Simplify input files

idaholab · Oct 15, 2024 · 4b57cac · 4b57cac
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diff --git a/doc/content/verification_and_validation/index.md b/doc/content/verification_and_validation/index.md
@@ -38,4 +38,5 @@ TMAP8 also contains [example cases](examples/tmap_index.md), which showcase how
 
 | Case   | Title                                          |
 | ------ | ---------------------------------------------- |
+| val-2a | [Ion Beam Experiment](val-2a.md) |
 | val-2b | [Diffusion Experiment in Beryllium](val-2b.md) |
diff --git a/test/tests/val-2a/gold/val-2a_TMAP4_out.e b/test/tests/val-2a/gold/val-2a_TMAP4_out.e
diff --git a/test/tests/val-2a/gold/val-2a_TMAP7_out.e b/test/tests/val-2a/gold/val-2a_TMAP7_out.e
diff --git a/test/tests/val-2a/tests b/test/tests/val-2a/tests
@@ -4,17 +4,13 @@
   validation = 'val-2a.md'
   [val-2a_TMAP7_csvdiff]
     type = CSVDiff
-    input = val-2a.i
+    input = 'val-2a_base.i val-2a_TMAP7.i'
     csvdiff = val-2a_TMAP7_out.csv
     requirement = 'The system shall be able to model Ion implantation based on the requirements and conditions listed in the TMAP7 V&V report'
   []
   [val-2a_TMAP4_csvdiff]
     type = CSVDiff
-    input = val-2a.i
-    cli_args = 'Mesh/active="cartesian_mesh_TMAP4"
-                Kernels/source/function=concentration_source_func_TMAP4
-                BCs/active="left_balance_TMAP4 right_balance"
-                Outputs/file_base="val-2a_TMAP4_out"'
+    input = 'val-2a_base.i val-2a_TMAP4.i'
     csvdiff = val-2a_TMAP4_out.csv
     requirement = 'The system shall be able to model Ion implantation based on the requirements and conditions listed in the TMAP4 V&V report'
   []

diff --git a/test/tests/val-2a/val-2a_TMAP4.i b/test/tests/val-2a/val-2a_TMAP4.i
@@ -0,0 +1,82 @@
+nx_scale = 1
+
+
+
+[Mesh]
+  [cartesian_mesh_TMAP4]
+    type = CartesianMeshGenerator
+    dim = 1
+    #     num
+    dx = '${fparse 5 * 4e-3}        1e-2        1e-1        1e0         1e1         ${fparse 10 * 4.88e1}'
+    ix = '${fparse 5 * ${nx_scale}} ${nx_scale} ${nx_scale} ${nx_scale} ${nx_scale} ${fparse 10 * ${nx_scale}}'
+  []
+[]
+
+[BCs]
+  # [left_balance]
+  #   type = ADFunctionNeumannBC
+  #   boundary = left
+  #   variable = concentration
+  #   function = 0
+  # []
+  [left_balance]
+    type = EquilibriumBC
+    Ko = '${fparse sqrt( ${dissociation_coefficient_parameter_enclos1} / ${recombination_coefficient_parameter_enclos1_TMAP4} )}'
+    boundary = left
+    enclosure_var = pressure_left
+    temperature = ${Temperature}
+    variable = concentration
+    p = 0.5
+  []
+[]
+
+[Functions]
+  ################# TMAP4
+  [Kd_left_func]
+    type = ParsedFunction
+    expression = '${dissociation_coefficient_parameter_enclos1} * (1 - 0.9999 * exp(-6e-5 * t))'
+  []
+
+  [Kr_left_func]
+    type = ParsedFunction
+    expression = '${recombination_coefficient_parameter_enclos1_TMAP4} * (1 - 0.9999 * exp(-6e-5 * t))'
+  []
+
+  [pressure_func]
+    type = ParsedFunction
+    expression = 'if(t<6420.0, ${pressure_high},
+                  if(t<9420.0, ${pressure_low},
+                  if(t<12480,  ${pressure_high},
+                  if(t<14940,  ${pressure_low},
+                  if(t<18180,  ${pressure_high}, ${pressure_low})))))'
+  []
+
+  [surface_flux_func]
+    type = ParsedFunction
+    expression = 'if(t<6420.0, ${flux_high},
+                  if(t<9420.0, ${flux_low},
+                  if(t<12480,  ${flux_high},
+                  if(t<14940,  ${flux_low},
+                  if(t<18180,  ${flux_high}, ${flux_low}))))) * 0.75'
+  []
+
+  [concentration_source_func]
+    type = ParsedFunction
+    symbol_names = 'surface_flux_func pressure_func Kd_left_func Kr_left_func'
+    symbol_values = 'surface_flux_func pressure_func Kd_left_func Kr_left_func'
+    expression = 'if(x<8e-3,  0,
+                  if(x<12e-3, sqrt((0.25 * surface_flux_func  + pressure_func * Kd_left_func) / Kr_left_func),
