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ncfunctions.cpp
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ncfunctions.cpp
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//#include"nctest.h"
#include "uebpgdecls.h"
#include <netcdf_par.h>
//writes the 1D array (TS values) at specified location in the netcdf
int WriteTSto3DNC(const char* FileName, const char* VarName, int dimOrd, int y_dim, int x_dim,int Nt_dim, float* var_inp, MPI::Intracomm inpComm, MPI::Info inpInfo) //ydim, xdim =the coordinate point the data to be written; Nt_dim =the length of the TS
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if ((retncval = nc_open_par(FileName, NC_WRITE|NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VarName, &v_varid)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch(dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = y_dim;
start[2] = x_dim;
count[0] = Nt_dim;
count[1] = 1;
count[2] = 1;
break;
case 1: //y,x,t
start[0] = y_dim;
start[1] = x_dim;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = Nt_dim;
break;
case 2: //x,t,y
start[0] = x_dim;
start[0] = 0;
start[2] = y_dim;
count[0] = 1;
count[1] = Nt_dim;
count[2] = 1;
break;
default:
cout<<"the dim order has to be between 0 and 2"<<endl;
getchar();
break;
}
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid,NC_COLLECTIVE)))
ERR(retncval);
//put variable values
if ((retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[0])))
ERR(retncval);
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//delte 3D array
//fflush(stdout);
return 0;
}
//writes multiple 1D arrays (TS values) at specified locations in the netcdf
int WriteTSto3DNC_Block(const char* FileName, const char* VarName, int dimOrd, int *YindArr, int *XindArr, int bSize, int Nt_dim, float** var_inp, MPI::Intracomm inpComm, MPI::Info inpInfo) //ydim, xdim =the coordinate point the data to be written; Nt_dim =the length of the TS
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if ((retncval = nc_open_par(FileName, NC_WRITE | NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VarName, &v_varid)))
ERR(retncval);
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid, NC_COLLECTIVE)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
for (int j = 0; j < bSize; j++)
{
switch (dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = YindArr[j]; // y_dim;
start[2] = XindArr[j]; // x_dim;
count[0] = Nt_dim;
count[1] = 1;
count[2] = 1;
break;
case 1: //y,x,t
start[0] = YindArr[j]; // y_dim;
start[1] = XindArr[j]; // x_dim;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = Nt_dim;
break;
case 2: //x,t,y
start[0] = XindArr[j]; // x_dim;
start[0] = 0;
start[2] = YindArr[j]; // y_dim;
count[0] = 1;
count[1] = Nt_dim;
count[2] = 1;
break;
default:
cout << "the dim order has to be between 0 and 2" << endl;
getchar();
break;
}
//put variable values
if (retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[j][0]))
ERR(retncval);
}
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//delte 3D array
//fflush(stdout);
return 0;
}
//aggregate outputs at specified zone in the netcdf
int Write_uebaggTS_toNC(const char* FileName, const char* VarName, int dimOrd, int z_dim, int Nt_dim, float* var_inp)
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if ((retncval = nc_open(FileName, NC_WRITE, &ncid))) //|NC_MPIIO, MPI::COMM_WORLD, MPI::INFO_NULL, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VarName, &v_varid)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch (dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = z_dim;
count[0] = Nt_dim;
count[1] = 1;
break;
case 1: //y,x,t
start[0] = z_dim;
start[1] = 0;
count[0] = 1;
count[1] = Nt_dim;
break;
default:
cout << "the dim order has to be 0 or 1" << endl;
getchar();
break;
}
//parallel access mode
/*if ((retncval = nc_var_par_access(ncid, v_varid,NC_INDEPENDENT)))
ERR(retncval); */
//put variable values
if (retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[0]))
ERR(retncval);
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//fflush(stdout);
return 0;
}
//aggregate outputs at specified zone in the netcdf in parallel
int Write_uebaggTS_toNC_par(const char* FileName, const char* VarName, int dimOrd, int z_dim, int Nt_dim, float* var_inp, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Open netcdf file.
