Reactor module test regoldings and add MOOSE tests for new Exodus out…

…put options / command line options

Refs idaholab#23386

framework/doc/content/source/actions/ElementIDOutputAction.md

@@ -0,0 +1,9 @@
+# ElementIDOutputAction
+
+!syntax description /Mesh/ElementIDOutputAction
+
+This action is triggered when [!param](/Outputs/Exodus/output_extra_element_ids) is set to `true`. AuxVariables and AuxKernels relevant to the extra element ids defined on the mesh are automatically added to the problem, and the resulting element integers are also outputted to the Exodus file.
+
+!listing test/tests/outputs/exodus/exodus_elem_id.i block=Outputs
+
+More information can be found on the [Exodus output documentation page](outputs/Exodus.md).

framework/src/actions/ElementIDOutputAction.C

@@ -11,6 +11,7 @@
 #include "ElementIDOutputAction.h"
 #include "MooseMesh.h"
 #include "FEProblemBase.h"
+#include "AddOutputAction.h"
 
 registerMooseAction("MooseApp", ElementIDOutputAction, "add_aux_kernel");
 
@@ -23,10 +24,7 @@ ElementIDOutputAction::validParams()
   return params;
 }
 
-ElementIDOutputAction::ElementIDOutputAction(const InputParameters & params)
-  : Action(params)
-{
-}
+ElementIDOutputAction::ElementIDOutputAction(const InputParameters & params) : Action(params) {}
 
 void
 ElementIDOutputAction::act()
@@ -52,8 +50,7 @@ ElementIDOutputAction::act()
         bool has_element_id_names = params.isParamValid("show_extra_element_ids");
         std::vector<std::string> element_id_names;
         if (has_element_id_names)
-          element_id_names =
-              params.get<std::vector<std::string>>("show_extra_element_ids");
+          element_id_names = params.get<std::vector<std::string>>("show_extra_element_ids");
 
         unsigned int n = _mesh->getMesh().n_elem_integers();
         auto var_params = _factory.getValidParams("MooseVariableConstMonomial");
@@ -62,7 +59,9 @@ ElementIDOutputAction::act()
         for (unsigned int i = 0; i < n; ++i)
         {
           auto & var_name = _mesh->getMesh().get_elem_integer_name(i);
-          if (!has_element_id_names || (std::find(element_id_names.begin(), element_id_names.end(), var_name) != element_id_names.end()))
+          if (!has_element_id_names ||
+              (std::find(element_id_names.begin(), element_id_names.end(), var_name) !=
+               element_id_names.end()))
           {
             // Create aux variables based on the extra element id name
             _problem->addAuxVariable("MooseVariableConstMonomial", var_name, var_params);

framework/src/actions/MeshOnlyAction.C

@@ -31,7 +31,9 @@ void
 MeshOnlyAction::act()
 {
   bool output_eeid_to_exodus = _app.isParamValid("initialize_only");
-  std::string mesh_file = output_eeid_to_exodus ? _app.parameters().get<std::string>("initialize_only") : _app.parameters().get<std::string>("mesh_only");
+  std::string mesh_file = output_eeid_to_exodus
+                              ? _app.parameters().get<std::string>("initialize_only")
+                              : _app.parameters().get<std::string>("mesh_only");
   auto & mesh_ptr = _app.actionWarehouse().mesh();
 
   // Print information about the mesh
@@ -104,7 +106,8 @@ MeshOnlyAction::act()
       std::vector<std::set<subdomain_id_type>> vars_active_subdomains;
       vars_active_subdomains.resize(n_eeid);
       exio_helper.initialize_element_variables(eeid_vars, vars_active_subdomains);
-      exio_helper.write_element_values(output_mesh, eeid_soln, empty_timestep, vars_active_subdomains);
+      exio_helper.write_element_values(
+          output_mesh, eeid_soln, empty_timestep, vars_active_subdomains);
     }
   }
   else if (mesh_file.find(".cpr") + 4 == mesh_file.size())

framework/src/base/MooseApp.C

@@ -105,10 +105,10 @@ MooseApp::validParams()
       "mesh_only",
       "--mesh-only [mesh_file_name]",
       "Setup and Output the input mesh only (Default: \"<input_file_name>_in.e\")");
-  params.addCommandLineParam<std::string>(
-      "initialize_only",
-      "--initialize-only [mesh_file_name]",
-      "Setup and Output the input mesh with extra element integers only (Default: \"<input_file_name>_in.e\")");
+  params.addCommandLineParam<std::string>("initialize_only",
+                                          "--initialize-only [mesh_file_name]",
+                                          "Setup and Output the input mesh with extra element "
+                                          "integers only (Default: \"<input_file_name>_in.e\")");
 
   params.addCommandLineParam<bool>("show_input",
                                    "--show-input",

framework/src/outputs/AdvancedOutput.C

@@ -701,9 +701,10 @@ AdvancedOutput::addValidParams(InputParameters & params, const MultiMooseEnum &
     params.addParamNamesToGroup("output_material_properties show_material_properties", "Materials");
 
