Fix SQA failures (idaholab#21885)

MengnanLi91 · Jan 4, 2023 · 46890c9 · 46890c9
1 parent 9aa657e
commit 46890c9
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Showing 18 changed files with 51 additions and 37 deletions.
diff --git a/modules/combined/test/tests/invOpt_nonlinear/tests b/modules/combined/test/tests/invOpt_nonlinear/tests
@@ -1,5 +1,5 @@
 [Tests]
-  issues = 'idaholab/isopod#25'
+  issues = '#22208'
   design = 'MaterialScaledGradientVector.md'
   requirement = "The system shall invert for a constant heat source with a temperature dependent "
                 "thermal condutivity using a"

diff --git a/modules/doc/config.yml b/modules/doc/config.yml
@@ -112,6 +112,7 @@ Extensions:
             meshgenerators: syntax/Mesh/index.md
             multiapps: syntax/MultiApps/index.md
             nodalkernels: syntax/NodalKernels/index.md
+            optimizationreporters: syntax/OptimizationReporter/index.md
             outputs: syntax/Outputs/index.md
             parser: source/parser/Parser.md
             partitioner: syntax/Mesh/Partitioner/index.md

diff --git a/modules/doc/sqa_reports.yml b/modules/doc/sqa_reports.yml
@@ -408,7 +408,7 @@ Requirements:
 
     optimization:
         directories:
-            - modules/navier_stokes
+            - modules/optimization
 
     phase_field:
         directories:

diff --git a/...s/optimization/doc/content/source/optimizationreporters/OptimizationReporter.md b/...s/optimization/doc/content/source/optimizationreporters/OptimizationReporter.md
@@ -0,0 +1 @@
+!template load file=stubs/moose_object.md.template name=OptimizationReporter syntax=/UserObjects/OptimizationReporter
diff --git a/modules/optimization/doc/sqa_reports.yml b/modules/optimization/doc/sqa_reports.yml
@@ -8,7 +8,8 @@ Applications:
             - ${MOOSE_DIR}/framework/doc/unregister.yml
         remove:
             - ${MOOSE_DIR}/framework/doc/remove.yml
-        log_missing_markdown: WARNING
+        # log_missing_markdown: WARNING
+        log_stub_files: WARNING
 
 Documents:
     software_quality_plan: sqa/inl_records.md#software_quality_plan
@@ -27,8 +28,8 @@ Documents:
     software_library_list: sqa/optimization_sll.md
     communication_and_contact_information: sqa/framework_cci.md
     software_coding_standards: sqa/framework_scs.md
-    log_user_manual: WARNING
-    log_theory_manual: WARNING
+    user_manual: getting_started/RunningOptimization.md
+    theory_manual: getting_started/InvOptTheory.md
 
 Requirements:
     optimization:

diff --git a/modules/optimization/examples/bimaterial/tests b/modules/optimization/examples/bimaterial/tests
@@ -1,5 +1,6 @@
 [Tests]
   issues = '#21885'
+  design = 'Optimize.md'
   [nm]
     type = CSVDiff
     input = main.i
@@ -8,7 +9,7 @@
     rel_err = 0.3
     cli_args = "Executioner/tao_solver=TAONM Executioner/petsc_options_iname='-tao_fmin'  "
                "Executioner/petsc_options_value='0.0001'"
-    requirement = "XXXX shall be able to use Nelder Mead to invert for material properties"
+    requirement = "The system shall be able to use Nelder Mead to invert for material properties"
   []
   [fd_grad]
     type = CSVDiff
@@ -18,8 +19,8 @@
     rel_err = 0.1
     cli_args = "Executioner/tao_solver=TAOBLMVM Executioner/petsc_options_iname='-tao_fd_gradient "
                "-tao_gatol'  Executioner/petsc_options_value='True 0.0005'"
-    requirement = "XXXX shall be able to use finite-differencing with a gradient method to invert "
-                  "for material properties"
+    requirement = "The system shall be able to use finite-differencing with a gradient method to "
+                  "invert for material properties"
   []
   [fd_hess]
     type = CSVDiff
@@ -29,7 +30,7 @@
     rel_err = 1.0
     cli_args = "Executioner/tao_solver=taobntr Executioner/petsc_options_iname='-tao_fd_gradient "
                "-tao_fd_hessian -tao_gatol'  Executioner/petsc_options_value='true True 0.1'"
-    requirement = "XXXX shall be able to use finite-differencing with a hessian method to invert for "
-                  "material properties"
+    requirement = "The system shall be able to use finite-differencing with a hessian method to "
+                  "invert for material properties"
   []
 []
diff --git a/modules/optimization/examples/simpleTransient/tests b/modules/optimization/examples/simpleTransient/tests
@@ -1,8 +1,8 @@
 [Tests]
   [transient]
-    design = 'ElementOptimizationSourceFunctionInnerProduct.md VectorNearestPointFunction.md  VectorPointSource.md'
+    design = "ElementOptimizationSourceFunctionInnerProduct.md VectorNearestPointFunction.md  VectorPointSource.md"
     issues = '#42'
-    requirement = 'The system shall be able to perform force-inversion optimization with time-dependent parameters and outputs with'
+    requirement = "The system shall be able to perform force-inversion optimization with time-dependent parameters and outputs with"
     [objective]
       type = JSONDiff
       input = main.i