if ((retncval = nc_open_par(FileName, NC_WRITE | NC_MPIIO, inpComm, inpInfo, &ncid))) //|NC_MPIIO, MPI::COMM_WORLD, MPI::INFO_NULL, &ncid)))
ERR(retncval);
// get variable id
if (retncval = nc_inq_varid(ncid, VarName, &v_varid))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch (dimOrd)
{
case 0: //t,y,x
start[0] = 0;
start[1] = z_dim;
count[0] = Nt_dim;
count[1] = 1;
break;
case 1: //y,x,t
start[0] = z_dim;
start[1] = 0;
count[0] = 1;
count[1] = Nt_dim;
break;
default:
cout << "the dim order has to be 0 or 1" << endl;
getchar();
break;
}
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid,NC_INDEPENDENT)))
ERR(retncval);
//put variable values
if (retncval = nc_put_vara_float(ncid, v_varid, start, count, &var_inp[0]))
ERR(retncval);
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//fflush(stdout);
return 0;
}
//creates 3D netcdf in PARALLEL mode, and stores dimension variables for UEB aggregated outputs; some attributes are copied from the watershed netCDF
int create3DNC_uebAggregatedOutputs(const char* FileName, aggOutput *aggOut, int naggOut, const char* tName, const char* tUnits, const char* tlong_name, const char* tcalendar, int Nt_dim, int dimOrd,
float* t_inp, float *fillVal, const char* ws_FileName, const char* ws_VarName, const char* yName, const char* xName, int nZones, const char * zName, float* y_inp, float* x_inp, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0;
//info from watershed nc
if ((retncval = nc_open_par(ws_FileName, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, ws_VarName, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, yName, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xName, &pxid)))
ERR(retncval);
//dimensions lengths
size_t Nzdim = nZones;
//3D outputs nc
int ncid_out = 0, pzid_out = 0, ptid_out = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0, gridmap_id = 0;
//attributes
int natts = 0;
size_t att_len;
void * attValue;
nc_type attType;
char attName[256]; // = {}; // "grid_mapping_or_any_other_long_enough_name";
char grid_mappingValue[256] = {NULL}; // "grid_mapping_or_any_other_long_enough_name";
const char* fillValueName = "_FillValue";
//float missVal = -9999;
const int NDIMS = 2;
int dimids[NDIMS];
int oldFill = 0;
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Create netcdf file.
if ((retncval = nc_create_par(FileName, NC_NETCDF4 | NC_MPIIO | NC_CLOBBER, inpComm, inpInfo, &ncid_out)))
ERR(retncval);
//?? set fill on
if ((retncval = nc_set_fill(ncid_out, NC_FILL, &oldFill)))
ERR(retncval);
//copy global attributes from the ws nc
if (retncval = nc_inq_natts(ncid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if ((retncval = nc_inq_attname(ncid, NC_GLOBAL, atti, attName)))
ERR(retncval);
if (retncval = nc_copy_att(ncid, NC_GLOBAL, (const char*)attName, ncid_out, NC_GLOBAL))
ERR(retncval);
}
/* Define the dimensions. record dim can be unlimited*/
if ((retncval = nc_def_dim(ncid_out, tName, Nt_dim, &ptid_out)))
ERR(retncval);
if ((retncval = nc_def_dim(ncid_out, zName, Nzdim, &pzid_out)))
ERR(retncval);
switch (dimOrd)
{
case 0:
dimids[0] = ptid_out;
dimids[1] = pzid_out;
break;
case 1:
dimids[0] = pzid_out;
dimids[1] = ptid_out;
break;
default:
cout << "the dim order has to be either 0 or 1" << endl;
getchar();
break;
}
// Define variables
for (int ivar = 0; ivar < naggOut; ivar++)
{
if (retncval = nc_def_var(ncid_out, (const char*)aggOut[ivar].symbol, NC_FLOAT, NDIMS, dimids, &v_varid))
ERR(retncval);
//assign fill value
if (retncval = nc_put_att_float(ncid_out, v_varid, fillValueName, NC_FLOAT, 1, fillVal))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if (retncval = nc_put_att_text(ncid_out, v_varid, "units", strlen((const char*)aggOut[ivar].units), (const char*)aggOut[ivar].units))
ERR(retncval);
//grid mapping (projection) attribute
if (retncval = nc_copy_att(ncid, pvarid, "grid_mapping", ncid_out, v_varid))
