idaholab · sapitts · Oct 17, 2023 · Oct 5, 2023 · Oct 5, 2023 · Oct 5, 2023
diff --git a/.coverage b/.coverage
@@ -6,5 +6,5 @@
 # - warn_new: Warns below this percentage of coverage for new lines added
 
 [default]
-require_total = 65
+require_total = 69
 warn_new = 90
diff --git a/doc/content/source/bcs/DisplaceBoundaryBC.md b/doc/content/source/bcs/DisplaceBoundaryBC.md
@@ -1,18 +1,12 @@
 # DisplaceBoundaryBC
 
-!alert construction title=Undocumented Class
-The DisplaceBoundaryBC has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /BCs/DisplaceBoundaryBC
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the DisplaceBoundaryBC object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the DisplaceBoundaryBC object.
 

diff --git a/doc/content/source/bcs/GaussianWeldEnergyFluxBC.md b/doc/content/source/bcs/GaussianWeldEnergyFluxBC.md
@@ -1,18 +1,12 @@
 # GaussianWeldEnergyFluxBC
 
-!alert construction title=Undocumented Class
-The GaussianWeldEnergyFluxBC has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /BCs/GaussianWeldEnergyFluxBC
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the GaussianWeldEnergyFluxBC object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the GaussianWeldEnergyFluxBC object.
 

diff --git a/doc/content/source/bcs/PenaltyDisplaceBoundaryBC.md b/doc/content/source/bcs/PenaltyDisplaceBoundaryBC.md
@@ -1,18 +1,12 @@
 # PenaltyDisplaceBoundaryBC
 
-!alert construction title=Undocumented Class
-The PenaltyDisplaceBoundaryBC has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /BCs/PenaltyDisplaceBoundaryBC
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the PenaltyDisplaceBoundaryBC object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the PenaltyDisplaceBoundaryBC object.
 

diff --git a/doc/content/source/bcs/RadiationEnergyFluxBC.md b/doc/content/source/bcs/RadiationEnergyFluxBC.md
@@ -1,18 +1,12 @@
 # RadiationEnergyFluxBC
 
-!alert construction title=Undocumented Class
-The RadiationEnergyFluxBC has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /BCs/RadiationEnergyFluxBC
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the RadiationEnergyFluxBC object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the RadiationEnergyFluxBC object.
 

diff --git a/doc/content/source/bcs/SurfaceTensionBC.md b/doc/content/source/bcs/SurfaceTensionBC.md
@@ -1,18 +1,12 @@
 # SurfaceTensionBC
 
-!alert construction title=Undocumented Class
-The SurfaceTensionBC has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /BCs/SurfaceTensionBC
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the SurfaceTensionBC object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the SurfaceTensionBC object.
 

diff --git a/doc/content/source/bcs/VaporRecoilPressureMomentumFluxBC.md b/doc/content/source/bcs/VaporRecoilPressureMomentumFluxBC.md
@@ -1,18 +1,12 @@
 # VaporRecoilPressureMomentumFluxBC
 
-!alert construction title=Undocumented Class
-The VaporRecoilPressureMomentumFluxBC has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /BCs/VaporRecoilPressureMomentumFluxBC
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the VaporRecoilPressureMomentumFluxBC object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the VaporRecoilPressureMomentumFluxBC object.
 

diff --git a/doc/content/source/indicators/AbsoluteValueIndicator.md b/doc/content/source/indicators/AbsoluteValueIndicator.md
@@ -1,18 +1,12 @@
 # AbsoluteValueIndicator
 
-!alert construction title=Undocumented Class
-The AbsoluteValueIndicator has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /Adaptivity/Indicators/AbsoluteValueIndicator
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the AbsoluteValueIndicator object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the AbsoluteValueIndicator object.
 

diff --git a/doc/content/source/kernels/ADStressDivergence.md b/doc/content/source/kernels/ADStressDivergence.md
@@ -1,18 +1,12 @@
 # ADStressDivergence
 
-!alert construction title=Undocumented Class
-The ADStressDivergence has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /Kernels/ADStressDivergence
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the ADStressDivergence object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the ADStressDivergence object.
 

diff --git a/doc/content/source/kernels/BaldrConvectedMesh.md b/doc/content/source/kernels/BaldrConvectedMesh.md
@@ -1,18 +1,12 @@
 # BaldrConvectedMesh
 