+                  if(x<16e-3, sqrt((1.00 * surface_flux_func  + pressure_func * Kd_left_func) / Kr_left_func),
+                  if(x<20e-3, sqrt((0.25 * surface_flux_func  + pressure_func * Kd_left_func) / Kr_left_func), 0))))'
+  []
+[]
+
+[Outputs]
+  # checkpoint = true
+  file_base = 'val-2a_TMAP4_out'
+  csv = true
+  [exodus]
+    type = Exodus
+    output_material_properties = true
+  []
+[]
diff --git a/test/tests/val-2a/val-2a_TMAP7.i b/test/tests/val-2a/val-2a_TMAP7.i
@@ -0,0 +1,87 @@
+
+nx_scale = 1
+
+[Mesh]
+  [cartesian_mesh_TMAP7]
+    type = CartesianMeshGenerator
+    dim = 1
+
+    # #     0    1    2    3    4    5    6    7    8    9    num
+    # dx = '1e-3 4e-3 4e-3 4e-3 4e-3 4e-3 1e-2 1e-1 1e-0 1e1
+    #       5.4319e1  5.4319e1  5.4319e1  5.4319e1  5.4319e1  5.4319e1  5.4319e1  5.4319e1  5.4319e1'
+    # #     10        11        12        13        14        15        16        17        18
+
+    #     num
+    dx = '1e-3        ${fparse 5 * 4e-3}        1e-2        1e-1        1e0         1e1         ${fparse 9 * 5.4319e1}'
+    ix = '${nx_scale} ${fparse 5 * ${nx_scale}} ${nx_scale} ${nx_scale} ${nx_scale} ${nx_scale} ${fparse 9 * ${nx_scale}}'
+  []
+[]
+
+[BCs]
+  # [left_balance]
+  #   type = ADFunctionNeumannBC
+  #   boundary = left
+  #   variable = concentration
+  #   function = 0
+  # []
+  [left_balance]
+    type = EquilibriumBC
+    Ko = '${fparse sqrt( ${dissociation_coefficient_parameter_enclos1} / ${recombination_coefficient_parameter_enclos1_TMAP7} )}'
+    boundary = left
+    enclosure_var = pressure_left
+    temperature = ${Temperature}
+    variable = concentration
+    p = 0.5
+  []
+[]
+
+[Functions]
+  ################## TMAP7
+  [Kd_left_func]
+    type = ParsedFunction
+    expression = '${dissociation_coefficient_parameter_enclos1} * (1 - 0.999997 * exp(-1.2e-4 * t))'
+  []
+
+  [Kr_left_func]
+    type = ParsedFunction
+    expression = '${recombination_coefficient_parameter_enclos1_TMAP7} * (1 - 0.999997 * exp(-1.2e-4 * t))'
+  []
+
+  [pressure_func]
+    type = ParsedFunction
+    expression = 'if(t<5820.0, ${pressure_high},
+                  if(t<9060.0, ${pressure_low},
+                  if(t<12160,  ${pressure_high},
+                  if(t<14472,  ${pressure_low},
+                  if(t<17678,  ${pressure_high}, ${pressure_low})))))'
+  []
+
+  [surface_flux_func]
+    type = ParsedFunction
+    expression = 'if(t<5820.0, ${flux_high},
+                  if(t<9060.0, ${flux_low},
+                  if(t<12160,  ${flux_high},
+                  if(t<14472,  ${flux_low},
+                  if(t<17678,  ${flux_high}, ${flux_low}))))) * 0.75'
+  []
+
+  [concentration_source_func]
+    type = ParsedFunction
+    symbol_names = 'surface_flux_func pressure_func Kd_left_func Kr_left_func'
+    symbol_values = 'surface_flux_func pressure_func Kd_left_func Kr_left_func'
+    expression = 'if(x<5e-3,  0,
+                  if(x<9e-3,  sqrt((0.15 * surface_flux_func  + pressure_func * Kd_left_func) / Kr_left_func),
+                  if(x<13e-3, sqrt((0.70 * surface_flux_func  + pressure_func * Kd_left_func) / Kr_left_func),
+                  if(x<17e-3, sqrt((0.15 * surface_flux_func  + pressure_func * Kd_left_func) / Kr_left_func), 0))))'
+  []
+[]
+
+[Outputs]
+  # checkpoint = true
+  file_base = 'val-2a_TMAP7_out'
+  csv = true
+  [exodus]
+    type = Exodus
+    output_material_properties = true
+  []
+[]
diff --git a/test/tests/val-2a/val-2a_base.i b/test/tests/val-2a/val-2a_base.i
@@ -0,0 +1,166 @@
+length_scale = '${units 1e6 num/m}'
+# length = '${units ${fparse 5e-4 * length_scale} m}'
+# nx_num = 100
+Temperature = '${units 703 K}'
+simulation_time = '${units 2e4 s}'
+diffusivity_D = '${units ${fparse 3e-10 * length_scale^2} m^2/s}'
+dissociation_parameter_enclos2 = '${units ${fparse 1.7918e15 / length_scale^2} at/m^2/s/Pa^0.5}' # d2/m^2/s/pa^0.5
+recombination_parameter_enclos2 = '${units ${fparse 2e-31 * length_scale^4} m^4/at/s}'    # m^4/atom/s
+pressure_high = '${units 4e-5 Pa}'