ERR(retncval);
}
//variable containing info about projection / grid mapping
if (retncval = nc_get_att_text(ncid, pvarid, "grid_mapping", grid_mappingValue))
ERR(retncval);
if (retncval = nc_inq_varid(ncid, (const char*)grid_mappingValue, &gridmap_id))
ERR(retncval);
if (retncval = nc_copy_var(ncid, gridmap_id, ncid_out))
ERR(retncval);
//time variable
if (retncval = nc_def_var(ncid_out, tName, NC_FLOAT, 1, &ptid_out, &t_varid))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "units", strlen(tUnits), tUnits))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "long_name", strlen(tlong_name), tlong_name))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "calendar", strlen(tcalendar), tcalendar))
ERR(retncval);
// y and x vars
if (retncval = nc_def_var(ncid_out, yName, NC_FLOAT, 1, &pzid_out, &y_varid))
ERR(retncval);
if (retncval = nc_def_var(ncid_out, xName, NC_FLOAT, 1, &pzid_out, &x_varid))
ERR(retncval);
if (retncval = nc_inq_varnatts(ncid, pyid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pyid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pyid, (const char*)attName, ncid_out, y_varid))
ERR(retncval);
}
if (retncval = nc_inq_varnatts(ncid, pxid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pxid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pxid, (const char*)attName, ncid_out, x_varid))
ERR(retncval);
}
//parallel access mode
if ((retncval = nc_var_par_access(ncid_out, v_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, t_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, y_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, x_varid, NC_COLLECTIVE)))
ERR(retncval);
//put values to dim variables
if (retncval = nc_put_var_float(ncid_out, t_varid, &t_inp[0]))
ERR(retncval);
if (retncval = nc_put_var_float(ncid_out, y_varid, &y_inp[0]))
ERR(retncval);
if (retncval = nc_put_var_float(ncid_out, x_varid, &x_inp[0]))
ERR(retncval);
//close files
if (retncval = nc_close(ncid))
ERR(retncval);
if (retncval = nc_close(ncid_out))
ERR(retncval);
cout << "Sucess creating and storing dimension vars in: " << FileName << endl;
//fflush(stdout);
return 0;
}
//creates 3D netcdf and stores dimension variables for a given UEB output; called once for a given output netcdf
//attributes are copied from the 2D (watershed) netCDF which the 3D netCDF spatial dimension follow
int create3DNC_uebOutputs(const char* FileName, const char* VarName, const char *varUnits, const char* tName, const char* tUnits, const char* tlong_name,
const char* tcalendar, int Nt_dim, int dimOrd, float* t_inp, float *fillVal, const char* ws_FileName, const char* ws_VarName, const char* yName, const char* xName, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//const char* yUnits, const char* xUnits;
float* y_inp;
float* x_inp;
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0, ndims = 0;
//dimensions lengths
size_t Nxdim = 0, Nydim = 0;
//array of dimensions
int pdimids[2];
if ((retncval = nc_open_par(ws_FileName, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, ws_VarName, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, yName, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xName, &pxid)))
ERR(retncval);
//var information, checking the dimension array
if (retncval = nc_inq_vardimid(ncid, pvarid, pdimids))
ERR(retncval);
//check dimension sizes
if ((retncval = nc_inq_dim(ncid, pdimids[0], NULL, &Nydim)))
ERR(retncval);
if ((retncval = nc_inq_dim(ncid, pdimids[1], NULL, &Nxdim)))
ERR(retncval);
//create the output arrays
y_inp = new float[Nydim];
x_inp = new float[Nxdim];
//parallel access mode
/*if ((retncval = nc_var_par_access(ncid, pvarid,NC_INDEPENDENT)))
ERR(retncval);*/
if ((retncval = nc_var_par_access(ncid, pyid,NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, pxid,NC_COLLECTIVE)))
ERR(retncval);
// Read the coordinate (dimensions) variable data.
