Add missing source documentation for doxygen

Refs #21275
idaholab · Jan 15, 2024 · 57fc371 · 57fc371
1 parent c0b7fe4
commit 57fc371
Show file tree

Hide file tree

Showing 16 changed files with 113 additions and 26 deletions.
diff --git a/modules/porous_flow/doc/content/source/fvbcs/FVPorousFlowAdvectiveFluxBC.md b/modules/porous_flow/doc/content/source/fvbcs/FVPorousFlowAdvectiveFluxBC.md
@@ -2,7 +2,7 @@
 
 !syntax description /FVBCs/FVPorousFlowAdvectiveFluxBC
 
-This boundary condition implements the weak form of
+This boundary condition implements the strong form of
 \begin{equation*}
   -\nabla\cdot \sum_{\beta}\chi_{\beta}^{\kappa} \rho_{\beta}\frac{k\,k_{\mathrm{r,}\beta}}{\mu_{\beta}}(\nabla P_{\beta} - \rho_{\beta} \mathbf{g})
 \end{equation*}

diff --git a/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowAdvectiveFlux.md b/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowAdvectiveFlux.md
@@ -2,7 +2,7 @@
 
 !syntax description /FVKernels/FVPorousFlowAdvectiveFlux
 
-This `FVKernel` implements the weak form of
+This `FVKernel` implements the strong form of
 \begin{equation*}
   -\nabla\cdot \sum_{\beta}\chi_{\beta}^{\kappa} \rho_{\beta}\frac{k\,k_{\mathrm{r,}\beta}}{\mu_{\beta}}(\nabla P_{\beta} - \rho_{\beta} \mathbf{g})
 \end{equation*}

diff --git a/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowDispersiveFlux.md b/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowDispersiveFlux.md
@@ -2,7 +2,7 @@
 
 !syntax description /FVKernels/FVPorousFlowDispersiveFlux
 
-This `FVKernel` implements the weak form of
+This `FVKernel` implements the strong form of
 \begin{equation*}
   -\nabla\cdot \sum_{\beta}\rho_{\beta}{\mathcal{D}}_{\beta}^{\kappa}\nabla \chi_{\beta}^{\kappa}
 \end{equation*}

diff --git a/...es/porous_flow/doc/content/source/fvkernels/FVPorousFlowEnergyTimeDerivative.md b/...es/porous_flow/doc/content/source/fvkernels/FVPorousFlowEnergyTimeDerivative.md
@@ -2,7 +2,7 @@
 
 !syntax description /FVKernels/FVPorousFlowEnergyTimeDerivative
 
-This `FVKernel` implements the weak form of
+This `FVKernel` implements the strong form of
 \begin{equation*}
   \frac{\partial}{\partial t}\left((1-\phi)\rho_{R}C_{R}T + \phi\sum_{\beta}S_{\beta}\rho_{\beta}\mathcal{E}_{\beta}\right)
 \end{equation*}

diff --git a/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowHeatAdvection.md b/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowHeatAdvection.md
@@ -2,7 +2,7 @@
 
 !syntax description /FVKernels/FVPorousFlowHeatAdvection
 
-This `FVKernel` implements the weak form of
+This `FVKernel` implements the strong form of
 \begin{equation*}
   -\nabla\cdot \sum_{\beta}h_{\beta} \rho_{\beta}\frac{k\,k_{\mathrm{r,}\beta}}{\mu_{\beta}}(\nabla P_{\beta} - \rho_{\beta} \mathbf{g})
 \end{equation*}

diff --git a/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowHeatConduction.md b/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowHeatConduction.md
@@ -2,7 +2,7 @@
 
 !syntax description /FVKernels/FVPorousFlowHeatConduction
 
-This `FVKernel` implements the weak form of
+This `FVKernel` implements the strong form of
 \begin{equation*}
   -\nabla\cdot \left(\lambda \nabla T\right)
 \end{equation*}

diff --git a/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowMassTimeDerivative.md b/modules/porous_flow/doc/content/source/fvkernels/FVPorousFlowMassTimeDerivative.md
@@ -2,7 +2,7 @@
 