diff --git a/modules/optimization/test/tests/dirackernels/tests b/modules/optimization/test/tests/dirackernels/tests
@@ -1,5 +1,5 @@
 [Tests]
-  issues = 'idaholab/isopod#42'
+  issues = '#22215'
   [vector_point_source]
     design = 'VectorPointSource.md'
     requirement = 'The system shall support point sources with locations, times, and values given by a vector values with '

diff --git a/modules/optimization/test/tests/executioners/tests b/modules/optimization/test/tests/executioners/tests
@@ -1,5 +1,6 @@
 [Tests]
   issues = '#21885'
+  design = 'Optimize.md'
   [quadratic_taonm]
     type = CSVDiff
     max_threads = 1

diff --git a/modules/optimization/test/tests/functions/piecewise_multilinear_from_reporter/tests b/modules/optimization/test/tests/functions/piecewise_multilinear_from_reporter/tests
@@ -1,5 +1,6 @@
 [Tests]
-  issues = 'idaholab/isopod#47'
+  issues = '#22217'
+  design = 'PiecewiseMultilinearFromReporter.md'
   [interp]
     requirement = "The PiecewiseMultilinearFromReporter object shall perform"
     [except1]

diff --git a/modules/optimization/test/tests/functions/vector_nearest_point/tests b/modules/optimization/test/tests/functions/vector_nearest_point/tests
@@ -1,7 +1,7 @@
 [Tests]
   [vector_nearest_point]
     design = 'VectorNearestPointFunction.md'
-    issues = 'idaholab/isopod#42'
+    issues = '#22215'
     requirement = 'The system shall be able to compute a auxiliary varible based on data from reporter values with '
     [x]
       type = Exodiff

