Elastodynamics

Makefile

@@ -40,7 +40,7 @@ POROUS_FLOW                 := no
 RDG                         := no
 RICHARDS                    := no
 SOLID_MECHANICS             := no
-STOCHASTIC_TOOLS            := no
+STOCHASTIC_TOOLS            := yes
 TENSOR_MECHANICS            := yes
 XFEM                        := no
 OPTIMIZATION                := yes

doc/content/sqa/isopod_rtm.md

@@ -1 +1 @@
-!template load file=app_rtm.md.template app=Isopod category=isopod stp_filename=isopod_stp.md
+!template load file=app_rtm.md.template app=Isopod category=isopod

doc/sqa_reports.yml

@@ -10,7 +10,7 @@ Documents:
     software_requirements_specification: sqa/isopod_srs.md
     software_design_description: sqa/isopod_sdd.md
     software_test_plan: sqa/isopod_stp.md
-    requirements_traceablity_matrix: sqa/isopod_rtm.md
+    requirements_traceability_matrix: sqa/isopod_rtm.md
     verification_validation_report: sqa/isopod_vvr.md
     failure_analysis_report: sqa/isopod_vvr.md
     log_safety_software_determination: WARNING

examples/bimaterialElastic/gold/main_auto_out_OptimizationReporter_0001.csv

@@ -0,0 +1,10 @@
+grad_lambda,grad_mu,lambda,measurement_time,measurement_values,measurement_xcoord,measurement_ycoord,measurement_zcoord,misfit_values,mu,simulation_values
+-4.3796599397474e-08,-8.1077586556456e-07,4.9999703676621,0,4.46462,-1,-1,0,-2.2288267853554e-07,1.0000005195792,4.4646197771173
+-6.2509348307711e-09,-1.7312856628588e-07,4.0001368580929,0,6.447155,-1,0,0,-1.9949611118619e-07,1.9999990912205,6.4471548005039
+-8.9816855038081e-10,-1.0424117832137e-08,3.0000053638196,0,8.434803,-1,1,0,-9.7586703162733e-08,3.0000073381577,8.4348029024133
+0,0,0,0,4.176264,0,-1,0,-1.4786177882087e-07,0,4.1762638521382
+0,0,0,0,6.172984,0,0,0,-2.477726290806e-08,0,6.1729839752227
+0,0,0,0,8.200859,0,1,0,4.4258881182202e-07,0,8.2008594425888
+0,0,0,0,4.049477,1,-1,0,-8.2262971545788e-08,0,4.049476917737
+0,0,0,0,6.052499,1,0,0,3.4381697400221e-07,0,6.052499343817
+0,0,0,0,8.079385,1,1,0,-8.3668947326032e-09,0,8.0793849916331

examples/bimaterialElastic/grad.i

@@ -153,11 +153,15 @@
   [grad_lambda]
      type = ElementOptimizationLameLambdaInnerProduct
      variable = dummy
+     adjoint_strain_name = mechanical_strain
+     forward_strain_name = forward_mechanical_strain
      function = lambda
   []
   [grad_mu]
      type = ElementOptimizationLameMuInnerProduct
      variable = dummy
+     adjoint_strain_name = mechanical_strain
+     forward_strain_name = forward_mechanical_strain
      function = mu
   []
 []

