this is just a placeholder + !----------------------------------------------------------------------- + + end function constructor + !------------------------------------------------------------------------ subroutine InitZender2003(this, bounds, NLFilename) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 7ba4e4b63e..4df64c7da3 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -9,6 +9,7 @@ module test_DustEmisZender2003 use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit use clm_varcon, only : clm_varcon_init, clm_varcon_clean use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean + use DustEmisBase use DustEmisZender2003 use shr_kind_mod , only : r8 => shr_kind_r8 use unittestFilterBuilderMod, only : filter_from_range @@ -20,6 +21,7 @@ module test_DustEmisZender2003 use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay + use DustEmisFactory, only : create_dust_emissions implicit none @@ -27,7 +29,7 @@ module test_DustEmisZender2003 @TestCase type, extends(TestCase) :: TestDustEmisZender2003 - type(dust_emis_zender2003_type) :: dust_emis + class(dust_emis_base_type), allocatable :: dust_emis integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) integer :: num_nolakep ! number of patches in non-lake filter type(atm2lnd_type) :: atm2lnd_inst @@ -79,7 +81,7 @@ contains endc = bounds%endc allocate( urb_em(begl:endl) ) - call this%dust_emis%Init( bounds, NLFilename ) + allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename)) call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & glcmec_downscale_longwave = .false., & diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 9e187f639c..ab690a92a6 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -45,7 +45,7 @@ module clm_instMod use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use CropType , only : crop_type use DryDepVelocity , only : drydepvel_type - use DustEmisZender2003 , only : dust_emis_zender2003_type + use DustEmisBase , only : dust_emis_base_type use EnergyFluxType , only : energyflux_type use FrictionVelocityMod , only : frictionvel_type use GlacierSurfaceMassBalanceMod , only : glacier_smb_type @@ -151,7 +151,7 @@ module clm_instMod ! General biogeochem types type(ch4_type) , public :: ch4_inst type(crop_type) , public :: crop_inst - type(dust_emis_zender2003_type) , public :: dust_emis_inst + class(dust_emis_base_type), public, allocatable :: dust_emis_inst type(vocemis_type) , public :: vocemis_inst type(fireemis_type) , public :: fireemis_inst type(drydepvel_type), public :: drydepvel_inst @@ -203,6 +203,7 @@ subroutine clm_instInit(bounds) use clm_varctl , only : use_hillslope use HillslopeHydrologyMod , only : SetHillslopeSoilThickness use initVerticalMod , only : setSoilLayerClass + use DustEmisFactory , only : create_dust_emissions ! ! !ARGUMENTS type(bounds_type), intent(in) :: bounds ! processor bounds @@ -350,7 +351,7 @@ subroutine clm_instInit(bounds) call surfrad_inst%Init(bounds) - call dust_emis_inst%Init(bounds, NLFilename) + allocate(dust_emis_inst, source = create_dust_emissions(bounds, NLFilename)) allocate(scf_method, source = CreateAndInitSnowCoverFraction( & snow_cover_fraction_method = snow_cover_fraction_method, & diff --git a/src/main/lnd2atmMod.F90 b/src/main/lnd2atmMod.F90 index 71f55b3b05..503f4b9585 100644 --- a/src/main/lnd2atmMod.F90 +++ b/src/main/lnd2atmMod.F90 @@ -20,7 +20,7 @@ module lnd2atmMod use lnd2atmType , only : lnd2atm_type use atm2lndType , only : atm2lnd_type use ch4Mod , only : ch4_type - use DustEmisZender2003 , only : dust_emis_zender2003_type + use DustEmisBase , only : dust_emis_base_type use DryDepVelocity , only : drydepvel_type use VocEmissionMod , only : vocemis_type use CNFireEmissionsMod , only : fireemis_type @@ -173,7 +173,7 @@ subroutine lnd2atm(bounds, & type(drydepvel_type) , intent(in) :: drydepvel_inst type(vocemis_type) , intent(in) :: vocemis_inst type(fireemis_type) , intent(in) :: fireemis_inst - type(dust_emis_zender2003_type) , intent(in) :: dust_emis_inst + class(dust_emis_base_type) , intent(in) :: dust_emis_inst type(ch4_type) , intent(in) :: ch4_inst type(glc_behavior_type) , intent(in) :: glc_behavior type(lnd2atm_type) , intent(inout) :: lnd2atm_inst From 779c9b51b15f6e0c7663df72590d4d5e36654e38 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 7 Jun 2024 12:07:37 -0600 Subject: [PATCH 248/408] Squashed '.lib/git-fleximod/' changes from a34070be0..4ff1e98de 4ff1e98de Merge tag 'v0.7.7' into tmp-release 87640adf4 Bump to 0.7.7 c124dc590 Merge pull request #43 from ESMCI/fix/root_dir 3ff935b83 update tests 0593149d3 one more improvement d95f5d61b fix status issue c304487af update complex test git-subtree-dir: .lib/git-fleximod git-subtree-split: 4ff1e98de895eb146de451e6d676ecc78d224662 --- git_fleximod/cli.py | 4 ++-- git_fleximod/git_fleximod.py | 22 +++++++++++++++++----- pyproject.toml | 2 +- tbump.toml | 2 +- tests/conftest.py | 4 ++-- tests/test_d_complex.py | 13 ++++++------- 6 files changed, 29 insertions(+), 18 deletions(-) diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py index 7d09abd83b..bc099fcbc0 100644 --- a/git_fleximod/cli.py +++ b/git_fleximod/cli.py @@ -2,7 +2,7 @@ import argparse from git_fleximod import utils -__version__ = "0.7.6" +__version__ = "0.7.7" def find_root_dir(filename=".gitmodules"): """ finds the highest directory in tree @@ -21,7 +21,7 @@ def find_root_dir(filename=".gitmodules"): attempt = dl / filename if attempt.is_file(): return str(dl) - utils.fatal_error("No .gitmodules found in directory tree") + return None def get_parser(): diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py index a003c0da8c..ca5f90622d 100755 --- a/git_fleximod/git_fleximod.py +++ b/git_fleximod/git_fleximod.py @@ -298,15 +298,25 @@ def submodules_status(gitmodules, root_dir, toplevel=False): # submodule commands use path, not name url = url.replace("git@github.com:", "https://github.com/") tags = rootgit.git_operation("ls-remote", "--tags", url) + result = rootgit.git_operation("submodule","status",newpath).split() + ahash = None + if result: + ahash = result[0][1:] + hhash = None atag = None needsupdate += 1 if not toplevel and level: continue for htag in tags.split("\n"): - if tag and tag in htag: + if htag.endswith('^{}'): + htag = htag[:-3] + if ahash and not atag and ahash in htag: atag = (htag.split()[1])[10:] + if tag and not hhash and htag.endswith(tag): + hhash = htag.split()[0] + if hhash and atag: break - if tag and tag == atag: + if tag and (ahash == hhash or atag == tag): print(f"e {name:>20} not checked out, aligned at tag {tag}") elif tag: ahash = rootgit.git_operation( @@ -565,10 +575,12 @@ def main(): logger.info("action is {} root_dir={} file_name={}".format(action, root_dir, file_name)) - if not os.path.isfile(os.path.join(root_dir, file_name)): - file_path = utils.find_upwards(root_dir, file_name) + if not root_dir or not os.path.isfile(os.path.join(root_dir, file_name)): + if root_dir: + file_path = utils.find_upwards(root_dir, file_name) - if file_path is None: + if root_dir is None or file_path is None: + root_dir = "." utils.fatal_error( "No {} found in {} or any of it's parents".format(file_name, root_dir) ) diff --git a/pyproject.toml b/pyproject.toml index 3c70c6c9c7..a316914bf5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "git-fleximod" -version = "0.7.6" +version = "0.7.7" description = "Extended support for git-submodule and git-sparse-checkout" authors = ["Jim Edwards "] maintainers = ["Jim Edwards "] diff --git a/tbump.toml b/tbump.toml index 3854682df4..c22637ccda 100644 --- a/tbump.toml +++ b/tbump.toml @@ -2,7 +2,7 @@ github_url = "https://github.com/jedwards4b/git-fleximod/" [version] -current = "0.7.6" +current = "0.7.7" # Example of a semver regexp. # Make sure this matches current_version before diff --git a/tests/conftest.py b/tests/conftest.py index 942a0efb97..1cc008eb1d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -32,7 +32,7 @@ def logger(): "submodule_name": "test_optional", "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", "status2" : "test_optional at tag MPIserial_2.4.0", - "status3" : "test_optional not checked out, aligned at tag MPIserial_2.4.0", + "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0", "status4" : "test_optional at tag MPIserial_2.4.0", "gitmodules_content": """ [submodule "test_optional"] @@ -46,7 +46,7 @@ def logger(): "submodule_name": "test_alwaysoptional", "status1" : "test_alwaysoptional MPIserial_2.3.0 is out of sync with .gitmodules e5cf35c", "status2" : "test_alwaysoptional at hash e5cf35c", - "status3" : "test_alwaysoptional not checked out, out of sync at tag MPIserial_2.3.0", + "status3" : "out of sync at tag None, expected tag is e5cf35c", "status4" : "test_alwaysoptional at hash e5cf35c", "gitmodules_content": """ [submodule "test_alwaysoptional"] diff --git a/tests/test_d_complex.py b/tests/test_d_complex.py index fdce516274..edde7d816d 100644 --- a/tests/test_d_complex.py +++ b/tests/test_d_complex.py @@ -7,8 +7,8 @@ def test_complex_checkout(git_fleximod, complex_repo, logger): assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) assert("ToplevelRequired not checked out, aligned at tag MPIserial_2.5.0" in status.stdout) assert("AlwaysRequired not checked out, aligned at tag MPIserial_2.4.0" in status.stdout) - assert("Complex not checked out, aligned at tag testtag01" in status.stdout) - assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) + assert("Complex not checked out, aligned at tag testtag02" in status.stdout) + assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout) # This should checkout and update test_submodule and complex_sub result = git_fleximod(complex_repo, "update") @@ -18,7 +18,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger): assert("ToplevelOptional not checked out, aligned at tag v5.3.2" in status.stdout) assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) - assert("Complex at tag testtag01" in status.stdout) + assert("Complex at tag testtag02" in status.stdout) # now check the complex_sub root = (complex_repo / "modules" / "complex") @@ -39,9 +39,8 @@ def test_complex_checkout(git_fleximod, complex_repo, logger): assert("ToplevelOptional at tag v5.3.2" in status.stdout) assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) - assert("Complex at tag testtag01" in status.stdout) - assert("AlwaysOptional not checked out, aligned at tag MPIserial_2.3.0" in status.stdout) - + assert("Complex at tag testtag02" in status.stdout) + assert("AlwaysOptional not checked out, out of sync at tag None, expected tag is MPIserial_2.3.0" in status.stdout) # Finally update optional result = git_fleximod(complex_repo, "update --optional") @@ -51,7 +50,7 @@ def test_complex_checkout(git_fleximod, complex_repo, logger): assert("ToplevelOptional at tag v5.3.2" in status.stdout) assert("ToplevelRequired at tag MPIserial_2.5.0" in status.stdout) assert("AlwaysRequired at tag MPIserial_2.4.0" in status.stdout) - assert("Complex at tag testtag01" in status.stdout) + assert("Complex at tag testtag02" in status.stdout) assert("AlwaysOptional at tag MPIserial_2.3.0" in status.stdout) # now check the complex_sub From 5eadc60c32d65b359fddee5947ffed57cdc02da8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 7 Jun 2024 13:18:22 -0600 Subject: [PATCH 249/408] Tweak the documenation a bit --- .gitignore | 4 --- README | 2 +- README_GITFLEXIMOD.rst | 31 ++++++++++--------- cime_config/testdefs/ExpectedTestFails.xml | 2 +- cime_config/testdefs/testlist_clm.xml | 2 +- .../PLUMBER2/defaults/user_nl_datm_streams | 2 +- doc/README.CHECKLIST.master_tags | 4 +-- python/ctsm/run_sys_tests.py | 6 ++-- ...st_unit_gen_mksurfdata_jobscript_single.py | 2 +- tools/mksurfdata_esmf/README.md | 2 +- 10 files changed, 28 insertions(+), 29 deletions(-) diff --git a/.gitignore b/.gitignore index a083a7853f..27823e7f54 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,3 @@ -# ignore svn directories -**/.svn/** -.svn/ - # netcdf files *.nc # but don't ignore netcdf files here: diff --git a/README b/README index 4d33638e7e..8b4e15e557 100644 --- a/README +++ b/README @@ -49,7 +49,7 @@ src --------------- CTSM Source code. lilac ------------- Lightweight Infrastructure for Land-Atmosphere Coupling (for coupling to a host atmosphere model) tools ------------- CTSM Offline tools to prepare input datasets and process output. cime_config ------- Configuration files of cime for compsets and CTSM settings -bin/git-fleximod -- Script to manage the external source directories +bin/git-fleximod -- Script to manage the needed sub-component source directories (handled with git submodule) py_env_create ----- Script to setup the python environment for CTSM python tools using conda python ------------ Python modules used in tools and testing and automated checking of ALL CTSM python scirpts diff --git a/README_GITFLEXIMOD.rst b/README_GITFLEXIMOD.rst index ab8c412cee..de6bbf392f 100644 --- a/README_GITFLEXIMOD.rst +++ b/README_GITFLEXIMOD.rst @@ -9,7 +9,7 @@ To obtain the CTSM code you need to do the following: #. Clone the repository. :: - git clone https://github.com/escomp/ctsm.git my_ctsm_sandbox + git clone https://github.com/ESCOMP/CTSM.git my_ctsm_sandbox This will create a directory ``my_ctsm_sandbox/`` in your current working directory. @@ -25,6 +25,10 @@ To obtain the CTSM code you need to do the following: Additional documentation for git-fleximod appears here: https://github.com/ESMCI/git-fleximod?tab=readme-ov-file#git-fleximod +"components" here refers to seperate git repositories for seperable parts of +the code (such as the MOSART or mizuRoute river models). Because they are +managed with "submodule" in git hereafter we will refer to them as "submodule(s)". + At this point you have a working version of CTSM. To see full details of how to set up a case, compile and run, see the CIME documentation at http://esmci.github.io/cime/ . @@ -33,19 +37,19 @@ More details on git-fleximod ---------------------------- The file **.gitmodules** in your top-level CTSM directory tells -**git-fleximod** which tag/branch of each component should be -brought in to generate your sandbox. +**git-fleximod** which tag/branch of each submodule +should be brought in to generate your sandbox. -NOTE: If you manually modify an external without updating .gitmodules, +NOTE: If you manually modify a submodule without updating .gitmodules, e.g. switch to a different tag, then rerunning git-fleximod will warn you of local changes you need to resolve. -git-fleximod will not change a modified external back to what is specified in +git-fleximod will not change a modified submodule back to what is specified in .gitmodules without the --force option. See below documentation `Customizing your CTSM sandbox`_ for more details. **You need to rerun git-fleximod whenever .gitmodules has changed** (unless you have already manually updated the relevant -external(s) to have the correct branch/tag checked out). Common times +submodule(s) to have the correct branch/tag checked out). Common times when this is needed are: * After checking out a new CTSM branch/tag @@ -74,7 +78,7 @@ changes, or if you have any ongoing CTSM cases that were created from this sandbox. In these cases, it is often easiest to do a second **git clone**. -Pointing to a different version of a component +Pointing to a different version of a submodule ---------------------------------------------- Each entry in **.gitmodules** has the following form (we use CIME as an @@ -92,11 +96,11 @@ Each entry specifies either a tag or a hash. To point to a new tag or hash: #. Modify the relevant entry/entries in **.gitmodules** (e.g., changing ``cime6.0.246`` to ``cime6.0.247`` above) -#. Checkout the new component(s):: +#. Checkout the new submodule(s):: - ./bin/git-fleximod update + ./bin/git-fleximod update -Keep in mind that changing individual components from a tag may result +Keep in mind that changing individual submodule from a tag may result in an invalid model (won't compile, won't run, not scientifically meaningful) and is unsupported. @@ -105,11 +109,10 @@ Committing your change to .gitmodules After making this change, it's a good idea to commit the change in your local CTSM git repository. First create a branch in your local -repository, then commit it. (Unlike with subversion, branches are stored -locally unless you explicitly push them up to GitHub. Feel free to -create whatever local branches you'd like.) For example:: +repository, then commit it. Feel free to create whatever local branches +you'd like in git. For example:: git checkout -b my_ctsm_branch git add .gitmodules - git commit -m "Update CIME to cime5.4.0-alpha.20" + git commit -m "Update CIME to cime6.0.247" diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 23e481222b..8b898a0627 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -272,7 +272,7 @@ - + diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 1ac2334ba8..b40f00d5a6 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2913,7 +2913,7 @@ - + diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams index 35071ff415..29a8c675ac 100644 --- a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams +++ b/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams @@ -21,7 +21,7 @@ ! foo:year_first = 1950 ! would change the stream year_first stream_entry to 1950 for the foo stream block !------------------------------------------------------------------------ -! This will come out when cdeps externals are updated +! This will come out when the cdeps submodule are updated CLM_USRDAT.PLUMBER2:datavars = ZBOT Sa_z, \ TBOT Sa_tbot, \ QBOT Sa_shum, \ diff --git a/doc/README.CHECKLIST.master_tags b/doc/README.CHECKLIST.master_tags index 0da52acaaa..51386c4238 100644 --- a/doc/README.CHECKLIST.master_tags +++ b/doc/README.CHECKLIST.master_tags @@ -14,7 +14,7 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow 2a -- run 'git pull' to pull in the latest version from GitHub 2b -- run 'git status' and/or 'git diff' to make sure you don't have any uncommitted local changes - 2c -- run './bin/git-fleximod status' to make sure all externals are + 2c -- run './bin/git-fleximod status' to make sure all submodules are updated and don't have any uncommitted changes. If any are marked with 's' in the first column, run './bin/git-fleximod update'. @@ -26,7 +26,7 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow $EDITOR cime_config/testdefs/ExpectedTestFails.xml 3c -- make sure you understand any changes to the baselines -- to document in ChangeLog 3d -- Check the log file for run_sys_tests (../run_sys_test.log), to make sure that - externals are correct (see 2c above) + submodules are correct (see 2c above) (4) Use diff and status to make sure any new files are in the repo and only the correct changes are on the branch diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index ecea2342a7..f5a7ed04dc 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -124,7 +124,7 @@ def run_sys_tests( cime_path (str): path to root of cime skip_testroot_creation (bool): if True, assume the testroot directory has already been created, so don't try to recreate it or re-make the link to it - skip_git_status (bool): if True, skip printing git and manage_externals status + skip_git_status (bool): if True, skip printing git and git-fleximod status dry_run (bool): if True, print commands to be run but don't run them suite_name (str): name of test suite/category to run testfile (str): path to file containing list of tests to run @@ -476,11 +476,11 @@ def _commandline_args(): parser.add_argument( "--skip-git-status", action="store_true", - help="Skip printing git and manage_externals status,\n" + help="Skip printing git and git-fleximod status,\n" "both to screen and to the SRCROOT_GIT_STATUS file in TESTROOT.\n" "This printing can often be helpful, but this option can be used to\n" "avoid extraneous output, to reduce the time needed to run this script,\n" - "or if git or manage_externals are currently broken in your sandbox.\n", + "or if git or git-fleximod are currently broken in your sandbox.\n", ) parser.add_argument( diff --git a/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py b/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py index 5038c6b3e1..8b8e2df32a 100755 --- a/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py +++ b/python/ctsm/test/test_unit_gen_mksurfdata_jobscript_single.py @@ -136,7 +136,7 @@ def test_simple_derecho_args(self): def test_derecho_mpirun(self): """ test derecho mpirun. This would've helped caught a problem we ran into - It will also be helpful when externals are updated to guide to solutions + It will also be helpful when sumodules are updated to guide to solutions to problems """ machine = "derecho" diff --git a/tools/mksurfdata_esmf/README.md b/tools/mksurfdata_esmf/README.md index 3d19c88ff0..a9c0b80de6 100644 --- a/tools/mksurfdata_esmf/README.md +++ b/tools/mksurfdata_esmf/README.md @@ -41,7 +41,7 @@ In addition for the build: python, bash-shell, CMake and GNU-Make are required These libraries need to be built such that they can all work together in the same executable. Hence, the above order may be required in building them. -CTSM externals that are required are: cime and ccs_config. See [Building](#building-the-executable) on getting +CTSM submodules that are required are: cime and ccs_config. See [Building](#building-the-executable) on getting those. A python environment that includes particular packages is also required we demonstrate how to use the ctsm_pylib environment that we support in CTSM. From e65c2034682afd9e5024361415c9002f8d82ca60 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 7 Jun 2024 13:49:07 -0600 Subject: [PATCH 250/408] Start the changelog --- doc/ChangeLog | 90 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 91 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 8b6bb8f0d2..4600af34be 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,94 @@ =============================================================== +Tag name: ctsm5.2.008 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Fri 07 Jun 2024 01:23:07 PM MDT +One-line Summary: Another update of git-fleximod + +Purpose and description of changes +---------------------------------- + +Just update the gitfleximod subtree to v0.7.7. This fixes an issue in identifying that a tag is out of sync in a submodule. +An issue about recursion on a submodule. Allows untracked files, and fixes a MS Window Memory error. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- + +List of CTSM issues fixed: + Fixes #2591 -- Start using submodule rather than external + +Notes of particular relevance for users +--------------------------------------- +Caveats for users (e.g., need to interpolate initial conditions): + doc-builder checkout seems to be required to use "git commit ." at the top level + +Changes to documentation: + Tweak some of the documentation around git-fleximod and use submodule rather than external. + +Notes of particular relevance for developers: +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] + + +Testing summary: minimual +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit + +Other details +------------- +List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): + git-fleximod subtree updated + +Pull Requests that document the changes (include PR ids): + #2577 -- Update git-fleximod +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== Tag name: ctsm5.2.007 Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD) Date: Fri 31 May 2024 13:49:29 AM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index b3f1632571..275c4a5cfa 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.008 erik 06/07/2024 Another update of git-fleximod ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems From dfebe5fdbdce10ba25cbdc6419c95f41f82f3848 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 7 Jun 2024 14:08:42 -0600 Subject: [PATCH 251/408] Remove user_nl_clm (added in 5431850) and replace 2 NIWO tests with HARV --- cime_config/testdefs/ExpectedTestFails.xml | 17 +---------------- cime_config/testdefs/testlist_clm.xml | 6 +++--- cime_config/usermods_dirs/NEON/NIWO/user_nl_clm | 8 -------- 3 files changed, 4 insertions(+), 27 deletions(-) delete mode 100644 cime_config/usermods_dirs/NEON/NIWO/user_nl_clm diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 03f60ad824..5968e73760 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -78,15 +78,11 @@ - + FAIL #2310 - - FAIL - #2310 - @@ -100,17 +96,6 @@ - - - FAIL - #2310 - - - FAIL - #2310 - - - FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 782af8bc34..9a2390bd58 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2257,7 +2257,7 @@ - + @@ -2268,7 +2268,7 @@ - + @@ -2276,7 +2276,7 @@ - + diff --git a/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm b/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm deleted file mode 100644 index cf427d738b..0000000000 --- a/cime_config/usermods_dirs/NEON/NIWO/user_nl_clm +++ /dev/null @@ -1,8 +0,0 @@ -! 20240604 slevis introduced this file to bypass test failures in the -! cnmatrix branch (so cnmatrix on by default) with two izumi tests: -! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO--clm-matrixcnOn -! SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-NIWO -! when the tests point to the default finidat, as documented in this post: -! https://github.com/ESCOMP/CTSM/pull/640#issuecomment-2143101361 -use_init_interp = .true. -finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc' From 628be7bd39fb48acab7a456504be05c424f4510f Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 11 Jun 2024 12:20:30 -0700 Subject: [PATCH 252/408] temporarily update fates to point to latest pull request commit hash --- .gitmodules | 4 ++-- src/fates | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.gitmodules b/.gitmodules index 699ad22969..5b679e62bf 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,7 +1,7 @@ [submodule "fates"] path = src/fates -url = https://github.com/NGEET/fates -fxtag = sci.1.73.0_api.35.0.0 +url = https://github.com/ckoven/fates +fxtag = 4b018eade498d063b21dddf26f77c9658ff80261 fxrequired = AlwaysRequired fxDONOTUSEurl = https://github.com/NCAR/fates-release diff --git a/src/fates b/src/fates index adfa664806..4b018eade4 160000 --- a/src/fates +++ b/src/fates @@ -1 +1 @@ -Subproject commit adfa6648063408d443f5cae671bd37f713d3e3e8 +Subproject commit 4b018eade498d063b21dddf26f77c9658ff80261 From c2f52d19f48f98d97183d447a77b7947b4ab3051 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 13 Jun 2024 13:02:09 -0600 Subject: [PATCH 253/408] Squashed '.lib/git-fleximod/' changes from 4ff1e98de..25ccc15de 25ccc15de Merge tag 'v0.7.8' into tmp-release 8eae7e3fb Bump to 0.7.8 34daa0657 Merge pull request #46 from ESMCI/add_optional_keyword af12c80ca fix spelling 7ea36dc44 remove manage_externals error 2ede18208 add optional to status output git-subtree-dir: .lib/git-fleximod git-subtree-split: 25ccc15de3b2e62554243300e69d44df69a65305 --- git_fleximod/cli.py | 4 ++-- git_fleximod/git_fleximod.py | 10 ++++++---- git_fleximod/utils.py | 12 ++++++------ pyproject.toml | 2 +- tbump.toml | 2 +- tests/conftest.py | 2 +- 6 files changed, 17 insertions(+), 15 deletions(-) diff --git a/git_fleximod/cli.py b/git_fleximod/cli.py index bc099fcbc0..a15a226de4 100644 --- a/git_fleximod/cli.py +++ b/git_fleximod/cli.py @@ -2,7 +2,7 @@ import argparse from git_fleximod import utils -__version__ = "0.7.7" +__version__ = "0.7.8" def find_root_dir(filename=".gitmodules"): """ finds the highest directory in tree @@ -26,7 +26,7 @@ def find_root_dir(filename=".gitmodules"): def get_parser(): description = """ - %(prog)s manages checking out groups of gitsubmodules with addtional support for Earth System Models + %(prog)s manages checking out groups of gitsubmodules with additional support for Earth System Models """ parser = argparse.ArgumentParser( description=description, formatter_class=argparse.RawDescriptionHelpFormatter diff --git a/git_fleximod/git_fleximod.py b/git_fleximod/git_fleximod.py index ca5f90622d..e1b8f484a5 100755 --- a/git_fleximod/git_fleximod.py +++ b/git_fleximod/git_fleximod.py @@ -304,6 +304,7 @@ def submodules_status(gitmodules, root_dir, toplevel=False): ahash = result[0][1:] hhash = None atag = None + needsupdate += 1 if not toplevel and level: continue @@ -316,22 +317,23 @@ def submodules_status(gitmodules, root_dir, toplevel=False): hhash = htag.split()[0] if hhash and atag: break + optional = " (optional)" if required and "Optional" in required else "" if tag and (ahash == hhash or atag == tag): - print(f"e {name:>20} not checked out, aligned at tag {tag}") + print(f"e {name:>20} not checked out, aligned at tag {tag}{optional}") elif tag: ahash = rootgit.git_operation( "submodule", "status", "{}".format(path) ).rstrip() ahash = ahash[1 : len(tag) + 1] if tag == ahash: - print(f"e {name:>20} not checked out, aligned at hash {ahash}") + print(f"e {name:>20} not checked out, aligned at hash {ahash}{optional}") else: print( - f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}" + f"e {name:>20} not checked out, out of sync at tag {atag}, expected tag is {tag}{optional}" ) testfails += 1 else: - print(f"e {name:>20} has no fxtag defined in .gitmodules") + print(f"e {name:>20} has no fxtag defined in .gitmodules{optional}") testfails += 1 else: with utils.pushd(newpath): diff --git a/git_fleximod/utils.py b/git_fleximod/utils.py index 7cc1de38cc..1a2d5ccf2f 100644 --- a/git_fleximod/utils.py +++ b/git_fleximod/utils.py @@ -241,12 +241,12 @@ def _hanging_msg(working_directory, command): has taken {hanging_sec} seconds. It may be hanging. The command will continue to run, but you may want to abort -manage_externals with ^C and investigate. A possible cause of hangs is -when svn or git require authentication to access a private -repository. On some systems, svn and git requests for authentication -information will not be displayed to the user. In this case, the program -will appear to hang. Ensure you can run svn and git manually and access -all repositories without entering your authentication information. +git-fleximod with ^C and investigate. A possible cause of hangs is git +requires authentication to access a private repository. On some +systems, git requests for authentication information will not +be displayed to the user. In this case, the program will appear to +hang. Ensure you can run git manually and access all +repositories without entering your authentication information. """.format( command=command, diff --git a/pyproject.toml b/pyproject.toml index a316914bf5..5b1332549c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "git-fleximod" -version = "0.7.7" +version = "0.7.8" description = "Extended support for git-submodule and git-sparse-checkout" authors = ["Jim Edwards "] maintainers = ["Jim Edwards "] diff --git a/tbump.toml b/tbump.toml index c22637ccda..c4f7ac96ea 100644 --- a/tbump.toml +++ b/tbump.toml @@ -2,7 +2,7 @@ github_url = "https://github.com/jedwards4b/git-fleximod/" [version] -current = "0.7.7" +current = "0.7.8" # Example of a semver regexp. # Make sure this matches current_version before diff --git a/tests/conftest.py b/tests/conftest.py index 1cc008eb1d..65ee85d23d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -32,7 +32,7 @@ def logger(): "submodule_name": "test_optional", "status1" : "test_optional MPIserial_2.5.0-3-gd82ce7c is out of sync with .gitmodules MPIserial_2.4.0", "status2" : "test_optional at tag MPIserial_2.4.0", - "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0", + "status3" : "test_optional not checked out, out of sync at tag None, expected tag is MPIserial_2.4.0 (optional)", "status4" : "test_optional at tag MPIserial_2.4.0", "gitmodules_content": """ [submodule "test_optional"] From 4deb704ebbfdb2accb099d79f58680c0f8fa4906 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 13 Jun 2024 13:14:02 -0600 Subject: [PATCH 254/408] Update changelog a bit --- doc/ChangeLog | 21 ++++++++++----------- doc/ChangeSum | 2 +- 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 4600af34be..984d6c1c2b 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,14 +1,15 @@ =============================================================== Tag name: ctsm5.2.008 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Fri 07 Jun 2024 01:23:07 PM MDT +Date: Thu 13 Jun 2024 01:13:24 PM MDT One-line Summary: Another update of git-fleximod Purpose and description of changes ---------------------------------- -Just update the gitfleximod subtree to v0.7.7. This fixes an issue in identifying that a tag is out of sync in a submodule. -An issue about recursion on a submodule. Allows untracked files, and fixes a MS Window Memory error. +Just update the gitfleximod subtree to v0.7.8. This fixes an issue in identifying that a tag is out of sync in a submodule. +An issue about recursion on a submodule. Allows untracked files, and fixes a MS Window Memory error. And +also git-fleximod status marks optional submodules, which helps explain why they are marked as not-checked out. Significant changes to scientifically-supported configurations @@ -39,7 +40,7 @@ List of CTSM issues fixed: Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): - doc-builder checkout seems to be required to use "git commit ." at the top level + doc-builder checkout requires use of "git commit ." at the top level Changes to documentation: Tweak some of the documentation around git-fleximod and use submodule rather than external. @@ -50,25 +51,23 @@ NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the [Remove any lines that don't apply. Remove entire section if nothing applies.] -Testing summary: minimual +Testing summary: regular ---------------- [PASS means all tests PASS; OK means tests PASS other than expected fails.] build-namelist tests (if CLMBuildNamelist.pm has changed): - derecho - + derecho - PASS python testing (if python code has changed; see instructions in python/README.md; document testing done): - (any machine) - + derecho - PASS regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- - izumi ------- - - any other testing (give details below): + derecho ----- OK + izumi ------- OK If the tag used for baseline comparisons was NOT the previous tag, note that here: diff --git a/doc/ChangeSum b/doc/ChangeSum index 275c4a5cfa..145279cdf6 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.008 erik 06/07/2024 Another update of git-fleximod + ctsm5.2.008 erik 06/13/2024 Another update of git-fleximod ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems From e947ea3017667327a671adce10942ec2b31c3d3f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 13 Jun 2024 14:27:41 -0600 Subject: [PATCH 255/408] Explicitly allocate arrays to start at 1, since izumi_gnu seems to need that --- src/biogeochem/DustEmisBase.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90 index dbc5729403..ef509add06 100644 --- a/src/biogeochem/DustEmisBase.F90 +++ b/src/biogeochem/DustEmisBase.F90 @@ -184,9 +184,9 @@ subroutine InitAllocate(this, bounds) allocate(this%vlc_trb_3_patch (begp:endp)) ; this%vlc_trb_3_patch (:) = nan allocate(this%vlc_trb_4_patch (begp:endp)) ; this%vlc_trb_4_patch (:) = nan - allocate (this%ovr_src_snk_mss(dst_src_nbr,ndst)) ; this%ovr_src_snk_mss (:,:) = nan - allocate (this%dmt_vwr(ndst)) ; this%dmt_vwr (:) = nan - allocate (this%stk_crc(ndst)) ; this%stk_crc (:) = nan + allocate (this%ovr_src_snk_mss(1:dst_src_nbr,1:ndst)) ; this%ovr_src_snk_mss (:,:) = nan + allocate (this%dmt_vwr(1:ndst)) ; this%dmt_vwr (:) = nan + allocate (this%stk_crc(1:ndst)) ; this%stk_crc (:) = nan end subroutine InitAllocate From d33ef3e5b3e695a627fa23dd4d56e85686794c2c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 3 Jun 2024 12:03:15 -0600 Subject: [PATCH 256/408] Add partial versions of RXCROPMATURITY test. Useful for troubleshooting: * RXCROPMATURITYSKIPRUN skips the build and run phases. * RXCROPMATURITYSKIPBUILD just skips the build phase. It still does the run phase so as to test everything before actual run submission. --- cime_config/SystemTests/rxcropmaturity.py | 444 +---------------- .../SystemTests/rxcropmaturityshared.py | 451 ++++++++++++++++++ .../SystemTests/rxcropmaturityskipbuild.py | 9 + .../SystemTests/rxcropmaturityskiprun.py | 9 + cime_config/config_tests.xml | 20 + 5 files changed, 492 insertions(+), 441 deletions(-) create mode 100644 cime_config/SystemTests/rxcropmaturityshared.py create mode 100644 cime_config/SystemTests/rxcropmaturityskipbuild.py create mode 100644 cime_config/SystemTests/rxcropmaturityskiprun.py diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index acb63bb000..12ec608898 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -1,444 +1,6 @@ -""" -CTSM-specific test that first performs a GDD-generating run, then calls -Python code to generate the maturity requirement file. This is then used -in a sowing+maturity forced run, which finally is tested to ensure -correct behavior. +from rxcropmaturityshared import RXCROPMATURITYSHARED -Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually, -this test should be able to generate its own files at whatever resolution it's -called at. Well, really, the ultimate goal would be to give CLM the files -at the original resolution (for GGCMI phase 3, 0.5°) and have the stream -code do the interpolation. However, that wouldn't act on harvest dates -(which are needed for generate_gdds.py). I could have Python interpolate -those, but this would cause a potential inconsistency. -""" - -import os -import re -import systemtest_utils as stu -import subprocess -from CIME.SystemTests.system_tests_common import SystemTestsCommon -from CIME.XML.standard_module_setup import * -from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files -import shutil, glob - -logger = logging.getLogger(__name__) - - -class RXCROPMATURITY(SystemTestsCommon): - def __init__(self, case): - # initialize an object interface to the SMS system test - SystemTestsCommon.__init__(self, case) - - # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency. - stop_n = self._case.get_value("STOP_N") - stop_option = self._case.get_value("STOP_OPTION") - stop_n_orig = stop_n - stop_option_orig = stop_option - if "nsecond" in stop_option: - stop_n /= 60 - stop_option = "nminutes" - if "nminute" in stop_option: - stop_n /= 60 - stop_option = "nhours" - if "nhour" in stop_option: - stop_n /= 24 - stop_option = "ndays" - if "nday" in stop_option: - stop_n /= 365 - stop_option = "nyears" - if "nmonth" in stop_option: - stop_n /= 12 - stop_option = "nyears" - error_message = None - if "nyear" not in stop_option: - error_message = ( - f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), " - + "nhour(s), nday(s), nmonth(s), or nyear(s)" - ) - elif stop_n < 5: - error_message = ( - "RXCROPMATURITY must be run for at least 5 years; you requested " - + f"{stop_n_orig} {stop_option_orig[1:]}" - ) - if error_message is not None: - logger.error(error_message) - raise RuntimeError(error_message) - - # Get the number of complete years that will be run - self._run_Nyears = int(stop_n) - - # Only allow RXCROPMATURITY to be called with test cropMonthOutput - casebaseid = self._case.get_value("CASEBASEID") - if casebaseid.split("-")[-1] != "cropMonthOutput": - error_message = ( - "Only call RXCROPMATURITY with test cropMonthOutput " - + "to avoid potentially huge sets of daily outputs." - ) - logger.error(error_message) - raise RuntimeError(error_message) - - # Get files with prescribed sowing and harvest dates - self._get_rx_dates() - - # Which conda environment should we use? - self._get_conda_env() +class RXCROPMATURITY(RXCROPMATURITYSHARED): def run_phase(self): - # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't - # want to be saved as baseline. - - # ------------------------------------------------------------------- - # (1) Set up GDD-generating run - # ------------------------------------------------------------------- - # Create clone to be GDD-Generating case - logger.info("RXCROPMATURITY log: cloning setup") - case_rxboth = self._case - caseroot = self._case.get_value("CASEROOT") - clone_path = f"{caseroot}.gddgen" - self._path_gddgen = clone_path - if os.path.exists(self._path_gddgen): - shutil.rmtree(self._path_gddgen) - logger.info("RXCROPMATURITY log: cloning") - case_gddgen = self._case.create_clone(clone_path, keepexe=True) - logger.info("RXCROPMATURITY log: done cloning") - - os.chdir(self._path_gddgen) - self._set_active_case(case_gddgen) - - # Set up stuff that applies to both tests - self._setup_all() - - # Add stuff specific to GDD-Generating run - logger.info("RXCROPMATURITY log: modify user_nl files: generate GDDs") - self._append_to_user_nl_clm( - [ - "generate_crop_gdds = .true.", - "use_mxmat = .false.", - " ", - "! (h2) Daily outputs for GDD generation and figure-making", - "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", - "hist_nhtfrq(3) = -24", - "hist_mfilt(3) = 365", - "hist_type1d_pertape(3) = 'PFTS'", - "hist_dov2xy(3) = .false.", - ] - ) - - # If flanduse_timeseries is defined, we need to make a static version for this test. This - # should have every crop in most of the world. - self._get_flanduse_timeseries_in(case_gddgen) - if self._flanduse_timeseries_in is not None: - - # Download files from the server, if needed - case_gddgen.check_all_input_data() - - # Make custom version of surface file - logger.info("RXCROPMATURITY log: run fsurdat_modifier") - self._run_fsurdat_modifier() - - # ------------------------------------------------------------------- - # (2) Perform GDD-generating run and generate prescribed GDDs file - # ------------------------------------------------------------------- - logger.info("RXCROPMATURITY log: Start GDD-Generating run") - - # As per SSP test: - # "No history files expected, set suffix=None to avoid compare error" - # We *do* expect history files here, but anyway. This works. - self._skip_pnl = False - self.run_indv(suffix=None, st_archive=True) - - self._run_generate_gdds(case_gddgen) - - # ------------------------------------------------------------------- - # (3) Set up and perform Prescribed Calendars run - # ------------------------------------------------------------------- - os.chdir(caseroot) - self._set_active_case(case_rxboth) - - # Set up stuff that applies to both tests - self._setup_all() - - # Add stuff specific to Prescribed Calendars run - logger.info("RXCROPMATURITY log: modify user_nl files: Prescribed Calendars") - self._append_to_user_nl_clm( - [ - "generate_crop_gdds = .false.", - f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", - ] - ) - - self.run_indv() - - # ------------------------------------------------------------------- - # (4) Check Prescribed Calendars run - # ------------------------------------------------------------------- - logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") - self._run_check_rxboth_run() - - # Get sowing and harvest dates for this resolution. - def _get_rx_dates(self): - # Eventually, I want to remove these hard-coded resolutions so that this test can generate - # its own sowing and harvest date files at whatever resolution is requested. - lnd_grid = self._case.get_value("LND_GRID") - input_data_root = self._case.get_value("DIN_LOC_ROOT") - processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed" - if lnd_grid == "10x15": - self._sdatefile = os.path.join( - processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", - ) - self._hdatefile = os.path.join( - processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", - ) - elif lnd_grid == "1.9x2.5": - self._sdatefile = os.path.join( - processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", - ) - self._hdatefile = os.path.join( - processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", - ) - elif lnd_grid == "0.9x1.25": - self._sdatefile = os.path.join( - processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc", - ) - self._hdatefile = os.path.join( - processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc", - ) - else: - error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" - logger.error(error_message) - raise RuntimeError(error_message) - - # Ensure files exist - error_message = None - if not os.path.exists(self._sdatefile): - error_message = f"ERROR: Sowing date file not found: {self._sdatefile}" - elif not os.path.exists(self._hdatefile): - error_message = f"ERROR: Harvest date file not found: {self._sdatefile}" - if error_message is not None: - logger.error(error_message) - raise RuntimeError(error_message) - - def _setup_all(self): - logger.info("RXCROPMATURITY log: _setup_all start") - - # Get some info - self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND") - run_startdate = self._case.get_value("RUN_STARTDATE") - self._run_startyear = int(run_startdate.split("-")[0]) - - # Set sowing dates file (and other crop calendar settings) for all runs - logger.info("RXCROPMATURITY log: modify user_nl files: all tests") - self._modify_user_nl_allruns() - logger.info("RXCROPMATURITY log: _setup_all done") - - # Make a surface dataset that has every crop in every gridcell - def _run_fsurdat_modifier(self): - - # fsurdat should be defined. Where is it? - self._fsurdat_in = None - with open(self._lnd_in_path, "r") as lnd_in: - for line in lnd_in: - fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line) - if