Merge pull request #27242 from GiudGiud/PR_modules_doco

Part 1 of finishing modules object & syntax documentation

modules/chemical_reactions/doc/content/modules/chemical_reactions/index.md

@@ -183,7 +183,7 @@ provided to define $\nabla u$ on a boundary.
 The total volume fraction of a given mineral species can be calculated using a
 [`TotalMineralVolumeFraction`](/TotalMineralVolumeFraction.md) postprocessor.
 
-## Reaction network parser
+## Reaction network parser id=parser
 
 The chemical reactions module includes a reaction network parser in the `Actions` system that enables
 chemical reactions to be specified in a natural form in the input file. The parser then adds all

modules/chemical_reactions/doc/content/source/actions/AddCoupledEqSpeciesAction.md

@@ -1 +1,15 @@
-!template load file=stubs/moose_action.md.template name=AddCoupledEqSpeciesAction syntax=/ReactionNetwork/AqueousEquilibriumReactions/AddCoupledEqSpeciesAction
+# AddCoupledEqSpeciesActions
+
+!syntax description /ReactionNetwork/AqueousEquilibriumReactions/AddCoupledEqSpeciesAction
+
+This action only creates the [Kernels](Kernels/index.md) and [AuxKernels](AuxKernels/index.md).
+The primary species are created as [nonlinear variables](Variables/index.md), by the [AddPrimarySpeciesAction.md].
+The reactions are parsed from the syntax described on this [page](modules/chemical_reactions/index.md#parser).
+Equilibrium species are output as [auxiliary variables](AuxVariables/index.md), by the [AddSecondarySpeciesAction.md].
+This action is the aqueous equilibrium pendant of the solid kinetic [AddCoupledSolidKinSpeciesAction.md].
+
+!syntax parameters /ReactionNetwork/AqueousEquilibriumReactions/AddCoupledEqSpeciesAction
+
+!syntax inputs /ReactionNetwork/AqueousEquilibriumReactions/AddCoupledEqSpeciesAction
+
+!syntax children /ReactionNetwork/AqueousEquilibriumReactions/AddCoupledEqSpeciesAction

modules/chemical_reactions/doc/content/source/actions/AddCoupledSolidKinSpeciesAction.md

@@ -1 +1,15 @@
-!template load file=stubs/moose_action.md.template name=AddCoupledSolidKinSpeciesAction syntax=/ReactionNetwork/SolidKineticReactions/AddCoupledSolidKinSpeciesAction
+# AddCoupledSolidKinSpeciesActions
+
+!syntax description /ReactionNetwork/SolidKineticReactions/AddCoupledSolidKinSpeciesAction
+
+This action only creates the [Kernels](Kernels/index.md) and [AuxKernels](AuxKernels/index.md).
+The primary species are created as [nonlinear variables](Variables/index.md), by the [AddPrimarySpeciesAction.md].
+The reactions are parsed from the syntax described on this [page](modules/chemical_reactions/index.md#parser).
+Equilibrium species are output as [auxiliary variables](AuxVariables/index.md), by the [AddSecondarySpeciesAction.md].
+This action is the solid kinetic pendant of the aqueous equilibrium [AddCoupledEqSpeciesAction.md].
+
+!syntax parameters /ReactionNetwork/SolidKineticReactions/AddCoupledSolidKinSpeciesAction
+
+!syntax inputs /ReactionNetwork/SolidKineticReactions/AddCoupledSolidKinSpeciesAction
+
+!syntax children /ReactionNetwork/SolidKineticReactions/AddCoupledSolidKinSpeciesAction