if ((retncval = nc_get_var_float(ncid, pyid, &y_inp[0])))
ERR(retncval);
if ((retncval = nc_get_var_float(ncid, pxid, &x_inp[0])))
ERR(retncval);
//3D outputs nc
int ncid_out = 0, pyid_out = 0, pxid_out = 0, ptid_out = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0, gridmap_id = 0;
//attributes
int natts = 0;
size_t att_len;
void * attValue;
nc_type attType;
char attName[256]; // = {}; // "grid_mapping_or_any_other_long_enough_name";
char grid_mappingValue[256] = { NULL }; // "grid_mapping_or_any_other_long_enough_name";
const char* fillValueName = "_FillValue";
//float missVal = -9999;
const int NDIMS = 3;
int dimids[NDIMS];
int oldFill = 0;
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Create netcdf file.
if ((retncval = nc_create_par(FileName, NC_NETCDF4 | NC_MPIIO | NC_CLOBBER, inpComm, inpInfo, &ncid_out)))
ERR(retncval);
//?? set fill on
if ((retncval = nc_set_fill(ncid_out, NC_FILL, &oldFill)))
ERR(retncval);
//copy global attributes from the ws nc
if (retncval = nc_inq_natts(ncid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid,NC_GLOBAL,atti, attName))
ERR(retncval);
/*if (retncval = nc_inq_atttype(ncid, NC_GLOBAL,(const char*)attName,&attType))
ERR(retncval);
if (retncval = nc_inq_attlen(ncid, NC_GLOBAL, (const char*)attName, &att_len))
ERR(retncval);
attValue = ::operator new (att_len*sizeof(attType));
if (retncval = nc_get_att(ncid, NC_GLOBAL, (const char*)attName,&attValue))
ERR(retncval);*/
if (retncval = nc_copy_att(ncid, NC_GLOBAL, (const char*)attName,ncid_out,NC_GLOBAL))
ERR(retncval);
}
/* Define the dimensions. record dim can be unlimited*/
if (retncval = nc_def_dim(ncid_out, tName, Nt_dim, &ptid_out))
ERR(retncval);
if (retncval = nc_def_dim(ncid_out, yName, Nydim, &pyid_out))
ERR(retncval);
if (retncval = nc_def_dim(ncid_out, xName, Nxdim, &pxid_out))
ERR(retncval);
switch (dimOrd)
{
case 0:
dimids[0] = ptid_out;
dimids[1] = pyid_out;
dimids[2] = pxid_out;
break;
case 1:
dimids[0] = pyid_out;
dimids[1] = pxid_out;
dimids[2] = ptid_out;
break;
case 2:
dimids[0] = pxid_out;
dimids[1] = ptid_out;
dimids[2] = pyid_out;
break;
default:
cout << "the dim order has to be between 0 and 2" << endl;
getchar();
break;
}
// Define the netCDF variables
if (retncval = nc_def_var(ncid_out, VarName, NC_FLOAT, NDIMS, dimids, &v_varid))
ERR(retncval);
//assign fill value
if (retncval = nc_put_att_float(ncid_out, v_varid, fillValueName, NC_FLOAT, 1, fillVal))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if (retncval = nc_put_att_text(ncid_out, v_varid, "units", strlen(varUnits), varUnits))
ERR(retncval);
//grid mapping
if (retncval = nc_get_att_text(ncid, pvarid, "grid_mapping",grid_mappingValue))
ERR(retncval);
//cout << grid_mappingValue << endl;
if (retncval = nc_copy_att(ncid, pvarid, "grid_mapping", ncid_out, v_varid))
ERR(retncval);
/*if (retncval = nc_put_att_text(ncid_out, v_varid, "grid_mapping", , (const char*)grid_mappingValue))
ERR(retncval);*/
if (retncval = nc_inq_varid(ncid,(const char*)grid_mappingValue, &gridmap_id))
ERR(retncval);
if (retncval = nc_copy_var(ncid, gridmap_id, ncid_out))
ERR(retncval);
//time variable
if (retncval = nc_def_var(ncid_out, tName, NC_FLOAT, 1, &ptid_out, &t_varid))
ERR(retncval);
// units attributes
if (retncval = nc_put_att_text(ncid_out, t_varid, "units", strlen(tUnits), tUnits))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "long_name", strlen(tlong_name), tlong_name))
ERR(retncval);
if (retncval = nc_put_att_text(ncid_out, t_varid, "calendar", strlen(tcalendar), tcalendar))
ERR(retncval);
// y and x vars
if (retncval = nc_def_var(ncid_out, yName, NC_FLOAT, 1, &pyid_out, &y_varid))
ERR(retncval);
if (retncval = nc_def_var(ncid_out, xName, NC_FLOAT, 1, &pxid_out, &x_varid))