examples/bimaterialElastic/main_auto.i

@@ -0,0 +1,96 @@
+[Optimization]
+[]
+
+[OptimizationReporter]
+  type = OptimizationReporter
+  parameter_names = 'lambda mu'
+  num_values = '3 3'
+  #initial_condition = '5 4 3 ; 1 2 1'
+  initial_condition = '5.0 5.0 5.0; 1.0 1.0 1.0'
+  lower_bounds = '0.1; 0.1'
+  upper_bounds = '10.0; 10.0'
+  measurement_points = '-1.0 -1.0 0.0
+                        -1.0  0.0 0.0
+                        -1.0  1.0 0.0
+                         0.0 -1.0 0.0
+                         0.0  0.0 0.0
+                         0.0  1.0 0.0
+                         1.0 -1.0 0.0
+                         1.0  0.0 0.0
+                         1.0  1.0 0.0'
+  measurement_values = '4.464620e+00 6.447155e+00 8.434803e+00
+                        4.176264e+00 6.172984e+00 8.200859e+00
+                        4.049477e+00 6.052499e+00 8.079385e+00'
+[]
+
+[Executioner]
+  type = Optimize
+  tao_solver = taobqnls #taobncg #taoblmvm
+  petsc_options_iname = '-tao_gatol -tao_ls_type -tao_max_it'
+  petsc_options_value = '1e-6 unit 500'
+
+  #THESE OPTIONS ARE FOR TESTING THE ADJOINT GRADIENT
+  #petsc_options_iname='-tao_max_it -tao_fd_test -tao_test_gradient -tao_fd_gradient -tao_fd_delta -tao_gatol'
+  #petsc_options_value='1 true true false 1e-8 0.1'
+  #petsc_options = '-tao_test_gradient_view'
+  verbose = true
+[]
+
+[MultiApps]
+  [forward]
+    type = FullSolveMultiApp
+    input_files = model_grad.i
+    execute_on = FORWARD
+  []
+[]
+
+[Transfers]
+  [set_model_grad]
+    type = MultiAppReporterTransfer
+    to_multi_app = forward
+    from_reporters = 'OptimizationReporter/measurement_xcoord
+                      OptimizationReporter/measurement_ycoord
+                      OptimizationReporter/measurement_zcoord
+                      OptimizationReporter/measurement_time
+                      OptimizationReporter/measurement_values
+                      OptimizationReporter/lambda
+                      OptimizationReporter/mu'
+    to_reporters = 'measure_data/measurement_xcoord
+                    measure_data/measurement_ycoord
+                    measure_data/measurement_zcoord
+                    measure_data/measurement_time
+                    measure_data/measurement_values
+                    parametrization/lambda
+                    parametrization/mu'
+  []
+  [get_simulation_values]
+    type = MultiAppReporterTransfer
+    from_multi_app = forward
+    from_reporters = 'measure_data/simulation_values'
+    to_reporters = 'OptimizationReporter/simulation_values'
+  []
+  [get_grad_lambda]
+    type = MultiAppReporterTransfer
+    from_multi_app = forward
+    from_reporters = 'grad_lambda/inner_product'
+    to_reporters = 'OptimizationReporter/grad_lambda'
+  []
+  [get_grad_mu]
+    type = MultiAppReporterTransfer
+    from_multi_app = forward
+    from_reporters = 'grad_mu/inner_product'
+    to_reporters = 'OptimizationReporter/grad_mu'
+  []
+[]
+
+[Reporters]
+  [optInfo]
+    type = OptimizationInfo
+    items = 'current_iterate function_value gnorm'
+  []
+[]
+
+[Outputs]
+  console = false
+  csv = true
+[]