     // Add mesh extra element id control, which are output via elemental variables
-    params.addParam<bool>("output_extra_element_ids",
-                          false,
-                          "Flag indicating if extra element ids defined on the mesh should be outputted");
+    params.addParam<bool>(
+        "output_extra_element_ids",
+        false,
+        "Flag indicating if extra element ids defined on the mesh should be outputted");
     params.addParam<std::vector<std::string>>(
         "show_extra_element_ids",
         "List of extra element ids defined on the mesh that should be written to the output");

test/tests/mesh/mesh_only/initialize_only.i

@@ -0,0 +1,60 @@
+[Mesh]
+  [gmg]
+    type = GeneratedMeshGenerator
+    dim = 2
+    nx = 10
+    ny = 10
+    xmax = 1
+    ymax = 1
+    subdomain_ids = '0 0 0 0 0 0 0 0 0 0
+                     0 1 0 0 0 0 0 0 0 0
+                     0 0 2 0 0 0 0 0 0 0
+                     0 0 0 3 0 0 0 0 0 0
+                     0 0 0 0 4 0 0 0 0 0
+                     0 0 0 0 0 5 0 0 0 0
+                     0 0 0 0 0 0 6 0 0 0
+                     0 0 0 0 0 0 0 7 0 0
+                     0 0 0 0 0 0 0 0 8 0
+                     0 0 0 0 0 0 0 0 0 9'
+    extra_element_integers = 'pin_id'
+  []
+  [pinid_1]
+    type = SubdomainBoundingBoxGenerator
+    input = gmg
+    bottom_left = '0 0 0'
+    top_right = '0.5 0.5 0'
+    block_id = 1
+    location = INSIDE
+    integer_name = pin_id
+  []
+  [pinid_2]
+    type = SubdomainBoundingBoxGenerator
+    input = pinid_1
+    bottom_left = '0.5 0 0'
+    top_right = '1 0.5 0'
+    block_id = 2
+    location = INSIDE
+    integer_name = pin_id
+  []
+  [pinid_3]
+    type = SubdomainBoundingBoxGenerator
+    input = pinid_2
+    bottom_left = '0 0.5 0'
+    top_right = '0.5 1 0'
+    block_id = 3
+    location = INSIDE
+    integer_name = pin_id
+  []
+  [pinid_4]
+    type = SubdomainBoundingBoxGenerator
+    input = pinid_3
+    bottom_left = '0.5 0.5 0'
+    top_right = '1 1 0'
+    block_id = 4
+    location = INSIDE
+    integer_name = pin_id
+  []
+[]
+
+# This input file is intended to be run with the "--initialize-only" option so
+# no other sections are required

test/tests/mesh/mesh_only/tests

@@ -1,7 +1,7 @@
 [Tests]
   design = 'Mesh/index.md'
 
-  [./mesh_only_test]
+  [mesh_only_test]
     type = 'Exodiff'
     input = 'mesh_only.i'
     cli_args = '--mesh-only 3d_chimney.e'
@@ -10,9 +10,9 @@
     method = '!dbg'
     issues = '#1568'
     requirement = 'The system shall allow writing out the mesh without running a simulation.'
-  [../]
+  []
 
-  [./mesh_info]
+  [mesh_info]
     type = 'RunApp'
     input = 'mesh_only.i'
     cli_args = '--mesh-only info_test.e'
@@ -21,9 +21,9 @@
     expect_out = 'Mesh Information'
     issues = '#11917 #11921'
     requirement = 'The system shall print out information about the mesh when writing out the mesh.'
-  [../]
+  []
 
-  [./mesh_only_warning]
+  [mesh_only_warning]
     type = RunApp
     input = 'mesh_only.i'
     # Intentional error (not a mesh filename)
@@ -32,9 +32,9 @@
     expect_out = 'The --mesh-only option should be followed by a file name.'
     issues = '#1568'
     requirement = 'The system shall warn when using --mesh-only and there is no clear filename to use'
-  [../]
+  []
 