ERR(retncval);
if (retncval = nc_inq_varnatts(ncid, pyid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pyid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pyid, (const char*)attName, ncid_out, y_varid))
ERR(retncval);
}
if (retncval = nc_inq_varnatts(ncid, pxid, &natts))
ERR(retncval);
for (int atti = 0; atti < natts; atti++)
{
if (retncval = nc_inq_attname(ncid, pxid, atti, attName))
ERR(retncval);
if (retncval = nc_copy_att(ncid, pxid, (const char*)attName, ncid_out, x_varid))
ERR(retncval);
}
/* Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, y_varid, vunits, strlen(yUnits), yUnits)))
ERR(retncval);
if ((retncval = nc_put_att_text(ncid, x_varid, vunits, strlen(xUnits), xUnits)))
ERR(retncval);
//y and x variables copy
if (retncval = nc_copy_var(ncid, pyid, ncid_out))
ERR(retncval);
if (retncval = nc_copy_var(ncid, pxid, ncid_out))
ERR(retncval); */
//parallel access mode
if ((retncval = nc_var_par_access(ncid_out, v_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, t_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, y_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid_out, x_varid, NC_COLLECTIVE)))
ERR(retncval);
//put values to dim variables
if ((retncval = nc_put_var_float(ncid_out, t_varid, &t_inp[0])))
ERR(retncval);
if ((retncval = nc_put_var_float(ncid_out, y_varid, &y_inp[0])))
ERR(retncval);
if ((retncval = nc_put_var_float(ncid_out, x_varid, &x_inp[0])))
ERR(retncval);
//close files
if (retncval = nc_close(ncid))
ERR(retncval);
if (retncval = nc_close(ncid_out))
ERR(retncval);
cout << "Sucess creating and storing dimension vars in: " << FileName << endl;
//fflush(stdout);
return 0;
}
//creates 3D netcdf and stores dimension variables; called once for a given output netcdf
int Create3DNC(const char* FileName, const char* VarName, const char *varUnits, const char* tName, const char* yName, const char* xName, const char* tUnits,
const char* yUnits, const char* xUnits, int Nt_dim, int Ny_dim, int Nx_dim, int dimOrd, float* t_inp, float* y_inp, float* x_inp, float* fillVal, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const char* fillValue = "_FillValue";
//float missVal = -9999;
const int NDIMS = 3;
int dimids[NDIMS];
int oldFill = 0;
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Create netcdf file.
if ((retncval = nc_create_par(FileName, NC_NETCDF4 | NC_MPIIO | NC_CLOBBER, inpComm, inpInfo, &ncid)))
ERR(retncval);
//set fill on
if ((retncval = nc_set_fill(ncid, NC_FILL, &oldFill)))
ERR(retncval);
/* Define the dimensions. record dim can be unlimited*/
if ((retncval = nc_def_dim(ncid, tName, Nt_dim, &t_dimid)))
ERR(retncval);
if ((retncval = nc_def_dim(ncid, yName, Ny_dim, &y_dimid)))
ERR(retncval);
if ((retncval = nc_def_dim(ncid, xName, Nx_dim, &x_dimid)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch(dimOrd)
{
case 0:
dimids[0] = t_dimid;
dimids[1] = y_dimid;
dimids[2] = x_dimid;
break;
case 1:
dimids[0] = y_dimid;
dimids[1] = x_dimid;
dimids[2] = t_dimid;
break;
case 2:
dimids[0] = x_dimid;
dimids[1] = t_dimid;
dimids[2] = y_dimid;
break;
default:
cout<<"the dim order has to be between 0 and 2"<<endl;
getchar();
break;
}
// Define the netCDF variables
if ((retncval = nc_def_var(ncid, VarName, NC_FLOAT, NDIMS, dimids, &v_varid)))
ERR(retncval);
//assign missing
if ((retncval = nc_put_att_float(ncid,v_varid, fillValue,NC_FLOAT,1, fillVal)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, v_varid, vunits, strlen(varUnits), varUnits)))
ERR(retncval);
if ((retncval = nc_def_var(ncid, tName, NC_FLOAT, 1, &t_dimid, &t_varid)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, t_varid, vunits, strlen(tUnits), tUnits)))
ERR(retncval);