examples/bimaterialElastic/model_grad.i

@@ -0,0 +1,197 @@
+[Problem]
+  nl_sys_names = 'nl0 adjoint'
+  kernel_coverage_check = false
+[]
+
+[Mesh]
+  [gmg]
+    type = GeneratedMeshGenerator
+    dim  =  2
+    nx   = 11
+    ny   = 11
+    xmin = -4
+    xmax =  4
+    ymin = -4
+    ymax =  4
+  []
+[]
+
+[Variables]
+  [ux]
+  []
+  [uy]
+  []
+  [ux_adjoint]
+    nl_sys = adjoint
+  []
+  [uy_adjoint]
+    nl_sys = adjoint
+  []
+[]
+
+[AuxVariables]
+  [dummy]
+  []
+[]
+
+[Kernels]
+  [div_sigma_x]
+    type = StressDivergenceTensors
+    variable      = ux
+    displacements = 'ux uy'
+    component     = 0
+    volumetric_locking_correction = false
+  []
+  [div_sigma_y]
+    type = StressDivergenceTensors
+    variable      = uy
+    displacements = 'ux uy'
+    component     = 1
+    volumetric_locking_correction = false
+  []
+[]
+
+[BCs]
+  [bottom_ux]
+    type = DirichletBC
+    variable = ux
+    boundary = bottom
+    value = 0.0
+  []
+  [bottom_uy]
+    type = DirichletBC
+    variable = uy
+    boundary = bottom
+    value = 0.0
+  []
+  [top_fx]
+    type = NeumannBC
+    variable = ux
+    boundary = top
+    value = 1.0
+  []
+  [top_fy]
+    type = NeumannBC
+    variable = uy
+    boundary = top
+    value = 1.0
+  []
+[]
+
+[Materials]
+  [stress]
+    type = ComputeLinearElasticStress
+  []
+  [strain]
+    type = ComputeSmallStrain
+    displacements = 'ux uy'
+  []
+  [adjoint_strain]
+    type = ComputeSmallStrain
+    displacements = 'ux_adjoint uy_adjoint'
+    base_name = 'adjoint'
+  []
+  [elasticity_tensor]
+     type = ComputeVariableIsotropicElasticityTensor
+     args = dummy
+     youngs_modulus = E_material
+     poissons_ratio = nu_material
+  []
+  [E_material]
+    type = GenericFunctionMaterial
+    prop_names = 'E_material'
+    prop_values = E
+  []
+  [nu_material]
+    type = GenericFunctionMaterial
+    prop_names = 'nu_material'
+    prop_values = nu
+  []
+[]
+
+[Functions]
+  [E]
+    type = ParsedFunction
+    expression = mu*(3*lambda+2*mu)/(lambda+mu)
+    symbol_names = 'lambda mu'
+    symbol_values = 'lambda mu'
+  []
+  [nu]
+    type = ParsedFunction
+    expression = lambda/2/(lambda+mu)
+    symbol_names = 'lambda mu'
+    symbol_values = 'lambda mu'
+  []
+  [lambda]
+    type = NearestReporterCoordinatesFunction
+    x_coord_name = parametrization/coordx
+    y_coord_name = parametrization/coordy
+    value_name = parametrization/lambda
+  []
+  [mu]
+    type = NearestReporterCoordinatesFunction
+    x_coord_name = parametrization/coordx
+    y_coord_name = parametrization/coordy
+    value_name = parametrization/mu
+  []
+[]
+
+[Executioner]
+  type = SteadyAndAdjoint
+  forward_system = nl0
+  adjoint_system = adjoint
+  petsc_options_iname='-pc_type'
+  petsc_options_value='lu'
+  nl_forced_its = 1
+  line_search = none
+  nl_abs_tol = 1e-8
+[]
+
+[Outputs]
+  console = false
+  csv = false
+[]
+
+[DiracKernels]
+  [misfit_is_adjoint_force]
+    type = ReporterPointSource
+    variable = ux_adjoint
+    x_coord_name = measure_data/measurement_xcoord
+    y_coord_name = measure_data/measurement_ycoord
+    z_coord_name = measure_data/measurement_zcoord
+    value_name = measure_data/misfit_values
+  []
+[]
+
+[Reporters]
+  [measure_data]
+    type = OptimizationData
+    variable = ux
+  []
+  [parametrization]
+    type = ConstantReporter
+    real_vector_names = 'coordx coordy lambda mu'
+    real_vector_values = '0 1 2; 0 1 2; 5 4 3; 1 2 3'
+  []
+[]
+
+[VectorPostprocessors]
+  [grad_lambda]
+    type = ElementOptimizationLameLambdaInnerProduct
+    forward_strain_name = 'mechanical_strain'
+    adjoint_strain_name = 'adjoint_mechanical_strain'
+    #adjoint_strain_name = 'adjoint_total_strain'
+    variable = dummy
+    function = lambda
+    execute_on = 'ADJOINT_TIMESTEP_END'
+  []
+  [grad_mu]
+    type = ElementOptimizationLameMuInnerProduct
+    forward_strain_name = 'mechanical_strain'
+    adjoint_strain_name = 'adjoint_mechanical_strain'
+    #adjoint_strain_name = 'adjoint_total_strain'
+    variable = dummy
+    function = mu
+    execute_on = 'ADJOINT_TIMESTEP_END'
+  []
+[]

examples/bimaterialElastic/tests

@@ -13,4 +13,18 @@
     # steady solve
     recover = false
   []
+  issues = '#9999' #modify this
+  design = 'OptimizationReporter.md'
+  [opt_auto]
+    requirement = "The system shall be able to invert for elastic moduli using automatic adjoint."
+    type = CSVDiff
+    abs_zero = 1E-3
+    rel_err = 1e-3
+    input = main_auto.i
+    csvdiff = main_auto_out_OptimizationReporter_0001.csv
+    max_threads = 1
+    method = opt
+    # steady solve
+    recover = false
+  []
 []

examples/incompressibleElastic/gold/inversion_out_OptimizationReporter_0001.csv

@@ -0,0 +1,10 @@
+grad_mu,measurement_time,measurement_values,measurement_xcoord,measurement_ycoord,measurement_zcoord,misfit_values,mu,simulation_values
+-3.9109922919115e-08,0,4.1613567552542,-1,-1,0,-0.00084769473057467,1.0016574936417,4.1605090605236
+-2.8552016042187e-09,0,5.9488957653438,-1,0,0,-0.00049305346803674,1.9964074643121,5.9484027118758
+1.7175434588979e-10,0,7.675869730064,-1,1,0,-0.0012184465245957,3.0592449960713,7.6746512835394
+0,0,3.7517712455797,0,-1,0,-2.7832529675642e-05,0,3.75174341305
+0,0,5.548762655743,0,0,0,0.0014059181715211,0,5.5501685739145
+0,0,7.3172699473444,0,1,0,5.9206744674967e-05,0,7.3173291540891
+0,0,3.5372009228108,1,-1,0,0.0010745903451448,0,3.5382755131559
+0,0,5.3435565114703,1,0,0,-0.00029167404059738,0,5.3432648374297
+0,0,7.156727075585,1,1,0,0.00075948676127702,0,7.1574865623463