fsurdat_in: - self._fsurdat_in = fsurdat_in.group(1) - break - if self._fsurdat_in is None: - error_message = "fsurdat not defined" - logger.error(error_message) - raise RuntimeError(error_message) - - # Where we will save the fsurdat version for this test - path, ext = os.path.splitext(self._fsurdat_in) - dir_in, filename_in_noext = os.path.split(path) - self._fsurdat_out = os.path.join( - self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}" - ) - - # Make fsurdat for this test, if not already done - if not os.path.exists(self._fsurdat_out): - tool_path = os.path.join( - self._ctsm_root, - "tools", - "modify_input_files", - "fsurdat_modifier", - ) - - # Create configuration file for fsurdat_modifier - self._cfg_path = os.path.join( - self._path_gddgen, - "modify_fsurdat_allcropseverywhere.cfg", - ) - self._create_config_file_evenlysplitcrop() - - command = f"python3 {tool_path} {self._cfg_path} " - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - # Modify namelist - logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") - self._append_to_user_nl_clm( - [ - "fsurdat = '{}'".format(self._fsurdat_out), - "do_transient_crops = .false.", - "flanduse_timeseries = ''", - "use_init_interp = .true.", - ] - ) - - def _create_config_file_evenlysplitcrop(self): - """ - Open the new and the template .cfg files - Loop line by line through the template .cfg file - When string matches, replace that line's content - """ - cfg_template_path = os.path.join( - self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg" - ) - - with open(self._cfg_path, "w", encoding="utf-8") as cfg_out: - # Copy template, replacing some lines - with open(cfg_template_path, "r", encoding="utf-8") as cfg_in: - for line in cfg_in: - if re.match(r" *evenly_split_cropland *=", line): - line = f"evenly_split_cropland = True" - elif re.match(r" *fsurdat_in *=", line): - line = f"fsurdat_in = {self._fsurdat_in}" - elif re.match(r" *fsurdat_out *=", line): - line = f"fsurdat_out = {self._fsurdat_out}" - elif re.match(r" *process_subgrid_section *=", line): - line = f"process_subgrid_section = True" - cfg_out.write(line) - - # Add new lines - cfg_out.write("\n") - cfg_out.write("[modify_fsurdat_subgrid_fractions]\n") - cfg_out.write("PCT_CROP = 100.0\n") - cfg_out.write("PCT_NATVEG = 0.0\n") - cfg_out.write("PCT_GLACIER = 0.0\n") - cfg_out.write("PCT_WETLAND = 0.0\n") - cfg_out.write("PCT_LAKE = 0.0\n") - cfg_out.write("PCT_OCEAN = 0.0\n") - cfg_out.write("PCT_URBAN = 0.0 0.0 0.0\n") - - def _run_check_rxboth_run(self): - - output_dir = os.path.join(self._get_caseroot(), "run") - first_usable_year = self._run_startyear + 2 - last_usable_year = self._run_startyear + self._run_Nyears - 2 - - tool_path = os.path.join( - self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py" - ) - command = ( - f"python3 {tool_path} " - + f"--directory {output_dir} " - + f"-y1 {first_usable_year} " - + f"-yN {last_usable_year} " - + f"--rx-sdates-file {self._sdatefile} " - + f"--rx-gdds-file {self._gdds_file} " - ) - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - def _modify_user_nl_allruns(self): - nl_additions = [ - "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")), - "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile), - "stream_fldFileName_swindow_end = '{}'".format(self._sdatefile), - "stream_year_first_cropcal = 2000", - "stream_year_last_cropcal = 2000", - "model_year_align_cropcal = 2000", - " ", - "! (h1) Annual outputs on sowing or harvest axis", - "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", - "hist_nhtfrq(2) = 17520", - "hist_mfilt(2) = 999", - "hist_type1d_pertape(2) = 'PFTS'", - "hist_dov2xy(2) = .false.", - ] - self._append_to_user_nl_clm(nl_additions) - - def _run_generate_gdds(self, case_gddgen): - self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out") - os.makedirs(self._generate_gdds_dir) - - # Get arguments to generate_gdds.py - dout_sr = case_gddgen.get_value("DOUT_S_ROOT") - input_dir = os.path.join(dout_sr, "lnd", "hist") - first_season = self._run_startyear + 2 - last_season = self._run_startyear + self._run_Nyears - 2 - sdates_file = self._sdatefile - hdates_file = self._hdatefile - - # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds. - tool_path = os.path.join( - self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py" - ) - command = " ".join( - [ - f"python3 {tool_path}", - f"--input-dir {input_dir}", - f"--first-season {first_season}", - f"--last-season {last_season}", - f"--sdates-file {sdates_file}", - f"--hdates-file {hdates_file}", - f"--output-dir generate_gdds_out", - f"--skip-crops miscanthus,irrigated_miscanthus", - ] - ) - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - # Where were the prescribed maturity requirements saved? - generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) - if len(generated_gdd_files) != 1: - error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" - logger.error(error_message) - raise RuntimeError(error_message) - self._gdds_file = generated_gdd_files[0] - - def _get_conda_env(self): - conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot()) - - # If npl conda environment is available, use that (It has dask, which - # enables chunking, which makes reading daily 1-degree netCDF files - # much more efficient. - if "npl " in os.popen(conda_setup_commands + "conda env list").read(): - self._this_conda_env = "npl" - else: - self._this_conda_env = "ctsm_pylib" - - def _append_to_user_nl_clm(self, additions): - caseroot = self._get_caseroot() - append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions) - - # Is flanduse_timeseries defined? If so, where is it? - def _get_flanduse_timeseries_in(self, case): - case.create_namelists(component="lnd") - self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in") - self._flanduse_timeseries_in = None - with open(self._lnd_in_path, "r") as lnd_in: - for line in lnd_in: - flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) - if flanduse_timeseries_in: - self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) - break + self._run_phase() diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py new file mode 100644 index 0000000000..6b3a3191de --- /dev/null +++ b/cime_config/SystemTests/rxcropmaturityshared.py @@ -0,0 +1,451 @@ +""" +CTSM-specific test that first performs a GDD-generating run, then calls +Python code to generate the maturity requirement file. This is then used +in a sowing+maturity forced run, which finally is tested to ensure +correct behavior. + +Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually, +this test should be able to generate its own files at whatever resolution it's +called at. Well, really, the ultimate goal would be to give CLM the files +at the original resolution (for GGCMI phase 3, 0.5°) and have the stream +code do the interpolation. However, that wouldn't act on harvest dates +(which are needed for generate_gdds.py). I could have Python interpolate +those, but this would cause a potential inconsistency. + +Note that this is just a parent class. The actual tests are RXCROPMATURITY and +RXCROPMATURITY_SKIPRUN, the latter of which does everything except perform and +check the CTSM runs. +""" + +import os +import re +import systemtest_utils as stu +import subprocess +from CIME.SystemTests.system_tests_common import SystemTestsCommon +from CIME.XML.standard_module_setup import * +from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files +import shutil, glob + +logger = logging.getLogger(__name__) + + +class RXCROPMATURITYSHARED(SystemTestsCommon): + def __init__(self, case): + # initialize an object interface to the SMS system test + SystemTestsCommon.__init__(self, case) + + # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency. + stop_n = self._case.get_value("STOP_N") + stop_option = self._case.get_value("STOP_OPTION") + stop_n_orig = stop_n + stop_option_orig = stop_option + if "nsecond" in stop_option: + stop_n /= 60 + stop_option = "nminutes" + if "nminute" in stop_option: + stop_n /= 60 + stop_option = "nhours" + if "nhour" in stop_option: + stop_n /= 24 + stop_option = "ndays" + if "nday" in stop_option: + stop_n /= 365 + stop_option = "nyears" + if "nmonth" in stop_option: + stop_n /= 12 + stop_option = "nyears" + error_message = None + if "nyear" not in stop_option: + error_message = ( + f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), " + + "nhour(s), nday(s), nmonth(s), or nyear(s)" + ) + elif stop_n < 5: + error_message = ( + "RXCROPMATURITY must be run for at least 5 years; you requested " + + f"{stop_n_orig} {stop_option_orig[1:]}" + ) + if error_message is not None: + logger.error(error_message) + raise RuntimeError(error_message) + + # Get the number of complete years that will be run + self._run_Nyears = int(stop_n) + + # Only allow RXCROPMATURITY to be called with test cropMonthOutput + casebaseid = self._case.get_value("CASEBASEID") + if casebaseid.split("-")[-1] != "cropMonthOutput": + error_message = ( + "Only call RXCROPMATURITY with test cropMonthOutput " + + "to avoid potentially huge sets of daily outputs." + ) + logger.error(error_message) + raise RuntimeError(error_message) + + # Get files with prescribed sowing and harvest dates + self._get_rx_dates() + + # Which conda environment should we use? + self._get_conda_env() + + def _run_phase(self, skip_run=False): + # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't + # want to be saved as baseline. + + # ------------------------------------------------------------------- + # (1) Set up GDD-generating run + # ------------------------------------------------------------------- + # Create clone to be GDD-Generating case + logger.info("RXCROPMATURITY log: cloning setup") + case_rxboth = self._case + caseroot = self._case.get_value("CASEROOT") + clone_path = f"{caseroot}.gddgen" + self._path_gddgen = clone_path + if os.path.exists(self._path_gddgen): + shutil.rmtree(self._path_gddgen) + logger.info("RXCROPMATURITY log: cloning") + case_gddgen = self._case.create_clone(clone_path, keepexe=True) + logger.info("RXCROPMATURITY log: done cloning") + + os.chdir(self._path_gddgen) + self._set_active_case(case_gddgen) + + # Set up stuff that applies to both tests + self._setup_all() + + # Add stuff specific to GDD-Generating run + logger.info("RXCROPMATURITY log: modify user_nl files: generate GDDs") + self._append_to_user_nl_clm( + [ + "generate_crop_gdds = .true.", + "use_mxmat = .false.", + " ", + "! (h2) Daily outputs for GDD generation and figure-making", + "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", + "hist_nhtfrq(3) = -24", + "hist_mfilt(3) = 365", + "hist_type1d_pertape(3) = 'PFTS'", + "hist_dov2xy(3) = .false.", + ] + ) + + # If flanduse_timeseries is defined, we need to make a static version for this test. This + # should have every crop in most of the world. + self._get_flanduse_timeseries_in(case_gddgen) + if self._flanduse_timeseries_in is not None: + + # Download files from the server, if needed + case_gddgen.check_all_input_data() + + # Make custom version of surface file + logger.info("RXCROPMATURITY log: run fsurdat_modifier") + self._run_fsurdat_modifier() + + # ------------------------------------------------------------------- + # (2) Perform GDD-generating run and generate prescribed GDDs file + # ------------------------------------------------------------------- + logger.info("RXCROPMATURITY log: Start GDD-Generating run") + + # As per SSP test: + # "No history files expected, set suffix=None to avoid compare error" + # We *do* expect history files here, but anyway. This works. + self._skip_pnl = False + + if not skip_run: + self.run_indv(suffix=None, st_archive=True) + self._run_generate_gdds(case_gddgen) + + # ------------------------------------------------------------------- + # (3) Set up and perform Prescribed Calendars run + # ------------------------------------------------------------------- + os.chdir(caseroot) + self._set_active_case(case_rxboth) + + # Set up stuff that applies to both tests + self._setup_all() + + # Add stuff specific to Prescribed Calendars run + logger.info("RXCROPMATURITY log: modify user_nl files: Prescribed Calendars") + self._append_to_user_nl_clm( + [ + "generate_crop_gdds = .false.", + f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", + ] + ) + + if not skip_run: + self.run_indv() + + # ------------------------------------------------------------------- + # (4) Check Prescribed Calendars run + # ------------------------------------------------------------------- + logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") + if not skip_run: + self._run_check_rxboth_run() + + # Get sowing and harvest dates for this resolution. + def _get_rx_dates(self): + # Eventually, I want to remove these hard-coded resolutions so that this test can generate + # its own sowing and harvest date files at whatever resolution is requested. + lnd_grid = self._case.get_value("LND_GRID") + input_data_root = self._case.get_value("DIN_LOC_ROOT") + processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed" + if lnd_grid == "10x15": + self._sdatefile = os.path.join( + processed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + ) + self._hdatefile = os.path.join( + processed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + ) + elif lnd_grid == "1.9x2.5": + self._sdatefile = os.path.join( + processed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + ) + self._hdatefile = os.path.join( + processed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + ) + elif lnd_grid == "0.9x1.25": + self._sdatefile = os.path.join( + processed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc", + ) + self._hdatefile = os.path.join( + processed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc", + ) + else: + error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" + logger.error(error_message) + raise RuntimeError(error_message) + + # Ensure files exist + error_message = None + if not os.path.exists(self._sdatefile): + error_message = f"ERROR: Sowing date file not found: {self._sdatefile}" + elif not os.path.exists(self._hdatefile): + error_message = f"ERROR: Harvest date file not found: {self._sdatefile}" + if error_message is not None: + logger.error(error_message) + raise RuntimeError(error_message) + + def _setup_all(self): + logger.info("RXCROPMATURITY log: _setup_all start") + + # Get some info + self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND") + run_startdate = self._case.get_value("RUN_STARTDATE") + self._run_startyear = int(run_startdate.split("-")[0]) + + # Set sowing dates file (and other crop calendar settings) for all runs + logger.info("RXCROPMATURITY log: modify user_nl files: all tests") + self._modify_user_nl_allruns() + logger.info("RXCROPMATURITY log: _setup_all done") + + # Make a surface dataset that has every crop in every gridcell + def _run_fsurdat_modifier(self): + + # fsurdat should be defined. Where is it? + self._fsurdat_in = None + with open(self._lnd_in_path, "r") as lnd_in: + for line in lnd_in: + fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line) + if fsurdat_in: + self._fsurdat_in = fsurdat_in.group(1) + break + if self._fsurdat_in is None: + error_message = "fsurdat not defined" + logger.error(error_message) + raise RuntimeError(error_message) + + # Where we will save the fsurdat version for this test + path, ext = os.path.splitext(self._fsurdat_in) + dir_in, filename_in_noext = os.path.split(path) + self._fsurdat_out = os.path.join( + self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}" + ) + + # Make fsurdat for this test, if not already done + if not os.path.exists(self._fsurdat_out): + tool_path = os.path.join( + self._ctsm_root, + "tools", + "modify_input_files", + "fsurdat_modifier", + ) + + # Create configuration file for fsurdat_modifier + self._cfg_path = os.path.join( + self._path_gddgen, + "modify_fsurdat_allcropseverywhere.cfg", + ) + self._create_config_file_evenlysplitcrop() + + command = f"python3 {tool_path} {self._cfg_path} " + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + + # Modify namelist + logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") + self._append_to_user_nl_clm( + [ + "fsurdat = '{}'".format(self._fsurdat_out), + "do_transient_crops = .false.", + "flanduse_timeseries = ''", + "use_init_interp = .true.", + ] + ) + + def _create_config_file_evenlysplitcrop(self): + """ + Open the new and the template .cfg files + Loop line by line through the template .cfg file + When string matches, replace that line's content + """ + cfg_template_path = os.path.join( + self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg" + ) + + with open(self._cfg_path, "w", encoding="utf-8") as cfg_out: + # Copy template, replacing some lines + with open(cfg_template_path, "r", encoding="utf-8") as cfg_in: + for line in cfg_in: + if re.match(r" *evenly_split_cropland *=", line): + line = f"evenly_split_cropland = True" + elif re.match(r" *fsurdat_in *=", line): + line = f"fsurdat_in = {self._fsurdat_in}" + elif re.match(r" *fsurdat_out *=", line): + line = f"fsurdat_out = {self._fsurdat_out}" + elif re.match(r" *process_subgrid_section *=", line): + line = f"process_subgrid_section = True" + cfg_out.write(line) + + # Add new lines + cfg_out.write("\n") + cfg_out.write("[modify_fsurdat_subgrid_fractions]\n") + cfg_out.write("PCT_CROP = 100.0\n") + cfg_out.write("PCT_NATVEG = 0.0\n") + cfg_out.write("PCT_GLACIER = 0.0\n") + cfg_out.write("PCT_WETLAND = 0.0\n") + cfg_out.write("PCT_LAKE = 0.0\n") + cfg_out.write("PCT_OCEAN = 0.0\n") + cfg_out.write("PCT_URBAN = 0.0 0.0 0.0\n") + + def _run_check_rxboth_run(self): + + output_dir = os.path.join(self._get_caseroot(), "run") + first_usable_year = self._run_startyear + 2 + last_usable_year = self._run_startyear + self._run_Nyears - 2 + + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py" + ) + command = ( + f"python3 {tool_path} " + + f"--directory {output_dir} " + + f"-y1 {first_usable_year} " + + f"-yN {last_usable_year} " + + f"--rx-sdates-file {self._sdatefile} " + + f"--rx-gdds-file {self._gdds_file} " + ) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + + def _modify_user_nl_allruns(self): + nl_additions = [ + "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")), + "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile), + "stream_fldFileName_swindow_end = '{}'".format(self._sdatefile), + "stream_year_first_cropcal = 2000", + "stream_year_last_cropcal = 2000", + "model_year_align_cropcal = 2000", + " ", + "! (h1) Annual outputs on sowing or harvest axis", + "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", + "hist_nhtfrq(2) = 17520", + "hist_mfilt(2) = 999", + "hist_type1d_pertape(2) = 'PFTS'", + "hist_dov2xy(2) = .false.", + ] + self._append_to_user_nl_clm(nl_additions) + + def _run_generate_gdds(self, case_gddgen): + self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out") + os.makedirs(self._generate_gdds_dir) + + # Get arguments to generate_gdds.py + dout_sr = case_gddgen.get_value("DOUT_S_ROOT") + input_dir = os.path.join(dout_sr, "lnd", "hist") + first_season = self._run_startyear + 2 + last_season = self._run_startyear + self._run_Nyears - 2 + sdates_file = self._sdatefile + hdates_file = self._hdatefile + + # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds. + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py" + ) + command = " ".join( + [ + f"python3 {tool_path}", + f"--input-dir {input_dir}", + f"--first-season {first_season}", + f"--last-season {last_season}", + f"--sdates-file {sdates_file}", + f"--hdates-file {hdates_file}", + f"--output-dir generate_gdds_out", + f"--skip-crops miscanthus,irrigated_miscanthus", + ] + ) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + + # Where were the prescribed maturity requirements saved? + generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) + if len(generated_gdd_files) != 1: + error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" + logger.error(error_message) + raise RuntimeError(error_message) + self._gdds_file = generated_gdd_files[0] + + def _get_conda_env(self): + conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot()) + + # If npl conda environment is available, use that (It has dask, which + # enables chunking, which makes reading daily 1-degree netCDF files + # much more efficient. + if "npl " in os.popen(conda_setup_commands + "conda env list").read(): + self._this_conda_env = "npl" + else: + self._this_conda_env = "ctsm_pylib" + + def _append_to_user_nl_clm(self, additions): + caseroot = self._get_caseroot() + append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions) + + # Is flanduse_timeseries defined? If so, where is it? + def _get_flanduse_timeseries_in(self, case): + case.create_namelists(component="lnd") + self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in") + self._flanduse_timeseries_in = None + with open(self._lnd_in_path, "r") as lnd_in: + for line in lnd_in: + flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) + if flanduse_timeseries_in: + self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) + break diff --git a/cime_config/SystemTests/rxcropmaturityskipbuild.py b/cime_config/SystemTests/rxcropmaturityskipbuild.py new file mode 100644 index 0000000000..0e16c757fc --- /dev/null +++ b/cime_config/SystemTests/rxcropmaturityskipbuild.py @@ -0,0 +1,9 @@ +from rxcropmaturityshared import RXCROPMATURITYSHARED + + +class RXCROPMATURITYSKIPBUILD(RXCROPMATURITYSHARED): + def build_indv(self, sharedlib_only=False, model_only=False): + self._case.set_value("BUILD_COMPLETE", "TRUE") + + def run_phase(self): + self._run_phase(skip_run=False) diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py new file mode 100644 index 0000000000..24fc288373 --- /dev/null +++ b/cime_config/SystemTests/rxcropmaturityskiprun.py @@ -0,0 +1,9 @@ +from rxcropmaturityshared import RXCROPMATURITYSHARED + + +class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED): + def build_indv(self, sharedlib_only=False, model_only=False): + self._case.set_value("BUILD_COMPLETE", "TRUE") + + def run_phase(self): + self._run_phase(skip_run=True) diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index c0b6afed9d..115f4c0e89 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -133,6 +133,26 @@ This defines various CTSM-specific system tests $STOP_N + + As RXCROPMATURITY but don't actually run or postprocess; just setup + 1 + FALSE + FALSE + never + $STOP_OPTION + $STOP_N + + + + As RXCROPMATURITY but don't actually build; just setup and then start "run." Will fail when run start is requested, but should successfully test preprocessing. + 1 + FALSE + FALSE + never + $STOP_OPTION + $STOP_N + + .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 37c457141c..1a6a5581a8 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -828,6 +828,11 @@ Toggle to turn on meteorological downscaling in hillslope model Toggle to turn on surface water routing in the hillslope hydrology model + +If true, set fsat to zero for hillslope columns + + Method for calculating hillslope saturated head gradient diff --git a/src/biogeophys/SaturatedExcessRunoffMod.F90 b/src/biogeophys/SaturatedExcessRunoffMod.F90 index 5643a95394..9956a7dfb8 100644 --- a/src/biogeophys/SaturatedExcessRunoffMod.F90 +++ b/src/biogeophys/SaturatedExcessRunoffMod.F90 @@ -12,8 +12,8 @@ module SaturatedExcessRunoffMod use shr_log_mod , only : errMsg => shr_log_errMsg use decompMod , only : bounds_type use abortutils , only : endrun - use clm_varctl , only : iulog, use_vichydro, crop_fsat_equals_zero - use clm_varcon , only : spval + use clm_varctl , only : iulog, use_vichydro, crop_fsat_equals_zero, hillslope_fsat_equals_zero + use clm_varcon , only : spval,ispval use LandunitType , only : landunit_type use landunit_varcon , only : istcrop use ColumnType , only : column_type @@ -266,6 +266,19 @@ subroutine SaturatedExcessRunoff (this, bounds, num_hydrologyc, filter_hydrology end do endif + ! ------------------------------------------------------------------------ + ! Set fsat to zero for upland hillslope columns + ! ------------------------------------------------------------------------ + if (hillslope_fsat_equals_zero) then + do fc = 1, num_hydrologyc + c = filter_hydrologyc(fc) + if(col%is_hillslope_column(c) .and. col%active(c)) then + ! Set fsat to zero for upland columns + if (col%cold(c) /= ispval) fsat(c) = 0._r8 + endif + end do + endif + ! ------------------------------------------------------------------------ ! Compute qflx_sat_excess_surf ! diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 0daedbbb1f..7423b5ad6a 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -414,6 +414,8 @@ module clm_varctl logical, public :: use_hillslope = .false. ! true => use multi-column hillslope hydrology logical, public :: downscale_hillslope_meteorology = .false. ! true => downscale meteorological forcing in hillslope model logical, public :: use_hillslope_routing = .false. ! true => use surface water routing in hillslope hydrology + logical, public :: hillslope_fsat_equals_zero = .false. ! set saturated excess runoff to zero for hillslope columns + !---------------------------------------------------------- ! excess ice physics switch diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 46d9e9958a..cde67aa12a 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -270,6 +270,8 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_hillslope_routing + namelist /clm_inparm/ hillslope_fsat_equals_zero + namelist /clm_inparm/ use_hydrstress namelist /clm_inparm/ use_dynroot @@ -840,6 +842,8 @@ subroutine control_spmd() call mpi_bcast (use_hillslope_routing, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (hillslope_fsat_equals_zero, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -1124,8 +1128,9 @@ subroutine control_print () write(iulog,*) ' land-ice albedos (unitless 0-1) = ', albice write(iulog,*) ' hillslope hydrology = ', use_hillslope - write(iulog,*) ' downscale hillslope meteorology = ', downscale_hillslope_meteorology + write(iulog,*) ' downscale hillslope meteorology = ', downscale_hillslope_meteorology write(iulog,*) ' hillslope routing = ', use_hillslope_routing + write(iulog,*) ' hillslope_fsat_equals_zero = ', hillslope_fsat_equals_zero write(iulog,*) ' pre-defined soil layer structure = ', soil_layerstruct_predefined write(iulog,*) ' user-defined soil layer structure = ', soil_layerstruct_userdefined write(iulog,*) ' user-defined number of soil layers = ', soil_layerstruct_userdefined_nlevsoi From bbd63275549c1ad6cfa51bccacccb01e169772d4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 11:09:53 -0600 Subject: [PATCH 260/408] Add RXCROPMATURITYSKIPGEN test. --- .../SystemTests/rxcropmaturityshared.py | 71 +++++++++++++++++-- .../SystemTests/rxcropmaturityskipgen.py | 7 ++ cime_config/config_tests.xml | 10 +++ 3 files changed, 81 insertions(+), 7 deletions(-) create mode 100644 cime_config/SystemTests/rxcropmaturityskipgen.py diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py index 0fc8a91cc2..991fe687b5 100644 --- a/cime_config/SystemTests/rxcropmaturityshared.py +++ b/cime_config/SystemTests/rxcropmaturityshared.py @@ -24,6 +24,7 @@ from CIME.SystemTests.system_tests_common import SystemTestsCommon from CIME.XML.standard_module_setup import * from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files +from CIME.case import Case import shutil, glob logger = logging.getLogger(__name__) @@ -34,6 +35,11 @@ def __init__(self, case): # initialize an object interface to the SMS system test SystemTestsCommon.__init__(self, case) + # Is this a real RXCROPMATURITY test or not? + casebaseid = self._case.get_value("CASEBASEID") + full_test = "RXCROPMATURITY_" in casebaseid + skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid + # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency. stop_n = self._case.get_value("STOP_N") stop_option = self._case.get_value("STOP_OPTION") @@ -60,11 +66,17 @@ def __init__(self, case): f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), " + "nhour(s), nday(s), nmonth(s), or nyear(s)" ) - elif stop_n < 5: + elif full_test and stop_n < 5: error_message = ( "RXCROPMATURITY must be run for at least 5 years; you requested " + f"{stop_n_orig} {stop_option_orig[1:]}" ) + elif skipgen_test and stop_n < 3: + # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish. + error_message = ( + "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested " + + f"{stop_n_orig} {stop_option_orig[1:]}" + ) if error_message is not None: logger.error(error_message) raise RuntimeError(error_message) @@ -73,7 +85,6 @@ def __init__(self, case): self._run_Nyears = int(stop_n) # Only allow RXCROPMATURITY to be called with test cropMonthOutput - casebaseid = self._case.get_value("CASEBASEID") if casebaseid.split("-")[-1] != "cropMonthOutput": error_message = ( "Only call RXCROPMATURITY with test cropMonthOutput " @@ -85,10 +96,17 @@ def __init__(self, case): # Get files with prescribed sowing and harvest dates self._get_rx_dates() + # Get cultivar maturity requirement file to fall back on if not generating it here + self._gdds_file = None + self._fallback_gdds_file = os.path.join( + os.path.dirname(self._sdatefile), + "gdds_20230829_161011.nc" + ) + # Which conda environment should we use? self._get_conda_env() - def _run_phase(self, skip_run=False): + def _run_phase(self, skip_run=False, skip_gen=False): # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't # want to be saved as baseline. @@ -157,8 +175,18 @@ def _run_phase(self, skip_run=False): # We *do* expect history files here, but anyway. This works. self._skip_pnl = False + # If not generating GDDs, only run a few days of this. + if skip_gen: + with Case(self._path_gddgen, read_only=False) as case: + case.set_value("STOP_N", 5) + case.set_value("STOP_OPTION", "ndays") + if not skip_run: self.run_indv(suffix=None, st_archive=True) + if skip_gen: + # Interpolate an existing GDD file. Needed to check obedience to GDD inputs. + self._run_interpolate_gdds() + else: self._run_generate_gdds(case_gddgen) # ------------------------------------------------------------------- @@ -187,7 +215,7 @@ def _run_phase(self, skip_run=False): # ------------------------------------------------------------------- logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") if not skip_run: - self._run_check_rxboth_run() + self._run_check_rxboth_run(skip_gen) # Get sowing and harvest dates for this resolution. def _get_rx_dates(self): @@ -344,11 +372,16 @@ def _create_config_file_evenlysplitcrop(self): cfg_out.write("PCT_OCEAN = 0.0\n") cfg_out.write("PCT_URBAN = 0.0 0.0 0.0\n") - def _run_check_rxboth_run(self): + def _run_check_rxboth_run(self, skip_gen): output_dir = os.path.join(self._get_caseroot(), "run") - first_usable_year = self._run_startyear + 2 - last_usable_year = self._run_startyear + self._run_Nyears - 2 + + if skip_gen: + first_usable_year = self._run_startyear + 1 + last_usable_year = first_usable_year + else: + first_usable_year = self._run_startyear + 2 + last_usable_year = self._run_startyear + self._run_Nyears - 2 tool_path = os.path.join( self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py" @@ -429,6 +462,30 @@ def _run_generate_gdds(self, case_gddgen): raise RuntimeError(error_message) self._gdds_file = generated_gdd_files[0] + def _run_interpolate_gdds(self): + # Save where? + self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc") + + # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds. + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py" + ) + command = " ".join( + [ + f"python3 {tool_path}", + f"--input-file {self._fallback_gdds_file}", + f"--target-file {self._sdatefile}", + f"--output-file {self._gdds_file}", + "--overwrite", + ] + ) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + def _get_conda_env(self): conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot()) diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py new file mode 100644 index 0000000000..4fb5257967 --- /dev/null +++ b/cime_config/SystemTests/rxcropmaturityskipgen.py @@ -0,0 +1,7 @@ +from rxcropmaturityshared import RXCROPMATURITYSHARED + + +class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED): + + def run_phase(self): + self._run_phase(skip_run=False, skip_gen=True) diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index 115f4c0e89..cbddc31b8d 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -133,6 +133,16 @@ This defines various CTSM-specific system tests $STOP_N + + As RXCROPMATURITY but don't actually generate GDDs. Allows short testing with existing GDD inputs. + 1 + FALSE + FALSE + never + $STOP_OPTION + $STOP_N + + As RXCROPMATURITY but don't actually run or postprocess; just setup 1 From 6bf99769d28391828b3cf72729ec8b120f0b839f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 15:33:24 -0600 Subject: [PATCH 261/408] interpolate_gdds: nearest-neighbor for safety. --- python/ctsm/crop_calendars/cropcal_module.py | 17 +++++++++++++---- python/ctsm/crop_calendars/interpolate_gdds.py | 18 +++++++++++------- 2 files changed, 24 insertions(+), 11 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 3fe6942f94..d25e16397e 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -13,6 +13,8 @@ from ctsm.crop_calendars.cropcal_constants import DEFAULT_GDD_MIN from ctsm.crop_calendars.import_ds import import_ds +MISSING_RX_GDD_VAL = -1 + def check_and_trim_years(year_1, year_n, ds_in): """ @@ -231,6 +233,13 @@ def import_max_gs_length(paramfile_dir, my_clm_ver, my_clm_subver): return mxmat_dict +def unexpected_negative_rx_gdd(data_array): + """ + Return True if there's a negative value not matching the designated missing value + """ + return np.any((data_array.values < 0) & (data_array.values != MISSING_RX_GDD_VAL)) + + def import_rx_dates(var_prefix, date_infile, dates_ds, set_neg1_to_nan=True): """ Import prescribed sowing/harvest dates @@ -260,19 +269,19 @@ def import_rx_dates(var_prefix, date_infile, dates_ds, set_neg1_to_nan=True): v_new = var.replace(var_prefix, "gs") this_ds = this_ds.rename({var: v_new}) - # Set -1 prescribed GDD values to NaN. Only warn the first time. + # Set GDD values matching MISSING_RX_GDD_VAL to NaN. Only warn the first time. if ( set_neg1_to_nan and var_prefix == "gdd" and v_new != var and np.any(this_ds[v_new].values < 0) ): - if np.any((this_ds[v_new].values < 0) & (this_ds[v_new].values != -1)): + if unexpected_negative_rx_gdd(this_ds[v_new]): raise RuntimeError(f"Unexpected negative value in {var}") if not did_warn: - print("Setting -1 rx GDD values to NaN") + print(f"Setting {MISSING_RX_GDD_VAL} rx GDD values to NaN") did_warn = True - this_ds[v_new] = this_ds[v_new].where(this_ds[v_new] != -1) + this_ds[v_new] = this_ds[v_new].where(this_ds[v_new] != MISSING_RX_GDD_VAL) return this_ds diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py index b740766d3b..e9491480e9 100755 --- a/python/ctsm/crop_calendars/interpolate_gdds.py +++ b/python/ctsm/crop_calendars/interpolate_gdds.py @@ -13,6 +13,9 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm import ctsm_logging # pylint: disable=wrong-import-position +from ctsm.crop_calendars.cropcal_module import ( # pylint: disable=wrong-import-position + unexpected_negative_rx_gdd, +) logger = logging.getLogger(__name__) @@ -113,13 +116,14 @@ def interpolate_gdds(args): continue # Interpolate - da_in = ds_in[var] - da_out = ds_in[var].interp_like(ds_target) - - # Ensure minimum GDD is respected - min_allowed = min(0, da_in.min()) - da_out = da_out.where(da_out >= min_allowed) - da_out = da_out.fillna(min_allowed) + da_out = ds_in[var].interp_like( + ds_target, + method="nearest", + kwargs={"fill_value": "extrapolate"}, # Otherwise you get NaNs at edges + ) + + if unexpected_negative_rx_gdd(da_out): + raise RuntimeError("Unexpected negative value") # Add to dataset ds_out[var] = da_out From e286f37c3ac736ad4c9b48967f705975c8ecf8fa Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 15:39:44 -0600 Subject: [PATCH 262/408] Add RXCROPMATURITYSKIPGEN test to aux_clm. Also adds rxcropmaturity test suite with that and a coarse version of the existing RXCROPMATURITY test. So: * RXCROPMATURITY_Lm61.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput * RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHistClm50BgcCrop.derecho_intel.clm-cropMonthOutput --- cime_config/testdefs/testlist_clm.xml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index c2a90507ba..432f8e3e9a 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3636,6 +3636,27 @@ + + + + + + + + + + + + + + + + + + + + + From 6f59eab9d04c93b0e67d5b2837ca3b71fd148ba3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 15:45:26 -0600 Subject: [PATCH 263/408] Remove RXCROPMATURITY SKIPRUN and SKIPBUILD tests. --- .../SystemTests/rxcropmaturityskipbuild.py | 9 --------- .../SystemTests/rxcropmaturityskiprun.py | 9 --------- cime_config/config_tests.xml | 20 ------------------- 3 files changed, 38 deletions(-) delete mode 100644 cime_config/SystemTests/rxcropmaturityskipbuild.py delete mode 100644 cime_config/SystemTests/rxcropmaturityskiprun.py diff --git a/cime_config/SystemTests/rxcropmaturityskipbuild.py b/cime_config/SystemTests/rxcropmaturityskipbuild.py deleted file mode 100644 index 0e16c757fc..0000000000 --- a/cime_config/SystemTests/rxcropmaturityskipbuild.py +++ /dev/null @@ -1,9 +0,0 @@ -from rxcropmaturityshared import RXCROPMATURITYSHARED - - -class RXCROPMATURITYSKIPBUILD(RXCROPMATURITYSHARED): - def build_indv(self, sharedlib_only=False, model_only=False): - self._case.set_value("BUILD_COMPLETE", "TRUE") - - def run_phase(self): - self._run_phase(skip_run=False) diff --git a/cime_config/SystemTests/rxcropmaturityskiprun.py b/cime_config/SystemTests/rxcropmaturityskiprun.py deleted file mode 100644 index 24fc288373..0000000000 --- a/cime_config/SystemTests/rxcropmaturityskiprun.py +++ /dev/null @@ -1,9 +0,0 @@ -from rxcropmaturityshared import RXCROPMATURITYSHARED - - -class RXCROPMATURITYSKIPRUN(RXCROPMATURITYSHARED): - def build_indv(self, sharedlib_only=False, model_only=False): - self._case.set_value("BUILD_COMPLETE", "TRUE") - - def run_phase(self): - self._run_phase(skip_run=True) diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index cbddc31b8d..5c5bdc2892 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -143,26 +143,6 @@ This defines various CTSM-specific system tests $STOP_N - - As RXCROPMATURITY but don't actually run or postprocess; just setup - 1 - FALSE - FALSE - never - $STOP_OPTION - $STOP_N - - - - As RXCROPMATURITY but don't actually build; just setup and then start "run." Will fail when run start is requested, but should successfully test preprocessing. - 1 - FALSE - FALSE - never - $STOP_OPTION - $STOP_N - - - - - PEND - #2460 - - - FAIL From dd6e0cb0b8f722c74a6819b48ff4ec534fbc7a87 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 15:50:47 -0600 Subject: [PATCH 265/408] Move RXCROPMATURITYSHARED into rxcropmaturity.py. --- cime_config/SystemTests/rxcropmaturity.py | 511 ++++++++++++++++- .../SystemTests/rxcropmaturityshared.py | 514 ------------------ .../SystemTests/rxcropmaturityskipgen.py | 2 +- 3 files changed, 511 insertions(+), 516 deletions(-) delete mode 100644 cime_config/SystemTests/rxcropmaturityshared.py diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 12ec608898..e0f6f4df21 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -1,4 +1,513 @@ -from rxcropmaturityshared import RXCROPMATURITYSHARED +""" +CTSM-specific test that first performs a GDD-generating run, then calls +Python code to generate the maturity requirement file. This is then used +in a sowing+maturity forced run, which finally is tested to ensure +correct behavior. + +Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually, +this test should be able to generate its own files at whatever resolution it's +called at. Well, really, the ultimate goal would be to give CLM the files +at the original resolution (for GGCMI phase 3, 0.5°) and have the stream +code do the interpolation. However, that wouldn't act on harvest dates +(which are needed for generate_gdds.py). I could have Python interpolate +those, but this would cause a potential inconsistency. +""" + +import os +import re +import systemtest_utils as stu +import subprocess +from CIME.SystemTests.system_tests_common import SystemTestsCommon +from CIME.XML.standard_module_setup import * +from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files +from CIME.case import Case +import shutil, glob + +logger = logging.getLogger(__name__) + + +class RXCROPMATURITYSHARED(SystemTestsCommon): + def __init__(self, case): + # initialize an object interface to the SMS system test + SystemTestsCommon.