if ((retncval = nc_def_var(ncid, yName, NC_FLOAT, 1, &y_dimid, &y_varid)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, y_varid, vunits, strlen(yUnits), yUnits)))
ERR(retncval);
if ((retncval = nc_def_var(ncid, xName, NC_FLOAT, 1, &x_dimid, &x_varid)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, x_varid, vunits, strlen(xUnits), xUnits)))
ERR(retncval);
// End define mode. not needed for nc4
/*if ((retncval = nc_enddef(ncid)))
ERR(retncval); */
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, t_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, y_varid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, x_varid, NC_COLLECTIVE)))
ERR(retncval);
//put values to dim variables
if ((retncval = nc_put_var_float(ncid, t_varid, &t_inp[0])))
ERR(retncval);
if ((retncval = nc_put_var_float(ncid, y_varid, &y_inp[0])))
ERR(retncval);
if ((retncval = nc_put_var_float(ncid, x_varid, &x_inp[0])))
ERR(retncval);
//put variable values
/*if ((retncval = nc_put_var_float(ncid, v_varid, &var_inp[0][0][0])))
ERR(retncval); */
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//delte 3D array
cout<<"Sucess creating and storing dimension vars in: "<<FileName<<endl;
//fflush(stdout);
return 0;
}
//This one creates and stores array passed to it at once
int Write3DNC(const char* FileName, const char* VarName, const char *varUnits, const char* tName, const char* yName, const char* xName, const char* tUnits, const char* yUnits, const char* xUnits,
int Nt_dim, int Ny_dim, int Nx_dim, int dimOrd, float* t_inp, float* y_inp, float* x_inp, float*** var_inp, MPI::Intracomm inpComm, MPI::Info inpInfo)// int &t_dimid, int &y_dimid, int &x_dimid) //time, y, x
{
// IDs for the netCDF file, dimensions, and variables.
int ncid = 0, y_dimid = 0, x_dimid = 0, t_dimid = 0;
int v_varid = 0, t_varid = 0, y_varid = 0, x_varid = 0;
const char* vunits = "UNITS";
const int NDIMS = 3;
int dimids[NDIMS];
// The start and count arrays will tell the netCDF library where to write our data.
size_t start[NDIMS], count[NDIMS];
// Error handling.
int retncval = 0;
// Create netcdf file.
if ((retncval = nc_create_par(FileName, NC_NETCDF4 | NC_MPIIO | NC_CLOBBER, inpComm, inpInfo, &ncid)))
ERR(retncval);
/* Define the dimensions. record dim can be unlimited*/
if ((retncval = nc_def_dim(ncid, tName, Nt_dim, &t_dimid)))
ERR(retncval);
if ((retncval = nc_def_dim(ncid, yName, Ny_dim, &y_dimid)))
ERR(retncval);
if ((retncval = nc_def_dim(ncid, xName, Nx_dim, &x_dimid)))
ERR(retncval);
/* The dimids array is used to pass the dimids of the dimensions of
the netCDF variables. In C, the unlimited dimension must come first on the list of dimids. */
switch(dimOrd)
{
case 0:
dimids[0] = t_dimid;
dimids[1] = y_dimid;
dimids[2] = x_dimid;
break;
case 1:
dimids[0] = y_dimid;
dimids[1] = x_dimid;
dimids[2] = t_dimid;
break;
case 2:
dimids[0] = x_dimid;
dimids[1] = t_dimid;
dimids[2] = y_dimid;
break;
default:
cout<<"the dim order has to be between 0 and 2"<<endl;
getchar();
break;
}
// Define the netCDF variables
if ((retncval = nc_def_var(ncid, VarName, NC_FLOAT, NDIMS,
dimids, &v_varid)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, v_varid, vunits,
strlen(varUnits), varUnits)))
ERR(retncval);
if ((retncval = nc_def_var(ncid, tName, NC_FLOAT, 1,
&t_dimid, &t_varid)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, t_varid, vunits,
strlen(tUnits), tUnits)))
ERR(retncval);
if ((retncval = nc_def_var(ncid, yName, NC_FLOAT, 1,
&y_dimid, &y_varid)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, y_varid, vunits,
strlen(yUnits), yUnits)))
ERR(retncval);
if ((retncval = nc_def_var(ncid, xName, NC_FLOAT, 1,
&x_dimid, &x_varid)))
ERR(retncval);
// Assign units attributes to the netCDF variables.