 !syntax description /FVKernels/FVPorousFlowMassTimeDerivative
 
-This `FVKernel` implements the weak form of
+This `FVKernel` implements the strong form of
 \begin{equation*}
   \frac{\partial}{\partial t}\left(\phi\sum_{\beta}S_{\beta}\rho_{\beta}\chi_{\beta}^{\kappa}\right)
 \end{equation*}

diff --git a/modules/porous_flow/include/fvbcs/FVPorousFlowAdvectiveFluxBC.h b/modules/porous_flow/include/fvbcs/FVPorousFlowAdvectiveFluxBC.h
@@ -13,6 +13,9 @@
 
 class PorousFlowDictator;
 
+/**
+ * Flux boundary condition where an advective flux is applied
+ */
 class FVPorousFlowAdvectiveFluxBC : public FVFluxBC
 {
 public:
@@ -22,29 +25,40 @@ class FVPorousFlowAdvectiveFluxBC : public FVFluxBC
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// UserObject that holds information (number of phases, components, etc)
   const PorousFlowDictator & _dictator;
+  /// Number of fluid phases present
   const unsigned int _num_phases;
+  /// Index of the fluid phase this BC applies to
   const unsigned int _phase;
+  /// Index of the fluid component this BC applies to
   const unsigned int _fluid_component;
 
+  /// Fluid density
   const ADMaterialProperty<std::vector<Real>> & _density;
   const ADMaterialProperty<std::vector<Real>> & _density_neighbor;
 
+  /// Fluid viscosity
   const ADMaterialProperty<std::vector<Real>> & _viscosity;
   const ADMaterialProperty<std::vector<Real>> & _viscosity_neighbor;
 
+  /// Relative permeability
   const ADMaterialProperty<std::vector<Real>> & _relperm;
   const ADMaterialProperty<std::vector<Real>> & _relperm_neighbor;
 
+  /// Mass fraction of fluid components in fluid phases
   const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions;
   const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions_neighbor;
 
+  /// Permeability
   const ADMaterialProperty<RealTensorValue> & _permeability;
   const ADMaterialProperty<RealTensorValue> & _permeability_neighbor;
 
+  /// Fluid pressure
   const ADMaterialProperty<std::vector<Real>> & _pressure;
   const ADMaterialProperty<std::vector<Real>> & _pressure_neighbor;
 
+  /// Gravity vector
   const RealVectorValue & _gravity;
 
   /// The porepressure value at the boundary

diff --git a/modules/porous_flow/include/fvkernels/FVPorousFlowAdvectiveFlux.h b/modules/porous_flow/include/fvkernels/FVPorousFlowAdvectiveFlux.h
@@ -13,6 +13,9 @@
 
 class PorousFlowDictator;
 
+/**
+ * Advective flux of fluid component k in fluid phase alpha
+ */
 class FVPorousFlowAdvectiveFlux : public FVFluxKernel
 {
 public:
@@ -22,28 +25,38 @@ class FVPorousFlowAdvectiveFlux : public FVFluxKernel
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// UserObject that holds information (number of phases, components, etc)
   const PorousFlowDictator & _dictator;
+  /// Number of fluid phases present
   const unsigned int _num_phases;
+  /// Index of the fluid component this kernel applies to
   const unsigned int _fluid_component;
 
+  /// Fluid density
   const ADMaterialProperty<std::vector<Real>> & _density;
   const ADMaterialProperty<std::vector<Real>> & _density_neighbor;
 
+  /// Fluid viscosity
   const ADMaterialProperty<std::vector<Real>> & _viscosity;
   const ADMaterialProperty<std::vector<Real>> & _viscosity_neighbor;
 
+  /// Relative permeability
   const ADMaterialProperty<std::vector<Real>> & _relperm;
   const ADMaterialProperty<std::vector<Real>> & _relperm_neighbor;
 
+  /// Mass fraction of fluid components in fluid phases
   const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions;
   const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions_neighbor;
 
+  /// Permeability
   const ADMaterialProperty<RealTensorValue> & _permeability;
   const ADMaterialProperty<RealTensorValue> & _permeability_neighbor;
 
+  /// Fluid pressure
   const ADMaterialProperty<std::vector<Real>> & _pressure;
   const ADMaterialProperty<std::vector<Real>> & _pressure_neighbor;
   const ADMaterialProperty<std::vector<RealGradient>> & _grad_p;
 