__init__(self, case) + + # Is this a real RXCROPMATURITY test or not? + casebaseid = self._case.get_value("CASEBASEID") + full_test = "RXCROPMATURITY_" in casebaseid + skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid + + # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency. + stop_n = self._case.get_value("STOP_N") + stop_option = self._case.get_value("STOP_OPTION") + stop_n_orig = stop_n + stop_option_orig = stop_option + if "nsecond" in stop_option: + stop_n /= 60 + stop_option = "nminutes" + if "nminute" in stop_option: + stop_n /= 60 + stop_option = "nhours" + if "nhour" in stop_option: + stop_n /= 24 + stop_option = "ndays" + if "nday" in stop_option: + stop_n /= 365 + stop_option = "nyears" + if "nmonth" in stop_option: + stop_n /= 12 + stop_option = "nyears" + error_message = None + if "nyear" not in stop_option: + error_message = ( + f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), " + + "nhour(s), nday(s), nmonth(s), or nyear(s)" + ) + elif full_test and stop_n < 5: + error_message = ( + "RXCROPMATURITY must be run for at least 5 years; you requested " + + f"{stop_n_orig} {stop_option_orig[1:]}" + ) + elif skipgen_test and stop_n < 3: + # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish. + error_message = ( + "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested " + + f"{stop_n_orig} {stop_option_orig[1:]}" + ) + if error_message is not None: + logger.error(error_message) + raise RuntimeError(error_message) + + # Get the number of complete years that will be run + self._run_Nyears = int(stop_n) + + # Only allow RXCROPMATURITY to be called with test cropMonthOutput + if casebaseid.split("-")[-1] != "cropMonthOutput": + error_message = ( + "Only call RXCROPMATURITY with test cropMonthOutput " + + "to avoid potentially huge sets of daily outputs." + ) + logger.error(error_message) + raise RuntimeError(error_message) + + # Get files with prescribed sowing and harvest dates + self._get_rx_dates() + + # Get cultivar maturity requirement file to fall back on if not generating it here + self._gdds_file = None + self._fallback_gdds_file = os.path.join( + os.path.dirname(self._sdatefile), + "gdds_20230829_161011.nc" + ) + + # Which conda environment should we use? + self._get_conda_env() + + def _run_phase(self, skip_run=False, skip_gen=False): + # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't + # want to be saved as baseline. + + # ------------------------------------------------------------------- + # (1) Set up GDD-generating run + # ------------------------------------------------------------------- + # Create clone to be GDD-Generating case + logger.info("RXCROPMATURITY log: cloning setup") + case_rxboth = self._case + caseroot = self._case.get_value("CASEROOT") + clone_path = f"{caseroot}.gddgen" + self._path_gddgen = clone_path + if os.path.exists(self._path_gddgen): + shutil.rmtree(self._path_gddgen) + logger.info("RXCROPMATURITY log: cloning") + case_gddgen = self._case.create_clone(clone_path, keepexe=True) + logger.info("RXCROPMATURITY log: done cloning") + + os.chdir(self._path_gddgen) + self._set_active_case(case_gddgen) + + # Set up stuff that applies to both tests + self._setup_all() + + # Add stuff specific to GDD-Generating run + logger.info("RXCROPMATURITY log: modify user_nl files: generate GDDs") + self._append_to_user_nl_clm( + [ + "generate_crop_gdds = .true.", + "use_mxmat = .false.", + " ", + "! (h2) Daily outputs for GDD generation and figure-making", + "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", + "hist_nhtfrq(3) = -24", + "hist_mfilt(3) = 365", + "hist_type1d_pertape(3) = 'PFTS'", + "hist_dov2xy(3) = .false.", + ] + ) + + # If flanduse_timeseries is defined, we need to make a static version for this test. This + # should have every crop in most of the world. + self._get_flanduse_timeseries_in(case_gddgen) + if self._flanduse_timeseries_in is not None: + + # Download files from the server, if needed + case_gddgen.check_all_input_data() + + # Copy needed file from original to gddgen directory + shutil.copyfile( + os.path.join(caseroot, ".env_mach_specific.sh"), + os.path.join(self._path_gddgen, ".env_mach_specific.sh"), + ) + + # Make custom version of surface file + logger.info("RXCROPMATURITY log: run fsurdat_modifier") + self._run_fsurdat_modifier() + + # ------------------------------------------------------------------- + # (2) Perform GDD-generating run and generate prescribed GDDs file + # ------------------------------------------------------------------- + logger.info("RXCROPMATURITY log: Start GDD-Generating run") + + # As per SSP test: + # "No history files expected, set suffix=None to avoid compare error" + # We *do* expect history files here, but anyway. This works. + self._skip_pnl = False + + # If not generating GDDs, only run a few days of this. + if skip_gen: + with Case(self._path_gddgen, read_only=False) as case: + case.set_value("STOP_N", 5) + case.set_value("STOP_OPTION", "ndays") + + if not skip_run: + self.run_indv(suffix=None, st_archive=True) + if skip_gen: + # Interpolate an existing GDD file. Needed to check obedience to GDD inputs. + self._run_interpolate_gdds() + else: + self._run_generate_gdds(case_gddgen) + + # ------------------------------------------------------------------- + # (3) Set up and perform Prescribed Calendars run + # ------------------------------------------------------------------- + os.chdir(caseroot) + self._set_active_case(case_rxboth) + + # Set up stuff that applies to both tests + self._setup_all() + + # Add stuff specific to Prescribed Calendars run + logger.info("RXCROPMATURITY log: modify user_nl files: Prescribed Calendars") + self._append_to_user_nl_clm( + [ + "generate_crop_gdds = .false.", + f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", + ] + ) + + if not skip_run: + self.run_indv() + + # ------------------------------------------------------------------- + # (4) Check Prescribed Calendars run + # ------------------------------------------------------------------- + logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") + if not skip_run: + self._run_check_rxboth_run(skip_gen) + + # Get sowing and harvest dates for this resolution. + def _get_rx_dates(self): + # Eventually, I want to remove these hard-coded resolutions so that this test can generate + # its own sowing and harvest date files at whatever resolution is requested. + lnd_grid = self._case.get_value("LND_GRID") + input_data_root = self._case.get_value("DIN_LOC_ROOT") + processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed" + if lnd_grid == "10x15": + self._sdatefile = os.path.join( + processed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + ) + self._hdatefile = os.path.join( + processed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + ) + elif lnd_grid == "1.9x2.5": + self._sdatefile = os.path.join( + processed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + ) + self._hdatefile = os.path.join( + processed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + ) + elif lnd_grid == "0.9x1.25": + self._sdatefile = os.path.join( + processed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc", + ) + self._hdatefile = os.path.join( + processed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc", + ) + else: + error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" + logger.error(error_message) + raise RuntimeError(error_message) + + # Ensure files exist + error_message = None + if not os.path.exists(self._sdatefile): + error_message = f"ERROR: Sowing date file not found: {self._sdatefile}" + elif not os.path.exists(self._hdatefile): + error_message = f"ERROR: Harvest date file not found: {self._sdatefile}" + if error_message is not None: + logger.error(error_message) + raise RuntimeError(error_message) + + def _setup_all(self): + logger.info("RXCROPMATURITY log: _setup_all start") + + # Get some info + self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND") + run_startdate = self._case.get_value("RUN_STARTDATE") + self._run_startyear = int(run_startdate.split("-")[0]) + + # Set sowing dates file (and other crop calendar settings) for all runs + logger.info("RXCROPMATURITY log: modify user_nl files: all tests") + self._modify_user_nl_allruns() + logger.info("RXCROPMATURITY log: _setup_all done") + + # Make a surface dataset that has every crop in every gridcell + def _run_fsurdat_modifier(self): + + # fsurdat should be defined. Where is it? + self._fsurdat_in = None + with open(self._lnd_in_path, "r") as lnd_in: + for line in lnd_in: + fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line) + if fsurdat_in: + self._fsurdat_in = fsurdat_in.group(1) + break + if self._fsurdat_in is None: + error_message = "fsurdat not defined" + logger.error(error_message) + raise RuntimeError(error_message) + + # Where we will save the fsurdat version for this test + path, ext = os.path.splitext(self._fsurdat_in) + dir_in, filename_in_noext = os.path.split(path) + self._fsurdat_out = os.path.join( + self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}" + ) + + # Make fsurdat for this test, if not already done + if not os.path.exists(self._fsurdat_out): + tool_path = os.path.join( + self._ctsm_root, + "tools", + "modify_input_files", + "fsurdat_modifier", + ) + + # Create configuration file for fsurdat_modifier + self._cfg_path = os.path.join( + self._path_gddgen, + "modify_fsurdat_allcropseverywhere.cfg", + ) + self._create_config_file_evenlysplitcrop() + + command = f"python3 {tool_path} {self._cfg_path} " + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + + # Modify namelist + logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") + self._append_to_user_nl_clm( + [ + "fsurdat = '{}'".format(self._fsurdat_out), + "do_transient_crops = .false.", + "flanduse_timeseries = ''", + "use_init_interp = .true.", + ] + ) + + def _create_config_file_evenlysplitcrop(self): + """ + Open the new and the template .cfg files + Loop line by line through the template .cfg file + When string matches, replace that line's content + """ + cfg_template_path = os.path.join( + self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg" + ) + + with open(self._cfg_path, "w", encoding="utf-8") as cfg_out: + # Copy template, replacing some lines + with open(cfg_template_path, "r", encoding="utf-8") as cfg_in: + for line in cfg_in: + if re.match(r" *evenly_split_cropland *=", line): + line = f"evenly_split_cropland = True" + elif re.match(r" *fsurdat_in *=", line): + line = f"fsurdat_in = {self._fsurdat_in}" + elif re.match(r" *fsurdat_out *=", line): + line = f"fsurdat_out = {self._fsurdat_out}" + elif re.match(r" *process_subgrid_section *=", line): + line = f"process_subgrid_section = True" + cfg_out.write(line) + + # Add new lines + cfg_out.write("\n") + cfg_out.write("[modify_fsurdat_subgrid_fractions]\n") + cfg_out.write("PCT_CROP = 100.0\n") + cfg_out.write("PCT_NATVEG = 0.0\n") + cfg_out.write("PCT_GLACIER = 0.0\n") + cfg_out.write("PCT_WETLAND = 0.0\n") + cfg_out.write("PCT_LAKE = 0.0\n") + cfg_out.write("PCT_OCEAN = 0.0\n") + cfg_out.write("PCT_URBAN = 0.0 0.0 0.0\n") + + def _run_check_rxboth_run(self, skip_gen): + + output_dir = os.path.join(self._get_caseroot(), "run") + + if skip_gen: + first_usable_year = self._run_startyear + 1 + last_usable_year = first_usable_year + else: + first_usable_year = self._run_startyear + 2 + last_usable_year = self._run_startyear + self._run_Nyears - 2 + + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py" + ) + command = ( + f"python3 {tool_path} " + + f"--directory {output_dir} " + + f"-y1 {first_usable_year} " + + f"-yN {last_usable_year} " + + f"--rx-sdates-file {self._sdatefile} " + + f"--rx-gdds-file {self._gdds_file} " + ) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + + def _modify_user_nl_allruns(self): + nl_additions = [ + "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")), + "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile), + "stream_fldFileName_swindow_end = '{}'".format(self._sdatefile), + "stream_year_first_cropcal = 2000", + "stream_year_last_cropcal = 2000", + "model_year_align_cropcal = 2000", + " ", + "! (h1) Annual outputs on sowing or harvest axis", + "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", + "hist_nhtfrq(2) = 17520", + "hist_mfilt(2) = 999", + "hist_type1d_pertape(2) = 'PFTS'", + "hist_dov2xy(2) = .false.", + ] + self._append_to_user_nl_clm(nl_additions) + + def _run_generate_gdds(self, case_gddgen): + self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out") + os.makedirs(self._generate_gdds_dir) + + # Get arguments to generate_gdds.py + dout_sr = case_gddgen.get_value("DOUT_S_ROOT") + input_dir = os.path.join(dout_sr, "lnd", "hist") + first_season = self._run_startyear + 2 + last_season = self._run_startyear + self._run_Nyears - 2 + sdates_file = self._sdatefile + hdates_file = self._hdatefile + + # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds. + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py" + ) + command = " ".join( + [ + f"python3 {tool_path}", + f"--input-dir {input_dir}", + f"--first-season {first_season}", + f"--last-season {last_season}", + f"--sdates-file {sdates_file}", + f"--hdates-file {hdates_file}", + f"--output-dir generate_gdds_out", + f"--skip-crops miscanthus,irrigated_miscanthus", + ] + ) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + + # Where were the prescribed maturity requirements saved? + generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) + if len(generated_gdd_files) != 1: + error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" + logger.error(error_message) + raise RuntimeError(error_message) + self._gdds_file = generated_gdd_files[0] + + def _run_interpolate_gdds(self): + # Save where? + self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc") + + # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds. + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py" + ) + command = " ".join( + [ + f"python3 {tool_path}", + f"--input-file {self._fallback_gdds_file}", + f"--target-file {self._sdatefile}", + f"--output-file {self._gdds_file}", + "--overwrite", + ] + ) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + + def _get_conda_env(self): + conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot()) + + # If npl conda environment is available, use that (It has dask, which + # enables chunking, which makes reading daily 1-degree netCDF files + # much more efficient. + if "npl " in os.popen(conda_setup_commands + "conda env list").read(): + self._this_conda_env = "npl" + else: + self._this_conda_env = "ctsm_pylib" + + def _append_to_user_nl_clm(self, additions): + caseroot = self._get_caseroot() + append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions) + + # Is flanduse_timeseries defined? If so, where is it? + def _get_flanduse_timeseries_in(self, case): + case.create_namelists(component="lnd") + self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in") + self._flanduse_timeseries_in = None + with open(self._lnd_in_path, "r") as lnd_in: + for line in lnd_in: + flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) + if flanduse_timeseries_in: + self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) + break class RXCROPMATURITY(RXCROPMATURITYSHARED): diff --git a/cime_config/SystemTests/rxcropmaturityshared.py b/cime_config/SystemTests/rxcropmaturityshared.py deleted file mode 100644 index 991fe687b5..0000000000 --- a/cime_config/SystemTests/rxcropmaturityshared.py +++ /dev/null @@ -1,514 +0,0 @@ -""" -CTSM-specific test that first performs a GDD-generating run, then calls -Python code to generate the maturity requirement file. This is then used -in a sowing+maturity forced run, which finally is tested to ensure -correct behavior. - -Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually, -this test should be able to generate its own files at whatever resolution it's -called at. Well, really, the ultimate goal would be to give CLM the files -at the original resolution (for GGCMI phase 3, 0.5°) and have the stream -code do the interpolation. However, that wouldn't act on harvest dates -(which are needed for generate_gdds.py). I could have Python interpolate -those, but this would cause a potential inconsistency. - -Note that this is just a parent class. The actual tests are RXCROPMATURITY and -RXCROPMATURITY_SKIPRUN, the latter of which does everything except perform and -check the CTSM runs. -""" - -import os -import re -import systemtest_utils as stu -import subprocess -from CIME.SystemTests.system_tests_common import SystemTestsCommon -from CIME.XML.standard_module_setup import * -from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files -from CIME.case import Case -import shutil, glob - -logger = logging.getLogger(__name__) - - -class RXCROPMATURITYSHARED(SystemTestsCommon): - def __init__(self, case): - # initialize an object interface to the SMS system test - SystemTestsCommon.__init__(self, case) - - # Is this a real RXCROPMATURITY test or not? - casebaseid = self._case.get_value("CASEBASEID") - full_test = "RXCROPMATURITY_" in casebaseid - skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid - - # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency. - stop_n = self._case.get_value("STOP_N") - stop_option = self._case.get_value("STOP_OPTION") - stop_n_orig = stop_n - stop_option_orig = stop_option - if "nsecond" in stop_option: - stop_n /= 60 - stop_option = "nminutes" - if "nminute" in stop_option: - stop_n /= 60 - stop_option = "nhours" - if "nhour" in stop_option: - stop_n /= 24 - stop_option = "ndays" - if "nday" in stop_option: - stop_n /= 365 - stop_option = "nyears" - if "nmonth" in stop_option: - stop_n /= 12 - stop_option = "nyears" - error_message = None - if "nyear" not in stop_option: - error_message = ( - f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), " - + "nhour(s), nday(s), nmonth(s), or nyear(s)" - ) - elif full_test and stop_n < 5: - error_message = ( - "RXCROPMATURITY must be run for at least 5 years; you requested " - + f"{stop_n_orig} {stop_option_orig[1:]}" - ) - elif skipgen_test and stop_n < 3: - # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish. - error_message = ( - "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested " - + f"{stop_n_orig} {stop_option_orig[1:]}" - ) - if error_message is not None: - logger.error(error_message) - raise RuntimeError(error_message) - - # Get the number of complete years that will be run - self._run_Nyears = int(stop_n) - - # Only allow RXCROPMATURITY to be called with test cropMonthOutput - if casebaseid.split("-")[-1] != "cropMonthOutput": - error_message = ( - "Only call RXCROPMATURITY with test cropMonthOutput " - + "to avoid potentially huge sets of daily outputs." - ) - logger.error(error_message) - raise RuntimeError(error_message) - - # Get files with prescribed sowing and harvest dates - self._get_rx_dates() - - # Get cultivar maturity requirement file to fall back on if not generating it here - self._gdds_file = None - self._fallback_gdds_file = os.path.join( - os.path.dirname(self._sdatefile), - "gdds_20230829_161011.nc" - ) - - # Which conda environment should we use? - self._get_conda_env() - - def _run_phase(self, skip_run=False, skip_gen=False): - # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't - # want to be saved as baseline. - - # ------------------------------------------------------------------- - # (1) Set up GDD-generating run - # ------------------------------------------------------------------- - # Create clone to be GDD-Generating case - logger.info("RXCROPMATURITY log: cloning setup") - case_rxboth = self._case - caseroot = self._case.get_value("CASEROOT") - clone_path = f"{caseroot}.gddgen" - self._path_gddgen = clone_path - if os.path.exists(self._path_gddgen): - shutil.rmtree(self._path_gddgen) - logger.info("RXCROPMATURITY log: cloning") - case_gddgen = self._case.create_clone(clone_path, keepexe=True) - logger.info("RXCROPMATURITY log: done cloning") - - os.chdir(self._path_gddgen) - self._set_active_case(case_gddgen) - - # Set up stuff that applies to both tests - self._setup_all() - - # Add stuff specific to GDD-Generating run - logger.info("RXCROPMATURITY log: modify user_nl files: generate GDDs") - self._append_to_user_nl_clm( - [ - "generate_crop_gdds = .true.", - "use_mxmat = .false.", - " ", - "! (h2) Daily outputs for GDD generation and figure-making", - "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", - "hist_nhtfrq(3) = -24", - "hist_mfilt(3) = 365", - "hist_type1d_pertape(3) = 'PFTS'", - "hist_dov2xy(3) = .false.", - ] - ) - - # If flanduse_timeseries is defined, we need to make a static version for this test. This - # should have every crop in most of the world. - self._get_flanduse_timeseries_in(case_gddgen) - if self._flanduse_timeseries_in is not None: - - # Download files from the server, if needed - case_gddgen.check_all_input_data() - - # Copy needed file from original to gddgen directory - shutil.copyfile( - os.path.join(caseroot, ".env_mach_specific.sh"), - os.path.join(self._path_gddgen, ".env_mach_specific.sh"), - ) - - # Make custom version of surface file - logger.info("RXCROPMATURITY log: run fsurdat_modifier") - self._run_fsurdat_modifier() - - # ------------------------------------------------------------------- - # (2) Perform GDD-generating run and generate prescribed GDDs file - # ------------------------------------------------------------------- - logger.info("RXCROPMATURITY log: Start GDD-Generating run") - - # As per SSP test: - # "No history files expected, set suffix=None to avoid compare error" - # We *do* expect history files here, but anyway. This works. - self._skip_pnl = False - - # If not generating GDDs, only run a few days of this. - if skip_gen: - with Case(self._path_gddgen, read_only=False) as case: - case.set_value("STOP_N", 5) - case.set_value("STOP_OPTION", "ndays") - - if not skip_run: - self.run_indv(suffix=None, st_archive=True) - if skip_gen: - # Interpolate an existing GDD file. Needed to check obedience to GDD inputs. - self._run_interpolate_gdds() - else: - self._run_generate_gdds(case_gddgen) - - # ------------------------------------------------------------------- - # (3) Set up and perform Prescribed Calendars run - # ------------------------------------------------------------------- - os.chdir(caseroot) - self._set_active_case(case_rxboth) - - # Set up stuff that applies to both tests - self._setup_all() - - # Add stuff specific to Prescribed Calendars run - logger.info("RXCROPMATURITY log: modify user_nl files: Prescribed Calendars") - self._append_to_user_nl_clm( - [ - "generate_crop_gdds = .false.", - f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", - ] - ) - - if not skip_run: - self.run_indv() - - # ------------------------------------------------------------------- - # (4) Check Prescribed Calendars run - # ------------------------------------------------------------------- - logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") - if not skip_run: - self._run_check_rxboth_run(skip_gen) - - # Get sowing and harvest dates for this resolution. - def _get_rx_dates(self): - # Eventually, I want to remove these hard-coded resolutions so that this test can generate - # its own sowing and harvest date files at whatever resolution is requested. - lnd_grid = self._case.get_value("LND_GRID") - input_data_root = self._case.get_value("DIN_LOC_ROOT") - processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed" - if lnd_grid == "10x15": - self._sdatefile = os.path.join( - processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", - ) - self._hdatefile = os.path.join( - processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", - ) - elif lnd_grid == "1.9x2.5": - self._sdatefile = os.path.join( - processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", - ) - self._hdatefile = os.path.join( - processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", - ) - elif lnd_grid == "0.9x1.25": - self._sdatefile = os.path.join( - processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc", - ) - self._hdatefile = os.path.join( - processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc", - ) - else: - error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" - logger.error(error_message) - raise RuntimeError(error_message) - - # Ensure files exist - error_message = None - if not os.path.exists(self._sdatefile): - error_message = f"ERROR: Sowing date file not found: {self._sdatefile}" - elif not os.path.exists(self._hdatefile): - error_message = f"ERROR: Harvest date file not found: {self._sdatefile}" - if error_message is not None: - logger.error(error_message) - raise RuntimeError(error_message) - - def _setup_all(self): - logger.info("RXCROPMATURITY log: _setup_all start") - - # Get some info - self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND") - run_startdate = self._case.get_value("RUN_STARTDATE") - self._run_startyear = int(run_startdate.split("-")[0]) - - # Set sowing dates file (and other crop calendar settings) for all runs - logger.info("RXCROPMATURITY log: modify user_nl files: all tests") - self._modify_user_nl_allruns() - logger.info("RXCROPMATURITY log: _setup_all done") - - # Make a surface dataset that has every crop in every gridcell - def _run_fsurdat_modifier(self): - - # fsurdat should be defined. Where is it? - self._fsurdat_in = None - with open(self._lnd_in_path, "r") as lnd_in: - for line in lnd_in: - fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line) - if fsurdat_in: - self._fsurdat_in = fsurdat_in.group(1) - break - if self._fsurdat_in is None: - error_message = "fsurdat not defined" - logger.error(error_message) - raise RuntimeError(error_message) - - # Where we will save the fsurdat version for this test - path, ext = os.path.splitext(self._fsurdat_in) - dir_in, filename_in_noext = os.path.split(path) - self._fsurdat_out = os.path.join( - self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}" - ) - - # Make fsurdat for this test, if not already done - if not os.path.exists(self._fsurdat_out): - tool_path = os.path.join( - self._ctsm_root, - "tools", - "modify_input_files", - "fsurdat_modifier", - ) - - # Create configuration file for fsurdat_modifier - self._cfg_path = os.path.join( - self._path_gddgen, - "modify_fsurdat_allcropseverywhere.cfg", - ) - self._create_config_file_evenlysplitcrop() - - command = f"python3 {tool_path} {self._cfg_path} " - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - # Modify namelist - logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") - self._append_to_user_nl_clm( - [ - "fsurdat = '{}'".format(self._fsurdat_out), - "do_transient_crops = .false.", - "flanduse_timeseries = ''", - "use_init_interp = .true.", - ] - ) - - def _create_config_file_evenlysplitcrop(self): - """ - Open the new and the template .cfg files - Loop line by line through the template .cfg file - When string matches, replace that line's content - """ - cfg_template_path = os.path.join( - self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg" - ) - - with open(self._cfg_path, "w", encoding="utf-8") as cfg_out: - # Copy template, replacing some lines - with open(cfg_template_path, "r", encoding="utf-8") as cfg_in: - for line in cfg_in: - if re.match(r" *evenly_split_cropland *=", line): - line = f"evenly_split_cropland = True" - elif re.match(r" *fsurdat_in *=", line): - line = f"fsurdat_in = {self._fsurdat_in}" - elif re.match(r" *fsurdat_out *=", line): - line = f"fsurdat_out = {self._fsurdat_out}" - elif re.match(r" *process_subgrid_section *=", line): - line = f"process_subgrid_section = True" - cfg_out.write(line) - - # Add new lines - cfg_out.write("\n") - cfg_out.write("[modify_fsurdat_subgrid_fractions]\n") - cfg_out.write("PCT_CROP = 100.0\n") - cfg_out.write("PCT_NATVEG = 0.0\n") - cfg_out.write("PCT_GLACIER = 0.0\n") - cfg_out.write("PCT_WETLAND = 0.0\n") - cfg_out.write("PCT_LAKE = 0.0\n") - cfg_out.write("PCT_OCEAN = 0.0\n") - cfg_out.write("PCT_URBAN = 0.0 0.0 0.0\n") - - def _run_check_rxboth_run(self, skip_gen): - - output_dir = os.path.join(self._get_caseroot(), "run") - - if skip_gen: - first_usable_year = self._run_startyear + 1 - last_usable_year = first_usable_year - else: - first_usable_year = self._run_startyear + 2 - last_usable_year = self._run_startyear + self._run_Nyears - 2 - - tool_path = os.path.join( - self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py" - ) - command = ( - f"python3 {tool_path} " - + f"--directory {output_dir} " - + f"-y1 {first_usable_year} " - + f"-yN {last_usable_year} " - + f"--rx-sdates-file {self._sdatefile} " - + f"--rx-gdds-file {self._gdds_file} " - ) - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - def _modify_user_nl_allruns(self): - nl_additions = [ - "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")), - "stream_fldFileName_swindow_start = '{}'".format(self._sdatefile), - "stream_fldFileName_swindow_end = '{}'".format(self._sdatefile), - "stream_year_first_cropcal = 2000", - "stream_year_last_cropcal = 2000", - "model_year_align_cropcal = 2000", - " ", - "! (h1) Annual outputs on sowing or harvest axis", - "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", - "hist_nhtfrq(2) = 17520", - "hist_mfilt(2) = 999", - "hist_type1d_pertape(2) = 'PFTS'", - "hist_dov2xy(2) = .false.", - ] - self._append_to_user_nl_clm(nl_additions) - - def _run_generate_gdds(self, case_gddgen): - self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out") - os.makedirs(self._generate_gdds_dir) - - # Get arguments to generate_gdds.py - dout_sr = case_gddgen.get_value("DOUT_S_ROOT") - input_dir = os.path.join(dout_sr, "lnd", "hist") - first_season = self._run_startyear + 2 - last_season = self._run_startyear + self._run_Nyears - 2 - sdates_file = self._sdatefile - hdates_file = self._hdatefile - - # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds. - tool_path = os.path.join( - self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py" - ) - command = " ".join( - [ - f"python3 {tool_path}", - f"--input-dir {input_dir}", - f"--first-season {first_season}", - f"--last-season {last_season}", - f"--sdates-file {sdates_file}", - f"--hdates-file {hdates_file}", - f"--output-dir generate_gdds_out", - f"--skip-crops miscanthus,irrigated_miscanthus", - ] - ) - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - # Where were the prescribed maturity requirements saved? - generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) - if len(generated_gdd_files) != 1: - error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" - logger.error(error_message) - raise RuntimeError(error_message) - self._gdds_file = generated_gdd_files[0] - - def _run_interpolate_gdds(self): - # Save where? - self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc") - - # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds. - tool_path = os.path.join( - self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py" - ) - command = " ".join( - [ - f"python3 {tool_path}", - f"--input-file {self._fallback_gdds_file}", - f"--target-file {self._sdatefile}", - f"--output-file {self._gdds_file}", - "--overwrite", - ] - ) - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - def _get_conda_env(self): - conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot()) - - # If npl conda environment is available, use that (It has dask, which - # enables chunking, which makes reading daily 1-degree netCDF files - # much more efficient. - if "npl " in os.popen(conda_setup_commands + "conda env list").read(): - self._this_conda_env = "npl" - else: - self._this_conda_env = "ctsm_pylib" - - def _append_to_user_nl_clm(self, additions): - caseroot = self._get_caseroot() - append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions) - - # Is flanduse_timeseries defined? If so, where is it? - def _get_flanduse_timeseries_in(self, case): - case.create_namelists(component="lnd") - self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in") - self._flanduse_timeseries_in = None - with open(self._lnd_in_path, "r") as lnd_in: - for line in lnd_in: - flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) - if flanduse_timeseries_in: - self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) - break diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py index 4fb5257967..7b836a7b17 100644 --- a/cime_config/SystemTests/rxcropmaturityskipgen.py +++ b/cime_config/SystemTests/rxcropmaturityskipgen.py @@ -1,4 +1,4 @@ -from rxcropmaturityshared import RXCROPMATURITYSHARED +from rxcropmaturity import RXCROPMATURITYSHARED class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED): From 6c5fdb1d735531f8aaf129420448b2ac1d635a4c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 15:56:50 -0600 Subject: [PATCH 266/408] Remove refs to skip_run. --- cime_config/SystemTests/rxcropmaturity.py | 11 ++++------- cime_config/SystemTests/rxcropmaturityskipgen.py | 2 +- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index e0f6f4df21..cffb832e8d 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -102,7 +102,7 @@ def __init__(self, case): # Which conda environment should we use? self._get_conda_env() - def _run_phase(self, skip_run=False, skip_gen=False): + def _run_phase(self, skip_gen=False): # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't # want to be saved as baseline. @@ -177,8 +177,7 @@ def _run_phase(self, skip_run=False, skip_gen=False): case.set_value("STOP_N", 5) case.set_value("STOP_OPTION", "ndays") - if not skip_run: - self.run_indv(suffix=None, st_archive=True) + self.run_indv(suffix=None, st_archive=True) if skip_gen: # Interpolate an existing GDD file. Needed to check obedience to GDD inputs. self._run_interpolate_gdds() @@ -203,15 +202,13 @@ def _run_phase(self, skip_run=False, skip_gen=False): ] ) - if not skip_run: - self.run_indv() + self.run_indv() # ------------------------------------------------------------------- # (4) Check Prescribed Calendars run # ------------------------------------------------------------------- logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") - if not skip_run: - self._run_check_rxboth_run(skip_gen) + self._run_check_rxboth_run(skip_gen) # Get sowing and harvest dates for this resolution. def _get_rx_dates(self): diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py index 7b836a7b17..4feb661037 100644 --- a/cime_config/SystemTests/rxcropmaturityskipgen.py +++ b/cime_config/SystemTests/rxcropmaturityskipgen.py @@ -4,4 +4,4 @@ class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED): def run_phase(self): - self._run_phase(skip_run=False, skip_gen=True) + self._run_phase(skip_gen=True) From 3efa49aec741b01d324b2236ca347fa4d4bf349f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 17:02:16 -0600 Subject: [PATCH 267/408] Unexpected behavior in rxboth run now errors check_rxboth_run.py. --- .../crop_calendars/check_constant_vars.py | 2 +- python/ctsm/crop_calendars/check_rx_obeyed.py | 5 +++++ .../ctsm/crop_calendars/check_rxboth_run.py | 19 +++++++++++++++---- python/ctsm/crop_calendars/cropcal_module.py | 10 ++++++++-- 4 files changed, 29 insertions(+), 7 deletions(-) diff --git a/python/ctsm/crop_calendars/check_constant_vars.py b/python/ctsm/crop_calendars/check_constant_vars.py index aa25a412fe..be7718256a 100644 --- a/python/ctsm/crop_calendars/check_constant_vars.py +++ b/python/ctsm/crop_calendars/check_constant_vars.py @@ -382,4 +382,4 @@ def check_constant_vars( raise RuntimeError("Stopping due to failed check_constant_vars().") bad_patches = np.unique(bad_patches) - return [int(p) for p in bad_patches] + return [int(p) for p in bad_patches], any_bad diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py index 99b8d80bde..8525f3e890 100644 --- a/python/ctsm/crop_calendars/check_rx_obeyed.py +++ b/python/ctsm/crop_calendars/check_rx_obeyed.py @@ -203,9 +203,12 @@ def check_rx_obeyed( else: break + bad = True if all_ok == 2: + bad = False print(f"✅ {which_ds}: Prescribed {output_var} always obeyed") elif all_ok == 1: + bad = False # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:") # for x in diff_str_list: print(x) print( @@ -214,3 +217,5 @@ def check_rx_obeyed( ) elif not verbose: print(f"⌠{which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}") + + return bad diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py index ae4decde30..8f416e9f8e 100644 --- a/python/ctsm/crop_calendars/check_rxboth_run.py +++ b/python/ctsm/crop_calendars/check_rxboth_run.py @@ -75,6 +75,8 @@ def main(argv): "HARVEST_REASON_PERHARV", ] + any_bad = False + annual_outfiles = glob.glob(os.path.join(args.directory, "*.clm2.h1.*.nc")) # These should be constant in a Prescribed Calendars (rxboth) run, as long as the inputs were @@ -85,13 +87,17 @@ def main(argv): "rx_gdds_file": args.rx_gdds_file, } - case["ds"] = cc.import_output( + case["ds"], any_bad_import_output = cc.import_output( annual_outfiles, my_vars=my_vars, year_1=args.first_usable_year, year_n=args.last_usable_year, + throw_errors=False, ) - check_constant_vars(case["ds"], case, ignore_nan=True, verbose=True, throw_error=True) + any_bad = any_bad or any_bad_import_output + + _, any_bad_check_const_vars = check_constant_vars(case["ds"], case, ignore_nan=True, verbose=True, throw_error=True) + any_bad = any_bad or any_bad_check_const_vars # Import GGCMI sowing and harvest dates, and check sims casename = "Prescribed Calendars" @@ -128,15 +134,16 @@ def main(argv): # Check if case["rx_sdates_file"]: - check_rx_obeyed( + sdate_not_obeyed = check_rx_obeyed( case["ds"].vegtype_str.values, case["rx_sdates_ds"].isel(time=0), case["ds"], casename, "SDATES", ) + any_bad = any_bad or sdate_not_obeyed if case["rx_gdds_file"]: - check_rx_obeyed( + gdds_not_obeyed = check_rx_obeyed( case["ds"].vegtype_str.values, case["rx_gdds_ds"].isel(time=0), case["ds"], @@ -144,6 +151,10 @@ def main(argv): "GDDHARV", gdd_min=gdd_min, ) + any_bad = any_bad or gdds_not_obeyed + + if any_bad: + raise RuntimeError("Unexpected behavior in rxboth run") if __name__ == "__main__": diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index d25e16397e..fa1cc30e7c 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -170,8 +170,10 @@ def check_v0_le_v1(this_ds, var_list, msg_txt=" ", both_nan_ok=False, throw_erro if both_nan_ok: gdd_lt_hui = gdd_lt_hui | (np.isnan(this_ds[var0]) & np.isnan(this_ds[var1])) if np.all(gdd_lt_hui): + any_bad = False print(f"✅{msg_txt}{var0} always <= {var1}") else: + any_bad = True msg = f"âŒ{msg_txt}{var0} *not* always <= {var1}" gdd_lt_hui_vals = gdd_lt_hui.values patch_index = np.where(~gdd_lt_hui_vals)[0][0] @@ -187,6 +189,7 @@ def check_v0_le_v1(this_ds, var_list, msg_txt=" ", both_nan_ok=False, throw_erro print(msg) else: raise RuntimeError(msg) + return any_bad def get_gs_len_da(this_da): @@ -346,10 +349,13 @@ def import_output( sdates_rx_ds=None, gdds_rx_ds=None, verbose=False, + throw_errors=True, ): """ Import CLM output """ + any_bad = False + # Import this_ds = import_ds(filename, my_vars=my_vars, my_vegtypes=my_vegtypes) @@ -419,7 +425,7 @@ def import_output( # Check that e.g., GDDACCUM <= HUI for var_list in [["GDDACCUM", "HUI"], ["SYEARS", "HYEARS"]]: if all(v in this_ds_gs for v in var_list): - check_v0_le_v1(this_ds_gs, var_list, both_nan_ok=True, throw_error=True) + any_bad = check_v0_le_v1(this_ds_gs, var_list, both_nan_ok=True, throw_error=throw_errors) # Check that prescribed calendars were obeyed if sdates_rx_ds: @@ -447,7 +453,7 @@ def import_output( raise RuntimeError("How to get NHARVEST_DISCREP for NHARVESTS > 2?") this_ds_gs["NHARVEST_DISCREP"] = (this_ds_gs["NHARVESTS"] == 2).astype(int) - return this_ds_gs + return this_ds_gs, any_bad def handle_zombie_crops(this_ds): From 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 17:08:21 -0600 Subject: [PATCH 268/408] Reformat with black. --- cime_config/SystemTests/rxcropmaturity.py | 3 +-- cime_config/SystemTests/rxcropmaturityskipgen.py | 1 - python/ctsm/crop_calendars/check_rxboth_run.py | 4 +++- python/ctsm/crop_calendars/cropcal_module.py | 4 +++- python/ctsm/crop_calendars/interpolate_gdds.py | 2 +- 5 files changed, 8 insertions(+), 6 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index cffb832e8d..a583432efe 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -95,8 +95,7 @@ def __init__(self, case): # Get cultivar maturity requirement file to fall back on if not generating it here self._gdds_file = None self._fallback_gdds_file = os.path.join( - os.path.dirname(self._sdatefile), - "gdds_20230829_161011.nc" + os.path.dirname(self._sdatefile), "gdds_20230829_161011.nc" ) # Which conda environment should we use? diff --git a/cime_config/SystemTests/rxcropmaturityskipgen.py b/cime_config/SystemTests/rxcropmaturityskipgen.py index 4feb661037..409f2b9847 100644 --- a/cime_config/SystemTests/rxcropmaturityskipgen.py +++ b/cime_config/SystemTests/rxcropmaturityskipgen.py @@ -2,6 +2,5 @@ class RXCROPMATURITYSKIPGEN(RXCROPMATURITYSHARED): - def run_phase(self): self._run_phase(skip_gen=True) diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py index 8f416e9f8e..a1014b5e66 100644 --- a/python/ctsm/crop_calendars/check_rxboth_run.py +++ b/python/ctsm/crop_calendars/check_rxboth_run.py @@ -96,7 +96,9 @@ def main(argv): ) any_bad = any_bad or any_bad_import_output - _, any_bad_check_const_vars = check_constant_vars(case["ds"], case, ignore_nan=True, verbose=True, throw_error=True) + _, any_bad_check_const_vars = check_constant_vars( + case["ds"], case, ignore_nan=True, verbose=True, throw_error=True + ) any_bad = any_bad or any_bad_check_const_vars # Import GGCMI sowing and harvest dates, and check sims diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index fa1cc30e7c..b87d26816f 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -425,7 +425,9 @@ def import_output( # Check that e.g., GDDACCUM <= HUI for var_list in [["GDDACCUM", "HUI"], ["SYEARS", "HYEARS"]]: if all(v in this_ds_gs for v in var_list): - any_bad = check_v0_le_v1(this_ds_gs, var_list, both_nan_ok=True, throw_error=throw_errors) + any_bad = check_v0_le_v1( + this_ds_gs, var_list, both_nan_ok=True, throw_error=throw_errors + ) # Check that prescribed calendars were obeyed if sdates_rx_ds: diff --git a/python/ctsm/crop_calendars/interpolate_gdds.py b/python/ctsm/crop_calendars/interpolate_gdds.py index e9491480e9..2aa0b79997 100755 --- a/python/ctsm/crop_calendars/interpolate_gdds.py +++ b/python/ctsm/crop_calendars/interpolate_gdds.py @@ -13,7 +13,7 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm import ctsm_logging # pylint: disable=wrong-import-position -from ctsm.crop_calendars.cropcal_module import ( # pylint: disable=wrong-import-position +from ctsm.crop_calendars.cropcal_module import ( # pylint: disable=wrong-import-position unexpected_negative_rx_gdd, ) From 6af704f3c6d3d55aa9f288f736db2977792ef45a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 17:09:16 -0600 Subject: [PATCH 269/408] Add previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index f86a330408..dc56c6b7e2 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -45,3 +45,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b 6c6f57e948bfa31e60b383536cc21663fedb8b70 9660667b1267dcd4150889f5f39db540158be74a 665cf86102e09b4c4c5a140700676dca23bc55a9 +045d90f1d80f713eb3ae0ac58f6c2352937f1eb0 From 76b7df7d9fb8be59118ac7b260acd46852e196f8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jun 2024 17:13:10 -0600 Subject: [PATCH 270/408] check_rx_obeyed.py: Satisfy pylint. --- python/ctsm/crop_calendars/check_rx_obeyed.py | 36 +++++++++++-------- 1 file changed, 22 insertions(+), 14 deletions(-) diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py index 8525f3e890..a38b946ec5 100644 --- a/python/ctsm/crop_calendars/check_rx_obeyed.py +++ b/python/ctsm/crop_calendars/check_rx_obeyed.py @@ -104,6 +104,27 @@ def get_extreme_info(diff_array, rx_array, mxn, dims, gs_da, patches1d_lon, patc return round(themxn, 3), round(this_lon, 3), round(this_lat, 3), this_gs, round(this_rx) +def summarize_results(which_ds, output_var, verbose, all_ok, gdd_tolerance, diffs_eg_txt): + """ + Summarize results + """ + bad = True + if all_ok == 2: + bad = False + print(f"✅ {which_ds}: Prescribed {output_var} always obeyed") + elif all_ok == 1: + bad = False + # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:") + # for x in diff_str_list: print(x) + print( + f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable (diffs <= " + + f"{gdd_tolerance})" + ) + elif not verbose: + print(f"⌠{which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}") + return bad + + def check_rx_obeyed( vegtype_list, rx_ds, dates_ds, which_ds, output_var, gdd_min=None, verbose=False ): @@ -203,19 +224,6 @@ def check_rx_obeyed( else: break - bad = True - if all_ok == 2: - bad = False - print(f"✅ {which_ds}: Prescribed {output_var} always obeyed") - elif all_ok == 1: - bad = False - # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:") - # for x in diff_str_list: print(x) - print( - f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable (diffs <= " - + f"{gdd_tolerance})" - ) - elif not verbose: - print(f"⌠{which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}") + bad = summarize_results(which_ds, output_var, verbose, all_ok, gdd_tolerance, diffs_eg_txt) return bad From ba6cc32662ec445f7725ce0221ebacb112f440e3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 14 Jun 2024 20:45:34 -0600 Subject: [PATCH 271/408] The gnu compiler on both Derecho and Izumi got confused about the InitAllocate methods in the base method as well as the Zender extension, I found this out in the debugger, this adds Base to the end of the ones in the Base class so they won't be confused with the Zender extension --- src/biogeochem/DustEmisBase.F90 | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/DustEmisBase.F90 b/src/biogeochem/DustEmisBase.F90 index ef509add06..c5e4260634 100644 --- a/src/biogeochem/DustEmisBase.F90 +++ b/src/biogeochem/DustEmisBase.F90 @@ -1,4 +1,5 @@ module DustEmisBase +#include "shr_assert.h" !----------------------------------------------------------------------- ! !DESCRIPTION: @@ -68,8 +69,8 @@ module DustEmisBase procedure , public :: GetConstVars ! Get important constant variables procedure , public :: CleanBase ! Base object deallocation (allows extension) procedure , public :: Clean => CleanBase ! Deallocation used by callers - procedure , private :: InitAllocate - procedure , private :: InitHistory + procedure , private :: InitAllocateBase + procedure , private :: InitHistoryBase procedure , private :: InitDustVars ! Initialize variables used in DustEmission method end type dust_emis_base_type @@ -130,8 +131,8 @@ subroutine InitBase(this, bounds, NLFilename) type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename - call this%InitAllocate (bounds) - call this%InitHistory (bounds) + call this%InitAllocateBase (bounds) + call this%InitHistoryBase (bounds) call this%InitDustVars (bounds) end subroutine InitBase @@ -162,7 +163,7 @@ subroutine CleanBase(this) end subroutine CleanBase !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds) + subroutine InitAllocateBase(this, bounds) ! ! !ARGUMENTS: class (dust_emis_base_type) :: this @@ -188,10 +189,10 @@ subroutine InitAllocate(this, bounds) allocate (this%dmt_vwr(1:ndst)) ; this%dmt_vwr (:) = nan allocate (this%stk_crc(1:ndst)) ; this%stk_crc (:) = nan - end subroutine InitAllocate + end subroutine InitAllocateBase !------------------------------------------------------------------------ - subroutine InitHistory(this, bounds) + subroutine InitHistoryBase(this, bounds) ! ! !USES: use histFileMod, only : hist_addfld1d @@ -234,7 +235,7 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='turbulent deposition velocity 4', & ptr_patch=this%vlc_trb_4_patch, default='inactive') - end subroutine InitHistory + end subroutine InitHistoryBase !----------------------------------------------------------------------- @@ -554,6 +555,8 @@ subroutine InitDustVars(this, bounds) real(r8), parameter :: dns_slt = 2650.0_r8 ! [kg m-3] Density of optimal saltation particles !------------------------------------------------------------------------ + call shr_assert_all((lbound(this%ovr_src_snk_mss) == (/1,1/) ), file=sourcefile, line=__LINE__) + call shr_assert_all((ubound(this%ovr_src_snk_mss) == (/dst_src_nbr,ndst/) ), file=sourcefile, line=__LINE__) ! allocate local variable allocate (dmt_vma_src(dst_src_nbr)) allocate (gsd_anl_src(dst_src_nbr)) From fda1ae2b57993f84dd96953538bba08b8c5d74fe Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 16 Jun 2024 08:48:17 -0600 Subject: [PATCH 272/408] check_rxboth_run: Handle diffs_eg_txt never assigned. --- python/ctsm/crop_calendars/check_rx_obeyed.py | 1 + 1 file changed, 1 insertion(+) diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py index a38b946ec5..383ebbf1e0 100644 --- a/python/ctsm/crop_calendars/check_rx_obeyed.py +++ b/python/ctsm/crop_calendars/check_rx_obeyed.py @@ -135,6 +135,7 @@ def check_rx_obeyed( dates_ds, which_ds, output_var, verbose ) + diffs_eg_txt = None for vegtype_str in vegtype_list: thisveg_patches = np.where(dates_ds.patches1d_itype_veg_str == vegtype_str)[0] if thisveg_patches.size == 0: From 682c52651105114c63fd8735a6204a58b94863da Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 12:18:49 -0600 Subject: [PATCH 273/408] Be explicit about the things needed from unittestSubGridMod, and remove two uneeded setttings --- .../test/DustEmis_test/test_DustEmisZender2003.pf | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 4df64c7da3..a8ac4630da 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -3,7 +3,7 @@ module test_DustEmisZender2003 ! Tests of DustEmisZender2003 use funit - use unittestSubgridMod + use unittestSubgridMod, only : bounds, unittest_subgrid_teardown use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit @@ -162,12 +162,6 @@ contains this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) end do - - ! Use longitude along Greenich so don't have to calculate offsets for longitudes (that's calculated in clm_time_manager) - grc%londeg(:) = 0.0_r8 - - grc%area(:) = 10.0_r8 - end subroutine setupEnvironment !