-!alert construction title=Undocumented Class
-The BaldrConvectedMesh has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /Kernels/BaldrConvectedMesh
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the BaldrConvectedMesh object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the BaldrConvectedMesh object.
 

diff --git a/doc/content/source/kernels/BaldrTemperatureConvectedMesh.md b/doc/content/source/kernels/BaldrTemperatureConvectedMesh.md
@@ -1,18 +1,12 @@
 # BaldrTemperatureConvectedMesh
 
-!alert construction title=Undocumented Class
-The BaldrTemperatureConvectedMesh has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /Kernels/BaldrTemperatureConvectedMesh
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the BaldrTemperatureConvectedMesh object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the BaldrTemperatureConvectedMesh object.
 

diff --git a/doc/content/source/materials/CrazyKCPlantFits.md b/doc/content/source/materials/CrazyKCPlantFits.md
@@ -1,18 +1,12 @@
 # CrazyKCPlantFits
 
-!alert construction title=Undocumented Class
-The CrazyKCPlantFits has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /Materials/CrazyKCPlantFits
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the CrazyKCPlantFits object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the CrazyKCPlantFits object.
 

diff --git a/doc/content/source/materials/CrazyKCPlantFitsBoundary.md b/doc/content/source/materials/CrazyKCPlantFitsBoundary.md
@@ -1,18 +1,12 @@
 # CrazyKCPlantFitsBoundary
 
-!alert construction title=Undocumented Class
-The CrazyKCPlantFitsBoundary has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /Materials/CrazyKCPlantFitsBoundary
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the CrazyKCPlantFitsBoundary object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the CrazyKCPlantFitsBoundary object.
 

diff --git a/doc/content/source/materials/PseudoSolidStress.md b/doc/content/source/materials/PseudoSolidStress.md
@@ -1,18 +1,12 @@
 # PseudoSolidStress
 
-!alert construction title=Undocumented Class
-The PseudoSolidStress has not been documented. The content listed below should be used as a starting point for
-documenting the class, which includes the typical automatic documentation associated with a
-MooseObject; however, what is contained is ultimately determined by what is necessary to make the
-documentation clear for users.
-
 !syntax description /Materials/PseudoSolidStress
 
-## Overview
+!! ## Overview
 
 !! Replace these lines with information regarding the PseudoSolidStress object.
 
-## Example Input File Syntax
+!! ## Example Input File Syntax
 
 !! Describe and include an example of how to use the PseudoSolidStress object.
 

diff --git a/doc/content/sqa/user_manual.md b/doc/content/sqa/user_manual.md
@@ -0,0 +1,4 @@
+# MALAMUTE User Manual
+
+Documentation for all MALAMUTE input file objects, and how they can be used in the creation of a
+multiphysics simulation, is contained in the [syntax/index.md] page.
diff --git a/doc/content/syntax/index.md b/doc/content/syntax/index.md
@@ -4,4 +4,6 @@ Listed below are all of the possible input parameter options for a MALAMUTE inpu
 file. Click the blue link shown to the right of each heading to see a more detailed
 description of its purpose.
 
+For a filtered list of MALAMUTE-only syntax, please [click here](syntax/malamute_only.md).
+
 !syntax complete
diff --git a/doc/content/syntax/malamute_only.md b/doc/content/syntax/malamute_only.md
@@ -0,0 +1,9 @@
+# MALAMUTE-only Input File Syntax
+
+Listed below are the input parameter options for a MALAMUTE input file for code contained solely
+within MALAMUTE (not within MOOSE or its modules). Click the blue link shown to the right of each
+heading to see a more detailed description of its purpose.
+
+To return to the complete code syntax, please [click here](syntax/index.md).
+
+!syntax complete groups=MalamuteApp
diff --git a/doc/sqa_reports.yml b/doc/sqa_reports.yml
@@ -5,7 +5,6 @@ Applications:
         content_directory: ${ROOT_DIR}/doc/content
         remove:
             - ${MOOSE_DIR}/framework/doc/remove.yml
-        log_default: WARNING
         show_warning: false
 