modules/chemical_reactions/doc/content/source/actions/AddPrimarySpeciesAction.md

@@ -1 +1,18 @@
-!template load file=stubs/moose_action.md.template name=AddPrimarySpeciesAction syntax=/ReactionNetwork/AqueousEquilibriumReactions/AddPrimarySpeciesAction
+# AddPrimarySpeciesAction
+
+!syntax description /ReactionNetwork/AqueousEquilibriumReactions/AddPrimarySpeciesAction
+
+All the variables are created with the same finite element family and order, and with the same nonlinear variable
+scaling.
+
+!syntax parameters /ReactionNetwork/AqueousEquilibriumReactions/AddPrimarySpeciesAction
+
+## Inputs for aqueous equilibrium reactions
+
+!syntax inputs /ReactionNetwork/AqueousEquilibriumReactions/AddPrimarySpeciesAction
+
+## Inputs for solid kinetics reactions
+
+!syntax inputs /ReactionNetwork/SolidKineticReactions/AddPrimarySpeciesAction
+
+!syntax children /ReactionNetwork/AqueousEquilibriumReactions/AddPrimarySpeciesAction

modules/chemical_reactions/doc/content/source/actions/AddSecondarySpeciesAction.md

@@ -1 +1,18 @@
-!template load file=stubs/moose_action.md.template name=AddSecondarySpeciesAction syntax=/ReactionNetwork/AqueousEquilibriumReactions/AddSecondarySpeciesAction
+# AddSecondarySpeciesAction
+
+!syntax description /ReactionNetwork/AqueousEquilibriumReactions/AddSecondarySpeciesAction
+
+All the variables are created with the same finite element family and order, which are also
+shared by the primary variables created within the same syntax by the [AddPrimarySpeciesAction.md].
+
+!syntax parameters /ReactionNetwork/AqueousEquilibriumReactions/AddSecondarySpeciesAction
+
+## Inputs for aqueous equilibrium reactions
+
+!syntax inputs /ReactionNetwork/AqueousEquilibriumReactions/AddSecondarySpeciesAction
+
+## Inputs for solid kinetics reactions
+
+!syntax inputs /ReactionNetwork/SolidKineticReactions/AddSecondarySpeciesAction
+
+!syntax children /ReactionNetwork/AqueousEquilibriumReactions/AddSecondarySpeciesAction

modules/chemical_reactions/doc/content/source/kernels/DesorptionFromMatrix.md

@@ -1 +1,20 @@
-!template load file=stubs/moose_object.md.template name=DesorptionFromMatrix syntax=/Kernels/DesorptionFromMatrix
+# DesorptionFromMatrix
+
+!syntax description /Kernels/DesorptionFromMatrix
+
+The weak form for this term is:
+
+!equation
+(\dot{m}, \psi)
+
+where $\dot{m}$ is the mass rate from the matrix to the porespace and $\psi$ the test function.
+The mass rates used in the kernel are retrieved directly from material properties, with the property name
+following the same convention as [LangmuirMaterial.md] and [MollifiedLangmuirMaterial.md], e.g. "mass_rate_from_matrix"
+for the mass rate, and "dmass_rate_from_matrix_dC" / "dmass_rate_from_matrix_dp" for its derivatives with regards to the
+nonlinear variables, concentration and pore pressure.
+
+!syntax parameters /Kernels/DesorptionFromMatrix
+
+!syntax inputs /Kernels/DesorptionFromMatrix
+
+!syntax children /Kernels/DesorptionFromMatrix

modules/chemical_reactions/doc/content/source/kernels/DesorptionToPorespace.md

@@ -1 +1,20 @@
-!template load file=stubs/moose_object.md.template name=DesorptionToPorespace syntax=/Kernels/DesorptionToPorespace
+# DesorptionToPorespace
+
+!syntax description /Kernels/DesorptionToPorespace
+
+The weak form for this term is:
+
+!equation
+(-\dot{m}, \psi)
+
+where $\dot{m}$ is the mass rate from the matrix to the porespace and $\psi$ the test function.
+The mass rates used in the kernel are retrieved directly from material properties, with the property name
+following the same convention as [LangmuirMaterial.md] and [MollifiedLangmuirMaterial.md], e.g. "mass_rate_from_matrix"
+for the mass rate, and "dmass_rate_from_matrix_dC" / "dmass_rate_from_matrix_dp" for its derivatives with regards to the
+nonlinear variables, concentration and pore pressure.
+
+!syntax parameters /Kernels/DesorptionToPorespace
+
+!syntax inputs /Kernels/DesorptionToPorespace
+
+!syntax children /Kernels/DesorptionToPorespace