-  [./output_dimension_override]
+  [output_dimension_override]
     type = 'Exodiff'
     input = 'output_dimension_override.i'
     cli_args = '--mesh-only output_dimension.e'
@@ -43,9 +43,9 @@
     method = '!dbg'
     issues = '#12757'
     requirement = 'The system shall support overriding output dimension when necessary to store coordinates in higher planes'
-  [../]
+  []
 
-  [./mesh_only_checkpoint]
+  [mesh_only_checkpoint]
     type = 'CheckFiles'
     input = 'mesh_only.i'
     cli_args = 'Mesh/parallel_type=distributed --mesh-only 3d_chimney.cpr'
@@ -56,5 +56,16 @@
     method = '!dbg'
     issues = '#14312'
     requirement = 'The system shall support writing parallel checkpoint files with --mesh-only'
-  [../]
+  []
+
+  [initialize_only]
+    type = 'Exodiff'
+    input = 'initialize_only.i'
+    cli_args = '--initialize-only'
+    exodiff = 'initialize_only_in.e'
+    recover = false
+    method = '!dbg'
+    issues = '#23386'
+    requirement = 'The system shall allow writing out the mesh with extra element ids without running a simulation.'
+  []
 []

test/tests/outputs/exodus/exodus_elem_id.i

@@ -0,0 +1,113 @@
+[Mesh]
+  [gmg]
+    type = GeneratedMeshGenerator
+    dim = 2
+    nx = 10
+    ny = 10
+    xmax = 1
+    ymax = 1
+    subdomain_ids = '0 0 0 0 0 0 0 0 0 0
+                     0 1 0 0 0 0 0 0 0 0
+                     0 0 2 0 0 0 0 0 0 0
+                     0 0 0 3 0 0 0 0 0 0
+                     0 0 0 0 4 0 0 0 0 0
+                     0 0 0 0 0 5 0 0 0 0
+                     0 0 0 0 0 0 6 0 0 0
+                     0 0 0 0 0 0 0 7 0 0
+                     0 0 0 0 0 0 0 0 8 0
+                     0 0 0 0 0 0 0 0 0 9'
+    extra_element_integers = 'pin_id temp_id'
+  []
+  [pinid_1]
+    type = SubdomainBoundingBoxGenerator
+    input = gmg
+    bottom_left = '0 0 0'
+    top_right = '0.5 0.5 0'
+    block_id = 1
+    location = INSIDE
+    integer_name = pin_id
+  []
+  [pinid_2]
+    type = SubdomainBoundingBoxGenerator
+    input = pinid_1
+    bottom_left = '0.5 0 0'
+    top_right = '1 0.5 0'
+    block_id = 2
+    location = INSIDE
+    integer_name = pin_id
+  []
+  [pinid_3]
+    type = SubdomainBoundingBoxGenerator
+    input = pinid_2
+    bottom_left = '0 0.5 0'
+    top_right = '0.5 1 0'
+    block_id = 3
+    location = INSIDE
+    integer_name = pin_id
+  []
+  [pinid_4]
+    type = SubdomainBoundingBoxGenerator
+    input = pinid_3
+    bottom_left = '0.5 0.5 0'
+    top_right = '1 1 0'
+    block_id = 4
+    location = INSIDE
+    integer_name = pin_id
+  []
+  [tempid_1]
+    type = SubdomainBoundingBoxGenerator
+    input = pinid_4
+    bottom_left = '0 0 0'
+    top_right = '0.5 0.5 0'
+    block_id = 1
+    location = INSIDE
+    integer_name = temp_id
+  []
+  [tempid_2]
+    type = SubdomainBoundingBoxGenerator
+    input = tempid_1
+    bottom_left = '0.5 0 0'
+    top_right = '1 0.5 0'
+    block_id = 2
+    location = INSIDE
+    integer_name = temp_id
+  []
+  [tempid_3]
+    type = SubdomainBoundingBoxGenerator
+    input = tempid_2
+    bottom_left = '0 0.5 0'
+    top_right = '0.5 1 0'
+    block_id = 3
+    location = INSIDE
+    integer_name = temp_id
+  []
+  [tempid_4]
+    type = SubdomainBoundingBoxGenerator
+    input = tempid_3
+    bottom_left = '0.5 0.5 0'
+    top_right = '1 1 0'
+    block_id = 4
+    location = INSIDE
+    integer_name = temp_id
+  []
+[]
+
+[Problem]
+  kernel_coverage_check = false
+  solve = false
+[]
+
+[Executioner]
+  type = Steady
+[]
+
+[Debug]
+  show_actions = true
+[]
+
+[Outputs]
+  [out]
+    type = Exodus
+    output_extra_element_ids = true
+  []
+[]