----------------------------------------------------------------------- From 67f4533a5c4fa6e6ab04563e2396532cb1b50dbf Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 12:26:21 -0600 Subject: [PATCH 274/408] Move dust emission object creation as last --- src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index a8ac4630da..856364e8db 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -81,7 +81,6 @@ contains endc = bounds%endc allocate( urb_em(begl:endl) ) - allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename)) call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & glcmec_downscale_longwave = .false., & @@ -111,6 +110,8 @@ contains is_simple_buildtemp=.true., is_prog_buildtemp=.false.) deallocate (snow_depth_col ) deallocate( urb_em ) + ! Create the dust emission object last + allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename)) end subroutine setUp !----------------------------------------------------------------------- From 499c4cfec445299e9e01be4e414372e26238f82a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 12:57:58 -0600 Subject: [PATCH 275/408] Remove setting of bedrock, which isn't needed --- src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 856364e8db..3d4f4c49c3 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -147,6 +147,7 @@ contains real(r8), parameter :: clay = 10.0_r8 !----------------------------------------------------------------------- + ! Setting the soil structrure is needed for water_state types col%dz(:,1:nlevgrnd) = 1.0_r8 do j = 1, nlevgrnd do c = bounds%begc, bounds%endc @@ -155,10 +156,6 @@ contains end do do c = bounds%begc, bounds%endc - ! Setting nbedrock to nlevsoi means that none of the layers from 1:nlevsoi are - ! considered bedrock - col%nbedrock(c) = nlevsoi - this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay ) this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) end do From 5e43b8f4aa71098b187b7719b3bf18e36aca0527 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 13:18:32 -0600 Subject: [PATCH 276/408] Add some comments about the setup, and move atm2lnd init more together --- .../test/DustEmis_test/test_DustEmisZender2003.pf | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 3d4f4c49c3..332f808283 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -64,16 +64,19 @@ contains integer :: c type(atm2lnd_params_type) :: atm2lnd_params + ! Settings needed for clm_varpar soil_layerstruct_predefined = '20SL_8.5m' create_crop_landunit = .true. use_crop = .false. call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) call clm_varcon_init( is_simple_buildtemp=.true.) + ! Water factor initialization call this%water_factory%init() call this%water_factory%setup_before_subgrid( & my_nlevsoi = nlevsoi, & nlevgrnd_additional = nlevgrnd - nlevsoi, & my_nlevsno = 3) + ! Setup the subgrid structure for a single bare-soil patch call setup_single_veg_patch( pft_type=0 ) begl = bounds%begl endl = bounds%endl @@ -81,15 +84,21 @@ contains endc = bounds%endc allocate( urb_em(begl:endl) ) + ! Create the nolake filter call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) + ! atmospher to land parameter object atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & glcmec_downscale_longwave = .false., & lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) ) + call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) + ! Hydrology and snow (needed for water types) allocate (snow_depth_col(begc:endc)) snow_depth_col(begc:endc) = 0.0_r8 call SnowHydrologySetControlForTesting() call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc)) + deallocate (snow_depth_col ) + ! Water and soil state -- after the subgrid setup call this%water_factory%setup_after_subgrid(snl = 3) call this%soilstate_inst%Init(bounds) do c = begc, endc @@ -97,7 +106,7 @@ contains end do call this%setupEnvironment( ) call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) - call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) + ! Canopy state, friction velocity, and temperature state ojects call this%canopystate_inst%SetNMLForTesting() call this%canopystate_inst%Init(bounds) call this%frictionvel_inst%InitForTesting(bounds) @@ -108,7 +117,6 @@ contains em_improad_lun=urb_em(begl:endl), & em_perroad_lun=urb_em(begl:endl), & is_simple_buildtemp=.true., is_prog_buildtemp=.false.) - deallocate (snow_depth_col ) deallocate( urb_em ) ! Create the dust emission object last allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename)) From 281fb7b6ba3b4f249a1bb3b5b4da65b3380bf3bd Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 13:35:17 -0600 Subject: [PATCH 277/408] Change name of setupEnvironment to setupSoilState and move the soil-state initialization together --- .../DustEmis_test/test_DustEmisZender2003.pf | 23 ++++++++++--------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 332f808283..d05dcbaa6f 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -42,7 +42,7 @@ module test_DustEmisZender2003 contains procedure :: setUp procedure :: tearDown - procedure :: setupEnvironment + procedure :: setupSoilState procedure :: create_atm2lnd procedure :: create_fv procedure :: print_values @@ -70,7 +70,7 @@ contains use_crop = .false. call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) call clm_varcon_init( is_simple_buildtemp=.true.) - ! Water factor initialization + ! Water object initialization -- before subgrid call this%water_factory%init() call this%water_factory%setup_before_subgrid( & my_nlevsoi = nlevsoi, & @@ -82,11 +82,10 @@ contains endl = bounds%endl begc = bounds%begc endc = bounds%endc - allocate( urb_em(begl:endl) ) ! Create the nolake filter call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) - ! atmospher to land parameter object + ! atmosphere to land parameter object atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & glcmec_downscale_longwave = .false., & lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) @@ -100,16 +99,13 @@ contains deallocate (snow_depth_col ) ! Water and soil state -- after the subgrid setup call this%water_factory%setup_after_subgrid(snl = 3) - call this%soilstate_inst%Init(bounds) - do c = begc, endc - this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1) - end do - call this%setupEnvironment( ) + call this%setupSoilState( ) ! This needs to happen before the water_type object creation call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) ! Canopy state, friction velocity, and temperature state ojects call this%canopystate_inst%SetNMLForTesting() call this%canopystate_inst%Init(bounds) call this%frictionvel_inst%InitForTesting(bounds) + allocate( urb_em(begl:endl) ) urb_em(begl:endl) = 0.99_r8 call this%temperature_inst%Init(bounds, & em_roof_lun=urb_em(begl:endl), & @@ -138,7 +134,7 @@ contains !----------------------------------------------------------------------- - subroutine setupEnvironment(this) + subroutine setupSoilState(this) ! ! !DESCRIPTION: ! Sets up the external environment used by Dust emissions - i.e., things accessed via @@ -163,12 +159,17 @@ contains end do end do + call this%soilstate_inst%Init(bounds) + do c = bounds%begc, bounds%endc + this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1) + end do + ! These are needed for dust emissions initialization do c = bounds%begc, bounds%endc this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay ) this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) end do - end subroutine setupEnvironment + end subroutine setupSoilState !----------------------------------------------------------------------- From 2db3f1c8200598f14cc64172b420b8241f224b43 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 14:00:29 -0600 Subject: [PATCH 278/408] Don't actually need clm_varcon here --- src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index d05dcbaa6f..90bc00803d 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -7,7 +7,6 @@ module test_DustEmisZender2003 use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit - use clm_varcon, only : clm_varcon_init, clm_varcon_clean use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean use DustEmisBase use DustEmisZender2003 @@ -69,7 +68,6 @@ contains create_crop_landunit = .true. use_crop = .false. call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) - call clm_varcon_init( is_simple_buildtemp=.true.) ! Water object initialization -- before subgrid call this%water_factory%init() call this%water_factory%setup_before_subgrid( & @@ -128,7 +126,6 @@ contains call SnowHydrologyClean() call unittest_subgrid_teardown() call this%atm2lnd_inst%Clean() - call clm_varcon_clean() deallocate( this%filter_nolakep ) end subroutine tearDown From b173ab575f2976c7b9e4880b2077e107dd905091 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 14:11:11 -0600 Subject: [PATCH 279/408] remove snowHydrology parts that weren't needed --- .../test/DustEmis_test/test_DustEmisZender2003.pf | 9 --------- 1 file changed, 9 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 90bc00803d..250b7b3a61 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -7,7 +7,6 @@ module test_DustEmisZender2003 use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit - use SnowHydrologyMod, only : InitSnowLayers, SnowHydrologySetControlForTesting, SnowHydrologyClean use DustEmisBase use DustEmisZender2003 use shr_kind_mod , only : r8 => shr_kind_r8 @@ -57,7 +56,6 @@ contains class(TestDustEmisZender2003), intent(inout) :: this character(len=5) :: NLFilename = 'none' - real(r8), allocatable :: snow_depth_col(:) real(r8), allocatable :: urb_em(:) integer :: begl, endl, begc, endc integer :: c @@ -89,12 +87,6 @@ contains lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) ) call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) - ! Hydrology and snow (needed for water types) - allocate (snow_depth_col(begc:endc)) - snow_depth_col(begc:endc) = 0.0_r8 - call SnowHydrologySetControlForTesting() - call InitSnowLayers(bounds, snow_depth_col(bounds%begc:bounds%endc)) - deallocate (snow_depth_col ) ! Water and soil state -- after the subgrid setup call this%water_factory%setup_after_subgrid(snl = 3) call this%setupSoilState( ) ! This needs to happen before the water_type object creation @@ -123,7 +115,6 @@ contains call this%dust_emis%Clean() call this%water_factory%teardown(this%water_inst) - call SnowHydrologyClean() call unittest_subgrid_teardown() call this%atm2lnd_inst%Clean() deallocate( this%filter_nolakep ) From 7ddcbb147acc7e66601e4e1182efbd5683c2c2ef Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 14:21:10 -0600 Subject: [PATCH 280/408] More notes, set snl with a parameter so consistent between two uses, and remove method not used --- .../test/DustEmis_test/test_DustEmisZender2003.pf | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 250b7b3a61..76bb036339 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -18,7 +18,7 @@ module test_DustEmisZender2003 use WaterType, only : water_type use FrictionVelocityMod, only : frictionvel_type use unittestWaterTypeFactory, only : unittest_water_type_factory_type - use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, ThresholdSoilMoistKok2014, MassFracClay + use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, MassFracClay use DustEmisFactory, only : create_dust_emissions implicit none @@ -54,12 +54,14 @@ contains subroutine setUp(this) use ColumnType, only : col class(TestDustEmisZender2003), intent(inout) :: this + ! Allocate and initiatlize the test object for input objects dust-emission needs character(len=5) :: NLFilename = 'none' real(r8), allocatable :: urb_em(:) integer :: begl, endl, begc, endc integer :: c type(atm2lnd_params_type) :: atm2lnd_params + integer, parameter :: snl = 3 ! Settings needed for clm_varpar soil_layerstruct_predefined = '20SL_8.5m' @@ -71,7 +73,7 @@ contains call this%water_factory%setup_before_subgrid( & my_nlevsoi = nlevsoi, & nlevgrnd_additional = nlevgrnd - nlevsoi, & - my_nlevsno = 3) + my_nlevsno = snl) ! Setup the subgrid structure for a single bare-soil patch call setup_single_veg_patch( pft_type=0 ) begl = bounds%begl @@ -88,7 +90,7 @@ contains ) call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) ! Water and soil state -- after the subgrid setup - call this%water_factory%setup_after_subgrid(snl = 3) + call this%water_factory%setup_after_subgrid(snl = snl) call this%setupSoilState( ) ! This needs to happen before the water_type object creation call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) ! Canopy state, friction velocity, and temperature state ojects @@ -96,7 +98,7 @@ contains call this%canopystate_inst%Init(bounds) call this%frictionvel_inst%InitForTesting(bounds) allocate( urb_em(begl:endl) ) - urb_em(begl:endl) = 0.99_r8 + urb_em(begl:endl) = 0.99_r8 ! Arbitrary won't matter here call this%temperature_inst%Init(bounds, & em_roof_lun=urb_em(begl:endl), & em_wall_lun=urb_em(begl:endl), & From 1633faac6bb4380f050e108af1220ac297080ea2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 15:56:31 -0600 Subject: [PATCH 281/408] Start moving dust emis inputs into it's own module to be shared by both Zender and Leung --- .../DustEmis_test/test_DustEmisZender2003.pf | 308 ++++-------------- src/unit_test_shr/CMakeLists.txt | 1 + src/unit_test_shr/unittestDustEmisInputs.F90 | 249 ++++++++++++++ 3 files changed, 315 insertions(+), 243 deletions(-) create mode 100644 src/unit_test_shr/unittestDustEmisInputs.F90 diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 76bb036339..a26e2a5a33 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -3,6 +3,7 @@ module test_DustEmisZender2003 ! Tests of DustEmisZender2003 use funit + use unittestDustEmisInputs, only : unittest_dust_emis_input_type use unittestSubgridMod, only : bounds, unittest_subgrid_teardown use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst @@ -28,21 +29,10 @@ module test_DustEmisZender2003 @TestCase type, extends(TestCase) :: TestDustEmisZender2003 class(dust_emis_base_type), allocatable :: dust_emis - integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) - integer :: num_nolakep ! number of patches in non-lake filter - type(atm2lnd_type) :: atm2lnd_inst - type(soilstate_type) :: soilstate_inst - type(canopystate_type) :: canopystate_inst - type(temperature_type) :: temperature_inst - type(unittest_water_type_factory_type) :: water_factory - type(water_type) :: water_inst - type(frictionvel_type) :: frictionvel_inst + type(unittest_dust_emis_input_type) :: input contains procedure :: setUp procedure :: tearDown - procedure :: setupSoilState - procedure :: create_atm2lnd - procedure :: create_fv procedure :: print_values procedure :: validate_patch end type TestDustEmisZender2003 @@ -52,60 +42,12 @@ contains !----------------------------------------------------------------------- subroutine setUp(this) - use ColumnType, only : col class(TestDustEmisZender2003), intent(inout) :: this - ! Allocate and initiatlize the test object for input objects dust-emission needs - + ! Allocate and initialize the test object for input objects dust-emission needs character(len=5) :: NLFilename = 'none' - real(r8), allocatable :: urb_em(:) - integer :: begl, endl, begc, endc - integer :: c - type(atm2lnd_params_type) :: atm2lnd_params - integer, parameter :: snl = 3 - - ! Settings needed for clm_varpar - soil_layerstruct_predefined = '20SL_8.5m' - create_crop_landunit = .true. - use_crop = .false. - call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) - ! Water object initialization -- before subgrid - call this%water_factory%init() - call this%water_factory%setup_before_subgrid( & - my_nlevsoi = nlevsoi, & - nlevgrnd_additional = nlevgrnd - nlevsoi, & - my_nlevsno = snl) - ! Setup the subgrid structure for a single bare-soil patch - call setup_single_veg_patch( pft_type=0 ) - begl = bounds%begl - endl = bounds%endl - begc = bounds%begc - endc = bounds%endc - - ! Create the nolake filter - call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) - ! atmosphere to land parameter object - atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & - glcmec_downscale_longwave = .false., & - lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) - ) - call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) - ! Water and soil state -- after the subgrid setup - call this%water_factory%setup_after_subgrid(snl = snl) - call this%setupSoilState( ) ! This needs to happen before the water_type object creation - call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) - ! Canopy state, friction velocity, and temperature state ojects - call this%canopystate_inst%SetNMLForTesting() - call this%canopystate_inst%Init(bounds) - call this%frictionvel_inst%InitForTesting(bounds) - allocate( urb_em(begl:endl) ) - urb_em(begl:endl) = 0.99_r8 ! Arbitrary won't matter here - call this%temperature_inst%Init(bounds, & - em_roof_lun=urb_em(begl:endl), & - em_wall_lun=urb_em(begl:endl), & - em_improad_lun=urb_em(begl:endl), & - em_perroad_lun=urb_em(begl:endl), & - is_simple_buildtemp=.true., is_prog_buildtemp=.false.) - deallocate( urb_em ) + + call this%input%setUp() + ! Create the dust emission object last allocate(this%dust_emis, source = create_dust_emissions(bounds, NLFilename)) end subroutine setUp @@ -116,153 +58,33 @@ contains class(TestDustEmisZender2003), intent(inout) :: this call this%dust_emis%Clean() - call this%water_factory%teardown(this%water_inst) - call unittest_subgrid_teardown() - call this%atm2lnd_inst%Clean() - deallocate( this%filter_nolakep ) + call this%input%tearDown() end subroutine tearDown !----------------------------------------------------------------------- - subroutine setupSoilState(this) - ! - ! !DESCRIPTION: - ! Sets up the external environment used by Dust emissions - i.e., things accessed via - ! 'use' statements. - ! - ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has - ! been completed. - ! - use ColumnType, only : col - use GridcellType, only : grc - class(TestDustEmisZender2003), intent(in) :: this - ! - integer :: c,j - real(r8), parameter :: clay = 10.0_r8 - - !----------------------------------------------------------------------- - ! Setting the soil structrure is needed for water_state types - col%dz(:,1:nlevgrnd) = 1.0_r8 - do j = 1, nlevgrnd - do c = bounds%begc, bounds%endc - col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j) - end do - end do - - call this%soilstate_inst%Init(bounds) - do c = bounds%begc, bounds%endc - this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1) - end do - ! These are needed for dust emissions initialization - do c = bounds%begc, bounds%endc - this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay ) - this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) - end do - - end subroutine setupSoilState - - !----------------------------------------------------------------------- - - subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho ) - ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets - ! forcing fields based on inputs. Excluded inputs are given a default value - class(TestDustEmisZender2003), intent(inout) :: this - real(r8), intent(in), optional :: forc_t(:) - real(r8), intent(in), optional :: forc_pbot(:) - real(r8), intent(in), optional :: forc_rho(:) - - real(r8), parameter :: forc_t_default = 301._r8 - real(r8), parameter :: forc_pbot_default = 100000._r8 - real(r8), parameter :: forc_rho_default = 1.1_r8 - ! ------------------------------------------------------------------------ - - if (present(forc_t)) then - this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:) - else - this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default - end if - - if (present(forc_pbot)) then - this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:) - else - this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default - end if - - if (present(forc_rho)) then - this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:) - else - this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default - end if - - end subroutine create_atm2lnd - - !----------------------------------------------------------------------- - - subroutine create_fv(this, fv, u10, ram1) - ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets - ! fields based on inputs. Excluded inputs are given a default value - class(TestDustEmisZender2003), intent(inout) :: this - real(r8), intent(in), optional :: fv - real(r8), intent(in), optional :: u10 - real(r8), intent(in), optional :: ram1 - - real(r8), parameter :: fv_default = 2.0_r8 - real(r8), parameter :: u10_default = 4._r8 - real(r8), parameter :: ram1_default = 200._r8 - ! ------------------------------------------------------------------------ - - if (present(fv)) then - this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv - else - this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default - end if - - if (present(u10)) then - this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10 - else - this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default - end if - - if (present(ram1)) then - this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1 - else - this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default - end if - - end subroutine create_fv - subroutine print_values(this) - use LandunitType, only : lun + ! For debugging use PatchType, only : patch class(TestDustEmisZender2003), intent(inout) :: this real(r8) :: SaltationFactor - integer :: p, c, l + integer :: p, c + call this%input%print_values() call this%dust_emis%GetConstVars( SaltationFactor ) - do l = bounds%begl, bounds%endl - print *, 'landunit type= ', lun%itype(l) - end do do c = bounds%begc, bounds%endc - print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1) - print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1) - print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c) - print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c) - print *, 'saltation per rho = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) + print *, 'saltation per rho = ', (SaltationFactor / this%input%atm2lnd_inst%forc_rho_downscaled_col(c)) end do do p = bounds%begp, bounds%endp - print *, 'patch type= ', patch%itype(p) - print *, 'patch weight= ', patch%wtgcell(p) - print *, 'patch active= ', patch%active(p) - print *, 'tlai = ', this%canopystate_inst%tlai_patch(p) - print *, 'tsai = ', this%canopystate_inst%tsai_patch(p) c = patch%column(p) - print *, 'Wind threshold fraction = ', (SaltationFactor / this%atm2lnd_inst%forc_rho_downscaled_col(c)) & - / this%frictionvel_inst%fv_patch(p) + print *, 'Wind threshold fraction = ', (SaltationFactor / this%input%atm2lnd_inst%forc_rho_downscaled_col(c)) & + / this%input%frictionvel_inst%fv_patch(p) call this%dust_emis%WritePatchToLog( p ) end do end subroutine print_values - + !----------------------------------------------------------------------- + subroutine validate_patch(this, p) class(TestDustEmisZender2003), intent(inout) :: this integer, intent(in) :: p @@ -283,12 +105,12 @@ contains real(r8) :: vlc_trb_3 real(r8) :: vlc_trb_4 - call this%create_atm2lnd() - call this%create_fv() - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%input%create_atm2lnd() + call this%input%create_fv() + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) do p = bounds%begp, bounds%endp call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, & @@ -314,15 +136,15 @@ contains real(r8) :: fv real(r8) :: SaltationFactor - call this%create_atm2lnd() + call this%input%create_atm2lnd() call this%dust_emis%GetConstVars( SaltationFactor ) ! Figure out what fv needs to be so that the wind threshold will be u10*(1/(1-eps)) - fv = ( SaltationFactor / sqrt( this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15 - call this%create_fv( fv=fv ) - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + fv = ( SaltationFactor / sqrt( this%input%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc)) ) - 1.d-15 + call this%input%create_fv( fv=fv ) + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) call this%print_values() do p = bounds%begp, bounds%endp call this%validate_patch(p) @@ -341,13 +163,13 @@ contains integer :: p real(r8) :: flx_mss_vrt_dst_tot - call this%create_atm2lnd() - this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 - call this%create_fv( ) - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%input%create_atm2lnd() + this%input%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + call this%input%create_fv( ) + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) do p = bounds%begp, bounds%endp call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) @@ -366,15 +188,15 @@ contains integer :: p, l real(r8) :: flx_mss_vrt_dst_tot - call this%create_atm2lnd() - call this%create_fv( ) + call this%input%create_atm2lnd() + call this%input%create_fv( ) ! Set the lanunit type for do l = istcrop+1, max_lunit lun%itype(bounds%begl:bounds%endl) = l - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) do p = bounds%begp, bounds%endp call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) @assertEqual( flx_mss_vrt_dst_tot, 0.0_r8 ) @@ -392,13 +214,13 @@ contains real(r8) :: flx_mss_vrt_dst_tot character(100) :: expected_msg - call this%create_atm2lnd() - call this%create_fv( ) + call this%input%create_atm2lnd() + call this%input%create_fv( ) ! Dust should abort with an error on dust mobility when snow fraction greater than 1 - this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + 1.e-15_r8 - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) + this%input%water_inst%waterdiagnosticbulk_inst%frac_sno_col(:) = 1.0_r8 + 1.e-15_r8 + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) expected_msg = "ABORTED: Bad value for dust mobilization fraction" @assertExceptionRaised(expected_msg) @@ -413,13 +235,13 @@ contains integer :: p real(r8) :: flx_mss_vrt_dst_tot - call this%create_atm2lnd() - call this%create_fv( ) - this%canopystate_inst%tlai_patch(:) = 0.3_r8 - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%input%create_atm2lnd() + call this%input%create_fv( ) + this%input%canopystate_inst%tlai_patch(:) = 0.3_r8 + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) do p = bounds%begp, bounds%endp call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) @@ -441,12 +263,12 @@ contains real(r8) :: total_dust0, total_dust_higher ! Run baseline u10 - call this%create_atm2lnd() - call this%create_fv( u10=u10, fv=fv ) - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%input%create_atm2lnd() + call this%input%create_fv( u10=u10, fv=fv ) + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) do p = bounds%begp, bounds%endp call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) @@ -454,11 +276,11 @@ contains @assertEqual( flx_mss_vrt_dst_tot, 2.273879554711299d-5, tolerance=tol ) end do ! Double u10 and show result is higher - call this%create_fv( u10=u10*2.0_r8, fv=fv) - call this%dust_emis%DustEmission(bounds, this%num_nolakep, this%filter_nolakep, this%atm2lnd_inst, & - this%soilstate_inst, this%canopystate_inst, this%water_inst%waterstatebulk_inst, & - this%water_inst%waterdiagnosticbulk_inst, this%frictionvel_inst) - call this%dust_emis%DustDryDep(bounds, this%atm2lnd_inst, this%frictionvel_inst) + call this%input%create_fv( u10=u10*2.0_r8, fv=fv) + call this%dust_emis%DustEmission(bounds, this%input%num_nolakep, this%input%filter_nolakep, this%input%atm2lnd_inst, & + this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & + this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) + call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) do p = bounds%begp, bounds%endp call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) diff --git a/src/unit_test_shr/CMakeLists.txt b/src/unit_test_shr/CMakeLists.txt index 9bf95c728f..f6a204bd72 100644 --- a/src/unit_test_shr/CMakeLists.txt +++ b/src/unit_test_shr/CMakeLists.txt @@ -9,6 +9,7 @@ sourcelist_to_parent(clm_genf90_sources) list(APPEND clm_sources "${clm_genf90_sources}") list(APPEND clm_sources + unittestDustEmisInputs.F90 unittestFilterBuilderMod.F90 unittestGlcMec.F90 unittestSimpleSubgridSetupsMod.F90 diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90 new file mode 100644 index 0000000000..4cc82fa55e --- /dev/null +++ b/src/unit_test_shr/unittestDustEmisInputs.F90 @@ -0,0 +1,249 @@ +module unittestDustEmisInputs + + ! unit testing dust emission inputs + + use unittestSubgridMod, only : bounds, unittest_subgrid_teardown + use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch + use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst + use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit + use shr_kind_mod , only : r8 => shr_kind_r8 + use unittestFilterBuilderMod, only : filter_from_range + use atm2lndType, only : atm2lnd_type, atm2lnd_params_type + use SoilStateType, only : soilstate_type + use CanopyStateType, only : canopystate_type + use TemperatureType, only : temperature_type + use WaterType, only : water_type + use FrictionVelocityMod, only : frictionvel_type + use unittestWaterTypeFactory, only : unittest_water_type_factory_type + use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, MassFracClay + + implicit none + private + + type, public :: unittest_dust_emis_input_type + integer, allocatable :: filter_nolakep(:) ! non-lake filter (patches) + integer :: num_nolakep ! number of patches in non-lake filter + type(atm2lnd_type) :: atm2lnd_inst + type(soilstate_type) :: soilstate_inst + type(canopystate_type) :: canopystate_inst + type(temperature_type) :: temperature_inst + type(unittest_water_type_factory_type) :: water_factory + type(water_type) :: water_inst + type(frictionvel_type) :: frictionvel_inst + contains + procedure, public :: setUp + procedure, public :: tearDown + procedure, private:: setupSoilState + procedure, public :: create_atm2lnd + procedure, public :: create_fv + procedure, public :: print_values + end type unittest_dust_emis_input_type + +contains + + !----------------------------------------------------------------------- + + subroutine setUp(this) + use ColumnType, only : col + class(unittest_dust_emis_input_type), intent(inout) :: this + ! Allocate and initiatlize the test object for input objects dust-emission needs + + character(len=5) :: NLFilename = 'none' + real(r8), allocatable :: urb_em(:) + integer :: begl, endl, begc, endc + integer :: c + type(atm2lnd_params_type) :: atm2lnd_params + integer, parameter :: snl = 3 + + ! Settings needed for clm_varpar + soil_layerstruct_predefined = '20SL_8.5m' + create_crop_landunit = .true. + use_crop = .false. + call clm_varpar_init( actual_maxsoil_patches=17, surf_numpft=15, surf_numcft=2, actual_nlevurb=5 ) + ! Water object initialization -- before subgrid + call this%water_factory%init() + call this%water_factory%setup_before_subgrid( & + my_nlevsoi = nlevsoi, & + nlevgrnd_additional = nlevgrnd - nlevsoi, & + my_nlevsno = snl) + ! Setup the subgrid structure for a single bare-soil patch + call setup_single_veg_patch( pft_type=0 ) + begl = bounds%begl + endl = bounds%endl + begc = bounds%begc + endc = bounds%endc + + ! Create the nolake filter + call filter_from_range(start=bounds%begp, end=bounds%endp, numf=this%num_nolakep, filter=this%filter_nolakep) + ! atmosphere to land parameter object + atm2lnd_params = atm2lnd_params_type( repartition_rain_snow = .false., & + glcmec_downscale_longwave = .false., & + lapse_rate = 0.01_r8 & ! arbitrary (this is unused for these tests) + ) + call this%atm2lnd_inst%InitForTesting(bounds, atm2lnd_params) + ! Water and soil state -- after the subgrid setup + call this%water_factory%setup_after_subgrid(snl = snl) + call this%setupSoilState( ) ! This needs to happen before the water_type object creation + call this%water_factory%create_water_type(this%water_inst, watsat_col=this%soilstate_inst%watsat_col) + ! Canopy state, friction velocity, and temperature state ojects + call this%canopystate_inst%SetNMLForTesting() + call this%canopystate_inst%Init(bounds) + call this%frictionvel_inst%InitForTesting(bounds) + allocate( urb_em(begl:endl) ) + urb_em(begl:endl) = 0.99_r8 ! Arbitrary won't matter here + call this%temperature_inst%Init(bounds, & + em_roof_lun=urb_em(begl:endl), & + em_wall_lun=urb_em(begl:endl), & + em_improad_lun=urb_em(begl:endl), & + em_perroad_lun=urb_em(begl:endl), & + is_simple_buildtemp=.true., is_prog_buildtemp=.false.) + deallocate( urb_em ) + end subroutine setUp + + !----------------------------------------------------------------------- + + subroutine tearDown(this) + class(unittest_dust_emis_input_type), intent(inout) :: this + + call this%water_factory%teardown(this%water_inst) + call unittest_subgrid_teardown() + call this%atm2lnd_inst%Clean() + deallocate( this%filter_nolakep ) + end subroutine tearDown + + !----------------------------------------------------------------------- + + subroutine setupSoilState(this) + ! + ! !DESCRIPTION: + ! Sets up the external environment used by Dust emissions - i.e., things accessed via + ! 'use' statements. + ! + ! Assumes nlevgrnd and nlevsoi have been set, and that all necessary subgrid setup has + ! been completed. + ! + use ColumnType, only : col + use GridcellType, only : grc + class(unittest_dust_emis_input_type), intent(in) :: this + ! + integer :: c,j + real(r8), parameter :: clay = 10.0_r8 + + !----------------------------------------------------------------------- + ! Setting the soil structrure is needed for water_state types + col%dz(:,1:nlevgrnd) = 1.0_r8 + do j = 1, nlevgrnd + do c = bounds%begc, bounds%endc + col%z(c,j) = sum(col%dz(c,1:j-1)) + 0.5_r8*col%dz(c,j) + end do + end do + + call this%soilstate_inst%Init(bounds) + do c = bounds%begc, bounds%endc + this%soilstate_inst%watsat_col(c,:) = 0.05_r8 * (c - bounds%begc + 1) + end do + ! These are needed for dust emissions initialization + do c = bounds%begc, bounds%endc + this%soilstate_inst%gwc_thr_col(c) = ThresholdSoilMoistZender2003( clay ) + this%soilstate_inst%mss_frc_cly_vld_col(c) = MassFracClay( clay ) + end do + + end subroutine setupSoilState + + !----------------------------------------------------------------------- + + subroutine create_atm2lnd(this, forc_t, forc_pbot, forc_rho ) + ! Initializes some fields needed for dust emissions in this%atm2lnd_inst, and sets + ! forcing fields based on inputs. Excluded inputs are given a default value + class(unittest_dust_emis_input_type), intent(inout) :: this + real(r8), intent(in), optional :: forc_t(:) + real(r8), intent(in), optional :: forc_pbot(:) + real(r8), intent(in), optional :: forc_rho(:) + + real(r8), parameter :: forc_t_default = 301._r8 + real(r8), parameter :: forc_pbot_default = 100000._r8 + real(r8), parameter :: forc_rho_default = 1.1_r8 + ! ------------------------------------------------------------------------ + + if (present(forc_t)) then + this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t(:) + else + this%atm2lnd_inst%forc_t_downscaled_col(bounds%begc:bounds%endc) = forc_t_default + end if + + if (present(forc_pbot)) then + this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot(:) + else + this%atm2lnd_inst%forc_pbot_downscaled_col(bounds%begc:bounds%endc) = forc_pbot_default + end if + + if (present(forc_rho)) then + this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho(:) + else + this%atm2lnd_inst%forc_rho_downscaled_col(bounds%begc:bounds%endc) = forc_rho_default + end if + + end subroutine create_atm2lnd + + !----------------------------------------------------------------------- + + subroutine create_fv(this, fv, u10, ram1) + ! Initializes some fields needed for dust emissions in this%frictionvel_inst, and sets + ! fields based on inputs. Excluded inputs are given a default value + class(unittest_dust_emis_input_type), intent(inout) :: this + real(r8), intent(in), optional :: fv + real(r8), intent(in), optional :: u10 + real(r8), intent(in), optional :: ram1 + + real(r8), parameter :: fv_default = 2.0_r8 + real(r8), parameter :: u10_default = 4._r8 + real(r8), parameter :: ram1_default = 200._r8 + ! ------------------------------------------------------------------------ + + if (present(fv)) then + this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv + else + this%frictionvel_inst%fv_patch(bounds%begp:bounds%endp) = fv_default + end if + + if (present(u10)) then + this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10 + else + this%frictionvel_inst%u10_patch(bounds%begp:bounds%endp) = u10_default + end if + + if (present(ram1)) then + this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1 + else + this%frictionvel_inst%ram1_patch(bounds%begp:bounds%endp) = ram1_default + end if + + end subroutine create_fv + + subroutine print_values(this) + use LandunitType, only : lun + use PatchType, only : patch + class(unittest_dust_emis_input_type), intent(inout) :: this + integer :: p, c, l + + do l = bounds%begl, bounds%endl + print *, 'landunit type= ', lun%itype(l) + end do + do c = bounds%begc, bounds%endc + print *, 'watsat = ', this%soilstate_inst%watsat_col(c,1) + print *, 'h2osoi_vol = ', this%water_inst%waterstatebulk_inst%h2osoi_vol_col(c,1) + print *, 'frac_sno = ', this%water_inst%waterdiagnosticbulk_inst%frac_sno_col(c) + print *, 'mss_frac_clay_vld = ', this%soilstate_inst%mss_frc_cly_vld_col(c) + end do + do p = bounds%begp, bounds%endp + print *, 'patch type= ', patch%itype(p) + print *, 'patch weight= ', patch%wtgcell(p) + print *, 'patch active= ', patch%active(p) + print *, 'tlai = ', this%canopystate_inst%tlai_patch(p) + print *, 'tsai = ', this%canopystate_inst%tsai_patch(p) + end do + end subroutine print_values + + !----------------------------------------------------------------------- + +end module unittestDustEmisInputs \ No newline at end of file From 65da9cf9c59b19f75e6621e3ca625c9443355dcf Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 16:06:40 -0600 Subject: [PATCH 282/408] Remove things not needed --- .../test/DustEmis_test/test_DustEmisZender2003.pf | 14 +------------- src/unit_test_shr/unittestDustEmisInputs.F90 | 8 +++++--- 2 files changed, 6 insertions(+), 16 deletions(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index a26e2a5a33..9bdaa685b0 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -4,22 +4,10 @@ module test_DustEmisZender2003 use funit use unittestDustEmisInputs, only : unittest_dust_emis_input_type - use unittestSubgridMod, only : bounds, unittest_subgrid_teardown - use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch - use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst - use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit + use unittestSubgridMod, only : bounds use DustEmisBase use DustEmisZender2003 use shr_kind_mod , only : r8 => shr_kind_r8 - use unittestFilterBuilderMod, only : filter_from_range - use atm2lndType, only : atm2lnd_type, atm2lnd_params_type - use SoilStateType, only : soilstate_type - use CanopyStateType, only : canopystate_type - use TemperatureType, only : temperature_type - use WaterType, only : water_type - use FrictionVelocityMod, only : frictionvel_type - use unittestWaterTypeFactory, only : unittest_water_type_factory_type - use SoilStateInitTimeConstMod, only : ThresholdSoilMoistZender2003, MassFracClay use DustEmisFactory, only : create_dust_emissions implicit none diff --git a/src/unit_test_shr/unittestDustEmisInputs.F90 b/src/unit_test_shr/unittestDustEmisInputs.F90 index 4cc82fa55e..6b15680ef7 100644 --- a/src/unit_test_shr/unittestDustEmisInputs.F90 +++ b/src/unit_test_shr/unittestDustEmisInputs.F90 @@ -4,7 +4,7 @@ module unittestDustEmisInputs use unittestSubgridMod, only : bounds, unittest_subgrid_teardown use unittestSimpleSubgridSetupsMod, only : setup_single_veg_patch - use clm_varpar, only : nlevsoi, nlevgrnd, nlevsno, clm_varpar_init, ndst + use clm_varpar, only : nlevsoi, nlevgrnd, clm_varpar_init use clm_varctl, only : soil_layerstruct_predefined, create_crop_landunit, use_crop, create_crop_landunit use shr_kind_mod , only : r8 => shr_kind_r8 use unittestFilterBuilderMod, only : filter_from_range @@ -26,8 +26,8 @@ module unittestDustEmisInputs type(atm2lnd_type) :: atm2lnd_inst type(soilstate_type) :: soilstate_inst type(canopystate_type) :: canopystate_inst - type(temperature_type) :: temperature_inst - type(unittest_water_type_factory_type) :: water_factory + type(temperature_type), private :: temperature_inst + type(unittest_water_type_factory_type), private :: water_factory type(water_type) :: water_inst type(frictionvel_type) :: frictionvel_inst contains @@ -220,6 +220,8 @@ subroutine create_fv(this, fv, u10, ram1) end subroutine create_fv + !----------------------------------------------------------------------- + subroutine print_values(this) use LandunitType, only : lun use PatchType, only : patch From eed6886a16996d823a49e0ffa0ae7aef06e56542 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 16:15:32 -0600 Subject: [PATCH 283/408] Add note about the call to print_values subroutine used for debugging --- src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index 9bdaa685b0..c8ffb87c32 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -99,6 +99,7 @@ contains this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) + call this%print_values() ! Call print subroutine just to make sure it can be used for debugging do p = bounds%begp, bounds%endp call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot, & @@ -133,7 +134,6 @@ contains this%input%soilstate_inst, this%input%canopystate_inst, this%input%water_inst%waterstatebulk_inst, & this%input%water_inst%waterdiagnosticbulk_inst, this%input%frictionvel_inst) call this%dust_emis%DustDryDep(bounds, this%input%atm2lnd_inst, this%input%frictionvel_inst) - call this%print_values() do p = bounds%begp, bounds%endp call this%validate_patch(p) call this%dust_emis%GetPatchVars( p, flx_mss_vrt_dst_tot=flx_mss_vrt_dst_tot ) From f5407e4c578665fad46438514b480a4738565015 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 17:55:49 -0600 Subject: [PATCH 284/408] Add some comments and change comment about dust-emis object by things asked for in the code review --- src/biogeochem/CNVegStateType.F90 | 2 +- src/biogeochem/DustEmisFactory.F90 | 18 ++++++++++++++++-- 2 files changed, 17 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index 98c1a6ce3a..d63752c5b7 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -519,7 +519,7 @@ subroutine InitCold(this, bounds) ! -------------------------------------------------------------------- ! Initialize terms needed for dust model - ! TODO - move these terms to DustEmisZender2003 module variables + ! TODO - move these terms to DustEmisBase object variables ! -------------------------------------------------------------------- do c = bounds%begc, bounds%endc diff --git a/src/biogeochem/DustEmisFactory.F90 b/src/biogeochem/DustEmisFactory.F90 index 29787c1855..aee4af0a55 100644 --- a/src/biogeochem/DustEmisFactory.F90 +++ b/src/biogeochem/DustEmisFactory.F90 @@ -1,5 +1,9 @@ module DustEmisFactory - + !--------------------------------------------------------------------------- + ! + ! Factory to figure out whihc dust emission method to instantiate + ! + !--------------------------------------------------------------------------- use abortutils , only : endrun use shr_log_mod , only : errMsg => shr_log_errMsg use clm_varctl , only : iulog @@ -15,16 +19,24 @@ module DustEmisFactory contains + !--------------------------------------------------------------------------- + function create_dust_emissions(bounds, NLFilename) result(dust_emis) + !--------------------------------------------------------------------------- + ! Create a dust_emission base class objecct + ! The method implemented depends on namelist input + !--------------------------------------------------------------------------- use DustEmisBase , only : dust_emis_base_type use DustEmisZender2003, only : dust_emis_zender2003_type use clm_varctl , only : dust_emis_method use decompMod , only : bounds_type use shr_kind_mod , only : CL => shr_kind_cl implicit none + ! Arguments class(dust_emis_base_type), allocatable :: dust_emis type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename + ! Local variables character(len=CL) :: method method = dust_emis_method @@ -48,4 +60,6 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis) end function create_dust_emissions -end module DustEmisFactory \ No newline at end of file + !