+  /// Gravity vector
   const RealVectorValue & _gravity;
 };
diff --git a/modules/porous_flow/include/fvkernels/FVPorousFlowDispersiveFlux.h b/modules/porous_flow/include/fvkernels/FVPorousFlowDispersiveFlux.h
@@ -14,6 +14,10 @@
 
 class PorousFlowDictator;
 
+/**
+ * Dispersive flux of component k in fluid phase alpha. Includes the effects
+ * of both molecular diffusion and hydrodynamic dispersion
+ */
 class FVPorousFlowDispersiveFlux : public FVFluxKernel
 {
 public:
@@ -23,30 +27,39 @@ class FVPorousFlowDispersiveFlux : public FVFluxKernel
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// UserObject that holds information (number of phases, components, etc)
   const PorousFlowDictator & _dictator;
+  /// Number of fluid phases present
   const unsigned int _num_phases;
+  /// Index of the fluid component this kernel applies to
   const unsigned int _fluid_component;
 
+  /// Fluid density
   const ADMaterialProperty<std::vector<Real>> & _density;
 
+  /// Fluid viscosity
   const ADMaterialProperty<std::vector<Real>> & _viscosity;
   const ADMaterialProperty<std::vector<Real>> & _viscosity_neighbor;
 
+  /// Relative permeability
   const ADMaterialProperty<std::vector<Real>> & _relperm;
   const ADMaterialProperty<std::vector<Real>> & _relperm_neighbor;
 
+  /// Mass fraction of fluid components in fluid phases
   const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions;
   const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions_neighbor;
   const ADMaterialProperty<std::vector<std::vector<RealGradient>>> & _grad_mass_frac;
 
+  /// Permeability
   const ADMaterialProperty<RealTensorValue> & _permeability;
   const ADMaterialProperty<RealTensorValue> & _permeability_neighbor;
 
+  /// Fluid pressure
   const ADMaterialProperty<std::vector<Real>> & _pressure;
   const ADMaterialProperty<std::vector<Real>> & _pressure_neighbor;
   const ADMaterialProperty<std::vector<RealGradient>> & _grad_p;
 
-  /// Porosity at the qps
+  /// Porosity
   const ADMaterialProperty<Real> & _porosity;
   const ADMaterialProperty<Real> & _porosity_neighbor;
 
@@ -58,6 +71,7 @@ class FVPorousFlowDispersiveFlux : public FVFluxKernel
   const MaterialProperty<std::vector<std::vector<Real>>> & _diffusion_coeff;
   const MaterialProperty<std::vector<std::vector<Real>>> & _diffusion_coeff_neighbor;
 
+  /// Gravity vector
   const RealVectorValue & _gravity;
   const ADRankTwoTensor _identity_tensor;
 

diff --git a/modules/porous_flow/include/fvkernels/FVPorousFlowEnergyTimeDerivative.h b/modules/porous_flow/include/fvkernels/FVPorousFlowEnergyTimeDerivative.h
@@ -12,6 +12,10 @@
 #include "FVTimeKernel.h"
 
 class PorousFlowDictator;
+
+/**
+ * Time derivative of energy
+ */
 class FVPorousFlowEnergyTimeDerivative : public FVTimeKernel
 {
 public:
@@ -21,18 +25,30 @@ class FVPorousFlowEnergyTimeDerivative : public FVTimeKernel
 protected:
   ADReal computeQpResidual() override;
 
+  /// UserObject that holds information (number of phases, components, etc)
   const PorousFlowDictator & _dictator;
+  /// Number of fluid phases
   const unsigned int _num_phases;
+  /// Whether fluid is present
   const bool _fluid_present;
 