+pressure_low =  '${units 9e-6 Pa}'
+pressure_right = '${units 2e-6 Pa}'
+flux_high = '${units ${fparse 4.9e19 / length_scale^2} atom/m^2/s}'
+flux_low =  '${units ${fparse 0 / length_scale^2}      atom/m^2/s}'
+dissociation_coefficient_parameter_enclos1 = '${units ${fparse 8.959e18 / length_scale^2} at/m^2/s/Pa^0.5}'  # d2/m^2/s/pa^0.5
+# Data in TMAP4
+recombination_coefficient_parameter_enclos1_TMAP4 = '${units ${fparse 1e-27 * length_scale^4} m^4/at/s}'    # m^4/atom/s
+# Data in TMAP7
+recombination_coefficient_parameter_enclos1_TMAP7 = '${units ${fparse 7e-27 * length_scale^4} m^4/at/s}'    # m^4/atom/s
+
+
+[Variables]
+  [concentration]
+    order = FIRST
+    family = LAGRANGE
+  []
+[]
+
+[Kernels]
+  [diffusion]
+    type = ADMatDiffusion
+    variable = concentration
+    diffusivity = ${diffusivity_D}
+  []
+  [time_diffusion]
+    type = ADTimeDerivative
+    variable = concentration
+  []
+  [source]
+    type = ADBodyForce
+    variable = concentration
+    function = concentration_source_func
+  []
+[]
+
+[AuxVariables]
+  [pressure_left]
+  []
+  [concentration_source]
+  []
+  [recombination_TMAP4]
+  []
+  [recombination_TMAP7]
+  []
+[]
+
+[AuxKernels]
+  [pressure_aux]
+    type = FunctionAux
+    variable = pressure_left
+    function = pressure_func
+    execute_on = 'INITIAL TIMESTEP_END'
+  []
+  [concentration_source_aux]
+    type = FunctionAux
+    variable = concentration_source
+    function = concentration_source_func
+    execute_on = 'INITIAL TIMESTEP_END'
+  []
+  [recombination_aux_TMAP4]
+    type = FunctionAux
+    variable = recombination_TMAP4
+    function = '${recombination_coefficient_parameter_enclos1_TMAP4}'
+    execute_on = 'INITIAL TIMESTEP_END'
+  []
+  [recombination_aux_TMAP7]
+    type = FunctionAux
+    variable = recombination_TMAP7
+    function = '${recombination_coefficient_parameter_enclos1_TMAP7}'
+    execute_on = 'INITIAL TIMESTEP_END'
+  []
+[]
+
+[BCs]
+  # [right_balance]
+  #   type = ADFunctionNeumannBC
+  #   boundary = right
+  #   variable = concentration
+  #   function = 0
+  # []
+  [right_balance]
+    type = EquilibriumBC
+    Ko = '${fparse sqrt( ${dissociation_parameter_enclos2} / ${recombination_parameter_enclos2} )}'
+    boundary = right
+    enclosure_var = ${pressure_right}
+    temperature = ${Temperature}
+    variable = concentration
+    p = 0.5
+  []
+[]
+
+[Postprocessors]
+  [flux_surface_left]
+    type = SideDiffusiveFluxIntegral
+    variable = concentration
+    diffusivity = '${diffusivity_D}'
+    boundary = 'left'
+    execute_on = 'initial nonlinear linear timestep_end'
+    outputs = 'console csv exodus'
+  []
+  [scaled_flux_surface_left]
+    type = ScalePostprocessor
+    scaling_factor = '${fparse ${length_scale}^2}'
+    value = flux_surface_left
+    execute_on = 'initial nonlinear linear timestep_end'
+    outputs = 'console csv exodus'
+  []
+  [flux_surface_right]
+    type = SideDiffusiveFluxIntegral
+    variable = concentration
+    diffusivity = '${diffusivity_D}'
+    boundary = 'right'
+    execute_on = 'initial nonlinear linear timestep_end'
+    outputs = 'console csv exodus'
+  []
+  [scaled_flux_surface_right]
+    type = ScalePostprocessor
+    scaling_factor = '${fparse ${length_scale}^2}'
+    value = flux_surface_right
+    execute_on = 'initial nonlinear linear timestep_end'
+    outputs = 'console csv exodus'
+  []
+[]
+
+[Preconditioning]
+  [SMP]
+    type = SMP
+    full = true
+  []
+[]
+
+[Executioner]
+  type = Transient
+  scheme = bdf2
+  solve_type = NEWTON
+  petsc_options_iname = '-pc_type'
+  petsc_options_value = 'lu'
+  nl_rel_tol = 1e-8
+  nl_abs_tol = 1e-7
+  l_tol = 1e-4
+  end_time = ${simulation_time}
+  automatic_scaling = true
+  line_search = 'none'
+  dtmax = 100
+
+  [TimeStepper]
+    type = IterationAdaptiveDT
+    dt = 0.1
+    optimal_iterations = 4
+    growth_factor = 1.1
+    cutback_factor = 0.5
+  []
+[]
+
+# [Debug]
+#   show_var_residual_norms = true
+# []