--------------------------------------------------------------------------- + +end module DustEmisFactory From 8e69f12020659b836bec06e7f50a1e2ffe9456fa Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 18:01:16 -0600 Subject: [PATCH 285/408] Use dust_emis_method directly as in the review --- src/biogeochem/DustEmisFactory.F90 | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/DustEmisFactory.F90 b/src/biogeochem/DustEmisFactory.F90 index aee4af0a55..371e77d6dc 100644 --- a/src/biogeochem/DustEmisFactory.F90 +++ b/src/biogeochem/DustEmisFactory.F90 @@ -37,11 +37,8 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis) type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename ! Local variables - character(len=CL) :: method - method = dust_emis_method - - select case ( trim(method) ) + select case ( trim(dust_emis_method) ) case( "Zender_2003" ) allocate(dust_emis, source=dust_emis_zender2003_type() ) @@ -50,7 +47,7 @@ function create_dust_emissions(bounds, NLFilename) result(dust_emis) !case( "Leung_2023" ) ! allocate(dust_emis, source=dust_emis_zender2003_type() ) case default - write(iulog,*) 'ERROR: unknown dust_emis_method: ', method, & + write(iulog,*) 'ERROR: unknown dust_emis_method: ', dust_emis_method, & errMsg(sourcefile, __LINE__) call endrun( "Unrecognized dust_emis_method" ) From e291534b6b058d6e6ea220432a22e2f8cb2fb97d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 18:08:07 -0600 Subject: [PATCH 286/408] Remove the ifs around different dust-emis methods for the Zender case as pointed out in the review --- src/biogeochem/DustEmisZender2003.F90 | 26 +++++--------------------- 1 file changed, 5 insertions(+), 21 deletions(-) diff --git a/src/biogeochem/DustEmisZender2003.F90 b/src/biogeochem/DustEmisZender2003.F90 index e3c4d4115e..cee704ad47 100644 --- a/src/biogeochem/DustEmisZender2003.F90 +++ b/src/biogeochem/DustEmisZender2003.F90 @@ -31,7 +31,6 @@ module DustEmisZender2003 use PatchType , only : patch use ZenderSoilErodStreamType, only : soil_erod_stream_type use DustEmisBase , only : dust_emis_base_type - use clm_varctl , only : dust_emis_method ! ! !PUBLIC TYPES implicit none @@ -160,6 +159,7 @@ end subroutine InitHistory subroutine InitCold(this, bounds) ! + ! Initialize values from a cold start ! !ARGUMENTS: class (dust_emis_zender2003_type) :: this type(bounds_type), intent(in) :: bounds @@ -168,27 +168,11 @@ subroutine InitCold(this, bounds) integer :: c,l !----------------------------------------------------------------------- - ! Set basin factor to 1 for now - - if (dust_emis_method == 'Leung_2023') then - !do c = bounds%begc, bounds%endc - ! l = col%landunit(c) - - ! if (.not.lun%lakpoi(l)) then - ! this%mbl_bsn_fct_col(c) = 1.0_r8 - ! end if - !end do - call endrun( msg="Leung_2023 dust_emis_method is currently not available"//errMsg(sourcefile, __LINE__)) - else if (dust_emis_method == 'Zender_2003') then - if ( this%soil_erod_stream%UseStreams() )then - call this%soil_erod_stream%CalcDustSource( bounds, & - this%mbl_bsn_fct_col(bounds%begc:bounds%endc) ) - else - this%mbl_bsn_fct_col(:) = 1.0_r8 - end if + if ( this%soil_erod_stream%UseStreams() )then + call this%soil_erod_stream%CalcDustSource( bounds, & + this%mbl_bsn_fct_col(bounds%begc:bounds%endc) ) else - write(iulog,*) 'dust_emis_method not recognized = ', trim(dust_emis_method) - call endrun( msg="dust_emis_method namelist item is not valid "//errMsg(sourcefile, __LINE__)) + this%mbl_bsn_fct_col(:) = 1.0_r8 end if end subroutine InitCold From 2060a9d77496feeadb106fdb311485f1b9b99c81 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Jun 2024 18:22:57 -0600 Subject: [PATCH 287/408] Set the veg patch type explicitly to 1 and add some comments regarding it, based on the code review --- .../test/DustEmis_test/test_DustEmisZender2003.pf | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf index c8ffb87c32..8641b8cceb 100644 --- a/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf +++ b/src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf @@ -218,11 +218,18 @@ contains @Test subroutine dust_zero_when_tlai_high(this) + use PatchType, only : patch ! Check dust emissions are zero when LAI is high enough class(TestDustEmisZender2003), intent(inout) :: this integer :: p real(r8) :: flx_mss_vrt_dst_tot + ! Explicitly set the patch type to a hard-coded 1 (so NOT bare-soil) + ! pft indices can't be used without reading them from the parameter file + ! + ! To do this fully the subgrid setup in unittestDustEmisInputs to baresoil + ! should really be run again. But, just doing this is likely sufficient for testing + patch%itype(bounds%begp:bounds%endp) = 1 call this%input%create_atm2lnd() call this%input%create_fv( ) this%input%canopystate_inst%tlai_patch(:) = 0.3_r8 From 787c2f2600212685ee4df732fe2bf33797084fb6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 18 Jun 2024 15:37:04 -0600 Subject: [PATCH 288/408] Improve a comment. --- cime_config/SystemTests/rxcropmaturity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index a583432efe..7a179cdf56 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -455,7 +455,7 @@ def _run_generate_gdds(self, case_gddgen): self._gdds_file = generated_gdd_files[0] def _run_interpolate_gdds(self): - # Save where? + # File where interpolated GDDs should be saved self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc") # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds. From 752ba73b9df6cf4997685789f2dc2fa1962768e8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 18 Jun 2024 15:38:39 -0600 Subject: [PATCH 289/408] Describe rxcropmaturity suite in testlist_clm.xml. --- cime_config/testdefs/testlist_clm.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 432f8e3e9a..5443acf2d7 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -10,6 +10,7 @@ prebeta: Run before CESM beta tags (more extensive, but should have tests outside of prealpha) (subset of aux_clm tests) aux_cime_baselines: CESM cime baselines (subset of aux_clm tests) hillslope: Experimental test list used for the hillslope option of the model + rxcropmaturity: Short tests to be run during development related to prescribed crop calendars --> From 400c4590ba07db052c6903bf48ee5cc54856497e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jun 2024 11:03:23 -0600 Subject: [PATCH 290/408] Remove some commented-out code from check_rx_obeyed. --- python/ctsm/crop_calendars/check_rx_obeyed.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/python/ctsm/crop_calendars/check_rx_obeyed.py b/python/ctsm/crop_calendars/check_rx_obeyed.py index 383ebbf1e0..4d8ccd1788 100644 --- a/python/ctsm/crop_calendars/check_rx_obeyed.py +++ b/python/ctsm/crop_calendars/check_rx_obeyed.py @@ -114,8 +114,6 @@ def summarize_results(which_ds, output_var, verbose, all_ok, gdd_tolerance, diff print(f"✅ {which_ds}: Prescribed {output_var} always obeyed") elif all_ok == 1: bad = False - # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:") - # for x in diff_str_list: print(x) print( f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable (diffs <= " + f"{gdd_tolerance})" From d01520b9000b32de107dcbef35b483ec966c9dc8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jun 2024 11:11:09 -0600 Subject: [PATCH 291/408] Add reference to issue ESCOMP/CTSM#2603. https://github.com/ESCOMP/CTSM/issues/2603 --- cime_config/SystemTests/rxcropmaturity.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 7a179cdf56..31deb1442b 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -424,6 +424,7 @@ def _run_generate_gdds(self, case_gddgen): hdates_file = self._hdatefile # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds. + # See https://github.com/ESCOMP/CTSM/issues/2603 tool_path = os.path.join( self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py" ) @@ -459,6 +460,7 @@ def _run_interpolate_gdds(self): self._gdds_file = os.path.join(self._get_caseroot(), "interpolated_gdds.nc") # It'd be much nicer to call interpolate_gdds.main(), but I can't import interpolate_gdds. + # See https://github.com/ESCOMP/CTSM/issues/2603 tool_path = os.path.join( self._ctsm_root, "python", "ctsm", "crop_calendars", "interpolate_gdds.py" ) From 98e3689e04a2ad2ef2de4c893cab2cf91007aebb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jun 2024 11:29:05 -0600 Subject: [PATCH 292/408] rxcropmaturity: Wrap two long comments. --- cime_config/SystemTests/rxcropmaturity.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 31deb1442b..d25bd015ca 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -36,7 +36,9 @@ def __init__(self, case): full_test = "RXCROPMATURITY_" in casebaseid skipgen_test = "RXCROPMATURITYSKIPGEN_" in casebaseid - # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency. + # Ensure run length is at least 5 years. Minimum to produce one complete growing season + # (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season + # usable for GDD generation, so you can't check for season-to-season consistency. stop_n = self._case.get_value("STOP_N") stop_option = self._case.get_value("STOP_OPTION") stop_n_orig = stop_n @@ -68,7 +70,10 @@ def __init__(self, case): + f"{stop_n_orig} {stop_option_orig[1:]}" ) elif skipgen_test and stop_n < 3: - # First year is discarded because crops are already in the ground at restart, and those aren't affected by the new crop calendar inputs. The second year is useable, but we need a third year so that all crops planted in the second year have a chance to finish. + # First year is discarded because crops are already in the ground at restart, and those + # aren't affected by the new crop calendar inputs. The second year is useable, but we + # need a third year so that all crops planted in the second year have a chance to + # finish. error_message = ( "RXCROPMATURITYSKIPGEN (both-forced part) must be run for at least 3 years; you requested " + f"{stop_n_orig} {stop_option_orig[1:]}" From 7f2a5c0192aa8f8b842e06259d46f8c095f2ee2b Mon Sep 17 00:00:00 2001 From: wwieder Date: Thu, 20 Jun 2024 14:25:27 -0600 Subject: [PATCH 293/408] addresses #2563 --- py_env_create | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/py_env_create b/py_env_create index 9a9b8d940c..ac705edb3c 100755 --- a/py_env_create +++ b/py_env_create @@ -122,7 +122,7 @@ if [ "$verbose" == "Yes" ]; then verbosity="--verbose" loglevel="INFO" fi -cmd="conda install --yes $verbosity --channel conda-forge --name $ctsm_python $condadir/$condafile $option" +cmd="conda install --yes $verbosity --channel conda-forge --name $ctsm_python --file $condadir/$condafile $option" echo "$cmd" $cmd if [ $? != 0 ]; then From 23b62613040d3c926a134e7068406289a2edfeae Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 20 Jun 2024 15:36:43 -0600 Subject: [PATCH 294/408] Draft ChangeLog/ChangeSum --- doc/ChangeLog | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 81 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 8b6bb8f0d2..e83b64c564 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,84 @@ =============================================================== +Tag name: tmp-240620.n01.ctsm5.2.007 +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Thu 20 Jun 2024 03:00:43 PM MDT +One-line Summary: Merge b4b-dev + +Purpose and description of changes +---------------------------------- + + Fix long names #2512 + Dust emissions moved to Object Oriented design #2552 + Fix RXCROPMATURITY test #2599 + + NB: This is the first temporary tag (n01, see full tag name above) in + a series of temporary tags while we wait for the completion of the + beta01 cesm tag. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: + Fixes #2512 + Fixes #2552 + Fixes #2599 + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: + Fix RXCROPMATURITY test #2599 + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- IN PROG + izumi ------- IN PROG + + any other testing (give details below): + + ctsm_sci + derecho ---- + +Answer changes +-------------- +Changes answers relative to baseline: No + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2604 + +=============================================================== +=============================================================== Tag name: ctsm5.2.007 Originator(s): jedwards4b (Jim Edwards, UCAR/CGD) slevis (Sam Levis, UCAR/CGD) Date: Fri 31 May 2024 13:49:29 AM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index b3f1632571..ace44b8037 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ +tmp-240620.n01.cts slevis 06/20/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems From d3e68143a2ca5e52568965a666cd6c53be7d0434 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 20 Jun 2024 17:30:14 -0600 Subject: [PATCH 295/408] Temporary .gitmodules points to the branches of the modules that changed --- .gitmodules | 20 ++++++++++---------- ccs_config | 2 +- components/cism | 2 +- components/cmeps | 2 +- components/mosart | 2 +- components/rtm | 2 +- 6 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.gitmodules b/.gitmodules index 699ad22969..e1df4e650c 100644 --- a/.gitmodules +++ b/.gitmodules @@ -7,22 +7,22 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release [submodule "cism"] path = components/cism -url = https://github.com/ESCOMP/CISM-wrapper -fxtag = cismwrap_2_2_001 +url = https://github.com/mvertens/CISM-wrapper +fxtag = 34339777afa7b810fd4822fce1039826668b33e4 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper [submodule "rtm"] path = components/rtm -url = https://github.com/ESCOMP/RTM -fxtag = rtm1_0_79 +url = https://github.com/swensosc/RTM +fxtag = 420c5979d8abf05184992fdfba5ac41c41c91c2e fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/RTM [submodule "mosart"] path = components/mosart -url = https://github.com/ESCOMP/MOSART -fxtag = mosart1_0_49 +url = https://github.com/mvertens/MOSART +fxtag = 01f40dcf589d4e6c5932c76128e3d42faea91e9f fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/MOSART @@ -35,8 +35,8 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute [submodule "ccs_config"] path = ccs_config -url = https://github.com/ESMCI/ccs_config_cesm.git -fxtag = ccs_config_cesm0.0.106 +url = https://github.com/mvertens/ccs_config_cesm.git +fxtag = dbb02c0ccd1492fe278885f8a07a71fa80064319 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git @@ -49,8 +49,8 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime [submodule "cmeps"] path = components/cmeps -url = https://github.com/ESCOMP/CMEPS.git -fxtag = cmeps0.14.63 +url = https://github.com/mvertens/CMEPS.git +fxtag = 4dca7c602e54189b74b1d0195c433d1b83475553 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git diff --git a/ccs_config b/ccs_config index 2ff978f92a..dbb02c0ccd 160000 --- a/ccs_config +++ b/ccs_config @@ -1 +1 @@ -Subproject commit 2ff978f92a5ac9a6ab243e5c14d06a7e2d2f5799 +Subproject commit dbb02c0ccd1492fe278885f8a07a71fa80064319 diff --git a/components/cism b/components/cism index c05dd5c4fc..34339777af 160000 --- a/components/cism +++ b/components/cism @@ -1 +1 @@ -Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928 +Subproject commit 34339777afa7b810fd4822fce1039826668b33e4 diff --git a/components/cmeps b/components/cmeps index 6384ff4e4a..4dca7c602e 160000 --- a/components/cmeps +++ b/components/cmeps @@ -1 +1 @@ -Subproject commit 6384ff4e4a6bc82a678f9419a43ffbd5d53ac209 +Subproject commit 4dca7c602e54189b74b1d0195c433d1b83475553 diff --git a/components/mosart b/components/mosart index 8c682b1b7f..01f40dcf58 160000 --- a/components/mosart +++ b/components/mosart @@ -1 +1 @@ -Subproject commit 8c682b1b7f15d146816de302e0d359da3e957056 +Subproject commit 01f40dcf589d4e6c5932c76128e3d42faea91e9f diff --git a/components/rtm b/components/rtm index 88503adbc2..420c5979d8 160000 --- a/components/rtm +++ b/components/rtm @@ -1 +1 @@ -Subproject commit 88503adbc275fb2ccbb6b598e460deaeb140e515 +Subproject commit 420c5979d8abf05184992fdfba5ac41c41c91c2e From a8f1daa14affaca9ddb21b51fe4cd49f6f1e8771 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 21 Jun 2024 09:20:45 -0600 Subject: [PATCH 296/408] Add header with notes on variables (copied from the CESM header) --- .gitmodules | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/.gitmodules b/.gitmodules index 699ad22969..8a173f0ddd 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +1,30 @@ +# This is a git submodule file with additional support for +# git-fleximod (https://github.com/ESMCI/git-fleximod) +# +# The additional flags supported by git-fleximod are +# fxtag - the tag associated with the submodule, this tag can be tested for +# consistancy with the submodule hash using git-fleximod status +# the hash can be updated to the tag using git-fleximod update +# +# fxrequired - indicates if a given submodule should be checked out on install +# submoudules can be toplevel or internal and required or optional +# toplevel means that the submodule should only be checked out if the +# module is the toplevel of the git repo (is not a submodule itself) +# internal means that the submodule is needed by the component whether +# the component is toplevel or the submodule of another repo +# required means that the submodule should always be checked out +# optional means that the submodule should only be checked out if the +# optional flag is provided to git-fleximod or the submodule name is +# explicitly listed on the git-fleximod command line. +# +# fxsparse - this is a path to a git sparse checkout file indicating that the +# submodule should be checked out in sparse mode +# +# fxDONOTUSEurl - this field is used by git-fleximod test to insure that the url is pointing +# to the official url of the repo and not to an unofficial fork. +# It is intended for use of github workflows to test commits to protected +# repository branches. +# [submodule "fates"] path = src/fates url = https://github.com/NGEET/fates From f7b9b29d686d88abef3e3b29a561598ae9a80da7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 21 Jun 2024 09:46:49 -0600 Subject: [PATCH 297/408] Update ChangeLog/ChangeSum --- doc/ChangeLog | 6 +++--- doc/ChangeSum | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index e83b64c564..e6e9215397 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: tmp-240620.n01.ctsm5.2.007 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Thu 20 Jun 2024 03:00:43 PM MDT +Date: Fri 21 Jun 2024 09:42:26 AM MDT One-line Summary: Merge b4b-dev Purpose and description of changes @@ -60,8 +60,8 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- IN PROG - izumi ------- IN PROG + derecho ----- OK + izumi ------- OK any other testing (give details below): diff --git a/doc/ChangeSum b/doc/ChangeSum index ace44b8037..a612b7d2d1 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ -tmp-240620.n01.cts slevis 06/20/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) +tmp-240620.n01.cts slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems From 64f1229cebd936536967a9522af703079379d7e3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 21 Jun 2024 13:56:04 -0600 Subject: [PATCH 298/408] Add note about each fxDONOTUSEurl line --- .gitmodules | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/.gitmodules b/.gitmodules index 8a173f0ddd..e437f56d61 100644 --- a/.gitmodules +++ b/.gitmodules @@ -30,6 +30,7 @@ path = src/fates url = https://github.com/NGEET/fates fxtag = sci.1.73.0_api.35.0.0 fxrequired = AlwaysRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/NCAR/fates-release [submodule "cism"] @@ -37,6 +38,7 @@ path = components/cism url = https://github.com/ESCOMP/CISM-wrapper fxtag = cismwrap_2_2_001 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper [submodule "rtm"] @@ -44,6 +46,7 @@ path = components/rtm url = https://github.com/ESCOMP/RTM fxtag = rtm1_0_79 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESCOMP/RTM [submodule "mosart"] @@ -51,6 +54,7 @@ path = components/mosart url = https://github.com/ESCOMP/MOSART fxtag = mosart1_0_49 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESCOMP/MOSART [submodule "mizuRoute"] @@ -58,6 +62,7 @@ path = components/mizuRoute url = https://github.com/ESCOMP/mizuRoute fxtag = cesm-coupling.n02_v2.1.2 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute [submodule "ccs_config"] @@ -65,6 +70,7 @@ path = ccs_config url = https://github.com/ESMCI/ccs_config_cesm.git fxtag = ccs_config_cesm0.0.106 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git [submodule "cime"] @@ -72,6 +78,7 @@ path = cime url = https://github.com/ESMCI/cime fxtag = cime6.0.246 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESMCI/cime [submodule "cmeps"] @@ -79,6 +86,7 @@ path = components/cmeps url = https://github.com/ESCOMP/CMEPS.git fxtag = cmeps0.14.63 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git [submodule "cdeps"] @@ -86,6 +94,7 @@ path = components/cdeps url = https://github.com/ESCOMP/CDEPS.git fxtag = cdeps1.0.34 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git [submodule "share"] @@ -93,6 +102,7 @@ path = share url = https://github.com/ESCOMP/CESM_share fxtag = share1.0.19 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share [submodule "mct"] @@ -100,6 +110,7 @@ path = libraries/mct url = https://github.com/MCSclimate/MCT fxtag = MCT_2.11.0 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/MCSclimate/MCT [submodule "parallelio"] @@ -107,6 +118,7 @@ path = libraries/parallelio url = https://github.com/NCAR/ParallelIO fxtag = pio2_6_2 fxrequired = ToplevelRequired +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/NCAR/ParallelIO [submodule "doc-builder"] @@ -114,4 +126,5 @@ path = doc/doc-builder url = https://github.com/ESMCI/doc-builder fxtag = v1.0.8 fxrequired = ToplevelOptional +# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/ESMCI/doc-builder From 540d87fcc791c68ecac02eb786ca58a2e6874b9c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 21 Jun 2024 16:34:58 -0600 Subject: [PATCH 299/408] Update .gitmodules with latest mosart commit --- .gitmodules | 2 +- components/mosart | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitmodules b/.gitmodules index e1df4e650c..3d3cb88e80 100644 --- a/.gitmodules +++ b/.gitmodules @@ -22,7 +22,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/RTM [submodule "mosart"] path = components/mosart url = https://github.com/mvertens/MOSART -fxtag = 01f40dcf589d4e6c5932c76128e3d42faea91e9f +fxtag = ca0acc0336365456bec653c4c233abb57d9bc62d fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/MOSART diff --git a/components/mosart b/components/mosart index 01f40dcf58..ca0acc0336 160000 --- a/components/mosart +++ b/components/mosart @@ -1 +1 @@ -Subproject commit 01f40dcf589d4e6c5932c76128e3d42faea91e9f +Subproject commit ca0acc0336365456bec653c4c233abb57d9bc62d From 596dc135a49918c225ce726122874ed55611ad87 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 21 Jun 2024 17:52:16 -0600 Subject: [PATCH 300/408] Update .gitmodules with new mosart and rtm tags --- .gitmodules | 8 ++++---- components/mosart | 2 +- components/rtm | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.gitmodules b/.gitmodules index 3d3cb88e80..6d4298befc 100644 --- a/.gitmodules +++ b/.gitmodules @@ -14,15 +14,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper [submodule "rtm"] path = components/rtm -url = https://github.com/swensosc/RTM -fxtag = 420c5979d8abf05184992fdfba5ac41c41c91c2e +url = https://github.com/ESCOMP/RTM +fxtag = rtm1_0_80 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/RTM [submodule "mosart"] path = components/mosart -url = https://github.com/mvertens/MOSART -fxtag = ca0acc0336365456bec653c4c233abb57d9bc62d +url = https://github.com/ESCOMP/MOSART +fxtag = mosart1.1.02 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/MOSART diff --git a/components/mosart b/components/mosart index ca0acc0336..e2ffe00004 160000 --- a/components/mosart +++ b/components/mosart @@ -1 +1 @@ -Subproject commit ca0acc0336365456bec653c4c233abb57d9bc62d +Subproject commit e2ffe00004cc416cfc8bcfae2a949474075c1d1f diff --git a/components/rtm b/components/rtm index 420c5979d8..b3dfcfbba5 160000 --- a/components/rtm +++ b/components/rtm @@ -1 +1 @@ -Subproject commit 420c5979d8abf05184992fdfba5ac41c41c91c2e +Subproject commit b3dfcfbba58c151ac5a6ab513b3515ef3deff798 From c2e471833dfbbb95bac1e3bf31ddf5de8d16e5f1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 21 Jun 2024 22:23:47 -0600 Subject: [PATCH 301/408] Update change files --- doc/ChangeLog | 4 +--- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 4da6b9379f..c4e7ca469e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: tmp-240620.n02.ctsm5.2.007 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Thu 13 Jun 2024 01:13:24 PM MDT +Date: Fri 21 Jun 2024 10:21:01 PM MDT One-line Summary: Another update of git-fleximod Purpose and description of changes @@ -47,8 +47,6 @@ Changes to documentation: Notes of particular relevance for developers: --------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -[Remove any lines that don't apply. Remove entire section if nothing applies.] Testing summary: regular diff --git a/doc/ChangeSum b/doc/ChangeSum index 029f88fe7e..0bffb18cf4 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ -tmp-240620.n02.ctsm5.2.007 erik 06/13/2024 Another update of git-fleximod +tmp-240620.n02.ctsm5.2.007 erik 06/21/2024 Another update of git-fleximod tmp-240620.n01.ctsm5.2.007 slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools From 5f5c10a30cb78b6d5b8a8c80d545ca5c980303de Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Mon, 24 Jun 2024 10:35:14 -0600 Subject: [PATCH 302/408] Turn off explicit ac for clm6_0 and clm5_1 --- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 4b8b7d3571..d0a45c5727 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -147,8 +147,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). NONE -.true. -.true. +.false. +.false. .false. .false. From 463fac1241827d975948a418dc6a9c90ee34fbc0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 24 Jun 2024 17:32:47 -0600 Subject: [PATCH 303/408] Minor comment updates --- bld/CLMBuildNamelist.pm | 4 ++-- bld/unit_testers/build-namelist_test.pl | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 44aa07ee28..d0d9328218 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4678,14 +4678,14 @@ sub setup_logic_cnmatrix { if ( &value_is_true($nl->get_value("use_matrixcn")) && &value_is_true($nl_flags->{"for_testing_use_repr_structure_pool"}) ) { $log->fatal_error("for_testing_use_repr_structure_pool can NOT be on when use_matrixcn is on" ); } - # If both matrixcn and soil_matrix are off outmatrix can't be on + # If both matrixcn and soil_matrix are off hist_wrt_matrixcn_diag can't be on if ( ! &value_is_true($nl->get_value("use_matrixcn")) && ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) { my $var = "hist_wrt_matrixcn_diag"; if ( &value_is_true($nl->get_value($var)) ) { $log->fatal_error("$var can NOT be on when both use_matrixcn and use_soil_matrixcn are off" ); } } - # If soil_matrix is off ispspinup can't be on + # If soil_matrix is off spinup_matrixcn can't be on if ( ! &value_is_true($nl_flags->{"use_soil_matrixcn"}) ) { my $var = "spinup_matrixcn"; if ( &value_is_true($nl->get_value($var)) ) { diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 28a2392736..9b83f9e7ec 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -942,12 +942,12 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, - "outmatrixWOmatrix" =>{ options=>"-envxml_dir . -bgc bgc", + "matrixcn_diagWOmatrix" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_soil_matrixcn=.false.,use_matrixcn=F,hist_wrt_matrixcn_diag=T", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", }, - "spinupWOsoilmatrix" =>{ options=>"-envxml_dir . -bgc bgc", + "spinupWOsoilmatrix" =>{ options=>"-envxml_dir . -bgc bgc", namelst=>"use_soil_matrixcn=F,use_matrixcn=T,spinup_matrixcn=T", GLC_TWO_WAY_COUPLING=>"TRUE", phys=>"clm5_0", From 47234a9d429e29612599bcf0590e647b895c28d2 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 24 Jun 2024 18:06:30 -0600 Subject: [PATCH 304/408] Add overridable warning that cnmatrix may fail in transient mode --- bld/CLMBuildNamelist.pm | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index d0d9328218..ffe1c4e522 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4650,6 +4650,16 @@ sub setup_logic_cnmatrix { , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); } @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" ); + # Matrix items can't be on for transient + $nl_flags->{'flanduse_timeseries'} = "null"; + my $flanduse_timeseries = $nl->get_value('flanduse_timeseries'); + if ( $flanduse_timeseries ne "null" ) { + foreach my $var ( @matrixlist ) { + if ( &value_is_true($nl->get_value($var)) ) { + $log->warning("$var may FAIL with balance error in transient mode" ); + } + } + } # Matrix items can't be on for SP mode if ( $nl_flags->{'bgc_mode'} eq "sp" ) { foreach my $var ( @matrixlist ) { From 18e63e354e604d43c6dd0bca4a43abef3f4480ee Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 25 Jun 2024 12:02:01 -0600 Subject: [PATCH 305/408] Abort if matrixcn is .true. and nrepr is not 1 --- src/biogeochem/CropReprPoolsMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/biogeochem/CropReprPoolsMod.F90 b/src/biogeochem/CropReprPoolsMod.F90 index dcbb4e4fd9..695af9f00e 100644 --- a/src/biogeochem/CropReprPoolsMod.F90 +++ b/src/biogeochem/CropReprPoolsMod.F90 @@ -98,6 +98,10 @@ subroutine crop_repr_pools_init() end if nrepr = nrepr_grain + nrepr_structure + ! matrixcn works with nrepr = 1 only + if (use_matrixcn .and. nrepr != 1) then + call endrun(msg="ERROR: nrepr should be 1 when use_matrixcn = .true."//errMsg(sourcefile, __LINE__)) + end if allocate(repr_hist_fnames(nrepr)) allocate(repr_rest_fnames(nrepr)) allocate(repr_longnames(nrepr)) From 422f06f7389094b32baa763628865a53467d0830 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 25 Jun 2024 13:33:42 -0700 Subject: [PATCH 306/408] add fates potential vegetation spin up to transient test mod --- cime_config/testdefs/testlist_clm.xml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 85824a4404..0706a1ef53 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2615,6 +2615,15 @@ + + + + + + + + + From f9d8349021458c56912edf626a0c8e229e4f58da Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 25 Jun 2024 13:53:01 -0700 Subject: [PATCH 307/408] rename fates luh2 harvest modes --- .../include_user_mods | 0 .../{FatesColdLUH2Mode3 => FatesColdLUH2HarvestArea}/user_nl_clm | 0 .../include_user_mods | 0 .../{FatesColdLUH2Mode1 => FatesColdLUH2HarvestEvent}/user_nl_clm | 0 .../include_user_mods | 0 .../{FatesColdLUH2Mode4 => FatesColdLUH2HarvestMass}/user_nl_clm | 0 .../include_user_mods | 0 .../{FatesColdLUH2Mode2 => FatesColdLUH2HarvestSurf}/user_nl_clm | 0 .../include_user_mods | 0 .../{FatesColdLUH2Mode0 => FatesColdLUH2NoHarvest}/user_nl_clm | 0 10 files changed, 0 insertions(+), 0 deletions(-) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode0 => FatesColdLUH2HarvestArea}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode3 => FatesColdLUH2HarvestArea}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode1 => FatesColdLUH2HarvestEvent}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode1 => FatesColdLUH2HarvestEvent}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode2 => FatesColdLUH2HarvestMass}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode4 => FatesColdLUH2HarvestMass}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode3 => FatesColdLUH2HarvestSurf}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode2 => FatesColdLUH2HarvestSurf}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode4 => FatesColdLUH2NoHarvest}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2Mode0 => FatesColdLUH2NoHarvest}/user_nl_clm (100%) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode1/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode3/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode2/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode4/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2Mode0/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm From f8330c9a7fba12652562efbc87a56f0de358b669 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 25 Jun 2024 17:16:45 -0600 Subject: [PATCH 308/408] Correct earlier commit 47234a9: warning about cnmatrix and transient --- bld/CLMBuildNamelist.pm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index ffe1c4e522..329030d985 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4651,9 +4651,7 @@ sub setup_logic_cnmatrix { } @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" ); # Matrix items can't be on for transient - $nl_flags->{'flanduse_timeseries'} = "null"; - my $flanduse_timeseries = $nl->get_value('flanduse_timeseries'); - if ( $flanduse_timeseries ne "null" ) { + if (not string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { foreach my $var ( @matrixlist ) { if ( &value_is_true($nl->get_value($var)) ) { $log->warning("$var may FAIL with balance error in transient mode" ); From 17143eea0e9c447eca85bde97b7f1dda7c2b1ffe Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 25 Jun 2024 17:24:15 -0600 Subject: [PATCH 309/408] Correct earlier commit 18e63e3: abort if matrixcn and nrepr not 1 --- src/biogeochem/CropReprPoolsMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CropReprPoolsMod.F90 b/src/biogeochem/CropReprPoolsMod.F90 index 695af9f00e..cbc2f3e2a2 100644 --- a/src/biogeochem/CropReprPoolsMod.F90 +++ b/src/biogeochem/CropReprPoolsMod.F90 @@ -99,7 +99,7 @@ subroutine crop_repr_pools_init() nrepr = nrepr_grain + nrepr_structure ! matrixcn works with nrepr = 1 only - if (use_matrixcn .and. nrepr != 1) then + if (use_matrixcn .and. nrepr /= 1) then call endrun(msg="ERROR: nrepr should be 1 when use_matrixcn = .true."//errMsg(sourcefile, __LINE__)) end if allocate(repr_hist_fnames(nrepr)) From 4b18e79ae14e8c56c51b718aad722ce679b37972 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 25 Jun 2024 17:29:56 -0600 Subject: [PATCH 310/408] Replace clm45_monthly_matrixcn_soilCN30 testmod and test with clm60 --- .../clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm | 2 -- .../include_user_mods | 0 .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm | 4 ++++ 3 files changed, 4 insertions(+), 2 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm rename cime_config/testdefs/testmods_dirs/clm/{clm45_monthly_matrixcn_soilCN30 => clm60_monthly_matrixcn_soilCN30}/include_user_mods (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm deleted file mode 100644 index c7436f5acb..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ - use_soil_matrixcn = .true. - paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm45_params.soilCN30.c220321.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/clm45_monthly_matrixcn_soilCN30/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm new file mode 100644 index 0000000000..d22154bef6 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm @@ -0,0 +1,4 @@ +use_soil_matrixcn = .true. +paramfile = '/glade/u/home/slevis/paramfiles/ctsm60_params_cn30.c240625.nc' +! If we keep this paramfile, it should move to the repository +! paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240625.nc' From 1761a7becb50cad2849db794243b1f2d37e602c3 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 25 Jun 2024 17:34:50 -0600 Subject: [PATCH 311/408] Move new param file to inputdata and rimport --- .../clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm index d22154bef6..df20ced9e8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm @@ -1,4 +1,2 @@ use_soil_matrixcn = .true. -paramfile = '/glade/u/home/slevis/paramfiles/ctsm60_params_cn30.c240625.nc' -! If we keep this paramfile, it should move to the repository -! paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240625.nc' +paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240625.nc' From 1e97001d0dc5e7359d8fb3b11c37118e3e429fe3 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 25 Jun 2024 17:59:00 -0600 Subject: [PATCH 312/408] Change use_matrixcn, use_soil_matrixcn to default .false. before merge --- bld/namelist_files/namelist_defaults_ctsm.xml | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 90e397d544..933b504606 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -618,19 +618,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case). +.false. .true. -.true. -.false. -.false. -.false. - +.false. .true. -.true. -.false. -.false. -.false. -.false. .false. .false. From 7feb6572d51e5d3ba2596ae9a1b4ededd045928d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 25 Jun 2024 18:04:46 -0600 Subject: [PATCH 313/408] Rm redunant LG* and LR* tests and corresponding expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 13 ------------- cime_config/testdefs/testlist_clm.xml | 20 -------------------- 2 files changed, 33 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 5968e73760..664b1c8e35 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -58,19 +58,6 @@ - - - FAIL - #640, same test with clm-ciso_soil_matrixcn_only works - - - - - FAIL - #640, same test with clm-ciso_soil_matrixcn_only works - - - FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 9a2390bd58..625a9f3504 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3386,26 +3386,6 @@ - - - - - - - - - - - - - - - - - - - - From 5a46b9382ee15fea803cb5e7091ed6915c2169a1 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 26 Jun 2024 10:53:02 -0700 Subject: [PATCH 314/408] remove fates land use no harvest due to overlap --- .../testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods | 1 - .../testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm | 1 - 2 files changed, 2 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods deleted file mode 100644 index 7eb8bb1579..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm deleted file mode 100644 index b3b338e232..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2NoHarvest/user_nl_clm +++ /dev/null @@ -1 +0,0 @@ -fates_harvest_mode = no_harvest From 3318d3b46df34013afcb5fadc4ad9f4184779f28 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 26 Jun 2024 11:03:10 -0700 Subject: [PATCH 315/408] update fates landuse harvest test mod names --- cime_config/testdefs/testlist_clm.xml | 19 +++++-------------- 1 file changed, 5 insertions(+), 14 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 0706a1ef53..ed0627f242 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2570,7 +2570,7 @@ - + @@ -2579,7 +2579,7 @@ - + @@ -2588,7 +2588,7 @@ - + @@ -2597,16 +2597,7 @@ - - - - - - - - - - + @@ -2621,7 +2612,7 @@ - + From f15eadec091721e236f0c83af26cc99ad2b1754e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 26 Jun 2024 12:10:24 -0600 Subject: [PATCH 316/408] Repl. NIWO with HARV in a test and update expected fails for two tests --- cime_config/testdefs/ExpectedTestFails.xml | 17 +---------------- cime_config/testdefs/testlist_clm.xml | 2 +- 2 files changed, 2 insertions(+), 17 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 156bee9f80..cf348c0f8d 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -58,15 +58,11 @@ - + FAIL #2310 - - FAIL - #2310 - @@ -80,17 +76,6 @@ - - - FAIL - #2310 - - - FAIL - #2310 - - - FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 049d9cf873..fee8e1a429 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1873,7 +1873,7 @@ - + From ddef21bdde3fdbe0990a45b6997393faaa70ccde Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 26 Jun 2024 12:35:58 -0600 Subject: [PATCH 317/408] Correction to the expected-fails update for one of the tests --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index cf348c0f8d..c5d8a85724 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -76,6 +76,13 @@ + + + FAIL + #2310 + + + FAIL From 5427891e02b3d6e4292e30ac3a1f827394a294d5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 26 Jun 2024 12:50:25 -0600 Subject: [PATCH 318/408] Revert last correction (it was fine to begin with) --- cime_config/testdefs/ExpectedTestFails.xml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index c5d8a85724..cf348c0f8d 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -76,13 +76,6 @@ - - - FAIL - #2310 - - - FAIL From b0c79e1c2ccde049102caf390656b123503a648a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 26 Jun 2024 12:54:34 -0600 Subject: [PATCH 319/408] Make one more update to expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index cf348c0f8d..a62a25151a 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -244,10 +244,6 @@ FAIL #2310 - - FAIL - #2310 - From 34c4db0b185b4cb62fc6fa22de96b23c949c0dfd Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 26 Jun 2024 23:47:14 -0700 Subject: [PATCH 320/408] Revert "Apply relevant changes from rgknox/fates-auto-params." This reverts commit 7216006b1c2400d1ca2932899671f9bcec85b6af. --- .../testdefs/testmods_dirs/clm/Fates/shell_commands | 5 ----- .../testdefs/testmods_dirs/clm/Fates/user_nl_clm | 1 - .../testdefs/testmods_dirs/clm/_scripts/README | 2 -- .../clm/_scripts/get_fates_shell_commands_vars.sh | 11 ----------- 4 files changed, 19 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/_scripts/README delete mode 100755 cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands index 3443bacef0..41a2342a51 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/shell_commands @@ -1,7 +1,2 @@ ./xmlchange CLM_BLDNML_OPTS="-no-megan" --append ./xmlchange BFBFLAG="TRUE" - -SRCROOT=`./xmlquery SRCROOT --value` -. "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh - -ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 57adea1ff6..91df3e2e61 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -4,7 +4,6 @@ hist_nhtfrq = -24 hist_empty_htapes = .true. hist_ndens = 1 fates_spitfire_mode = 1 -fates_paramfile='${SRCROOT}/src/fates/parameter_files/binaries/${CASE}-params.nc' hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', 'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON', diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/README b/cime_config/testdefs/testmods_dirs/clm/_scripts/README deleted file mode 100644 index 66eb22a375..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/_scripts/README +++ /dev/null @@ -1,2 +0,0 @@ -This directory contains scripts that can be called in -shell_commands of multiple testmods. diff --git a/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh b/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh deleted file mode 100755 index 382fb4e53e..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh +++ /dev/null @@ -1,11 +0,0 @@ -# This script should be called in shell_commands with -# . "${SRCROOT}"/cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh -# where the leading period ensures it's run in the same shell. - -CASE=`./xmlquery CASE --value` -FATESDIR="${SRCROOT}/src/fates" -FATESPARAMDIR="${SRCROOT}/src/fates/parameter_files/binaries" -mkdir -p "${FATESPARAMDIR}" -FATESPARAMFILE="${FATESPARAMDIR}/${CASE}-params.nc" - -# No exit status because it should be called in the same shell. From 6f3a068cc301039ce7eb6ce98fc062f4a1257bb0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Jun 2024 14:22:32 -0600 Subject: [PATCH 321/408] Finish fsat_hillslope merge (update ChangeLog/Sum). --- doc/ChangeLog | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 60 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index c4e7ca469e..05b43c20ab 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,63 @@ =============================================================== +Tag name: tmp-240620.n03.ctsm5.2.007 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Thu Jun 27 14:17:02 MDT 2024 +One-line Summary: Set upland hillslope column fsat values to zero + +Purpose and description of changes +---------------------------------- + +The topmodel-based fsat surface runoff scheme is not appropriate for upland hillslope columns, so set upland hillslope column fsat values to zero. User can revert this behavior by setting hillslope_fsat_equals_zero to false. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- Added parameter hillslope_fsat_equals_zero (default true). Set to false for previous behavior. + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- DIFF + izumi ------- DIFF + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, but only for hillslope tests. + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +- ESCOMP/CTSM#2600 (https://github.com/ESCOMP/CTSM/pull/2600) + +=============================================================== +=============================================================== Tag name: tmp-240620.n02.ctsm5.2.007 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Fri 21 Jun 2024 10:21:01 PM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index 0bffb18cf4..7dd063df45 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ +tmp-240620.n03.ctsm5.2.007 samrabin 06/27/2024 Set upland hillslope column fsat values to zero tmp-240620.n02.ctsm5.2.007 erik 06/21/2024 Another update of git-fleximod tmp-240620.n01.ctsm5.2.007 slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly From 99d0f2bb4c93c739e5875781070a3d66c6bb8cbd Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jun 2024 16:56:21 -0700 Subject: [PATCH 322/408] move fates landuse test mods to fates suite --- cime_config/testdefs/testlist_clm.xml | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index ef4358f763..347fd33e8e 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2573,8 +2573,7 @@ - - + @@ -2582,8 +2581,7 @@ - - + @@ -2591,8 +2589,7 @@ - - + @@ -2600,8 +2597,7 @@ - - + @@ -2609,8 +2605,7 @@ - - + From 535033b959f6eab9c5d39d7edff410c47dfacb80 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jun 2024 17:11:47 -0700 Subject: [PATCH 323/408] remove flandusepft and fluh_times pointers for testmod Use default currently. --- .../testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm | 2 -- 1 file changed, 2 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm index 970e7df7cd..e25490ffbb 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm @@ -2,10 +2,8 @@ ! Run a transient case, with vegetation starting from bare ground, but land use starting from LUH state vector on starting date, in a nocomp configuration. ! From Charlie's list of valid FATES configurations: ! https://docs.google.com/spreadsheets/d/1eE3sRMYxfocZKbT8uIQhXpjjtfM2feXPRSWXJNoo4jM/edit#gid=0 -flandusepftdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc' use_fates_luh = .true. use_fates_nocomp = .true. use_fates_fixed_biogeog = .true. use_fates_sp = .false. use_fates_potentialveg = .false. -fluh_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc' From 8793f477483bf0332bf423e3c7b3bb66b31f88aa Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jun 2024 17:15:29 -0700 Subject: [PATCH 324/408] add readme noting grid resolution limitation --- cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README new file mode 100644 index 0000000000..79d6511d17 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README @@ -0,0 +1,2 @@ +Currently the FATES LUH2 category of test mods currently only supports +4x5 grid resolutions. From 35d5a5081c6b95690276f43d78e965792d7b3dd6 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 28 Jun 2024 12:26:54 -0600 Subject: [PATCH 325/408] Update Change files --- doc/ChangeLog | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 7 +++--- 2 files changed, 72 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 05b43c20ab..2ab7676ddc 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,72 @@ =============================================================== +Tag name: ctsm5.2.008 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Fri 28 Jun 2024 12:22:46 PM MDT +One-line Summary: Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat + +Purpose and description of changes +---------------------------------- + +Bring in changes that came in on the tmp-240620 branch to master now that cesm3_0_beta01 has +been made. The changes are documented in below but include the following tags: + + tmp-240620.n03.ctsm5.2.007 samrabin -- upland hillslope column fsat values to zero + tmp-240620.n02.ctsm5.2.007 erik ------ Another update of git-fleximod + tmp-240620.n01.ctsm5.2.007 slevis ---- Merge b4b-dev + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- + +Notes of particular relevance for users +--------------------------------------- + +Notes of particular relevance for developers: +--------------------------------------------- + +Testing summary: +---------------- + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + +Answer changes +-------------- + +Changes answers relative to baseline: No bit-for-bit with branch_tags/tmp-240620.n03.ctsm5.2.007 + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== Tag name: tmp-240620.n03.ctsm5.2.007 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Thu Jun 27 14:17:02 MDT 2024 diff --git a/doc/ChangeSum b/doc/ChangeSum index 7dd063df45..ea9417fe41 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,8 +1,9 @@ Tag Who Date Summary ============================================================================================================================ -tmp-240620.n03.ctsm5.2.007 samrabin 06/27/2024 Set upland hillslope column fsat values to zero -tmp-240620.n02.ctsm5.2.007 erik 06/21/2024 Another update of git-fleximod -tmp-240620.n01.ctsm5.2.007 slevis 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) + ctsm5.2.008 erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat +tmp-240620.n03.ctsm5.2.007 06/27/2024 Set upland hillslope column fsat values to zero (samrabin) +tmp-240620.n02.ctsm5.2.007 06/21/2024 Another update of git-fleximod (erik) +tmp-240620.n01.ctsm5.2.007 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) (slevis) ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems From 95bf3f82fb09d4022ac1af285569e9c1fd1aefa0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 13:52:40 -0700 Subject: [PATCH 326/408] add fates harvest event expected failure --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ cime_config/testdefs/testlist_clm.xml | 3 ++- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 65419a5903..de864aeee6 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -165,6 +165,13 @@ + + + FAIL + FATES#1216 + + + FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 347fd33e8e..16359b88be 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2579,7 +2579,7 @@ - + @@ -2609,6 +2609,7 @@ + From 889cc97d4172e85edc7f6c53f4a71ec89048a4d5 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jun 2024 17:51:13 -0600 Subject: [PATCH 327/408] update seed dispersal test mod to put on-the-fly generated paramfile in the case directory --- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands | 2 +- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands index 94a832af25..db5a1f8672 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands @@ -1,7 +1,7 @@ SRCDIR=`./xmlquery SRCROOT --value` CASEDIR=`./xmlquery CASEROOT --value` FATESDIR=$SRCDIR/src/fates/ -FATESPARAMFILE=$SRCDIR/fates_params_seeddisp_4x5.nc +FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index e8d24253c1..ecd1dc8b57 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1,3 +1,3 @@ -fates_paramfile = '$SRCROOT/fates_params_seeddisp_4x5.nc' +fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc' fates_seeddisp_cadence = 1 hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF' From f58cd7ee463f5ad7d8838a618f6e51bc7c37fb07 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jun 2024 23:43:20 -0600 Subject: [PATCH 328/408] reinstate fates-landuse as a second, shorter test list --- cime_config/testdefs/testlist_clm.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 16359b88be..68862c0dce 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2565,6 +2565,7 @@ + @@ -2574,6 +2575,7 @@ + @@ -2582,6 +2584,7 @@ + @@ -2590,6 +2593,7 @@ + @@ -2598,6 +2602,7 @@ + @@ -2606,6 +2611,7 @@ + From 9465da6202b0fd2ca8cbd9d39b6ffb5cc2e9f1e0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jun 2024 23:44:49 -0600 Subject: [PATCH 329/408] fix luh2 harvest testmod --- .../testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm | 2 +- .../testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm index d760105e68..426b41b49e 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestArea/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = luhdata_area +fates_harvest_mode = 'luhdata_area' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm index bb5f30f75d..7b6bc24f5a 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestMass/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = luhdata_mass +fates_harvest_mode = 'luhdata_mass' From c2deb25a278e7b177c47b5ae189f1c8697cd8d58 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jun 2024 23:48:18 -0600 Subject: [PATCH 330/408] rename fates landuse to luh2harvestevent --- .../testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm | 3 ++- .../testmods_dirs/clm/FatesColdLandUse/include_user_mods | 1 - .../testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm | 2 -- 3 files changed, 2 insertions(+), 4 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm index 61e1daaa93..a23336f36c 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm @@ -1 +1,2 @@ -fates_harvest_mode = surfdata_file +flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_hist_16_CMIP6_1850-2015_c230620.nc' +fates_harvest_mode = 'surfdata_file' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods deleted file mode 100644 index 14f7591b72..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm deleted file mode 100644 index 668f9c861d..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_4x5_hist_16_CMIP6_1850-2015_c230620.nc' -do_harvest = .true. From 4d0b49a81fa68653ba92ca59cfdd791cc053378a Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 12:32:36 -0600 Subject: [PATCH 331/408] fix fates harvest event code testmod --- .../testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm index c0e1c476be..d2079d9e43 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm @@ -1 +1 @@ -fates_harvest_mode = event_code +fates_harvest_mode = 'event_code' From 387ac5ed9163f77bd037ff8f935e56e73a832702 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 14:49:55 -0600 Subject: [PATCH 332/408] add description to flandusepftdat definition --- bld/namelist_files/namelist_definition_ctsm.xml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index c12cb75ab6..fd3020f320 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -826,7 +826,13 @@ types to vary over time. -Full pathname of fates landuse x pft static data map. +Full pathname of fates landuse x pft association static data map. +The file associates land use types with pfts across a static global map. +This file is necessary for running FATES with use_fates_luh, +use_fates_nocomp, and use_fates_fixedbiogeo engaged. The file is output +by the FATES land use data tool (https://github.com/NGEET/tools-fates-landusedata) +which processes the raw land use data from the THEMIS tool data sets +(https://doi.org/10.5065/29s7-7b41) Date: Fri, 28 Jun 2024 14:04:09 -0700 Subject: [PATCH 333/408] update flandusepftdat description with note about use_fates_lupft --- bld/namelist_files/namelist_definition_ctsm.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index fd3020f320..fb4f5d07a9 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -829,7 +829,8 @@ types to vary over time. Full pathname of fates landuse x pft association static data map. The file associates land use types with pfts across a static global map. This file is necessary for running FATES with use_fates_luh, -use_fates_nocomp, and use_fates_fixedbiogeo engaged. The file is output +use_fates_nocomp, and use_fates_fixedbiogeo engaged (note that use_fates_lupft +is provided as a namelist option to engage all necessary options). The file is output by the FATES land use data tool (https://github.com/NGEET/tools-fates-landusedata) which processes the raw land use data from the THEMIS tool data sets (https://doi.org/10.5065/29s7-7b41) From f985fbafafd5710e944d7715522966e042743361 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 14:23:29 -0700 Subject: [PATCH 334/408] rename misleading surfdata_file option name to the landuse_timeseries --- bld/CLMBuildNamelist.pm | 4 ++-- bld/namelist_files/namelist_definition_ctsm.xml | 7 ++++--- .../testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm | 2 +- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 2 +- 4 files changed, 8 insertions(+), 7 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c336d41ca9..0fb7963c67 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4652,7 +4652,7 @@ sub setup_logic_fates { if ( ! &value_is_true($nl->get_value('use_fates_luh')) ) { $log->fatal_error("use_fates_luh is required to be true when $var is luhdata_mass or luhdata_area" ); } - } elsif ( $mode eq 'surfdata_file' ) { + } elsif ( $mode eq 'landuse_timeseries' ) { # Check to make sure that the user set the flanduse_timeseries file # Since the flanduse_timeseries logic checking is upstream of the fates logic, # don't add the default here. The onus is on the user to match the correct timeseries @@ -4660,7 +4660,7 @@ sub setup_logic_fates { my $var = "flanduse_timeseries"; my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { - $log->fatal_error("$var is required when fates_harvest_mode is surfdata_file" ); + $log->fatal_error("$var is required when fates_harvest_mode is landuse_timeseries" ); } elsif ( ! -f "$fname" ) { $log->fatal_error("$var does NOT point to a valid filename" ); } diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index fb4f5d07a9..046de32c11 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -734,15 +734,16 @@ Toggle to turn on no competition mode (only relevant if FATES is being used). Toggle to turn on FATES satellite phenology mode (only relevant if FATES is being used). - + Set FATES harvesting mode by setting fates_harvest_mode to a valid string option. Allowed values are: no_harvest: no fates harvesting of any kind event_code: fates logging via fates logging event codes (see fates parameter file) only - surfdata_file: fates harvest driven by CLM landuse timeseries data (dynHarvestMod) + landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod) luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod) luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod) +Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file. Date: Fri, 28 Jun 2024 14:25:37 -0700 Subject: [PATCH 335/408] add language about age and possible future deprication of landuse_timeseries option --- bld/namelist_files/namelist_definition_ctsm.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 046de32c11..9b495ccda4 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -744,6 +744,7 @@ Allowed values are: luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod) luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod) Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file. +This option is older than the luhdata options and may be depricated at some point in the future. Date: Fri, 28 Jun 2024 14:29:38 -0700 Subject: [PATCH 336/408] fix copy/paste typo --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 9b495ccda4..b80bbda2d6 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -806,7 +806,7 @@ This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harv + group="clm_inparm" valid_values="" value=".false."> If TRUE, enable use of fates land use x pft mapping data file. (Only valid for use_fates = true and is incompatible with transient runs currently.) From 32b2554189d6cbdb11361ed376eb53c4bb8d2857 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 14:32:39 -0700 Subject: [PATCH 337/408] add clarifying language for use_fates_potentialveg --- bld/namelist_files/namelist_definition_ctsm.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index b80bbda2d6..bbc860df6c 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -814,7 +814,9 @@ If TRUE, enable use of fates land use x pft mapping data file. If TRUE, ignore the land-use state vector and transitions, and assert that all lands -are primary, and that there is no harvest. +are primary, and that there is no harvest. This mode is only relevant for FATES +spin-up workflows that are intending to use the spin-up restart output to start a +FATES land use transient case using the use_fates_lupft namelist option. From aaaff224b18585a4f93c4b83595b2017ee96f607 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 14:40:32 -0700 Subject: [PATCH 338/408] add clearer instructions about when to use_fates_potentialveg --- bld/namelist_files/namelist_definition_ctsm.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index bbc860df6c..252d83aa21 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -816,7 +816,8 @@ If TRUE, enable use of fates land use x pft mapping data file. If TRUE, ignore the land-use state vector and transitions, and assert that all lands are primary, and that there is no harvest. This mode is only relevant for FATES spin-up workflows that are intending to use the spin-up restart output to start a -FATES land use transient case using the use_fates_lupft namelist option. +FATES land use transient case using the use_fates_lupft namelist option. The option +should be set to true for the spin-up case and false for the transient case. From f6f7b2d135253f5a13dbd6e5ae66328a01c97d76 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 14:45:13 -0700 Subject: [PATCH 339/408] add language explaining what use_fates_lupft does --- bld/namelist_files/namelist_definition_ctsm.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 252d83aa21..5a478f0bfa 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -807,7 +807,9 @@ This is enabled by default if fates_harvest_mode is set to use the raw LUH2 harv -If TRUE, enable use of fates land use x pft mapping data file. +If TRUE, enable use of FATES land use with no competition and fixed biogeography. This mode +requires the use of the land use x pft association static data map file. See the +flandusepftdat definition entry in this file for more information. (Only valid for use_fates = true and is incompatible with transient runs currently.) From 2539cea91b481f4680e2696c6c517df3d952befa Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 28 Jun 2024 16:31:36 -0700 Subject: [PATCH 340/408] add readme to FatesLUPFT test mod --- cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README new file mode 100644 index 0000000000..88f5c2c8fb --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesLUPFT/README @@ -0,0 +1,9 @@ +This test mod does not use cold start and is intended to +be used in conjunction with a test workflow that provides +an initialization file. Currently this is accomplished +by using the test mod in conjunction with the PVT +system test. The PVT system test runs a FATES spin-up +case using the use_fates_potentialveg mode and then +references the restart output to run a use_fates_lupft +transient mode case. + From bf46d33d289f85077082dc01ec79c1945c42c3f4 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sun, 30 Jun 2024 23:04:07 -0700 Subject: [PATCH 341/408] update fates logging test with new harvest event code Remove duplicate and misnamed FatesColdLUH2HarvestEvent --- .../clm/FatesColdLUH2HarvestEvent/include_user_mods | 1 - .../testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm | 1 - .../testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm | 3 +-- 3 files changed, 1 insertion(+), 4 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods deleted file mode 100644 index 7eb8bb1579..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm deleted file mode 100644 index d2079d9e43..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestEvent/user_nl_clm +++ /dev/null @@ -1 +0,0 @@ -fates_harvest_mode = 'event_code' diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm index 5f457f3f1c..d2079d9e43 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm @@ -1,2 +1 @@ -! TODO SSR: Replace this with fates_harvest_mode -use_fates_logging= .true. +fates_harvest_mode = 'event_code' From 96d1a78b3c28c9f1bc8185e646f6a4f975236a42 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sun, 30 Jun 2024 23:07:59 -0700 Subject: [PATCH 342/408] reinstate FatesColdLandUse This will provide continuity to the previous test and fixes the incorrect use of FatesColdLUH2 as the test to inherit from --- .../testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods | 1 - .../testmods_dirs/clm/FatesColdLandUse/include_user_mods | 1 + .../{FatesColdLUH2HarvestSurf => FatesColdLandUse}/user_nl_clm | 0 3 files changed, 1 insertion(+), 1 deletion(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdLUH2HarvestSurf => FatesColdLandUse}/user_nl_clm (100%) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods deleted file mode 100644 index 7eb8bb1579..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdLUH2 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2HarvestSurf/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm From f47e2bfe035571268743f5bed11b2b97169d31e0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sun, 30 Jun 2024 23:10:43 -0700 Subject: [PATCH 343/408] remove duplicate tests --- cime_config/testdefs/testlist_clm.xml | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 68862c0dce..272d4093d8 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2581,15 +2581,6 @@ - - - - - - - - - @@ -2599,15 +2590,6 @@ - - - - - - - - - From 6dd55eeef55c093e53f500867d516df1beb16f39 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 1 Jul 2024 11:31:06 -0600 Subject: [PATCH 344/408] Update .gitmodules with new cismwrapper, cmeps, and ccs_config tags --- .gitmodules | 12 ++++++------ ccs_config | 2 +- components/cism | 2 +- components/cmeps | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.gitmodules b/.gitmodules index 6d4298befc..eb2a0980f4 100644 --- a/.gitmodules +++ b/.gitmodules @@ -7,8 +7,8 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release [submodule "cism"] path = components/cism -url = https://github.com/mvertens/CISM-wrapper -fxtag = 34339777afa7b810fd4822fce1039826668b33e4 +url = https://github.com/ESCOMP/CISM-wrapper +fxtag = cismwrap_2_2_001 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper @@ -35,8 +35,8 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute [submodule "ccs_config"] path = ccs_config -url = https://github.com/mvertens/ccs_config_cesm.git -fxtag = dbb02c0ccd1492fe278885f8a07a71fa80064319 +url = https://github.com/ESMCI/ccs_config_cesm.git +fxtag = ccs_config_cesm0.0.110 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git @@ -49,8 +49,8 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime [submodule "cmeps"] path = components/cmeps -url = https://github.com/mvertens/CMEPS.git -fxtag = 4dca7c602e54189b74b1d0195c433d1b83475553 +url = https://github.com/ESCOMP/CMEPS.git +fxtag = cmeps0.14.67 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git diff --git a/ccs_config b/ccs_config index dbb02c0ccd..c30a283155 160000 --- a/ccs_config +++ b/ccs_config @@ -1 +1 @@ -Subproject commit dbb02c0ccd1492fe278885f8a07a71fa80064319 +Subproject commit c30a2831556f269675971b11c5c156ea92599878 diff --git a/components/cism b/components/cism index 34339777af..c05dd5c4fc 160000 --- a/components/cism +++ b/components/cism @@ -1 +1 @@ -Subproject commit 34339777afa7b810fd4822fce1039826668b33e4 +Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928 diff --git a/components/cmeps b/components/cmeps index 4dca7c602e..90f815ba9e 160000 --- a/components/cmeps +++ b/components/cmeps @@ -1 +1 @@ -Subproject commit 4dca7c602e54189b74b1d0195c433d1b83475553 +Subproject commit 90f815ba9e7493d71043b5d8e627a3f20bd5dc78 From fb9529577c1e1f294cce17c0a0285f78b98554ce Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 1 Jul 2024 12:59:23 -0600 Subject: [PATCH 345/408] Update cismwrapper tag to the correct new one --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index eb2a0980f4..615de28b6f 100644 --- a/.gitmodules +++ b/.gitmodules @@ -8,7 +8,7 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release [submodule "cism"] path = components/cism url = https://github.com/ESCOMP/CISM-wrapper -fxtag = cismwrap_2_2_001 +fxtag = cismwrap_2_2_002 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper From de1b44ca4c9ef7c9116b41f1969a7998bcf21a84 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 1 Jul 2024 13:01:37 -0600 Subject: [PATCH 346/408] Ran ./bin/git-fleximod update, so now update the cism module itself --- components/cism | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/components/cism b/components/cism index c05dd5c4fc..c84cc9f5b3 160000 --- a/components/cism +++ b/components/cism @@ -1 +1 @@ -Subproject commit c05dd5c4fc85327e76523aaea9cfe1e388748928 +Subproject commit c84cc9f5b3103766a35d0a7ddd5e9dbd7deae762 From e1b2bdabb4b2c74a27bbf12d4cca677452396de7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 2 Jul 2024 17:03:19 -0600 Subject: [PATCH 347/408] Correct the tags that I used for ccs_config and cmeps --- .gitmodules | 4 ++-- ccs_config | 2 +- components/cmeps | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.gitmodules b/.gitmodules index 615de28b6f..897824e9cc 100644 --- a/.gitmodules +++ b/.gitmodules @@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute [submodule "ccs_config"] path = ccs_config url = https://github.com/ESMCI/ccs_config_cesm.git -fxtag = ccs_config_cesm0.0.110 +fxtag = ccs_config_cesm1.0.0 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git @@ -50,7 +50,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime [submodule "cmeps"] path = components/cmeps url = https://github.com/ESCOMP/CMEPS.git -fxtag = cmeps0.14.67 +fxtag = cmeps0.14.77 fxrequired = ToplevelRequired fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git diff --git a/ccs_config b/ccs_config index c30a283155..69a958581e 160000 --- a/ccs_config +++ b/ccs_config @@ -1 +1 @@ -Subproject commit c30a2831556f269675971b11c5c156ea92599878 +Subproject commit 69a958581ecd2d32ee9cb1c38bcd3847b8b920bf diff --git a/components/cmeps b/components/cmeps index 90f815ba9e..47fb4e633a 160000 --- a/components/cmeps +++ b/components/cmeps @@ -1 +1 @@ -Subproject commit 90f815ba9e7493d71043b5d8e627a3f20bd5dc78 +Subproject commit 47fb4e633a76ec6d60969b1af751f90790387246 From 0e6eed5f399eb85744410ecf1962c0416c7846ba Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 5 Jul 2024 10:57:34 -0700 Subject: [PATCH 348/408] Revert "update seed dispersal test mod to put on-the-fly generated paramfile in the case directory" This reverts commit 889cc97d4172e85edc7f6c53f4a71ec89048a4d5. I forgot that #2322 prevents this from working. --- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands | 2 +- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands index db5a1f8672..94a832af25 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands @@ -1,7 +1,7 @@ SRCDIR=`./xmlquery SRCROOT --value` CASEDIR=`./xmlquery CASEROOT --value` FATESDIR=$SRCDIR/src/fates/ -FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc +FATESPARAMFILE=$SRCDIR/fates_params_seeddisp_4x5.nc ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index ecd1dc8b57..e8d24253c1 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1,3 +1,3 @@ -fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc' +fates_paramfile = '$SRCROOT/fates_params_seeddisp_4x5.nc' fates_seeddisp_cadence = 1 hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF' From 8ae9c3329165f8f5f63cd35a415e3ba9478d52f8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 5 Jul 2024 13:53:49 -0600 Subject: [PATCH 349/408] Add cam7 lnd_tuning moode options and settings --- bld/namelist_files/namelist_defaults_ctsm.xml | 468 ++++++++++++++++++ .../namelist_definition_ctsm.xml | 4 +- bld/unit_testers/build-namelist_test.pl | 4 +- 3 files changed, 472 insertions(+), 4 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index e04db59cae..8656389103 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -243,18 +243,24 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >30.0d00 30.0d00 +20.0d00 20.0d00 20.0d00 20.0d00 +20.0d00 20.0d00 20.0d00 20.0d00 +20.0d00 20.0d00 0.010d00 0.010d00 +0.008d00 0.008d00 0.008d00 0.008d00 +0.008d00 0.008d00 0.008d00 0.008d00 +0.008d00 0.008d00 + + +.true. +.true. +.true. +.true. + +.true. + + +.true. + + +.true. +.true. +.true. +.true. + +.true. + + +.true. + + + +.true. +.true. +.true. +.true. + +.true. + + +.true. + @@ -701,6 +772,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. .true. +.true. .true. @@ -734,6 +806,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. + + hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. @@ -755,6 +831,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. + + hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. @@ -777,6 +857,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. +hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. @@ -800,6 +884,150 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + + +hgrid=ne120np4.pg3 maxpft=79 mask=tx0.1v3 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + + +hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=ne0np4.ARCTIC.ne30x4 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + +hgrid=1.9x2.5 maxpft=17 mask=gx1v7 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + +hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + + + lnd/clm2/initdata_map/clmi.I1850Clm45BgcCruGs.1101-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc +lnd/clm2/initdata_map/clmi.B1850Clm45BgcGs.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200806.nc + + lnd/clm2/initdata_esmf/ctsm5.2/clmi.I1850Clm50BgcCropCru-ciso.1526-01-01.0.9x1.25_gx1v7_simyr1850_c240223.nc +lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc + lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc + + lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc + + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + + + +lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc + + + + +lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc + + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + + + +lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc + + + + +lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr1979_c200806.nc + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.1.9x2.5_gx1v7_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTIC_ne30x4_mt12_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.FHISTSp.1979-01-01.ARCTICGRIS_ne30x8_mt12_simyr1979_c200806.nc + + + +lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc + + + +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + + + +lnd/clm2/initdata_map/clmi.BHISTSp.2000-01-01.1.9x2.5_gx1v7_simyr2003_c200807.nc + + + + +lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc + + @@ -1951,6 +2407,12 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c Zender_2003 atm bilinear +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc - + + valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam7.0,clm4_5_cam6.0,clm4_5_cam5.0,clm4_5_cam4_0,clm5_0_cam7.0,clm5_0_cam6.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_CRUv7,clm5_1_cam7.0,clm5_1_cam6.0,clm5_1_cam5.0,clm5_1_cam4.0,clm6_0_GSWP3v1,clm6_0_cam7.0,clm6_0_cam6.0,clm6_0_cam5.0,clm6_0_cam4.0"> General configuration of model version and atmospheric forcing to tune the model to run under. This sets the model to run with constants and initial conditions that were set to run well under the configuration of model version and atmospheric forcing. To run well constants would need to be changed diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 53c71ae0e9..2147fdea31 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 3254; +my $ntests = 3278; if ( defined($opts{'compare'}) ) { $ntests += 2001; @@ -1802,7 +1802,7 @@ sub cat_and_create_namelistinfile { my $mode = "-phys $phys"; &make_config_cache($phys); my @forclist = (); - @forclist = ( "CRUv7", "GSWP3v1", "cam6.0", "cam5.0", "cam4.0" ); + @forclist = ( "CRUv7", "GSWP3v1", "cam7.0", "cam6.0", "cam5.0", "cam4.0" ); foreach my $forc ( @forclist ) { foreach my $bgc ( "sp", "bgc" ) { my $lndtuningmode = "${phys}_${forc}"; From f303264ff62cfc0f9752573a0bc404573287c787 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 5 Jul 2024 15:11:58 -0600 Subject: [PATCH 350/408] Fix cam4.0 clm4_5 lnd_tuning_mode name --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 02b7356b52..5e65a3a603 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2043,7 +2043,7 @@ Land mask description + valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam7.0,clm4_5_cam6.0,clm4_5_cam5.0,clm4_5_cam4.0,clm5_0_cam7.0,clm5_0_cam6.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_CRUv7,clm5_1_cam7.0,clm5_1_cam6.0,clm5_1_cam5.0,clm5_1_cam4.0,clm6_0_GSWP3v1,clm6_0_cam7.0,clm6_0_cam6.0,clm6_0_cam5.0,clm6_0_cam4.0"> General configuration of model version and atmospheric forcing to tune the model to run under. This sets the model to run with constants and initial conditions that were set to run well under the configuration of model version and atmospheric forcing. To run well constants would need to be changed From 4670b6e2c3df9af6d03eb900cd0eed4877eaab59 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 5 Jul 2024 15:57:35 -0600 Subject: [PATCH 351/408] Allow a C or E to follow the period, which is needed by cesm3 all active compsets --- cime_config/config_component.xml | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index d69bdbc302..859883db8e 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -199,22 +199,22 @@ UNSET - 2010_control - 2000_control - 1850_control + 2010_control + 2000_control + 1850_control 1850_noanthro_control 1850_noanthro_control - 20thC_transient - 1850-2100_SSP5-8.5_transient - 1850-2100_SSP1-2.6_transient - 1850-2100_SSP3-7.0_transient - 1850-2100_SSP5-3.4_transient - 1850-2100_SSP2-4.5_transient + 20thC_transient + 1850-2100_SSP5-8.5_transient + 1850-2100_SSP1-2.6_transient + 1850-2100_SSP3-7.0_transient + 1850-2100_SSP5-3.4_transient + 1850-2100_SSP2-4.5_transient 1850-2100_SSP2-4.5_transient - 1850-2100_SSP1-1.9_transient - 1850-2100_SSP4-3.4_transient - 1850-2100_SSP4-6.0_transient - 1850-2100_SSP5-8.5_transient + 1850-2100_SSP1-1.9_transient + 1850-2100_SSP4-3.4_transient + 1850-2100_SSP4-6.0_transient + 1850-2100_SSP5-8.5_transient 20thC_transient 1850-2100_SSP5-8.5_transient From 03fb25a2a6d94753d7abbb4300fa32b917883969 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 5 Jul 2024 16:18:47 -0600 Subject: [PATCH 352/408] Two new tests in testlist_clm and two new tests in expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 15 +++++++++++++++ cime_config/testdefs/testlist_clm.xml | 20 ++++++++++++++++++++ 2 files changed, 35 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 664b1c8e35..59802d9109 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,6 +44,21 @@ + + + FAIL + #2619 + This failure relates to the following REP failure. + + + + + FAIL + #2619 + This failure relates to the preceding ERP failure. + + + FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 625a9f3504..23cc5ebcc5 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1445,6 +1445,26 @@ + + + + + + + + + + + + + + + + + + + + From 0efd37fe16814134389b9c49a30c7c033828c462 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 5 Jul 2024 17:55:44 -0600 Subject: [PATCH 353/408] New testmods /matrixcnOn_Hist to use -ignore_warnings in IHist compsets --- cime_config/testdefs/ExpectedTestFails.xml | 4 +-- cime_config/testdefs/testlist_clm.xml | 28 +++++++++---------- .../clm/matrixcnOn_Hist/include_user_mods | 1 + .../clm/matrixcnOn_Hist/shell_commands | 3 ++ 4 files changed, 20 insertions(+), 16 deletions(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 59802d9109..1243c125c0 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,14 +44,14 @@ - + FAIL #2619 This failure relates to the following REP failure. - + FAIL #2619 diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 23cc5ebcc5..1fe5ed770d 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -548,7 +548,7 @@ - + @@ -794,7 +794,7 @@ - + @@ -1002,7 +1002,7 @@ - + @@ -1020,7 +1020,7 @@ - + @@ -1038,7 +1038,7 @@ - + @@ -1234,7 +1234,7 @@ - + @@ -1354,7 +1354,7 @@ - + @@ -1435,7 +1435,7 @@ - + @@ -1445,7 +1445,7 @@ - + @@ -1455,7 +1455,7 @@ - + @@ -1793,7 +1793,7 @@ - + @@ -1849,7 +1849,7 @@ - + @@ -1925,7 +1925,7 @@ - + @@ -2369,7 +2369,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods new file mode 100644 index 0000000000..a3c70cba11 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods @@ -0,0 +1 @@ +../matrixcnOn diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands new file mode 100644 index 0000000000..f0547f3f26 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands @@ -0,0 +1,3 @@ +#!/bin/bash + +./xmlchange CLM_BLDNML_OPTS="-ignore_warnings" --append From a486e86065223a882790a6078647a82c592ffdaf Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 5 Jul 2024 17:15:08 -0700 Subject: [PATCH 354/408] update harvest parameter variables lengths Updating all lengths to account for the update to the clmlanduse name option change --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index b440b55dc9..681d39f38c 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -35,11 +35,11 @@ module dynFATESLandUseChangeMod integer, public, parameter :: num_landuse_harvest_vars = 5 ! Define the fates landuse namelist mode switch values - character(len=13), public, parameter :: fates_harvest_no_logging = 'no_harvest' - character(len=13), public, parameter :: fates_harvest_logging_only = 'event_code' - character(len=13), public, parameter :: fates_harvest_clmlanduse = 'landuse_timeseries' - character(len=13), public, parameter :: fates_harvest_luh_area = 'luhdata_area' - character(len=13), public, parameter :: fates_harvest_luh_mass = 'luhdata_mass' + character(len=18), public, parameter :: fates_harvest_no_logging = 'no_harvest' + character(len=18), public, parameter :: fates_harvest_logging_only = 'event_code' + character(len=18), public, parameter :: fates_harvest_clmlanduse = 'landuse_timeseries' + character(len=18), public, parameter :: fates_harvest_luh_area = 'luhdata_area' + character(len=18), public, parameter :: fates_harvest_luh_mass = 'luhdata_mass' ! Define landuse harvest unit integer representation integer, public, parameter :: landuse_harvest_area_units = 1 From de689e418343c903193bbb4e0f7075a91a94dc1b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 8 Jul 2024 11:23:22 -0600 Subject: [PATCH 355/408] Update bld/namelist_files/namelist_defaults_ctsm.xml Co-authored-by: Samuel Levis --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 8656389103..e81cd6dab9 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2407,11 +2407,11 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c Zender_2003 atm bilinear -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc From f745c21641baa3cbabd0e2dbe5e734a237a31e22 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 8 Jul 2024 13:33:10 -0600 Subject: [PATCH 356/408] Consistency in RE and don't require a C or E Make the Regular Expressions more consistent. Don't allow the use of CLM51 for all options. Make CPLHIST CAM version depend on which CLM version is used. Make sure explicit matches for CAM60 are there. --- cime_config/config_component.xml | 68 +++++++++++++++++--------------- 1 file changed, 36 insertions(+), 32 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 859883db8e..04306c0e40 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -87,10 +87,11 @@ clm4_5_CRUv7 clm4_5_GSWP3v1 clm4_5_cam6.0 - clm4_5_cam4.0 - clm4_5_cam5.0 - clm4_5_cam7.0 - clm4_5_cam6.0 + clm4_5_cam4.0 + clm4_5_cam5.0 + clm4_5_cam6.0 + clm4_5_cam7.0 + clm4_5_cam5.0 clm4_5_QIAN clm4_5_QIAN clm4_5_1PT @@ -102,9 +103,10 @@ clm5_0_GSWP3v1 clm5_0_GSWP3v1 clm5_0_cam6.0 - clm5_0_cam4.0 - clm5_0_cam5.0 - clm5_0_cam7.0 + clm5_0_cam4.0 + clm5_0_cam5.0 + clm5_0_cam6.0 + clm5_0_cam7.0 clm5_0_cam6.0 clm5_0_QIAN clm5_0_QIAN @@ -112,22 +114,24 @@ clm5_0_NLDAS2 clm5_0_ERA5 - clm5_1_GSWP3v1 clm5_1_GSWP3v1 - clm5_1_cam6.0 - clm5_1_cam4.0 - clm5_1_cam5.0 - clm5_1_cam6.0 + INVALID_USE_CLM60_NOT_CLM51 + clm5_1_cam4.0 + clm5_1_cam5.0 + clm5_1_cam6.0 + INVALID_USE_CLM60_NOT_CLM51_FOR_CAM70 + INVALID_USE_CLM60_NOT_CLM51_FOR_CPLHIST clm6_0_CRUv7 clm6_0_CRUv7 clm6_0_GSWP3v1 clm6_0_GSWP3v1 clm6_0_cam6.0 - clm6_0_cam4.0 - clm6_0_cam5.0 - clm6_0_cam7.0 - clm6_0_cam6.0 + clm6_0_cam4.0 + clm6_0_cam5.0 + clm6_0_cam6.0 + clm6_0_cam7.0 + clm6_0_cam7.0 clm6_0_QIAN clm6_0_QIAN clm6_0_1PT @@ -199,24 +203,24 @@ UNSET - 2010_control - 2000_control - 1850_control + 2010_control + 2000_control + 1850_control 1850_noanthro_control 1850_noanthro_control - 20thC_transient - 1850-2100_SSP5-8.5_transient - 1850-2100_SSP1-2.6_transient - 1850-2100_SSP3-7.0_transient - 1850-2100_SSP5-3.4_transient - 1850-2100_SSP2-4.5_transient - 1850-2100_SSP2-4.5_transient - 1850-2100_SSP1-1.9_transient - 1850-2100_SSP4-3.4_transient - 1850-2100_SSP4-6.0_transient - 1850-2100_SSP5-8.5_transient - 20thC_transient - 1850-2100_SSP5-8.5_transient + 20thC_transient + 1850-2100_SSP5-8.5_transient + 1850-2100_SSP1-2.6_transient + 1850-2100_SSP3-7.0_transient + 1850-2100_SSP5-3.4_transient + 1850-2100_SSP2-4.5_transient + 1850-2100_SSP2-4.5_transient + 1850-2100_SSP1-1.9_transient + 1850-2100_SSP4-3.4_transient + 1850-2100_SSP4-6.0_transient + 1850-2100_SSP5-8.5_transient + 20thC_transient + 1850-2100_SSP5-8.5_transient run_component_ctsm env_run.xml From bf02a881a6e18c137e5e7917754d381d62c2b94b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 8 Jul 2024 13:51:42 -0600 Subject: [PATCH 357/408] Change some comments to respond to @slevis-lmwg review --- bld/namelist_files/namelist_defaults_ctsm.xml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index e81cd6dab9..eb25cbf486 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -706,7 +706,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). maxpft="17" use_cn=".false." use_crop=".false." hgrid="ne0np4CONUS.ne30x8" >.true. .true. lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc - + lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc - + lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc - + lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc - + lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc - + lnd/clm2/initdata_map/clmi.F2000.2000-01-01.ne120pg3_mt13_simyr2000_c200728.nc - + Date: Mon, 8 Jul 2024 14:07:35 -0600 Subject: [PATCH 358/408] More lines to describe the finidat sections Add some comments to talk about what kind of land tuning mode is being done for a section of finidat files. --- bld/namelist_files/namelist_defaults_ctsm.xml | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index eb25cbf486..c6430bfff2 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1326,7 +1326,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). - + lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + + lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + - + lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc + lnd/clm2/initdata_map/clmi.FHISTSp.2013-01-01.ne0CONUSne30x8_mt12_simyr2013_c200806.nc + Date: Mon, 8 Jul 2024 14:30:22 -0600 Subject: [PATCH 359/408] Update test number --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 2147fdea31..3464dfadef 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -166,7 +166,7 @@ sub cat_and_create_namelistinfile { my $ntests = 3278; if ( defined($opts{'compare'}) ) { - $ntests += 2001; + $ntests += 1981; } plan( tests=>$ntests ); From fafc8137baeb39c07c65e697def4488b86aab612 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 8 Jul 2024 14:53:52 -0700 Subject: [PATCH 360/408] update fates submodule to api 36 --- .gitmodules | 4 ++-- src/fates | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.gitmodules b/.gitmodules index 049c62ade8..9ed4402c7e 100644 --- a/.gitmodules +++ b/.gitmodules @@ -27,8 +27,8 @@ # [submodule "fates"] path = src/fates -url = https://github.com/ckoven/fates -fxtag = 4b018eade498d063b21dddf26f77c9658ff80261 +url = https://github.com/NGEET/fates +fxtag = sci.1.77.0_api.36.0.0 fxrequired = AlwaysRequired # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/NCAR/fates-release diff --git a/src/fates b/src/fates index 4b018eade4..fd7f3438c2 160000 --- a/src/fates +++ b/src/fates @@ -1 +1 @@ -Subproject commit 4b018eade498d063b21dddf26f77c9658ff80261 +Subproject commit fd7f3438c2ff821672b703050e7011f293649ee9 From 7fac3e9c5c205391b0e359a4838bc48447b58240 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 8 Jul 2024 16:46:10 -0600 Subject: [PATCH 361/408] Change cam6 lnd_tuning_mode to cam7, and remove the cam7 Zender Dust tests (as Zender won't be the option for cam7) --- cime_config/testdefs/testlist_clm.xml | 79 ++++++++++--------- .../include_user_mods | 1 - .../clm60cam6LndTuningModeCiso/user_nl_clm | 5 -- .../include_user_mods | 1 - .../user_nl_clm | 3 - .../include_user_mods | 1 - .../include_user_mods | 1 - .../include_user_mods | 1 + .../shell_commands | 0 .../include_user_mods | 1 + .../shell_commands | 0 11 files changed, 42 insertions(+), 51 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeCiso/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningModeZDustSoilErod/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_1979Start/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam6LndTuningMode_2013Start/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_1979Start/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{clm60cam6LndTuningMode_1979Start => clm60cam7LndTuningMode_1979Start}/shell_commands (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode_2013Start/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{clm60cam6LndTuningMode_2013Start => clm60cam7LndTuningMode_2013Start}/shell_commands (100%) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 707a310f89..4b6f1dc46f 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -63,6 +63,7 @@ + @@ -80,22 +81,22 @@ - + - + - + - + @@ -109,7 +110,7 @@ - + @@ -118,7 +119,7 @@ - + @@ -127,7 +128,7 @@ - + @@ -136,7 +137,7 @@ - + @@ -145,7 +146,7 @@ - + @@ -155,7 +156,7 @@ - + @@ -182,7 +183,7 @@ - + @@ -191,7 +192,7 @@ - + @@ -200,7 +201,7 @@ - + @@ -209,7 +210,7 @@ - + @@ -218,7 +219,7 @@ - + @@ -227,7 +228,7 @@ - + @@ -236,7 +237,7 @@ - + @@ -246,7 +247,7 @@ lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1650-2015_c240216.nc + >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr0850-2015_c240216.nc .false. From 03ab3bdefa98b776263c057b50cf4b803f6c4fd7 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 9 Jul 2024 10:41:40 -0700 Subject: [PATCH 365/408] remove out-dated-comment Checking the landuse x pft data is handled on the fates-side --- src/utils/clmfates_interfaceMod.F90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 43a574d6e3..d15288d3a3 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -3915,8 +3915,6 @@ subroutine GetLandusePFTData(bounds, landuse_pft_file, landuse_pft_map, landuse_ deallocate(arraylocal_bareground) call ncd_pio_closefile(ncid) - ! Check that sums equal to unity - end subroutine GetLandusePFTData From 272f99f405e95adec9774519323a34c0f2f9c874 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 9 Jul 2024 13:41:55 -0700 Subject: [PATCH 366/408] remove unused land use mod subroutine --- src/utils/clmfates_interfaceMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index d15288d3a3..e3e7644b90 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -182,7 +182,6 @@ module CLMFatesInterfaceMod use dynFATESLandUseChangeMod, only : num_landuse_transition_vars, num_landuse_state_vars use dynFATESLandUseChangeMod, only : landuse_transitions, landuse_states use dynFATESLandUseChangeMod, only : landuse_transition_varnames, landuse_state_varnames - use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp use dynFATESLandUseChangeMod, only : num_landuse_harvest_vars use dynFATESLandUseChangeMod, only : fates_harvest_no_logging use dynFATESLandUseChangeMod, only : fates_harvest_clmlanduse From 72ab1cbf97522984acaceda494b5279fb4ea3621 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 9 Jul 2024 15:48:06 -0600 Subject: [PATCH 367/408] Remove use_dynroot and corresponding code and testing --- bld/CLMBuildNamelist.pm | 20 -- bld/namelist_files/namelist_defaults_ctsm.xml | 3 - .../namelist_definition_ctsm.xml | 5 - bld/unit_testers/build-namelist_test.pl | 5 - cime_config/testdefs/testlist_clm.xml | 17 -- .../clm/clm50dynroots/include_user_mods | 1 - .../clm/clm50dynroots/user_nl_clm | 2 - src/biogeochem/CNDriverMod.F90 | 17 +- src/biogeochem/CNRootDynMod.F90 | 271 ------------------ src/biogeophys/IrrigationMod.F90 | 5 +- src/biogeophys/SoilStateType.F90 | 26 +- src/main/clm_varctl.F90 | 6 - src/main/controlMod.F90 | 10 - src/main/pftconMod.F90 | 14 +- 14 files changed, 7 insertions(+), 395 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm delete mode 100644 src/biogeochem/CNRootDynMod.F90 diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index f65414e4af..146cf5bd32 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1582,7 +1582,6 @@ sub process_namelist_inline_logic { setup_logic_hillslope($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_o3_veg_stress_method($opts, $nl_flags, $definition, $defaults, $nl,$physv); setup_logic_hydrstress($opts, $nl_flags, $definition, $defaults, $nl); - setup_logic_dynamic_roots($opts, $nl_flags, $definition, $defaults, $nl, $physv); setup_logic_params_file($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_create_crop_landunit($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_subgrid($opts, $nl_flags, $definition, $defaults, $nl); @@ -3581,25 +3580,6 @@ sub setup_logic_grainproduct { #------------------------------------------------------------------------------- -sub setup_logic_dynamic_roots { - # - # dynamic root model - # - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_dynroot', 'phys'=>$physv->as_string(), 'bgc_mode'=>$nl_flags->{'bgc_mode'}); - my $use_dynroot = $nl->get_value('use_dynroot'); - if ( &value_is_true($use_dynroot) && ($nl_flags->{'bgc_mode'} eq "sp") ) { - $log->fatal_error("Cannot turn dynroot mode on mode bgc=sp\n" . - "Set the bgc mode to 'bgc'."); - } - if ( &value_is_true( $use_dynroot ) && &value_is_true( $nl_flags->{'use_hydrstress'} ) ) { - $log->fatal_error("Cannot turn use_dynroot on when use_hydrstress is on" ); - } -} - -#------------------------------------------------------------------------------- - sub setup_logic_c_isotope { # # Error checking for C-isotope options diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 655e97c47c..794c9278ca 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -568,9 +568,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. - -.false. - .false. .true. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 37c457141c..e13d8f867a 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1364,11 +1364,6 @@ Percentage threshold above which the model keeps the urban landunits. Selecting Default: 0 - -Toggle to turn on the dynamic root model - - Toggle to turn on on diagnostic Snow Radiative Effect diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 53c71ae0e9..e754883785 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1062,11 +1062,6 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "useHYDSTwithdynroot" =>{ options=>"-bgc bgc -envxml_dir . -megan", - namelst=>"use_hydrstress=.true., use_dynroot=.true.", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm5_0", - }, "specWOfireemis" =>{ options=>"-envxml_dir . -no-fire_emis", namelst=>"fire_emis_specifier='bc_a1 = BC'", GLC_TWO_WAY_COUPLING=>"FALSE", diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index fee8e1a429..e3c0053698 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1345,15 +1345,6 @@ - - - - - - - - - @@ -2134,14 +2125,6 @@ - - - - - - - - diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods deleted file mode 100644 index fe0e18cf88..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../default diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm deleted file mode 100644 index e493c3e8e7..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/clm50dynroots/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -use_dynroot = .true. -use_hydrstress = .false. diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index b23019eb23..0381711258 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -6,7 +6,7 @@ module CNDriverMod ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_varctl , only : use_c13, use_c14, use_fates, use_fates_bgc, use_dynroot + use clm_varctl , only : use_c13, use_c14, use_fates, use_fates_bgc use dynSubgridControlMod , only : get_do_harvest, get_do_grossunrep use decompMod , only : bounds_type use perf_mod , only : t_startf, t_stopf @@ -147,7 +147,6 @@ subroutine CNDriverNoLeaching(bounds, use SoilBiogeochemNitrifDenitrifMod , only: SoilBiogeochemNitrifDenitrif use SoilBiogeochemNStateUpdate1Mod , only: SoilBiogeochemNStateUpdate1 use NutrientCompetitionMethodMod , only: nutrient_competition_method_type - use CNRootDynMod , only: CNRootDyn use CNPrecisionControlMod , only: CNPrecisionControl ! ! !ARGUMENTS: @@ -564,20 +563,6 @@ subroutine CNDriverNoLeaching(bounds, call t_stopf('CNGResp') - !-------------------------------------------- - ! Dynamic Roots - !-------------------------------------------- - - if( use_dynroot ) then - call t_startf('CNRootDyn') - - call CNRootDyn(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, & - cnveg_state_inst, crop_inst, soilstate_inst, soilbiogeochem_nitrogenstate_inst) - - call t_stopf('CNRootDyn') - end if - !-------------------------------------------------------------------------- ! CNUpdate0 ! The state updates are still called for the matrix solution (use_matrixn diff --git a/src/biogeochem/CNRootDynMod.F90 b/src/biogeochem/CNRootDynMod.F90 deleted file mode 100644 index 3f43424cfa..0000000000 --- a/src/biogeochem/CNRootDynMod.F90 +++ /dev/null @@ -1,271 +0,0 @@ -module CNRootDynMod - -!----------------------------------------------------------------------- -! !DESCRIPTION: -! Module holding routines used for determining fine root distribution for all pfts. -! Includes dynamic root depth for crops -! -! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_time_manager , only : get_step_size_real - use abortutils , only : endrun - use clm_varpar , only : nlevsoi, nlevgrnd - use clm_varctl , only : use_bedrock - use decompMod , only : bounds_type - use pftconMod , only : noveg, npcropmin, pftcon - use ColumnType , only : col - use PatchType , only : patch - use CNVegStateType , only : cnveg_state_type - use CNVegCarbonStateType , only : cnveg_carbonstate_type - use CNVegCarbonFluxType , only : cnveg_carbonflux_type - use CNVegnitrogenstateType , only : cnveg_nitrogenstate_type - use SoilStateType , only : soilstate_type - use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type - use CropType , only : crop_type - -! !PUBLIC TYPES: - implicit none - save - private - public :: CNRootDyn -!----------------------------------------------------------------------- - -contains - -!----------------------------------------------------------------------- -! -subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, & - cnveg_state_inst, crop_inst, soilstate_inst, soilbiogeochem_nitrogenstate_inst) -! -! !DESCRIPTION: -! This routine determine the fine root distribution -! Needs to be called after the photosynthesis calculation -! May need to update other subroutines that use the fixed root profile for calculations -! i.e. CNVerticalProfileMod -! -! !USES: - - -! !ARGUMENTS: - type(bounds_type), intent(in) :: bounds ! bounds - integer, intent(in) :: num_soilc - integer, intent(in) :: filter_soilc(:) - integer, intent(in) :: num_soilp ! number of soil pfts in filter - integer, intent(in) :: filter_soilp(:) ! filter for soil pfts - type(cnveg_state_type) , intent(in) :: cnveg_state_inst - type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst - type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst - type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst - type(crop_type) , intent(in) :: crop_inst - type(soilbiogeochem_nitrogenstate_type) , intent(in) :: soilbiogeochem_nitrogenstate_inst - type(soilstate_type) , intent(inout) :: soilstate_inst - -! -! !LOCAL VARIABLES: - - integer :: f,c,p,lev,j ! indices - real(r8):: dt ! radiation time step delta t (seconds) - real(r8), allocatable :: w_limit(:) - real(r8), allocatable :: rswa(:,:) ! soil water availability in each soil layer - real(r8), allocatable :: rsmn(:,:) ! soil nitrogen availability in each soil layer - real(r8), allocatable :: sumrswa(:) ! scaling soil water availability in each soil layer - real(r8), allocatable :: sumrsmn(:) ! scaling soil mineral N availability in each soil layer - real(r8) :: frootc_dz(bounds%begp:bounds%endp, 1:nlevgrnd) - real(r8), allocatable :: sumfrootc(:) ! fine root carbon total before turnover in each step - real(r8):: minpsi ! minimum soil moisture potential - real(r8):: psi - real(r8):: maxpsi - real(r8):: new_growth - -!----------------------------------------------------------------------- - ! Assign local pointers to derived type arrays (in) - associate(& - ivt => patch%itype , & ! Input: [integer (:)] pft vegetation type - pcolumn => patch%column , & ! Input: [integer (:)] pft's column index - roota_par => pftcon%roota_par , & ! Input: [real(r8) (:)] pft's roota index - rootb_par => pftcon%rootb_par , & ! Input: [real(r8) (:)] pft's rootb index - root_dmx => pftcon%root_dmx , & ! Input: [real(r8) (:)] crop maximum root depth - cpool_to_frootc => cnveg_carbonflux_inst%cpool_to_frootc_patch , & ! Input: [real(r8) (:)] allocation to fine root C (gC/m2/s) - frootc_xfer_to_frootc => cnveg_carbonflux_inst%frootc_xfer_to_frootc_patch , & ! Input: [real(r8) (:)] fine root C growth from storage (gC/m2/s) - dormant_flag => cnveg_state_inst%dormant_flag_patch , & ! Input: [real(r8) (:)] dormancy flag - root_depth => soilstate_inst%root_depth_patch , & ! InOut: [real(r8) (:)] current root depth - dz => col%dz , & ! Input: layer thickness (m) (-nlevsno+1:nlevgrnd) - zi => col%zi , & ! Input: interface level below a "z" level (m) (-nlevsno+0:nlevgrnd) - rootfr => soilstate_inst%rootfr_patch , & ! Output: [real(r8) (:,:)] fraction of roots in each soil layer - sucsat => soilstate_inst%sucsat_col , & ! Input: minimum soil suction (mm) - soilpsi => soilstate_inst%soilpsi_col , & ! Input: soil water potential in each soil layer (MPa) - sminn_vr => soilbiogeochem_nitrogenstate_inst%sminn_vr_col , & ! Iniput: [real(r8) (:,:)] (gN/m3) soil mineral N - frootc => cnveg_carbonstate_inst%frootc_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:)] crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest - croplive => crop_inst%croplive_patch , & ! Input: [logical (:)] flag, true if planted, not harvested - huigrain => cnveg_state_inst%huigrain_patch & ! Input: [real(r8) (:)] same to reach vegetative maturity - ) - -! set time steps - dt = get_step_size_real() - -! set minpsi to permanent wilting point - minpsi = -1.5_r8 - - allocate(sumrswa(bounds%begp:bounds%endp)) - allocate(sumrsmn(bounds%begp:bounds%endp)) - allocate(sumfrootc(bounds%begp:bounds%endp)) - allocate(rswa(bounds%begp:bounds%endp,nlevgrnd)) - allocate(rsmn(bounds%begp:bounds%endp,nlevgrnd)) - allocate(w_limit(bounds%begp:bounds%endp)) - -!initialize to 0 - w_limit(bounds%begp:bounds%endp) = 0._r8 - sumrswa(bounds%begp:bounds%endp) = 0._r8 - sumrsmn(bounds%begp:bounds%endp) = 0._r8 - sumfrootc(bounds%begp:bounds%endp) = 0._r8 - rswa(bounds%begp:bounds%endp,:) = 0._r8 - rsmn(bounds%begp:bounds%endp,:) = 0._r8 - - frootc_dz(bounds%begp:bounds%endp,1:nlevgrnd) = 0._r8 - - -!--------------------------------------------------------------- -! Set root depth, dynamic for crops, fixed for other vegetation -!--------------------------------------------------------------- - - do f = 1, num_soilp - p = filter_soilp(f) - c = pcolumn(p) - if (ivt(p) /= noveg) then - if((ivt(p)) >= npcropmin)then !skip generic crop types - if (.not. croplive(p)) then - root_depth(p) = 0._r8 - else if(huigrain(p) > 0._r8)then - root_depth(p) = max(zi(c,2), min(hui(p)/huigrain(p)* root_dmx(ivt(p)), root_dmx(ivt(p)))) - end if - else - ! this can be changed to any depth (i.e. the maximum soil depth) - root_depth(p) = zi(c,nlevsoi) - end if - if (use_bedrock) then - root_depth(p) = min(root_depth(p),zi(c,col%nbedrock(c))) - end if - else - root_depth(p) = 0._r8 - end if - end do - -!---------------------------------------------------------------- -! ! calculate a weighting function by soil depth that depends on the - ! fine root distribution per pft and depth and the pft weight on the column. - ! This will be used to weight the temperature and water potential scalars - ! for decomposition control. - - ! calculate the rate constant scalar for soil water content. - ! Uses the log relationship with water potential given in - ! Andren, O., and K. Paustian, 1987. Barley straw decomposition in the field: - ! a comparison of models. Ecology, 68(5):1190-1200. - ! and supported by data in - ! Orchard, V.A., and F.J. Cook, 1983. Relationship between soil respiration - ! and soil moisture. Soil Biol. Biochem., 15(4):447-453. - - do j = 1,nlevsoi - do f = 1,num_soilp - p = filter_soilp(f) - c = pcolumn(p) - maxpsi = sucsat(c,j) * (-9.8e-6_r8) - psi = min(soilpsi(c,j),maxpsi) - if (psi > minpsi) then -! First calculate water in the root zone - if(root_depth(p) > 0.15_r8 .and. (zi(c,j) <= root_depth(p) .or. & - (zi(c,j-1) < root_depth(p) .and. zi(c,j) > root_depth(p)))) then - w_limit(p) = w_limit(p) + max(0._r8,log(minpsi/psi)/log(minpsi/maxpsi))*rootfr(p,j) - end if -! Calculate the water in each soil layer - if (root_depth(p) >= zi(c,j) .or. & - (zi(c,j-1) < root_depth(p) .and. zi(c,j) > root_depth(p))) then - rswa(p,j) = max(0._r8, (log(minpsi/psi)/log(minpsi/maxpsi))) - end if - end if - sumrswa(p) = sumrswa(p) + rswa(p,j) - -! Calculate the nitrogen profile in each layer -! For now, the profile for each PFT is equivilent to the -! column profile, in the future, this could be changed to a weighted profile - rsmn(p,j) = sminn_vr(c,j) - if (root_depth(p) >= zi(c,j).or. & - (zi(c,j-1) < root_depth(p) .and. zi(c,j) > root_depth(p))) then - sumrsmn(p) = sumrsmn(p) + rsmn(p,j) - end if - end do - end do - - -!-------------------------------------------------------------------- -! Now calculate the density of roots in each soil layer for each pft -! based on this timesteps growth -!-------------------------------------------------------------------- - do lev = 1, nlevgrnd - - do f = 1, num_soilp - p = filter_soilp(f) - c = pcolumn(p) - - new_growth = (cpool_to_frootc(p) + frootc_xfer_to_frootc(p))*dt - if(zi(c,lev) <= root_depth(p) .or. & - (zi(c,lev-1) < root_depth(p) .and. zi(c,lev) > root_depth(p))) then - if(sumrswa(p) <= 0._r8 .or. sumrsmn(p) <= 0._r8) then -! when sumrswa or sumrsmn are less than or equal to 0 rootfr will not be updated - else - frootc_dz(p,lev) = (frootc(p))*rootfr(p,lev) & - + new_growth * ((1._r8 - w_limit(p)) * rswa(p,lev) / sumrswa(p) & - + w_limit(p) * rsmn(p,lev) / sumrsmn(p)) - end if - else - frootc_dz(p,lev) = 0._r8 - end if - - sumfrootc(p) = sumfrootc(p) + frootc_dz(p,lev) - - end do - end do -!---------------------------------- -!Calculate root fraction -!---------------------------------- - - do lev = 1, nlevgrnd - do f = 1, num_soilp - p = filter_soilp(f) - c = pcolumn(p) - if(sumfrootc(p) > 0._r8)then - rootfr(p,lev) = frootc_dz(p,lev)/sumfrootc(p) - end if - if(ivt(p) >= npcropmin .and. .not. croplive(p))then -! CROPS are dormant, there are no roots! -! but, need an initial frootr so crops can start root production - if (lev < 2)then - rootfr(p,lev) = .5_r8*( exp(-roota_par(patch%itype(p)) * zi(c,lev-1)) & - + exp(-rootb_par(patch%itype(p)) * zi(c,lev-1)) & - - exp(-roota_par(patch%itype(p)) * zi(c,lev )) & - - exp(-rootb_par(patch%itype(p)) * zi(c,lev )) ) - elseif (lev == 2) then - rootfr(p,lev) = .5_r8*( exp(-roota_par(patch%itype(p)) * zi(c,lev-1)) & - + exp(-rootb_par(patch%itype(p)) * zi(c,lev-1)) ) - else - rootfr(p,lev) = 0.0_r8 - end if - - end if - end do - end do - -!********************** - deallocate(sumrswa) - deallocate(sumrsmn) - deallocate(sumfrootc) - deallocate(rsmn) - deallocate(rswa) - deallocate(w_limit) - - end associate - - end subroutine CNRootDyn - -end module CNRootDynMod diff --git a/src/biogeophys/IrrigationMod.F90 b/src/biogeophys/IrrigationMod.F90 index 27cf050dd3..11c9132eea 100644 --- a/src/biogeophys/IrrigationMod.F90 +++ b/src/biogeophys/IrrigationMod.F90 @@ -221,9 +221,8 @@ module IrrigationMod ! There is no reason to make this a tunable parameter, because the behavior it governs ! (the trigger for irrigation) can be tuned via other parameters. ! - ! TODO(wjs, 2016-09-08) It looks like there is other code in CLM that also uses an - ! assumed wilting point (CNRootDynMod, maybe others). We should probably make this a - ! shared parameter, e.g., in clm_varcon. + ! TODO(wjs, 2016-09-08, updated by slevis 2024-07-06) assumed wilting point: + ! Make this a shared parameter? E.g., in clm_varcon real(r8), parameter, private :: wilting_point_smp = -150000._r8 ! Conversion factors diff --git a/src/biogeophys/SoilStateType.F90 b/src/biogeophys/SoilStateType.F90 index e301cc27b9..2e7225f962 100644 --- a/src/biogeophys/SoilStateType.F90 +++ b/src/biogeophys/SoilStateType.F90 @@ -9,7 +9,7 @@ module SoilStateType use abortutils , only : endrun use clm_varpar , only : nlevsoi, nlevgrnd, nlevlak, nlayer, nlevsno, nlevmaxurbgrnd use clm_varcon , only : spval - use clm_varctl , only : use_hydrstress, use_cn, use_lch4, use_dynroot, use_fates + use clm_varctl , only : use_hydrstress, use_cn, use_lch4, use_fates use clm_varctl , only : iulog, hist_wrtch4diag use LandunitType , only : lun use ColumnType , only : col @@ -231,20 +231,6 @@ subroutine InitHistory(this, bounds) ptr_col=this%bsw_col, default='inactive') end if - if (use_dynroot) then - this%rootfr_patch(begp:endp,:) = spval - call hist_addfld2d (fname='ROOTFR', units='proportion', type2d='levgrnd', & - avgflag='A', long_name='fraction of roots in each soil layer', & - ptr_patch=this%rootfr_patch, default='active') - end if - - if ( use_dynroot ) then - this%root_depth_patch(begp:endp) = spval - call hist_addfld1d (fname='ROOT_DEPTH', units="m", & - avgflag='A', long_name='rooting depth', & - ptr_patch=this%root_depth_patch ) - end if - if (use_cn) then this%rootr_patch(begp:endp,:) = spval call hist_addfld2d (fname='ROOTR', units='proportion', type2d='levgrnd', & @@ -393,15 +379,7 @@ subroutine Restart(this, bounds, ncid, flag) scale_by_thickness=.true., & interpinic_flag='interp', readvar=readvar, data=this%hk_l_col) - if( use_dynroot ) then - call restartvar(ncid=ncid, flag=flag, varname='rootfr', xtype=ncd_double, & - dim1name='pft', dim2name='levgrnd', switchdim=.true., & - long_name='root fraction', units='', & - scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readrootfr, data=this%rootfr_patch) - else - readrootfr = .false. - end if + readrootfr = .false. if (flag=='read' .and. .not. readrootfr ) then if (masterproc) then write(iulog,*) "can't find rootfr in restart (or initial) file..." diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 0daedbbb1f..cbfcbfd8ea 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -426,12 +426,6 @@ module clm_varctl logical, public :: use_hydrstress = .false. ! true => use plant hydraulic stress calculation - !---------------------------------------------------------- - ! dynamic root switch - !---------------------------------------------------------- - - logical, public :: use_dynroot = .false. ! true => use dynamic root module - !---------------------------------------------------------- ! glacier_mec control variables: default values (may be overwritten by namelist) !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 46d9e9958a..4773cc6921 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -272,8 +272,6 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_hydrstress - namelist /clm_inparm/ use_dynroot - namelist /clm_inparm/ & use_c14_bombspike, atm_c14_filename, use_c13_timeseries, atm_c13_filename @@ -613,11 +611,6 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if - if ( use_dynroot .and. use_hydrstress ) then - call endrun(msg=' ERROR:: dynroot and hydrstress can NOT be on at the same time'//& - errMsg(sourcefile, __LINE__)) - end if - ! Check on run type if (nsrest == iundef) then call endrun(msg=' ERROR:: must set nsrest'//& @@ -842,8 +835,6 @@ subroutine control_spmd() call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier) - if (use_cn .or. use_fates) then ! vertical soil mixing variables call mpi_bcast (som_adv_flux, 1, MPI_REAL8, 0, mpicom, ier) @@ -1130,7 +1121,6 @@ subroutine control_print () write(iulog,*) ' user-defined soil layer structure = ', soil_layerstruct_userdefined write(iulog,*) ' user-defined number of soil layers = ', soil_layerstruct_userdefined_nlevsoi write(iulog,*) ' plant hydraulic stress = ', use_hydrstress - write(iulog,*) ' dynamic roots = ', use_dynroot if (nsrest == nsrContinue) then write(iulog,*) 'restart warning:' write(iulog,*) ' Namelist not checked for agreement with initial run.' diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index e5379100e0..7988b57e75 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -280,9 +280,6 @@ module pftconMod real(r8), allocatable :: FUN_fracfixers(:) ! Fraction of C that can be used for fixation. - ! pft parameters for dynamic root code - real(r8), allocatable :: root_dmx(:) !maximum root depth - contains procedure, public :: Init @@ -494,7 +491,6 @@ subroutine InitAllocate (this) allocate( this%kn_nonmyc (0:mxpft) ) allocate( this%kr_resorb (0:mxpft) ) allocate( this%perecm (0:mxpft) ) - allocate( this%root_dmx (0:mxpft) ) allocate( this%fun_cn_flex_a (0:mxpft) ) allocate( this%fun_cn_flex_b (0:mxpft) ) allocate( this%fun_cn_flex_c (0:mxpft) ) @@ -520,7 +516,7 @@ subroutine InitRead(this) use fileutils , only : getfil use ncdio_pio , only : ncd_io, ncd_pio_closefile, ncd_pio_openfile, file_desc_t use ncdio_pio , only : ncd_inqdid, ncd_inqdlen - use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage, z0param_method + use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_biomass_heat_storage, z0param_method use spmdMod , only : masterproc use CLMFatesParamInterfaceMod, only : FatesReadPFTs use SoilBiogeochemDecompCascadeConType, only : mimics_decomp, decomp_method @@ -1105,13 +1101,8 @@ subroutine InitRead(this) end if ! - ! Dynamic Root variables for crops ! - if ( use_crop .and. use_dynroot )then - call ncd_io('root_dmx', this%root_dmx, 'read', ncid, readvar=readv) - if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) - end if - + ! call ncd_io('nstem',this%nstem, 'read', ncid, readvar=readv) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) call ncd_io('taper',this%taper, 'read', ncid, readvar=readv) @@ -1583,7 +1574,6 @@ subroutine Clean(this) deallocate( this%kn_nonmyc) deallocate( this%kr_resorb) deallocate( this%perecm) - deallocate( this%root_dmx) deallocate( this%fun_cn_flex_a) deallocate( this%fun_cn_flex_b) deallocate( this%fun_cn_flex_c) From a5b4d34720d81eac9f052ea7e8230af57955dee8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 9 Jul 2024 21:57:55 -0600 Subject: [PATCH 368/408] Fix the lnd_tuning_mode for the zendersoil files --- bld/namelist_files/namelist_defaults_ctsm.xml | 48 +++++++++---------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index c6430bfff2..c535bc96e4 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2419,53 +2419,53 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc -lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc Date: Tue, 9 Jul 2024 23:54:45 -0600 Subject: [PATCH 369/408] Add clm6_0 for Zdust --- bld/namelist_files/namelist_defaults_ctsm.xml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index c535bc96e4..a2200cb7fa 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2419,54 +2419,72 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c >lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc +lnd/clm2/dustemisdata/dst_source2x2_cam5.4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc +lnd/clm2/dustemisdata/dst_source2x2tuned-cam4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc +lnd/clm2/dustemisdata/dst_source1x1tuned-cam4-forCLM_cdf5_c240202.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc +lnd/clm2/dustemisdata/dst_source2x2tunedcam6-2x2-forCLM_cdf5_c230312.nc lnd/clm2/dustemisdata/dust_2x2_ESMFmesh_cdf5_c230730.nc From 97b8c552f4df54eff77f05cb1dad078c2fa2908e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 10 Jul 2024 00:07:48 -0600 Subject: [PATCH 370/408] Add files for the new clm60cam7 test mod --- .../clm/clm60cam7LndTuningMode/include_user_mods | 1 + .../testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands | 5 +++++ 2 files changed, 6 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands new file mode 100644 index 0000000000..7dd25a08bf --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/shell_commands @@ -0,0 +1,5 @@ +#!/bin/bash + +./xmlchange LND_TUNING_MODE="clm6_0_cam7.0" +./xmlchange ROF_NCPL='$ATM_NCPL' + From 197e8abb184425d1ed46c53435340a2803efdd3a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 10 Jul 2024 00:14:35 -0600 Subject: [PATCH 371/408] Update expected fail for new test --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index dad6acb63d..3c3bde2ff6 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,7 +44,7 @@ - + FAIL #2542 From 334b144b59ce0d649116408be1d67007c0ff6d14 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 10 Jul 2024 01:38:21 -0600 Subject: [PATCH 372/408] Fix typo in lnd_tuning_mode for Zender dust emission soil eroditability file --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index fbf7b9a8bc..b3141f1b42 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4002,7 +4002,7 @@ sub setup_logic_dust_emis { foreach my $option ( @zender_files_in_lnd_opts ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $option, 'dust_emis_method'=>$dust_emis_method, 'zender_soil_erod_source'=>$zender_source, - 'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mod'=>$nl_flags->{'lnd_tuning_mode'} ); + 'hgrid'=>$nl_flags->{'res'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); } } else { foreach my $option ( @zender_files_in_lnd_opts ) { From 734dbf2e24b7f98d108e3ab9a6605f978cdb5787 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 10 Jul 2024 13:34:29 -0600 Subject: [PATCH 373/408] Update change files --- doc/ChangeLog | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 95 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 2ab7676ddc..9f62ca5a87 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,98 @@ =============================================================== +Tag name: ctsm5.2.009 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Wed 10 Jul 2024 12:21:23 PM MDT +One-line Summary: Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names + +Purpose and description of changes +---------------------------------- + +Changes so that CAM7 is allowed for the land-tuning mode. Allow "C" and "E" after period designation in long compset names. Fix an +issue with Zender dust emission soil eroditability files. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- + +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: + Fixes #2480 -- cam7 lnd_tuning_mode + Fixes #2634 -- allow period part of long-compset name to have a "C" or "E" + Fixes #2637 -- bad lnd_tuning_mode for Zender soil eroditability file settings + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + LND_TUNING_MODE will fail with an error for CAM (that's NOT cam4/cam5/cam6), or CPLHIST with CLM51 + use CLM60 instead + +Changes made to namelist defaults (e.g., changed parameter values): + Add lnd_tuning_mode options for cam7.0 to namelist defaults + +Notes of particular relevance for developers: +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + lnd_tuning_mode options duplicate a bunch of XML code lines and should be refactored + +Changes to tests or testing: + Add cam7.0 test mod directories + Change tests for clm6_0_cam6.0 lnd_tuning_mode to clm6_0_cam7.0 + +Testing summary: regular +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- OK + +Answer changes +-------------- + +Changes answers relative to baseline: Only the cam4/cam5 lnd_tuning_mode tests + + Summarize any changes to answers, i.e., + - what code configurations: lnd_tuning_mode ending with _cam4.0 or _cam5.0 suffix with zender_soil_erod_source='lnd' + - what platforms/compilers: All + - nature of change: new dust emissions + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #2632 -- Handle CAM7 + +=============================================================== +=============================================================== Tag name: ctsm5.2.008 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Fri 28 Jun 2024 12:22:46 PM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index ea9417fe41..22a9b12230 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.009 erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names ctsm5.2.008 erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat tmp-240620.n03.ctsm5.2.007 06/27/2024 Set upland hillslope column fsat values to zero (samrabin) tmp-240620.n02.ctsm5.2.007 06/21/2024 Another update of git-fleximod (erik) From 525914480cdbb7aab6963942c284ae80972b37d8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 10 Jul 2024 13:47:58 -0600 Subject: [PATCH 374/408] Add cam7 testing and change tests for cam6.0 to cam7.0 --- bld/unit_testers/build-namelist_test.pl | 26 ++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 53c71ae0e9..183a511020 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,10 +163,10 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 3254; +my $ntests = 3278; if ( defined($opts{'compare'}) ) { - $ntests += 2001; + $ntests += 1981; } plan( tests=>$ntests ); @@ -414,17 +414,17 @@ sub cat_and_create_namelistinfile { $mode = "-phys $phys"; &make_config_cache($phys); foreach my $options ( - "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res ne0np4.ARCTICGRIS.ne30x8 -bgc sp -use_case 1850_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res 0.9x1.25 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res 0.9x1.25 -bgc bgc -crop -use_case 20thC_transient -namelist '&a start_ymd=19500101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res ne0np4CONUS.ne30x8 -bgc sp -use_case 2000_control -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20030101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res 1.9x2.5 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res ne0np4.ARCTICGRIS.ne30x8 -bgc sp -use_case 1850_control -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res 0.9x1.25 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=19790101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res 0.9x1.25 -bgc bgc -crop -use_case 20thC_transient -namelist '&a start_ymd=19500101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res ne0np4CONUS.ne30x8 -bgc sp -use_case 2000_control -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res 1.9x2.5 -bgc sp -use_case 20thC_transient -namelist '&a start_ymd=20030101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res 1.9x2.5 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam7.0", "-res 1x1_brazil -no-megan -use_case 2000_control -lnd_tuning_mode ${phys}_CRUv7", - "-res C96 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam6.0", - "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam6.0", + "-res C96 -bgc sp -use_case 2010_control -namelist '&a start_ymd=20100101/' -lnd_tuning_mode ${phys}_cam7.0", + "-res ne0np4.ARCTIC.ne30x4 -bgc sp -use_case 2000_control -namelist '&a start_ymd=20130101/' -lnd_tuning_mode ${phys}_cam7.0", ) { &make_env_run(); eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); }; @@ -1802,7 +1802,7 @@ sub cat_and_create_namelistinfile { my $mode = "-phys $phys"; &make_config_cache($phys); my @forclist = (); - @forclist = ( "CRUv7", "GSWP3v1", "cam6.0", "cam5.0", "cam4.0" ); + @forclist = ( "CRUv7", "GSWP3v1", "cam7.0", "cam6.0", "cam5.0", "cam4.0" ); foreach my $forc ( @forclist ) { foreach my $bgc ( "sp", "bgc" ) { my $lndtuningmode = "${phys}_${forc}"; From ee3e6a678ff3c336fdc1bc17c5a61ed8557d92e9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 10 Jul 2024 17:21:18 -0600 Subject: [PATCH 375/408] Update ChangeLog/ChangeSum --- doc/ChangeLog | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 78 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 9f62ca5a87..f9fa259a05 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,81 @@ =============================================================== +Tag name: ctsm5.2.010 +Originator(s): @cathyxinchangli (Cathy Xinchang Li, U of Illinois - Urbana-Champaign), @Face2sea, @olyson, @fang-bowen, @keerzhang1 +Date: Wed 10 Jul 2024 05:00:24 PM MDT +One-line Summary: Explicit A/C adoption + +Purpose and description of changes +---------------------------------- + + Code changes for adding an explicit air-conditioning (AC) adoption parameterization scheme in CLMU. This includes adding a new time-varying input variable (AC adoption rate, p_ac), changes to building energy calculations, and a toggle (new namelist variable urban_explicit_ac) + + In this tag we keep the change off by default in order to show that answers do not change: + - If explicit AC adoption is off, the p_ac_[TBD/HD/MD] variables are set to 1 universally, and the building interior setpoints (tbuildmax_[TBD/HD/MD]) remain unchanged, to ensure the model reproduces previous results. + - If explicit AC adoption is on, the p_ac_[TBD/HD/MD] variables take on actual AC adoption rate values (present-day global data were developed together with the code change), and tbuildmax_[TBD/HD/MD] are set to 300K/27°C universally. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: + Fixes #2254 Explicitly representing air-conditioning adoption in CESM + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist variable urban_explicit_ac = .false. by default + +Changes to the datasets (e.g., parameter, surface or initial files): + The default urban time-varying input data file (namelist variable stream_fldfilename_urbantv) now includes p_ac_[TBD/HD/MD] variables, whether or not the explicit-AC-adoption scheme is on and the new file has been rimported to svn: CTSM52_urbantv_Li_2024_0.9x1.25_simyr1849-2106_c20230621.nc + +Changes to documentation: + +Substantial timing or memory changes: +[e.g., check PFS test in the test suite and look at timings, if you +expect possible significant timing changes] + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- IN PROGRESS + izumi ------- + +Answer changes +-------------- + +Changes answers relative to baseline: + No, because we have introduced the changes as default .false. at this time + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2275 + +=============================================================== +=============================================================== Tag name: ctsm5.2.009 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Wed 10 Jul 2024 12:21:23 PM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index 22a9b12230..be04c9c22e 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.010 multiple 07/10/2024 Explicit A/C adoption ctsm5.2.009 erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names ctsm5.2.008 erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat tmp-240620.n03.ctsm5.2.007 06/27/2024 Set upland hillslope column fsat values to zero (samrabin) From 4ca2b6aeeb3388efa9b4026b826d902d8a9f6f95 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 10 Jul 2024 18:17:29 -0600 Subject: [PATCH 376/408] Add error: matrixcn not ok with NTHRDS_LND > 1 (the check does not work) --- bld/CLMBuildNamelist.pm | 16 ++++++++++++++-- bld/unit_testers/build-namelist_test.pl | 2 +- 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 329030d985..7038351688 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1655,7 +1655,7 @@ sub process_namelist_inline_logic { if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) { setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv); } - setup_logic_cnmatrix($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_cnmatrix($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); setup_logic_spinup($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl); @@ -4640,7 +4640,7 @@ sub setup_logic_cnmatrix { # # Set some default options related to the CN Matrix options # - my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref) = @_; my @matrixlist = ( "use_matrixcn", "hist_wrt_matrixcn_diag" ); foreach my $var ( @matrixlist ) { @@ -4650,6 +4650,18 @@ sub setup_logic_cnmatrix { , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); } @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" ); + # Matrix items can't be on for NTHRDS_LND > 1 + my $var_xml = "NTHRDS_LND"; + my $val_xml = int($envxml_ref->{$var_xml}); + print "$var_xml = $val_xml"; + if ( $val_xml > 1) { + foreach my $var ( @matrixlist ) { + if ( &value_is_true($nl->get_value($var)) ) { + $log->warning("$var and $var_xml > 1 causes a clm threading test to FAIL (as of 2024/7/10), so use at your own risk." ); + } + } + } + # Matrix items can't be on for transient if (not string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { foreach my $var ( @matrixlist ) { diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 9b83f9e7ec..df159a8870 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -42,7 +42,7 @@ sub make_env_run { my %settings = @_; # Set default settings - my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" ); + my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NTHRDS_LND=>"1", NEONSITE=>"" ); # Set any settings that came in from function call foreach my $item ( keys(%settings) ) { $env_vars{$item} = $settings{$item}; From 18084b8614d36b6ec24860af95e34df400aa8872 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 11 Jul 2024 11:59:22 -0600 Subject: [PATCH 377/408] Final ChangeLog/ChangeSum --- doc/ChangeLog | 10 +++------- doc/ChangeSum | 2 +- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index f9fa259a05..beca7fbd7f 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.010 Originator(s): @cathyxinchangli (Cathy Xinchang Li, U of Illinois - Urbana-Champaign), @Face2sea, @olyson, @fang-bowen, @keerzhang1 -Date: Wed 10 Jul 2024 05:00:24 PM MDT +Date: Thu 11 Jul 2024 11:57:15 AM MDT One-line Summary: Explicit A/C adoption Purpose and description of changes @@ -48,10 +48,6 @@ Changes to the datasets (e.g., parameter, surface or initial files): Changes to documentation: -Substantial timing or memory changes: -[e.g., check PFS test in the test suite and look at timings, if you -expect possible significant timing changes] - Testing summary: ---------------- @@ -60,8 +56,8 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- IN PROGRESS - izumi ------- + derecho ----- OK + izumi ------- OK Answer changes -------------- diff --git a/doc/ChangeSum b/doc/ChangeSum index be04c9c22e..5df9aa34cf 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.010 multiple 07/10/2024 Explicit A/C adoption + ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption ctsm5.2.009 erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names ctsm5.2.008 erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat tmp-240620.n03.ctsm5.2.007 06/27/2024 Set upland hillslope column fsat values to zero (samrabin) From d67a354298714a5de2357a0216770b1b74603d09 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 11 Jul 2024 13:46:45 -0600 Subject: [PATCH 378/408] Correct number of tests in build-namelist_test and update ChangeLog --- bld/unit_testers/build-namelist_test.pl | 2 +- doc/ChangeLog | 78 +++++++++++++++++++++++++ doc/ChangeSum | 3 +- 3 files changed, 81 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 7c2be32719..02088eecbe 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 3278; +my $ntests = 3277; if ( defined($opts{'compare'}) ) { $ntests += 1981; diff --git a/doc/ChangeLog b/doc/ChangeLog index beca7fbd7f..3a33553f64 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,82 @@ =============================================================== +Tag name: ctsm5.2.011 +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Thu 11 Jul 2024 01:14:12 PM MDT +One-line Summary: Merge b4b-dev + +Purpose and description of changes +---------------------------------- + +#2638 Remove use_dynroot and corresponding code and testing (slevis) +#2623 Change a NIWO test to HARV and update expected failures (slevis) +#2607 Fix py env create (wwieder) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: +Fixes #2451 Remove use_dynroot from clm codes and testing +Fixes #2563 Unable to install ctsm_pylib environment for mksurfdata_esmf in CTSM5.2.005 + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +Change a NIWO test to HARV and update expected failures + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - OK + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - OK + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- IN PROG + izumi ------- NOT STARTED + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Other details +------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2638 + https://github.com/ESCOMP/ctsm/pull/2623 + https://github.com/ESCOMP/ctsm/pull/2607 + +=============================================================== +=============================================================== Tag name: ctsm5.2.010 Originator(s): @cathyxinchangli (Cathy Xinchang Li, U of Illinois - Urbana-Champaign), @Face2sea, @olyson, @fang-bowen, @keerzhang1 Date: Thu 11 Jul 2024 11:57:15 AM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index 5df9aa34cf..892913c52f 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,11 +1,12 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.011 slevis 07/11/2024 Merge b4b-dev ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption ctsm5.2.009 erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names ctsm5.2.008 erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat tmp-240620.n03.ctsm5.2.007 06/27/2024 Set upland hillslope column fsat values to zero (samrabin) tmp-240620.n02.ctsm5.2.007 06/21/2024 Another update of git-fleximod (erik) -tmp-240620.n01.ctsm5.2.007 06/21/2024 Merge b4b-dev (full tag name is tmp-240620.n01.ctsm5.2.007) (slevis) +tmp-240620.n01.ctsm5.2.007 06/21/2024 Merge b4b-dev (slevis) ctsm5.2.007 multiple 05/31/2024 Rm manage_externals and update documentation accordingly ctsm5.2.006 slevis 05/28/2024 Update externals to cesm2_3_beta17, remove mct, retire /test/tools ctsm5.2.005 erik 05/13/2024 Fix clm6_0 defaults and CESM testing issues, add tests to detect these problems From 4f436dcc855d00d0daf69c8d351cf8b19f525924 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 11 Jul 2024 15:48:50 -0600 Subject: [PATCH 379/408] Draft ChangeLog/ChangeSum files --- doc/ChangeLog | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 67 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 2ab7676ddc..4ebd09163a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,70 @@ =============================================================== +Tag name: ctsm5.2.013 +Originator(s): sacks (Bill Sacks, UCAR/NCAR/CGD) +Date: Thu 11 Jul 2024 03:38:12 PM MDT +One-line Summary: Relax tolerance for truncating small snocan values in CanopyFluxes + +Purpose and description of changes +---------------------------------- + +Details in the PR #2457. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: +Fixes #2444 Failing water isotope test on the ctsm5.2 branch + +Notes of particular relevance for users +--------------------------------------- +Changes to documentation: None + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- OK + +Answer changes +-------------- + +Changes answers relative to baseline: + Yes, roundoff. + + - what code configurations: All + - what platforms/compilers: All + - nature of change: Changes start roundoff level and grow over time. + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2457 + +=============================================================== +=============================================================== Tag name: ctsm5.2.008 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Fri 28 Jun 2024 12:22:46 PM MDT diff --git a/doc/ChangeSum b/doc/ChangeSum index ea9417fe41..1af9fcf58e 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.013 sacks 07/??