if ((retncval = nc_put_att_text(ncid, x_varid, vunits,
strlen(xUnits), xUnits)))
ERR(retncval);
// End define mode.
if ((retncval = nc_enddef(ncid)))
ERR(retncval);
//parallel access mode
if ((retncval = nc_var_par_access(ncid, v_varid,NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, t_varid,NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, y_varid,NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, x_varid,NC_COLLECTIVE)))
ERR(retncval);
//put values to dim variables
if ((retncval = nc_put_var_float(ncid, t_varid, &t_inp[0])))
ERR(retncval);
if ((retncval = nc_put_var_float(ncid, y_varid, &y_inp[0])))
ERR(retncval);
if ((retncval = nc_put_var_float(ncid, x_varid, &x_inp[0])))
ERR(retncval);
//put variable values
if ((retncval = nc_put_var_float(ncid, v_varid, &var_inp[0][0][0])))
ERR(retncval);
//close file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//delte 3D array
cout<<" SUCCESS writing file: "<< FileName<<endl;
//fflush(stdout);
return 0;
}
//read 3d nc to contiguous array; y,x,time coordinate names are same as index names
int read3DNC_Contiguous(const char* FILE_NAME, const char* VAR_NAME, const char* tcor_NAME, const char* ycor_NAME, const char* xcor_NAME,
float* tcorvar, float* ycorvar, float* xcorvar, size_t &Ntdim, size_t &Nydim, size_t &Nxdim, float*** &pvar_in, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0, ptid = 0, ndims = 0;
//dimensions lengths
size_t pdim_sizes;
//variable data type
nc_type varType;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error message otherwise
//dimension names
char pdim_Names[80];
size_t start[3], count[3];
//dimensions lengths
//size_t Ntdim = 0, Nxdim = 0, Nydim = 0;
//Open the file.
if ((retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, tcor_NAME, &ptid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, ycor_NAME, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xcor_NAME, &pxid)))
ERR(retncval);
//var information, checking the dimension array
if ((retncval = nc_inq_var(ncid,pvarid,NULL,&varType,NULL,pdimids,NULL)))
ERR(retncval);
//check dimension info and set start and count arrays;
for (int i = 0; i < 3; i++)
{
if ((retncval = nc_inq_dim(ncid, pdimids[i], pdim_Names, &pdim_sizes)))
ERR(retncval);
if (strcmp(pdim_Names, tcor_NAME) == 0)
{
start[i] = 0;
Ntdim = pdim_sizes;
count[i] = Ntdim;
tcorvar = new float[Ntdim];
}
else if (strcmp(pdim_Names, ycor_NAME) == 0)
{
start[i] = 0;
Nydim = pdim_sizes;
count[i] = Nydim;
ycorvar = new float[Nydim];
}
else
{
start[i] = 0;
Nxdim = pdim_sizes;
count[i] = Nxdim;
xcorvar = new float[Nxdim];
}
}
//create the output arrays
pvar_in = create3DArrayblock_Contiguous(count[0], count[1], count[2]); // (Ntdim, Nydim, Nxdim);
//parallel access mode
if (retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, ptid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, pyid, NC_COLLECTIVE))
ERR(retncval);
if (retncval = nc_var_par_access(ncid, pxid, NC_COLLECTIVE))
ERR(retncval);
/* Read the coordinate (dimensions) variable data. */
if (retncval = nc_get_var_float(ncid, ptid, &tcorvar[0]))
ERR(retncval);
if (retncval = nc_get_var_float(ncid, pyid, &ycorvar[0]))
ERR(retncval);
if (retncval = nc_get_var_float(ncid, pxid, &xcorvar[0]))
ERR(retncval);
//read variable (input data)
if (retncval = nc_get_var_float(ncid, pvarid,&pvar_in[0][0][0]))
ERR(retncval);
//close netcdf file
if ((retncval = nc_close(ncid)))
ERR(retncval);
//cout<<"SUCCESS reading input file: "<< FILE_NAME<<endl;
return 0;
}
int read3DNC(const char* FILE_NAME, const char* VAR_NAME, const char* xcor_NAME, const char* ycor_NAME, const char* tcor_NAME,
float* xcorvar, float* ycorvar, float* tcorvar, float*** pvar_in, MPI::Intracomm inpComm, MPI::Info inpInfo)
{
//ids for variable, axes,...