modules/chemical_reactions/doc/content/source/materials/LangmuirMaterial.md

@@ -1 +1,26 @@
-!template load file=stubs/moose_object.md.template name=LangmuirMaterial syntax=/Materials/LangmuirMaterial
+# LangmuirMaterial
+
+!syntax description /Materials/LangmuirMaterial
+
+This material computes the mass rates from the matrix to the porespace, as well as the derivatives
+of the mass rates with regards to the gas species and with regards to the pressure.
+
+If the concentration is above the equilibrium concentration, desorption occurs and the mass rate is
+equal to
+
+!equation
+\dot{m}_{m\rightarrow p} = \dfrac{C-C_{eq}}{K_d} 
+
+else adsorption is happening and:
+
+!equation
+\dot{m}_{m\rightarrow p} = \dfrac{C-C_{eq}}{K_a} 
+
+where $m_{m\rightarrow p}$ is the mass rate from the matrix to the porespace, $C$ the species concentration, $C_{eq}$ the
+equilibrium concentration and $K_d$ / $K_a$ are the desorption and adsorption time constants (in seconds).
+
+!syntax parameters /Materials/LangmuirMaterial
+
+!syntax inputs /Materials/LangmuirMaterial
+
+!syntax children /Materials/LangmuirMaterial

modules/chemical_reactions/doc/content/source/materials/MollifiedLangmuirMaterial.md

@@ -1 +1,30 @@
-!template load file=stubs/moose_object.md.template name=MollifiedLangmuirMaterial syntax=/Materials/MollifiedLangmuirMaterial
+# MollifiedLangmuirMaterial
+
+!syntax description /Materials/MollifiedLangmuirMaterial
+
+This material computes the mollified mass rates from the matrix to the porespace, as well as the derivatives
+of the mollified mass rates with regards to the gas species and with regards to the pressure.
+
+If the concentration is above the equilibrium concentration, desorption occurs and the mass rate is
+equal to
+
+!equation
+\dot{m}_{m\rightarrow p} = A_{mol} * \dfrac{C-C_{eq}}{K_d} 
+
+else adsorption is happening and:
+
+!equation
+\dot{m}_{m\rightarrow p} = A_{mol} * \dfrac{C-C_{eq}}{K_a} 
+
+where $m_{m\rightarrow p}$ is the mass rate from the matrix to the porespace, $C$ the species concentration, $C_{eq}$ the
+equilibrium concentration and $K_d$ / $K_a$ are the desorption and adsorption time constants (in seconds). The mollifier term
+$A_{mol}$ is equal to
+
+!equation
+A_{mol} = tanh(\dfrac{C - C_{eq}}{ \text{mollifier} * \text{Langmuir density}})
+
+!syntax parameters /Materials/MollifiedLangmuirMaterial
+
+!syntax inputs /Materials/MollifiedLangmuirMaterial
+
+!syntax children /Materials/MollifiedLangmuirMaterial

modules/chemical_reactions/doc/content/syntax/ReactionNetwork/AqueousEquilibriumReactions/index.md

@@ -1 +1,15 @@
-!template load file=stubs/moose_system.md.template name=AqueousEquilibriumReactions syntax=/ReactionNetwork/AqueousEquilibriumReactions
+# AqueousEquilibriumReactions syntax
+
+This syntax, nesting parameters in the `[ReactionNetwork/AqueousEquilibriumReactions]` block, is used to describe aqueous equilibrium chemical reactions.
+The following actions use the parameters defined in this syntax:
+
+- [AddCoupledEqSpeciesAction.md] to define the kernels and auxiliary kernels for the equations describing the chemical reactions.
+- [AddPrimarySpeciesAction.md] to define the nonlinear variables for the primary species.
+- [AddSecondarySpeciesAction.md] to define the auxiliary variables for the secondary species.
+
+!syntax list /ReactionNetwork/AqueousEquilibriumReactions objects=True actions=False subsystems=False
+
+!syntax list /ReactionNetwork/AqueousEquilibriumReactions objects=False actions=False subsystems=True
+
+!syntax list /ReactionNetwork/AqueousEquilibriumReactions objects=False actions=True subsystems=False
+