diff --git a/modules/optimization/test/tests/optimizationreporter/base/tests b/modules/optimization/test/tests/optimizationreporter/base/tests
@@ -1,19 +1,21 @@
 [Tests]
-  issues = 'idaholab/isopod#34'
+  issues = '#22212'
   design = 'OptimizationReporter/index.md'
-  requirement = "The system shall correctly read in "
-  [input]
-    type = JSONDiff
-    input = optRep_fromInput.i
-    jsondiff = optRep_fromInput_out.json
-    allow_test_objects = true
-    detail = "parameter data from the input file and and measurment data from the input file."
-  []
-  [csv]
-    type = JSONDiff
-    input = optRep_fromCsv.i
-    jsondiff = optRep_fromCsv_out.json
-    allow_test_objects = true
-    detail = "parameter data from the input file and and measurment data from a CSV file."
+  [read_data]
+    requirement = "The system shall correctly read in "
+    [input]
+      type = JSONDiff
+      input = optRep_fromInput.i
+      jsondiff = optRep_fromInput_out.json
+      allow_test_objects = true
+      detail = "parameter data from the input file and and measurment data from the input file."
+    []
+    [csv]
+      type = JSONDiff
+      input = optRep_fromCsv.i
+      jsondiff = optRep_fromCsv_out.json
+      allow_test_objects = true
+      detail = "parameter data from the input file and and measurment data from a CSV file."
+    []
   []
 []
diff --git a/modules/optimization/test/tests/optimizationreporter/bc_convective/tests b/modules/optimization/test/tests/optimizationreporter/bc_convective/tests
@@ -1,4 +1,6 @@
 [Tests]
+  issues = '#21885'
+  design = 'Optimize.md'
   [taolmvm]
     type = CSVDiff
     max_threads = 1
@@ -7,5 +9,6 @@
     csvdiff = forward_vertical_0001.csv
     # steady solve
     recover = false
+    requirement = 'The system shall be able to solve an inverse boundary value problem using TAO.'
   []
 []
diff --git a/modules/optimization/test/tests/optimizationreporter/bimaterial/tests b/modules/optimization/test/tests/optimizationreporter/bimaterial/tests
@@ -1,13 +1,13 @@
 [Tests]
   issues = '#21885'
   design = 'DiffusionVariableIntegral.md'
-  requirement = 'The system shall be able to invert for the material properties of two seperate materials'
   [taoblmvm]
     type = CSVDiff
     max_threads = 1
     input = main.i
     abs_zero = 1e-2
     csvdiff = main_out_OptimizationReporter_0001.csv
     recover = false
+    requirement = 'The system shall be able to invert for the material properties of two seperate materials'
   []
 []
diff --git a/modules/optimization/test/tests/optimizationreporter/point_loads/tests b/modules/optimization/test/tests/optimizationreporter/point_loads/tests
@@ -1,7 +1,6 @@
 [Tests]
   issues = '#21885'
   design = 'ReporterPointSource.md'
-  requirement = "The system shall be able to invert for point loads using "
   [hessian]
     type = CSVDiff
     max_threads = 1
@@ -11,7 +10,8 @@
                "-tao_max_it -tao_nls_pc_type -tao_nls_ksp_type' "
                "Executioner/petsc_options_value='1e-5 10 none cg'"
     csvdiff = main_out_receiver_0001.csv
-    detail = " Hessian based optimimization;"
+    requirement = "The system shall be able to invert for point loads using Hessian based "
+                  "optimimization;"
     # steady solve
     recover = false
   []
@@ -21,7 +21,8 @@
     rel_err = 0.1
     input = main.i
     csvdiff = main_out_receiver_0001.csv
-    detail = " gradient based optimization;"
+    requirement = "The system shall be able to invert for point loads using gradient based "
+                  "optimization;"
     # steady solve
     recover = false
   []

diff --git a/modules/optimization/test/tests/reporter/GriddedDataReporter/tests b/modules/optimization/test/tests/reporter/GriddedDataReporter/tests
@@ -3,6 +3,8 @@
     requirement = "This tests that a reporter is able to read in a gridded data file and produce the "
                   "appropriate grid from it that can be used in PiecewiseMultiInterpolation like "
                   "functions."
+    issues = '#21885'
+    design = 'GriddedDataReporter.md'
     type = JSONDiff
     input = 'griddedData.i'
     jsondiff = 'griddedData_out.json'

diff --git a/modules/optimization/test/tests/vectorpostprocessors/element_source_inner_product/tests b/modules/optimization/test/tests/vectorpostprocessors/element_source_inner_product/tests
@@ -5,7 +5,7 @@
     input = element_source_inner_product.i
     csvdiff = element_source_inner_product_out_inner_product_0011.csv
     recover = false # Can't do recover since there is no mesh
-    issues = '#42'
+    issues = '#22215'
     requirement = 'They system shall be able to compute the inner product of a variable and a nearest node optimization volumetric source function.'
   []
 []
diff --git a/modules/optimization/test/tests/vectorpostprocessors/measured_data_point_sampler/tests b/modules/optimization/test/tests/vectorpostprocessors/measured_data_point_sampler/tests
@@ -1,6 +1,6 @@
 [Tests]
-  design = 'None'
-  issues = 'None'
+  design = 'MeasuredDataPointSampler.md'
+  issues = '#21885'
 
   [sort]
     requirement = "Measured point value sampler can hold a vector of measurement data and sortit the "