 Documents:
@@ -19,13 +18,14 @@ Documents:
     software_requirements_specification: sqa/malamute_srs.md
     software_design_description: sqa/malamute_sdd.md
     software_test_plan: sqa/malamute_stp.md
-    requirements_traceablity_matrix: sqa/malamute_rtm.md
+    requirements_traceability_matrix: sqa/malamute_rtm.md
     verification_validation_report: sqa/malamute_vvr.md
     failure_analysis_report: sqa/malamute_far.md
     software_library_list: sqa/malamute_sll.md
     communication_and_contact_information: sqa/malamute_cci.md
     software_coding_standards: sqa/malamute_scs.md
-    log_default: WARNING
+    user_manual: sqa/user_manual.md
+    log_theory_manual: NONE   # all theory is contained within example, benchmark, or design docs
     show_warning: false
     working_dirs:
         - ${ROOT_DIR}/doc/content
@@ -49,6 +49,5 @@ Requirements:
             - ${MOOSE_DIR}/modules/tensor_mechanics/doc/content
         directories:
             - ${ROOT_DIR}/test
-            - ${ROOT_DIR}/examples
-        log_default: WARNING
+            # - ${ROOT_DIR}/examples   TODO: add back in when examples is more stable and less R&D
         show_warning: false
diff --git a/examples/melt_pool_2d/tests b/examples/melt_pool_2d/tests
@@ -4,5 +4,6 @@
     input = 'melt_pool.i'
     check_input = True
     method = opt
+    issues = '#4'
   [../]
 []
diff --git a/examples/melt_pool_3d/tests b/examples/melt_pool_3d/tests
@@ -4,5 +4,6 @@
     input = 'melt_pool.i'
     check_input = True
     method = opt
+    issues = '#4'
   [../]
 []
diff --git a/examples/sps/engineering_scale/validation/dcs5/empty_die/stepped_20mm/tests b/examples/sps/engineering_scale/validation/dcs5/empty_die/stepped_20mm/tests
@@ -1,14 +1,13 @@
 [Tests]
-  requirement = 'The system shall compute the electro-thermo-mechanical response '
-                'of a 2D-axisymmetric representation of the DCS-5 stepped 20mm diameter '
-                'punch graphite tooling stack,'
   [dcs5_stepped20mm_empty_constant_properties]
     type = RunApp
     input = 'dcs5_stepped20mm_empty_constant_properties.i'
     check_input = True
     method = opt
     issues = '#91'
-    detail = 'using constant graphite material properties, which signficantly '
-             'overestimates the temperature profile during the SPS run.'
+    requirement = 'The system shall compute the electro-thermo-mechanical response '
+                  'of a 2D-axisymmetric representation of the DCS-5 stepped 20mm diameter '
+                  'punch graphite tooling stack, using constant graphite material properties, '
+                  'which signficantly overestimates the temperature profile during the SPS run.'
   []
 []
diff --git a/src/bcs/GaussianWeldEnergyFluxBC.C b/src/bcs/GaussianWeldEnergyFluxBC.C
@@ -16,6 +16,8 @@ InputParameters
 GaussianWeldEnergyFluxBC::validParams()
 {
   InputParameters params = ADIntegratedBC::validParams();
+  params.addClassDescription("Calculates the boundary condition residual contribution of the heat "
+                             "flux of a Gaussian laser beam impinging on a surface.");
   params.addRequiredParam<Real>("reff",
                                 "The effective radius describing the radial distribution of the "
                                 "beam energy. This should be non-dimensional.");

diff --git a/src/indicators/AbsoluteValueIndicator.C b/src/indicators/AbsoluteValueIndicator.C
@@ -16,6 +16,8 @@ InputParameters
 AbsoluteValueIndicator::validParams()
 {
   InputParameters params = ElementIntegralIndicator::validParams();
+  params.addClassDescription(
+      "Compute the absolute value of the provided variable for use as an error indicator.");
   return params;
 }
 

diff --git a/src/kernels/ADStressDivergence.C b/src/kernels/ADStressDivergence.C
@@ -15,6 +15,8 @@ InputParameters
 ADStressDivergence::validParams()
 {
   InputParameters params = ADKernel::validParams();
+  params.addClassDescription(
+      "Computes a stress divergence term for a given displacement component.");
   params.addRequiredParam<int>("component", "The displacement component");
   return params;
 }