modules/chemical_reactions/doc/content/syntax/ReactionNetwork/SolidKineticReactions/index.md

@@ -1 +1,14 @@
-!template load file=stubs/moose_system.md.template name=SolidKineticReactions syntax=/ReactionNetwork/SolidKineticReactions
+# SolidKineticReactions syntax
+
+This syntax, nesting parameters in the `[ReactionNetwork/SolidKineticReactions]` block, is used to describe solid kinetic reactions.
+The following actions use the parameters defined in this syntax:
+
+- [AddCoupledSolidKinSpeciesAction.md] to define the kernels and auxiliary kernels for the equations describing the chemical reactions.
+- [AddPrimarySpeciesAction.md] to define the nonlinear variables for the primary species.
+- [AddSecondarySpeciesAction.md] to define the auxiliary variables for the secondary species.
+
+!syntax list /ReactionNetwork/SolidKineticReactions objects=True actions=False subsystems=False
+
+!syntax list /ReactionNetwork/SolidKineticReactions objects=False actions=False subsystems=True
+
+!syntax list /ReactionNetwork/SolidKineticReactions objects=False actions=True subsystems=False

modules/chemical_reactions/doc/content/syntax/ReactionNetwork/index.md

@@ -1 +1,11 @@
-!template load file=stubs/moose_system.md.template name=ReactionNetwork syntax=/ReactionNetwork
+# ReactionNetwork syntax
+
+The `ReactionNetwork` parent block syntax is shared by the [aqueous equilibrium reactions](AqueousEquilibriumReactions/index.md)
+and [solid kinetics reactions](SolidKineticReactions/index.md) syntaxes. Both are nested under their respective sub-block, and can be
+defined simultaneously.
+
+!syntax list /ReactionNetwork objects=True actions=False subsystems=False
+
+!syntax list /ReactionNetwork objects=False actions=False subsystems=True
+
+!syntax list /ReactionNetwork objects=False actions=True subsystems=False

modules/contact/doc/content/source/postprocessors/NumAugmentedLagrangeIterations.md

@@ -0,0 +1,13 @@
+# NumAugmentedLagrangeIterations
+
+!syntax description /Postprocessors/NumAugmentedLagrangeIterations
+
+Defaults to 0 if the problem is not an [AugmentedLagrangianContactProblem.md].
+The reader is referred to the [AugmentedLagrangianContactProblem.md] for more explanation
+on the augmented Lagrangian iteration.
+
+!syntax parameters /Postprocessors/NumAugmentedLagrangeIterations
+
+!syntax inputs /Postprocessors/NumAugmentedLagrangeIterations
+
+!syntax children /Postprocessors/NumAugmentedLagrangeIterations

modules/navier_stokes/doc/content/source/bcs/INSFEFluidEnergyBC.md

@@ -1,20 +1,25 @@
 # INSFEFluidEnergyBC
 
-!alert construction title=Undocumented Class
-The INSFEFluidEnergyBC 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/INSFEFluidEnergyBC
 
-## Overview
-
-!! Replace these lines with information regarding the INSFEFluidEnergyBC object.
+This boundary condition can be used for porous media flow using the [!param](/BCs/INSFEFluidEnergyBC/porosity) parameter
+to define the porosity.
 