int retncval = 0, ncid = 0, pvarid = 0, pxid = 0, pyid = 0, ptid = 0, ndims = 0;
//dimensions lengths
size_t Ntdim = 0, Nxdim = 0, Nydim = 0;
//variable data type
nc_type varType;
//array of dimensions
int pdimids[3]; //NC_MAX_DIMS]; 3D file only being read here; expected to get error messege otherwise
size_t start[3], count[3];
//Open the file.
if ((retncval = nc_open_par(FILE_NAME, NC_MPIIO, inpComm, inpInfo, &ncid)))
ERR(retncval);
// get variable id
if ((retncval = nc_inq_varid(ncid, VAR_NAME, &pvarid)))
ERR(retncval);
// Get the varids of the coordinate variables
if ((retncval = nc_inq_varid(ncid, tcor_NAME, &ptid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, ycor_NAME, &pyid)))
ERR(retncval);
if ((retncval = nc_inq_varid(ncid, xcor_NAME, &pxid)))
ERR(retncval);
//var information, checking the dimension array
if ((retncval = nc_inq_var(ncid,pvarid,NULL,&varType,NULL,pdimids,NULL)))
ERR(retncval);
//check dimension sizes
if ((retncval = nc_inq_dim(ncid,pdimids[0],NULL,&Ntdim)))
ERR(retncval);
if ((retncval = nc_inq_dim(ncid,pdimids[1],NULL,&Nydim)))
ERR(retncval);
if ((retncval = nc_inq_dim(ncid,pdimids[2],NULL,&Nxdim)))
ERR(retncval);
//create the output arrays
pvar_in = Create3DArray(Ntdim,Nydim,Nxdim);
tcorvar = new float[Ntdim];
ycorvar = new float[Nydim];
xcorvar = new float[Nxdim];
//set start and count arrays; time, if exists, is expected to to come first
//although in this code the effect may not be noticed
//#_1 (need a check 5/19/13)
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = Nydim;
count[2] = Nxdim;
//temporary 2D array to help in data read
//#_2 (need check 5/19/13) should read 3d @ once
float** pvar_inp = new float*[Nydim];
for(size_t j=0; j< Nydim; j++)
pvar_inp[j] = new float [Nydim];
//parallel access mode
if ((retncval = nc_var_par_access(ncid, pvarid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, ptid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, pyid, NC_COLLECTIVE)))
ERR(retncval);
if ((retncval = nc_var_par_access(ncid, pxid, NC_COLLECTIVE)))
ERR(retncval);
/* Read the coordinate (dimensions) variable data. */
if ((retncval = nc_get_var_float(ncid, ptid, &tcorvar[0])))
ERR(retncval);
if ((retncval = nc_get_var_float(ncid, pyid, &ycorvar[0])))
ERR(retncval);
if ((retncval = nc_get_var_float(ncid, pxid, &xcorvar[0])))
ERR(retncval);
//read variable (input data)
//the readings below are done as Double data type; expected type conversion
//to float if input is float (no data loss than the vice versa)
//#_3 tbc 3.19.13
for (size_t kt = 0; kt < Ntdim; kt++)
{
start[0] = kt;
if ((retncval = nc_get_vara_float(ncid, pvarid,start,count, &pvar_inp[0][0])))
ERR(retncval);
for(size_t i=0; i< Nydim; i++)