/2024 Relax tolerance for truncating small snocan values in CanopyFluxes ctsm5.2.008 erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat tmp-240620.n03.ctsm5.2.007 06/27/2024 Set upland hillslope column fsat values to zero (samrabin) tmp-240620.n02.ctsm5.2.007 06/21/2024 Another update of git-fleximod (erik) From 3ce1bb42c09670d87cd9fdca86cdbd24b19fd1f2 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 11 Jul 2024 17:34:25 -0600 Subject: [PATCH 380/408] Code mods to get the error check in the previous commit to work --- bld/CLMBuildNamelist.pm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 7038351688..caa116e3bc 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4650,14 +4650,13 @@ sub setup_logic_cnmatrix { , 'spinup_matrixcn'=>$nl_flags->{'spinup_matrixcn'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); } @matrixlist = ( "use_matrixcn", "use_soil_matrixcn", "hist_wrt_matrixcn_diag", "spinup_matrixcn" ); - # Matrix items can't be on for NTHRDS_LND > 1 - my $var_xml = "NTHRDS_LND"; - my $val_xml = int($envxml_ref->{$var_xml}); - print "$var_xml = $val_xml"; + # Matrix items can't be on for OMP_NUM_THREADS (also known as NTHRDS_LND) > 1 + my $var_xml = "OMP_NUM_THREADS"; + my $val_xml = $ENV{$var_xml}; if ( $val_xml > 1) { foreach my $var ( @matrixlist ) { if ( &value_is_true($nl->get_value($var)) ) { - $log->warning("$var and $var_xml > 1 causes a clm threading test to FAIL (as of 2024/7/10), so use at your own risk." ); + $log->warning("$var and $var_xml > 1 (in this case $val_xml) causes a clm threading test to FAIL (as of 2024/7/10), so use at your own risk." ); } } } From c6fba2250092ac1ad776b0ab2fbff9a09db6ad46 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 12 Jul 2024 09:47:27 -0600 Subject: [PATCH 381/408] Final ChangeLog/ChangeSum files --- doc/ChangeLog | 6 +++--- doc/ChangeSum | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 3a33553f64..d12c30e731 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.011 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Thu 11 Jul 2024 01:14:12 PM MDT +Date: Fri 12 Jul 2024 09:45:59 AM MDT One-line Summary: Merge b4b-dev Purpose and description of changes @@ -56,8 +56,8 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- IN PROG - izumi ------- NOT STARTED + derecho ----- OK + izumi ------- OK Answer changes -------------- diff --git a/doc/ChangeSum b/doc/ChangeSum index 892913c52f..79ee06377d 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.011 slevis 07/11/2024 Merge b4b-dev + ctsm5.2.011 slevis 07/12/2024 Merge b4b-dev ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption ctsm5.2.009 erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names ctsm5.2.008 erik 06/28/2024 Bring changes on temp-branch to master: b4b-dev, git-fleximod, hillslope fsat From 093f5fb615988c4ec3cf9e41997178ca45e4808c Mon Sep 17 00:00:00 2001 From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com> Date: Fri, 12 Jul 2024 09:55:43 -0700 Subject: [PATCH 382/408] Update bld/namelist_files/namelist_definition_ctsm.xml with note asterisks --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index c8118031cc..ce2c1b3c5a 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -740,7 +740,7 @@ Set FATES harvesting mode by setting fates_harvest_mode to a valid string option Allowed values are: no_harvest: no fates harvesting of any kind event_code: fates logging via fates logging event codes (see fates parameter file) only - landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod) + landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod)** luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod) luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod) Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file. From 63c458254274edf650aac6bb0da359630446bfca Mon Sep 17 00:00:00 2001 From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com> Date: Fri, 12 Jul 2024 09:57:09 -0700 Subject: [PATCH 383/408] Update bld/namelist_files/namelist_definition_ctsm.xml with astericks Link to note --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index ce2c1b3c5a..208c42038e 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -743,7 +743,7 @@ Allowed values are: landuse_timeseries: fates harvest driven by CLM flanduse_timeseries file (dynHarvestMod)** luhdata_area: fates harvest driven by LUH2 raw harvest data, area-based (dynFATESLandUseChangeMod) luhdata_mass: fates harvest driven by LUH2 raw harvest data, mass-based (dynFATESLandUseChangeMod) -Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file. +**Note that the landuse_timeseries option is not the same as the FATES fluh_timeseries data file. This option is older than the luhdata options and may be depricated at some point in the future. From 7417640e49d9b83932b0ba608b13987b5e62de2c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 12 Jul 2024 11:07:12 -0600 Subject: [PATCH 384/408] Allow tests with threading to proceed with -ignore_warnings --- cime_config/testdefs/testlist_clm.xml | 42 +++++++++---------- .../clm/matrixcnOn_Hist/shell_commands | 3 -- .../include_user_mods | 0 .../matrixcnOn_ignore_warnings/shell_commands | 7 ++++ 4 files changed, 28 insertions(+), 24 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands rename cime_config/testdefs/testmods_dirs/clm/{matrixcnOn_Hist => matrixcnOn_ignore_warnings}/include_user_mods (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 1fe5ed770d..7ead363a6d 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -548,7 +548,7 @@ - + @@ -794,7 +794,7 @@ - + @@ -1002,7 +1002,7 @@ - + @@ -1020,7 +1020,7 @@ - + @@ -1038,7 +1038,7 @@ - + @@ -1074,7 +1074,7 @@ - + @@ -1092,7 +1092,7 @@ - + @@ -1145,7 +1145,7 @@ - + @@ -1162,7 +1162,7 @@ - + @@ -1234,7 +1234,7 @@ - + @@ -1354,7 +1354,7 @@ - + @@ -1390,7 +1390,7 @@ - + @@ -1435,7 +1435,7 @@ - + @@ -1445,7 +1445,7 @@ - + @@ -1455,7 +1455,7 @@ - + @@ -1793,7 +1793,7 @@ - + @@ -1849,7 +1849,7 @@ - + @@ -1897,7 +1897,7 @@ - + @@ -1925,7 +1925,7 @@ - + @@ -1982,7 +1982,7 @@ - + @@ -2369,7 +2369,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands deleted file mode 100644 index f0547f3f26..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/shell_commands +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -./xmlchange CLM_BLDNML_OPTS="-ignore_warnings" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/matrixcnOn_Hist/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands new file mode 100644 index 0000000000..d94ef06a5c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/matrixcnOn_ignore_warnings/shell_commands @@ -0,0 +1,7 @@ +#!/bin/bash + +./xmlchange CLM_BLDNML_OPTS="-ignore_warnings" --append + +# In this testmod directory we are ignoring warnings about running +# matrixcn in transient simulations AND/OR +# warnings about running matrixcn with threading NTHRDS_LND > 1. From 1e9df4973fdfcb9e685026ecaed2b56745b24663 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com> Date: Fri, 12 Jul 2024 10:27:07 -0700 Subject: [PATCH 385/408] update comment regarding landuse x pft data set Pre-generating files is a more likely next step relative to auto-gen --- cime_config/SystemTests/pvt.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py index feef6cb04c..2a3dbafdc3 100644 --- a/cime_config/SystemTests/pvt.py +++ b/cime_config/SystemTests/pvt.py @@ -30,9 +30,8 @@ def __init__(self,case): error_message = (f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected.") # Only allow to run if resolution is 4x5 for now - # Eventually we could set this up to generate the necessary land use x pft mapping - # on the fly, although this would also require generating the land use timeseries - # regridding on the fly which is a more time consuming endevour currently + # Other grid resolutions will be pre-processed and included in the namelist defaults at a future date. + # Potentially we could generate these on the fly although doing so would result in increased build time lnd_grid = self._case.get_value("LND_GRID") if lnd_grid != "4x5": error_message = (f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected.") From 48aeb43c9575c80a1547a85c1b02b529b690ac05 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux <7565064+glemieux@users.noreply.github.com> Date: Fri, 12 Jul 2024 10:40:15 -0700 Subject: [PATCH 386/408] Update README with suggested clarification --- cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README index 79d6511d17..9b782cb2a7 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/README @@ -1,2 +1,4 @@ Currently the FATES LUH2 category of test mods currently only supports -4x5 grid resolutions. +4x5 grid resolutions. This is because we only have one LUH2 time series +dataset for the 4x5 resolution. In the future we will provide more resolutions +which will be added to the namelist defaults. From 9ee75610973c32376f6dc407c99a0bc8d55cad83 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 12 Jul 2024 14:09:26 -0700 Subject: [PATCH 387/408] fix how harvest mode is passed to add_default for use_fates_luh --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 47e0fff402..ac87d6f4ca 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4522,7 +4522,7 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_luh', 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), 'use_fates_potentialveg'=>$nl->get_value('use_fates_potentialveg'), - 'fates_harvest_mode'=>$nl->get_value('fates_harvest_mode') ); + 'fates_harvest_mode'=>remove_leading_and_trailing_quotes($nl->get_value('fates_harvest_mode')) ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_nocomp', 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_lupft'=>$nl->get_value('use_fates_lupft'), 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); From 48368ac9a5fd2c36fb57cd21c3be76f773e3744d Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 12 Jul 2024 15:11:48 -0700 Subject: [PATCH 388/408] add comment pointing to luh2 data set readme --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index 681d39f38c..1bc6ab929e 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -50,6 +50,7 @@ module dynFATESLandUseChangeMod type(dyn_file_type), target :: dynFatesLandUse_file ! LUH2 raw wood harvest area fraction + ! LUH2 data set variable names can be found at https://luh.umd.edu/LUH2/LUH2_v2h_README.pdf character(len=10), target :: landuse_harvest_area_varnames(num_landuse_harvest_vars) = & [character(len=10) :: 'primf_harv', 'primn_harv', 'secmf_harv', 'secyf_harv', 'secnf_harv'] From b0e6565a8d802db3c1a4a2ad3322726ed680b09f Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 12 Jul 2024 15:18:54 -0700 Subject: [PATCH 389/408] add single quotes around fates_harvest_mode in unit tests --- bld/unit_testers/build-namelist_test.pl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index b343e3d194..e60a411ccb 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1009,7 +1009,7 @@ sub cat_and_create_namelistinfile { phys=>"clm5_0", }, "useloggingButNOTFATES" =>{ options=>"-envxml_dir . -no-megan", - namelst=>"fates_harvest_mode=event_code", + namelst=>"fates_harvest_mode='event_code'", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, @@ -1064,12 +1064,12 @@ sub cat_and_create_namelistinfile { phys=>"clm5_0", }, "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan", - namelst=>"use_fates_potentialveg=T,fates_harvest_mode=event_code", + namelst=>"use_fates_potentialveg=T,fates_harvest_mode='event_code'", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, "useFATESHARVEST3WOLUH" =>{ options=>"-bgc fates -envxml_dir . -no-megan", - namelst=>"use_fates_luh=F,fates_harvest_mode=luhdata_area", + namelst=>"use_fates_luh=F,fates_harvest_mode='luhdata_area'", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, From 8e618bb5384ba72d2b53b45a778aad29be542221 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 12 Jul 2024 16:44:47 -0600 Subject: [PATCH 390/408] Add new test to build-namelist_test.pl (currently failing) --- bld/unit_testers/build-namelist_test.pl | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 005f2c3f96..1810d4434b 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -41,7 +41,7 @@ sub make_env_run { # my %settings = @_; - # Set default settings + # Set default settings TODO slevis: NTHRDS_LND fails, OMP_NUM_THREADS fails my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NTHRDS_LND=>"1", NEONSITE=>"" ); # Set any settings that came in from function call foreach my $item ( keys(%settings) ) { @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 3306; +my $ntests = 3309; if ( defined($opts{'compare'}) ) { $ntests += 2045; @@ -1320,6 +1320,12 @@ sub cat_and_create_namelistinfile { my %warntest = ( # Warnings without the -ignore_warnings option given + "matrixcnOn_with_threading" =>{ options=>"-envxml_dir . -bgc bgc", + namelst=>"use_matrixcn=.true.", + GLC_TWO_WAY_COUPLING=>"TRUE", + NTHRDS_LND=>"2", + phys=>"clm5_0", + }, "dustemisLeung" =>{ options=>"-envxml_dir .", namelst=>"dust_emis_method = 'Leung_2023'", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -1376,7 +1382,13 @@ sub cat_and_create_namelistinfile { &make_config_cache($warntest{$key}{"phys"}); my $options = $warntest{$key}{"options"}; my $namelist = $warntest{$key}{"namelst"}; - &make_env_run( GLC_TWO_WAY_COUPLING=>$warntest{$key}{"GLC_TWO_WAY_COUPLING"} ); + my %settings; + foreach my $xmlvar ( "GLC_TWO_WAY_COUPLING", "NTHRDS_LND") { + if ( defined($failtest{$key}{$xmlvar}) ) { + $settings{$xmlvar} = $failtest{$key}{$xmlvar}; + } + } + &make_env_run( %settings ); eval{ system( "$bldnml $options -namelist \"&clmexp $namelist /\" > $tempfile 2>&1 " ); }; isnt( $?, 0, $key ); system( "cat $tempfile" ); From 12c60f3de477bbdaa2cf7a8afe0d089886d2c960 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 12 Jul 2024 16:01:12 -0700 Subject: [PATCH 391/408] correct POTVEG fail unit test This needs to have use_fates_luh to avoid the false negative of failing due to not having this mode with use_fates_potentialveg --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index fc1e83f162..741964d8a1 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1063,7 +1063,7 @@ sub cat_and_create_namelistinfile { phys=>"clm5_0", }, "useFATESPOTVEGwithHARVEST" =>{ options=>"-bgc fates -envxml_dir . -no-megan", - namelst=>"use_fates_potentialveg=T,fates_harvest_mode='event_code'", + namelst=>"use_fates_potentialveg=T,fates_harvest_mode='event_code',use_fates_luh=T", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, From af11aaab0644357cbff66aecbbc2f94a25778ab7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 15 Jul 2024 14:02:15 -0600 Subject: [PATCH 392/408] Remove new test from build-namelist_test.pl for now --- bld/unit_testers/build-namelist_test.pl | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 1810d4434b..16f6ba2a62 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -41,8 +41,8 @@ sub make_env_run { # my %settings = @_; - # Set default settings TODO slevis: NTHRDS_LND fails, OMP_NUM_THREADS fails - my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NTHRDS_LND=>"1", NEONSITE=>"" ); + # Set default settings + my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" ); # Set any settings that came in from function call foreach my $item ( keys(%settings) ) { $env_vars{$item} = $settings{$item}; @@ -1320,12 +1320,6 @@ sub cat_and_create_namelistinfile { my %warntest = ( # Warnings without the -ignore_warnings option given - "matrixcnOn_with_threading" =>{ options=>"-envxml_dir . -bgc bgc", - namelst=>"use_matrixcn=.true.", - GLC_TWO_WAY_COUPLING=>"TRUE", - NTHRDS_LND=>"2", - phys=>"clm5_0", - }, "dustemisLeung" =>{ options=>"-envxml_dir .", namelst=>"dust_emis_method = 'Leung_2023'", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -1383,7 +1377,7 @@ sub cat_and_create_namelistinfile { my $options = $warntest{$key}{"options"}; my $namelist = $warntest{$key}{"namelst"}; my %settings; - foreach my $xmlvar ( "GLC_TWO_WAY_COUPLING", "NTHRDS_LND") { + foreach my $xmlvar ( "GLC_TWO_WAY_COUPLING" ) { if ( defined($failtest{$key}{$xmlvar}) ) { $settings{$xmlvar} = $failtest{$key}{$xmlvar}; } From 322097f0a2b5cf0c3b6bdd5a3eccb70845cb6990 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 15 Jul 2024 13:05:59 -0700 Subject: [PATCH 393/408] change folder name for fates land use x pft files This matches the corresponding fates tag that also impliments using this file --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6f29513e6b..d4167228b9 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2019,7 +2019,7 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc -lnd/clm2/surfdata_map/fates-sci.1.73.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc +lnd/clm2/surfdata_map/fates-sci.1.77.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc Date: Tue, 16 Jul 2024 08:58:38 -0600 Subject: [PATCH 394/408] Final ChangeLog/ChangeSum --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index b723b849ae..00c576d0d8 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.012 Originator(s): sacks (Bill Sacks, UCAR/NCAR/CGD) -Date: Mon 15 Jul 2024 11:55:45 AM MDT +Date: Tue 16 Jul 2024 08:57:42 AM MDT One-line Summary: Relax tolerance for truncating small snocan values in CanopyFluxes Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index 034c02429c..381b0db858 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.012 sacks 07/15/2024 Relax tolerance for truncating small snocan values in CanopyFluxes + ctsm5.2.012 sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes ctsm5.2.011 slevis 07/12/2024 Merge b4b-dev ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption ctsm5.2.009 erik 07/10/2024 Allow for CAM7 in lnd_tuning_mode and handle C or E in long compset names From aa923a4d2dc279cd9a85c2f691fd73ab7ab83e56 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 16 Jul 2024 12:12:33 -0600 Subject: [PATCH 395/408] Correct two test names in ExpectedTestFails.xml --- cime_config/testdefs/ExpectedTestFails.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 6a2186d6d9..7a07a056f7 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -37,14 +37,14 @@ - + FAIL #2619 This failure relates to the following REP failure. - + FAIL #2619 From ef970e2e8062e0852583216acda18c4ade60cd5e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 16 Jul 2024 12:13:21 -0600 Subject: [PATCH 396/408] Make hillslope_fsat_equals_zero .false. unless use_hillslope = .true. --- bld/namelist_files/namelist_defaults_ctsm.xml | 3 ++- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0777f423ca..e2ba2de74b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -625,7 +625,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Standard Uniform .true. -.true. +.false. +.true. .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 52f5aee138..bc92dafbf0 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -829,7 +829,7 @@ Toggle to turn on surface water routing in the hillslope hydrology model + group="clm_inparm" valid_values="" value=".false."> If true, set fsat to zero for hillslope columns From 9db4d48623697669e5120830ded96ea2cb7047e0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 16 Jul 2024 15:38:28 -0700 Subject: [PATCH 397/408] add izumi luh2 failure to expected list --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index a4033aa6cd..ee1f188f15 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -150,6 +150,13 @@ + + + FAIL + #2653 + + + FAIL From 1de58fbb04d862245f69239835a00c15e062dc54 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 17 Jul 2024 12:37:45 -0700 Subject: [PATCH 398/408] update fates to sci.1.77.1_api.36.0.0 --- .gitmodules | 2 +- src/fates | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitmodules b/.gitmodules index 9ed4402c7e..8127cac482 100644 --- a/.gitmodules +++ b/.gitmodules @@ -28,7 +28,7 @@ [submodule "fates"] path = src/fates url = https://github.com/NGEET/fates -fxtag = sci.1.77.0_api.36.0.0 +fxtag = sci.1.77.1_api.36.0.0 fxrequired = AlwaysRequired # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed fxDONOTUSEurl = https://github.com/NCAR/fates-release diff --git a/src/fates b/src/fates index fd7f3438c2..1982b0032c 160000 --- a/src/fates +++ b/src/fates @@ -1 +1 @@ -Subproject commit fd7f3438c2ff821672b703050e7011f293649ee9 +Subproject commit 1982b0032c3cab6278892eccb85f643114ffb1af From 47571d844674d836a7501c3cd98f65ac545f4e39 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 17 Jul 2024 13:23:11 -0700 Subject: [PATCH 399/408] formatting fixed for changelog --- doc/ChangeLog | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 71b07aa2f2..54e3b4cc4b 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,3 +1,5 @@ +=============================================================== +Tag name: ctsm5.2.013 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) Date: Wed 17 Jul 2024 01:20:00 PM MDT From e4142b96425712afa44cb6ab440d297a56aeaae1 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 17 Jul 2024 13:26:45 -0700 Subject: [PATCH 400/408] fixing bad merge with changelog --- doc/ChangeLog | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 54e3b4cc4b..3c6a104725 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -79,7 +79,6 @@ Changes to tests or testing: and use_fates_lupft namelist options. Additoinally a new system text prefix, PVT, has been added to test the use_fates_potentialveg spin-up to use_fates_lupft transient workflow. These have been added to the fates test suite. -======= Bugs fixed ---------- @@ -154,6 +153,19 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm4_5 + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: +Fixes #2444 Failing water isotope test on the ctsm5.2 branch + +Notes of particular relevance for users +--------------------------------------- +Changes to documentation: None + +Testing summary: +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): From 75cd2f4c866bd8148dff0e310e1ba0711bef13f3 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 17 Jul 2024 14:07:23 -0700 Subject: [PATCH 401/408] reformat new and updated systests with black --- cime_config/SystemTests/pvt.py | 15 +++++++++------ cime_config/SystemTests/systemtest_utils.py | 7 ++++--- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/cime_config/SystemTests/pvt.py b/cime_config/SystemTests/pvt.py index 2a3dbafdc3..cf923dd334 100644 --- a/cime_config/SystemTests/pvt.py +++ b/cime_config/SystemTests/pvt.py @@ -16,9 +16,10 @@ logger = logging.getLogger(__name__) + class PVT(SystemTestsCommon): - def __init__(self,case): - SystemTestsCommon.__init__(self,case) + def __init__(self, case): + SystemTestsCommon.__init__(self, case) # Do not allow PVT to be run with certain testmods # Should this be targeted to a specific testmod for simplicity for now? @@ -27,14 +28,16 @@ def __init__(self,case): casebaseid = self._case.get_value("CASEBASEID") casebaseid = casebaseid.split("-")[-1] if casebaseid[0:10] != "FatesLUPFT": - error_message = (f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected.") + error_message = f"Only call PVT with testmod FatesLUPFT. {casebaseid} selected." # Only allow to run if resolution is 4x5 for now # Other grid resolutions will be pre-processed and included in the namelist defaults at a future date. # Potentially we could generate these on the fly although doing so would result in increased build time lnd_grid = self._case.get_value("LND_GRID") if lnd_grid != "4x5": - error_message = (f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected.") + error_message = ( + f"PVT can currently only be run with 4x5 resolution. {lnd_grid} selected." + ) if error_message is not None: logger.error(error_message) @@ -79,7 +82,7 @@ def run_phase(self): # Turn off fates_harvest_mode for the spin up. logger.info("PVT log: modify user_nl_clm file for spin up run") - added_content = ["use_fates_potentialveg = .true.","fates_harvest_mode = 'no_harvest'"] + added_content = ["use_fates_potentialveg = .true.", "fates_harvest_mode = 'no_harvest'"] append_to_user_nl_files(clone_path, "clm", added_content) # Run the spin up case @@ -100,7 +103,7 @@ def run_phase(self): # obtain rpointer files and necessary restart files from short term archiving directory rundir = self._case.get_value("RUNDIR") - refdate = str(refcase_year) + '-01-01-00000' + refdate = str(refcase_year) + "-01-01-00000" rest_path = os.path.join(dout_sr, "rest", "{}".format(refdate)) for item in glob.glob("{}/*{}*".format(rest_path, refdate)): diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index c39f5171ba..c252f73251 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -86,14 +86,15 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): print(f"ERROR trying to run {tool_name}.") raise + # Read a user_nl file and return the namelist option if found def find_user_nl_option(caseroot, component, namelist_option): - + # This is a copy of the CIME _get_list_of_user_nl_files # which could be used if this moved into the CIME project file_pattern = "user_nl_" + component + "*" file_list = glob.glob(os.path.join(caseroot, file_pattern)) - + # Check that there is at least one file if len(file_list) == 0: raise RuntimeError("No user_nl files found for component " + component) @@ -103,7 +104,7 @@ def find_user_nl_option(caseroot, component, namelist_option): for one_file in file_list: with open(one_file, "r") as user_nl_file: user_nl_text = user_nl_file.read() - reg = fr'{namelist_option}.*?(?=,|\n)' + reg = rf"{namelist_option}.*?(?=,|\n)" find_out = re.findall(reg, user_nl_text) output[one_file] = find_out return output From 3416574a862e2f1df62d29abb82efe76686084dd Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 18 Jul 2024 10:51:28 -0600 Subject: [PATCH 402/408] update date --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 3c6a104725..8cc3198fae 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -2,7 +2,7 @@ Tag name: ctsm5.2.013 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) -Date: Wed 17 Jul 2024 01:20:00 PM MDT +Date: Thu Jul 18 10:51:11 MDT 2024 One-line Summary: FATES Land Use V2 Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index 92ca8281cf..df8e6dcf6a 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.013 glemieux 07/17/2024 FATES Land Use V2 + ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2 ctsm5.2.012 sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes ctsm5.2.011 slevis 07/12/2024 Merge b4b-dev ctsm5.2.010 multiple 07/11/2024 Explicit A/C adoption From c031e1c699be02a96123df5c0ed780f4c9ce73bc Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 18 Jul 2024 15:14:14 -0600 Subject: [PATCH 403/408] Update ntests in build-namelist_test.pl --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 16f6ba2a62..9b283af334 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 3309; +my $ntests = 3306; if ( defined($opts{'compare'}) ) { $ntests += 2045; From c2b6c43f44c0dc3b6b9ad65b5dc979951090c3da Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 18 Jul 2024 17:35:07 -0600 Subject: [PATCH 404/408] Draft ChangeLog/ChangeSum --- doc/ChangeLog | 144 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 145 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 8cc3198fae..5f2896ebc9 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,148 @@ =============================================================== +Tag name: ctsm5.2.014 +Originator(s): chrislxj (Xingjie Lu, Northern Arizona U., xingjie.lu@nau.edu) +Date: Thu 18 Jul 2024 03:50:56 PM MDT +One-line Summary: use_matrixcn, use_soil_matrixcn come in but as default .false. + +Purpose and description of changes +---------------------------------- + + Currently set as default .false.: + - Add matrix module for vegetation and soil C and N cycle + - Add diagnostic variables C and N storage capacity in history files + - Add Sparse matrix module to increase the code efficiency + - Create spin-up switch, and be ready for matrix spin up development + + Additional contributors: Yuanyuan Huang, Zhenggang Du, and Yiqi Luo from + Professor Yiqi Luo's EcoLab at Northern Arizona University, now at Cornell U. + + In TSS/CGD/NCAR, contributors in the last year include slevis, ekluzek, wwieder. + Others may have been involved prior. I apologize for omissions. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: + Fixes #903 Bring CN-Matrix solution into CTSM + Fixes #2450 Cn-matrix testing in the aux_clm test-suites + Fixes #2621 matrixcn does not work with nrepr != 1 (number of crop reproductive pools) + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc spin-ups + and NOT recommended for + - transient simulations (e.g. IHist) + - simulations that use threading (e.g. see tests with P64x2) + - NWP compsets + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New: use_matrixcn, use_soil_matrixcn, hist_wrt_matrixcn_diag. + All three are default .false. at this time. + +Changes made to namelist defaults (e.g., changed parameter values): + Changed hillslope_fsat_equals_zero to default .false. when + use_hillslope = .false. as per issue #2652 + clm_accelerated_spinup can be set to off, on, sasu, the latter being + the setting that uses matrixcn + +Changes to the datasets (e.g., parameter, surface or initial files): + No. + +Changes to documentation: + None at this time. A description of the spinup procedure appears in + https://github.com/NCAR/LMWG_dev/issues/58 + +Substantial timing or memory changes: + ***Check PFS test in the test suite and look at timings + + +Notes of particular relevance for developers: +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + - Future changes to the bgc will likely require changes in both + matrix and non-matrix parts of the code. + - I have found matrixcn to be sensitive to changes in the subgrid + heterogeneity and other subtleties. For example, matrixcn simulations + have failed from using a finidat file from a different simulation (#2592), + from running in transient mode (#2592), from running with threading (#2619), + and from setting hillslope_fsat_equals_zero = .true. (issue #2652). + - We recommend using matrixcn to accelerate bgc spin-ups and not for + most (possibly any) other purposes. + +Changes to tests or testing: + Numerous new tests in aux_clm and in build-namelist_test.pl that can be + identified by searching "matr" + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- IN PROG + izumi ------- IN PROG + + ctsm_sci + derecho ---- IN PROG + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, roundoff + + Summarize any changes to answers, i.e., + - what code configurations: All + - what platforms/compilers: All + - nature of change: roundoff + use_matrixcn and use_soil_matrixcn are default .false.. We get + roundoff diffs due to order-of-operation changes in a few locations, + done to improve code readability and streamlining in the presence of matrix. + + Testing with the non-default use_matrixcn = .true. and use_soil_matrixcn = .true. + appears here: https://github.com/NCAR/LMWG_dev/issues/58 + + PR #640 associated with this tag explains how answers are expected to + change from non-matrix to matrix simulations. + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/640 + +=============================================================== +=============================================================== Tag name: ctsm5.2.013 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) diff --git a/doc/ChangeSum b/doc/ChangeSum index df8e6dcf6a..8579fbee98 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.014 chrislxj 07/18/2024 use_matrixcn, use_soil_matrixcn come in but as default .false. ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2 ctsm5.2.012 sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes ctsm5.2.011 slevis 07/12/2024 Merge b4b-dev From 5aeb618ebffdb8ab49521d47aa2d04037f76aa6f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 19 Jul 2024 11:53:37 -0600 Subject: [PATCH 405/408] Update ChangeLog/ChangeSum --- doc/ChangeLog | 57 +++++++++++++++++++++++++-------------------------- doc/ChangeSum | 2 +- 2 files changed, 29 insertions(+), 30 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 5f2896ebc9..35ad747636 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,8 +1,8 @@ =============================================================== Tag name: ctsm5.2.014 Originator(s): chrislxj (Xingjie Lu, Northern Arizona U., xingjie.lu@nau.edu) -Date: Thu 18 Jul 2024 03:50:56 PM MDT -One-line Summary: use_matrixcn, use_soil_matrixcn come in but as default .false. +Date: Fri 19 Jul 2024 11:04:17 AM MDT +One-line Summary: use_matrixcn, use_soil_matrixcn come in as default .false. Purpose and description of changes ---------------------------------- @@ -16,8 +16,9 @@ Purpose and description of changes Additional contributors: Yuanyuan Huang, Zhenggang Du, and Yiqi Luo from Professor Yiqi Luo's EcoLab at Northern Arizona University, now at Cornell U. - In TSS/CGD/NCAR, contributors in the last year include slevis, ekluzek, wwieder. - Others may have been involved prior. I apologize for omissions. + In TSS/CGD/NCAR/UCAR, contributors in the last year include slevis, ekluzek, wwieder. + I apologize if I have omitted others who may have been involved prior. + Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -45,12 +46,13 @@ List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: Fixes #2450 Cn-matrix testing in the aux_clm test-suites Fixes #2621 matrixcn does not work with nrepr != 1 (number of crop reproductive pools) + Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): - use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc spin-ups - and NOT recommended for + use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc + spin-ups (keep reading for more info) and NOT recommended for - transient simulations (e.g. IHist) - simulations that use threading (e.g. see tests with P64x2) - NWP compsets @@ -60,21 +62,17 @@ Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): All three are default .false. at this time. Changes made to namelist defaults (e.g., changed parameter values): - Changed hillslope_fsat_equals_zero to default .false. when + - hillslope_fsat_equals_zero is now default .false. when use_hillslope = .false. as per issue #2652 - clm_accelerated_spinup can be set to off, on, sasu, the latter being - the setting that uses matrixcn - -Changes to the datasets (e.g., parameter, surface or initial files): - No. + - clm_accelerated_spinup can be set to on, sasu, off; matrixcn spin-up + is performed in that order (on, sasu, off); in the "on" phase, matrixcn + is not active, in the "sasu" phase matrixcn is active, and in the "off" + phase, matrixcn may be active Changes to documentation: None at this time. A description of the spinup procedure appears in https://github.com/NCAR/LMWG_dev/issues/58 -Substantial timing or memory changes: - ***Check PFS test in the test suite and look at timings - Notes of particular relevance for developers: --------------------------------------------- @@ -82,17 +80,17 @@ Notes of particular relevance for developers: Caveats for developers (e.g., code that is duplicated that requires double maintenance): - Future changes to the bgc will likely require changes in both matrix and non-matrix parts of the code. - - I have found matrixcn to be sensitive to changes in the subgrid - heterogeneity and other subtleties. For example, matrixcn simulations - have failed from using a finidat file from a different simulation (#2592), + - matrixcn seems sensitive to changes in subgrid heterogeneity and + other subtleties. For example, matrixcn simulations have failed from + using a finidat file from a different simulation (#2592), from running in transient mode (#2592), from running with threading (#2619), and from setting hillslope_fsat_equals_zero = .true. (issue #2652). - We recommend using matrixcn to accelerate bgc spin-ups and not for - most (possibly any) other purposes. + most (any?) other purposes. Changes to tests or testing: - Numerous new tests in aux_clm and in build-namelist_test.pl that can be - identified by searching "matr" + We introduced numerous new tests to the aux_clm and build-namelist_test.pl + test-suites that can be identified by searching "matrix" Testing summary: @@ -110,11 +108,11 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- IN PROG - izumi ------- IN PROG + derecho ----- OK + izumi ------- OK ctsm_sci - derecho ---- IN PROG + derecho ---- OK Answer changes @@ -123,17 +121,18 @@ Answer changes Changes answers relative to baseline: Yes, roundoff Summarize any changes to answers, i.e., - - what code configurations: All + - what code configurations: Non-matrix - what platforms/compilers: All - nature of change: roundoff use_matrixcn and use_soil_matrixcn are default .false.. We get - roundoff diffs due to order-of-operation changes in a few locations, - done to improve code readability and streamlining in the presence of matrix. + roundoff diffs due to order-of-operation changes in a few sections + of code, which improve readability and streamlining of the code + in the presence of matrix. - Testing with the non-default use_matrixcn = .true. and use_soil_matrixcn = .true. + Testing with the non-default use_matrixcn and use_soil_matrixcn = .true. appears here: https://github.com/NCAR/LMWG_dev/issues/58 - PR #640 associated with this tag explains how answers are expected to + PR #640 explains how answers are expected to change from non-matrix to matrix simulations. Other details diff --git a/doc/ChangeSum b/doc/ChangeSum index 8579fbee98..21237cbac8 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.014 chrislxj 07/18/2024 use_matrixcn, use_soil_matrixcn come in but as default .false. + ctsm5.2.014 chrislxj 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false. ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2 ctsm5.2.012 sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes ctsm5.2.011 slevis 07/12/2024 Merge b4b-dev From 63b3c3fdfa8e9d5aec763bd872a81a69b2832d8e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 19 Jul 2024 17:19:36 -0600 Subject: [PATCH 406/408] Namelist corrections after an izumi test failed ERS_D.f19_g17.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup failed during the build because a namelist variable needed renaming --- .../user_nl_mosart | 2 +- .../testmods_dirs/clm/rtmColdSSP/user_nl_rtm | 8 +++---- lilac/bld_templates/mosart_in | 22 +++++++++---------- 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart index 9e109fc131..82243d7d3d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_monthly_matrixcn_spinup/user_nl_mosart @@ -1 +1 @@ -frivinp_rtm = '/dev/null' +frivinp = '/dev/null' diff --git a/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm b/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm index d1a0254a0b..e78d13a51c 100644 --- a/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm +++ b/cime_config/testdefs/testmods_dirs/clm/rtmColdSSP/user_nl_rtm @@ -1,4 +1,4 @@ -finidat_rtm = " " -rtmhist_mfilt = 1 -rtmhist_ndens = 2 -rtmhist_nhtfrq = 0 +finidat = " " +mfilt = 1 +ndens = 2 +nhtfrq = 0 diff --git a/lilac/bld_templates/mosart_in b/lilac/bld_templates/mosart_in index 091ec69285..0bc2242dda 100644 --- a/lilac/bld_templates/mosart_in +++ b/lilac/bld_templates/mosart_in @@ -4,18 +4,18 @@ delt_mosart = 1800 do_rtm = .true. do_rtmflood = .false. - finidat_rtm = " " - frivinp_rtm = "/glade/campaign/cesm/cesmdata/cseg/inputdata/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc" + finidat = " " + frivinp = "/glade/campaign/cesm/cesmdata/cseg/inputdata/rof/mosart/MOSART_routing_Global_0.5x0.5_c170601.nc" ice_runoff = .true. qgwl_runoff_option = "threshold" - rtmhist_fexcl1 = "" - rtmhist_fexcl2 = "" - rtmhist_fexcl3 = "" - rtmhist_fincl1 = "" - rtmhist_fincl2 = "" - rtmhist_fincl3 = "" - rtmhist_mfilt = 1 - rtmhist_ndens = 1 - rtmhist_nhtfrq = 0 + fexcl1 = "" + fexcl2 = "" + fexcl3 = "" + fincl1 = "" + fincl2 = "" + fincl3 = "" + mfilt = 1 + ndens = 1 + nhtfrq = 0 smat_option = "Xonly" / From a32a9eb121af3fcb7de1af94b5812f51eac49666 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 19 Jul 2024 18:42:31 -0600 Subject: [PATCH 407/408] Draft ChangeLog/ChangeSum (comments welcome) --- doc/ChangeLog | 130 +++++++++++++++++++++++++++++++++++++++++++++++++- doc/ChangeSum | 3 +- 2 files changed, 131 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 35ad747636..785b26db9e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,131 @@ =============================================================== +Tag name: ctsm5.2.015 +Originator(s): multiple (Samuel Levis,UCAR/TSS,303-665-1310, @mvertens, @jedwards4b, @billsacks, @Katetc) +Date: Fri 19 Jul 2024 06:02:22 PM MDT +One-line Summary: Update submodule tags to pass runoff from cism to rof + +Purpose and description of changes +---------------------------------- + + - Update MOSART, CMEPS, and CISM so CISM runoff goes to ROF rather than CTSM + - Update RTM with fix needed for Paleo LGM work + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm6_0 + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +List of CTSM issues fixed (include CTSM Issue # and description) [one per line]: + Fixes #2590 Update CMEPS/MOSART/CISM/RTM tags + Fixes https://github.com/ESCOMP/RTM/issues/50 Likely wrong RTM river flux to MOM6 within cesm2_3_beta17 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + Issue https://github.com/ESCOMP/RTM/issues/50 + Likely wrong RTM river flux to MOM6 within cesm2_3_beta17 is now fixed with + https://github.com/ESCOMP/RTM/pull/51 + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + Differences in namelist 'mosart_inparm': + missing variable: 'do_rtmflood' + missing variable: 'finidat_rtm' + missing variable: 'frivinp_rtm' + missing variable: 'rtmhist_fexcl1' + missing variable: 'rtmhist_fexcl2' + missing variable: 'rtmhist_fexcl3' + missing variable: 'rtmhist_fincl1' + missing variable: 'rtmhist_fincl2' + missing variable: 'rtmhist_fincl3' + missing variable: 'rtmhist_mfilt' + missing variable: 'rtmhist_ndens' + missing variable: 'rtmhist_nhtfrq' + found extra variable: 'budget_frq' + found extra variable: 'fexcl1' + found extra variable: 'fexcl2' + found extra variable: 'fexcl3' + found extra variable: 'fincl1' + found extra variable: 'fincl2' + found extra variable: 'fincl3' + found extra variable: 'finidat' + found extra variable: 'frivinp' + found extra variable: 'mfilt' + found extra variable: 'mosart_euler_calc' + found extra variable: 'mosart_tracers' + found extra variable: 'ndens' + found extra variable: 'nhtfrq' + found extra variable: 'use_halo_option' + +Changes to documentation: + Not that I am aware of + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- OK + + ctsm_sci + derecho ---- OK (while in tag ctsm5.2.007; I did not repeat with the latest; see checklist in #2590) + + +Answer changes +-------------- + +Changes answers relative to baseline: Yes + + Summarize any changes to answers, i.e., + - what code configurations: mosart and rtm + - what platforms/compilers: all + - nature of change: mosart roundoff; rtm larger than roundoff due to bug fix + + +Other details +------------- +List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): + See .gitmodules: cism, rtm, mosart, ccs_config, cmeps + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2605 + https://github.com/ESCOMP/RTM/pull/51 + https://github.com/ESCOMP/MOSART/pull/94 + https://github.com/ESCOMP/CISM-wrapper/pull/100 + https://github.com/ESCOMP/CMEPS/pull/463 + https://github.com/ESMCI/ccs_config_cesm/pull/174 + +=============================================================== +=============================================================== Tag name: ctsm5.2.014 Originator(s): chrislxj (Xingjie Lu, Northern Arizona U., xingjie.lu@nau.edu) Date: Fri 19 Jul 2024 11:04:17 AM MDT @@ -51,7 +178,8 @@ Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): - use_matrixcn and use_soil_matrixcn ARE recommended for accelerating bgc + use_matrixcn and use_soil_matrixcn ARE NOT available for clm4_5 + and ARE recommended for accelerating bgc spin-ups (keep reading for more info) and NOT recommended for - transient simulations (e.g. IHist) - simulations that use threading (e.g. see tests with P64x2) diff --git a/doc/ChangeSum b/doc/ChangeSum index 21237cbac8..5c7123b5e0 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,7 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.014 chrislxj 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false. + ctsm5.2.015 multiple 07/19/2024 Update submodule tags to pass runoff from cism to rof + ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false. ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2 ctsm5.2.012 sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes ctsm5.2.011 slevis 07/12/2024 Merge b4b-dev From a4a9ede604eb36e1b1f6541fb1e40b712176ffa5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 22 Jul 2024 16:04:00 -0600 Subject: [PATCH 408/408] Update ChangeLog/ChangeSum --- doc/ChangeLog | 4 +++- doc/ChangeSum | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 785b26db9e..506b3d5ad0 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.2.015 Originator(s): multiple (Samuel Levis,UCAR/TSS,303-665-1310, @mvertens, @jedwards4b, @billsacks, @Katetc) -Date: Fri 19 Jul 2024 06:02:22 PM MDT +Date: Mon 22 Jul 2024 12:46:17 PM MDT One-line Summary: Update submodule tags to pass runoff from cism to rof Purpose and description of changes @@ -110,6 +110,8 @@ Changes answers relative to baseline: Yes - what platforms/compilers: all - nature of change: mosart roundoff; rtm larger than roundoff due to bug fix + We are ignoring strange diffs from baseline in two tests in variable + FATES_TRANSITION_MATRIX_LULU as explained in issue #2656. Other details ------------- diff --git a/doc/ChangeSum b/doc/ChangeSum index 5c7123b5e0..9c6524b33d 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.015 multiple 07/19/2024 Update submodule tags to pass runoff from cism to rof + ctsm5.2.015 multiple 07/22/2024 Update submodule tags to pass runoff from cism to rof ctsm5.2.014 multiple 07/19/2024 use_matrixcn, use_soil_matrixcn come in as default .false. ctsm5.2.013 glemieux 07/18/2024 FATES Land Use V2 ctsm5.2.012 sacks 07/16/2024 Relax tolerance for truncating small snocan values in CanopyFluxes