-## Example Input File Syntax
+## Overview
 
-!! Describe and include an example of how to use the INSFEFluidEnergyBC object.
+This boundary condition can be used for porous media flow using the [!param](/BCs/INSFEFluidEnergyBC/porosity_elem) parameter
+to define the porosity.
+
+If the [!param](/BCs/INSFEFluidEnergyBC/v_fn) parameter is specified, it is used to compute the boundary fluid
+velocity. If not, the domain velocity variables are used.
+This kind of setup makes this boundary condition flexible to handle both specified velocity and specified pressure (thus velocity is part of the solutions) situations.
+This boundary condition is reversible. If the velocity is outgoing from the boundary,
+then the temperature considered for the heat flux is computed using the [!param](/BCs/INSFEFluidEnergyBC/temperature)
+parameter variable.
+If the velocity is such that the fluid enters the boundary, the fluid temperature is computed using the
+[!param](/BCs/INSFEFluidEnergyBC/T_fn) parameter function, or the [!param](/BCs/INSFEFluidEnergyBC/T_branch)
+parameter scalar variable, depending on which is specified.
+The use of scalar variables is intended for coupling with thermal hydraulics components (in SAM).
 
 !syntax parameters /BCs/INSFEFluidEnergyBC
 

modules/navier_stokes/doc/content/source/bcs/INSFEFluidEnergyDirichletBC.md

@@ -1,20 +1,20 @@
 # INSFEFluidEnergyDirichletBC
 
-!alert construction title=Undocumented Class
-The INSFEFluidEnergyDirichletBC 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/INSFEFluidEnergyDirichletBC
 
 ## Overview
 
-!! Replace these lines with information regarding the INSFEFluidEnergyDirichletBC object.
-
-## Example Input File Syntax
-
-!! Describe and include an example of how to use the INSFEFluidEnergyDirichletBC object.
+If the [!param](/BCs/INSFEFluidEnergyBC/v_fn) parameter is specified, it is used to compute the boundary fluid
+velocity. If not, the domain velocity variables are used. The velocity is used to determine whether the boundary is
+an inlet.
+
+This boundary condition provides a `conditional' Dirichlet temperature boundary condition for the energy equation, given that no integration by parts is applied to the energy advection term.
+Without applying integration by parts to the advection term, the energy equation needs a Dirichlet temperature boundary condition for an inlet condition.
+This object additionally introduces a natural boundary condition at outlets.
+This conditional Dirichlet boundary condition relies on its `shouldApply()' function to determine if it should be applied.
+The fluid temperature is computed using the
+[!param](/BCs/INSFEFluidEnergyDirichletBC/T_fn) parameter function, or the [!param](/BCs/INSFEFluidEnergyDirichletBC/T_scalar)
+parameter scalar variable, depending on which is specified. The use of scalar variables is intended for coupling with thermal hydraulics components (in SAM).
 
 !syntax parameters /BCs/INSFEFluidEnergyDirichletBC
 

modules/navier_stokes/doc/content/source/bcs/INSFEFluidMassBC.md

@@ -1,20 +1,21 @@
 # INSFEFluidMassBC
 
-!alert construction title=Undocumented Class
-The INSFEFluidMassBC 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/INSFEFluidMassBC
 
+This boundary condition can be used for porous media flow using the [!param](/BCs/INSFEFluidEnergyBC/porosity) parameter
+to define the porosity.
+This boundary condition can describe both an inlet and an outlet.
+
 ## Overview
 
-!! Replace these lines with information regarding the INSFEFluidMassBC object.
+If either the [!param](/BCs/INSFEFluidMassBC/v_fn) or [!param](/BCs/INSFEFluidMassBC/v_pps) parameters are specified, they are used to compute the boundary fluid velocity. If not, the domain velocity variables are used.
+The mass flux is computed as
 
-## Example Input File Syntax
+!equation
+\rho v_{bc}
 
-!! Describe and include an example of how to use the INSFEFluidMassBC object.
+where $\rho$ is the local fluid density and $v_{bc}$ is the boundary fluid velocity. The mass flux times the test
+function is the contribution of this boundary condition to the residual.
 
 !syntax parameters /BCs/INSFEFluidMassBC