+  /// Porosity
   const ADMaterialProperty<Real> & _porosity;
-  const ADMaterialProperty<std::vector<Real>> * const _density;
-  const ADMaterialProperty<Real> & _rock_energy;
-  const ADMaterialProperty<std::vector<Real>> * const _energy;
-  const ADMaterialProperty<std::vector<Real>> * const _saturation;
   const MaterialProperty<Real> & _porosity_old;
+
+  /// Fluid density
+  const ADMaterialProperty<std::vector<Real>> * const _density;
   const MaterialProperty<std::vector<Real>> * const _density_old;
+
+  /// Internal energy of porous matrix
+  const ADMaterialProperty<Real> & _rock_energy;
   const MaterialProperty<Real> & _rock_energy_old;
+
+  /// Internal energy of fluid
+  const ADMaterialProperty<std::vector<Real>> * const _energy;
   const MaterialProperty<std::vector<Real>> * const _energy_old;
+
+  /// Fluid phase saturation
+  const ADMaterialProperty<std::vector<Real>> * const _saturation;
   const MaterialProperty<std::vector<Real>> * const _saturation_old;
 };
diff --git a/modules/porous_flow/include/fvkernels/FVPorousFlowHeatAdvection.h b/modules/porous_flow/include/fvkernels/FVPorousFlowHeatAdvection.h
@@ -13,6 +13,9 @@
 
 class PorousFlowDictator;
 
+/**
+ * Advective flux of heat energy
+ */
 class FVPorousFlowHeatAdvection : public FVFluxKernel
 {
 public:
@@ -22,27 +25,36 @@ class FVPorousFlowHeatAdvection : public FVFluxKernel
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// UserObject that holds information (number of phases, components, etc)
   const PorousFlowDictator & _dictator;
+  /// Number of fluid phases present
   const unsigned int _num_phases;
 
+  /// Fluid density
   const ADMaterialProperty<std::vector<Real>> & _density;
   const ADMaterialProperty<std::vector<Real>> & _density_neighbor;
 
+  /// Fluid viscosity
   const ADMaterialProperty<std::vector<Real>> & _viscosity;
   const ADMaterialProperty<std::vector<Real>> & _viscosity_neighbor;
 
+  /// Fluid enthalpy
   const ADMaterialProperty<std::vector<Real>> & _enthalpy;
   const ADMaterialProperty<std::vector<Real>> & _enthalpy_neighbor;
 
+  /// Relative permeability
   const ADMaterialProperty<std::vector<Real>> & _relperm;
   const ADMaterialProperty<std::vector<Real>> & _relperm_neighbor;
 
+  /// Permeability
   const ADMaterialProperty<RealTensorValue> & _permeability;
   const ADMaterialProperty<RealTensorValue> & _permeability_neighbor;
 
+  /// Fluid pressure
   const ADMaterialProperty<std::vector<Real>> & _pressure;
   const ADMaterialProperty<std::vector<Real>> & _pressure_neighbor;
   const ADMaterialProperty<std::vector<RealGradient>> & _grad_p;
 
+  /// Gravity vector
   const RealVectorValue & _gravity;
 };
diff --git a/modules/porous_flow/include/fvkernels/FVPorousFlowHeatConduction.h b/modules/porous_flow/include/fvkernels/FVPorousFlowHeatConduction.h
@@ -13,6 +13,9 @@
 
 class PorousFlowDictator;
 
+/**
+ * Heat conduction kernel
+ */
 class FVPorousFlowHeatConduction : public FVFluxKernel
 {
 public:
@@ -22,6 +25,7 @@ class FVPorousFlowHeatConduction : public FVFluxKernel
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// UserObject that holds information (number of phases, components, etc)
   const PorousFlowDictator & _dictator;
 
   /// Thermal conductivity

diff --git a/modules/porous_flow/include/fvkernels/FVPorousFlowMassTimeDerivative.h b/modules/porous_flow/include/fvkernels/FVPorousFlowMassTimeDerivative.h
@@ -12,6 +12,10 @@
 #include "FVTimeKernel.h"
 
 class PorousFlowDictator;
+
+/**
+ * Time derivative of fluid mass
+ */
 class FVPorousFlowMassTimeDerivative : public FVTimeKernel
 {
 public:
@@ -21,16 +25,26 @@ class FVPorousFlowMassTimeDerivative : public FVTimeKernel
 protected:
   ADReal computeQpResidual() override;
 
+  /// UserObject that holds information (number of phases, components, etc)
   const PorousFlowDictator & _dictator;
+  /// Number of fluid phases present
   const unsigned int _num_phases;
+  /// Index of the fluid component this kernel applies to
   const unsigned int _fluid_component;
 
+  /// Porosity
   const ADMaterialProperty<Real> & _porosity;
-  const ADMaterialProperty<std::vector<Real>> & _density;
-  const ADMaterialProperty<std::vector<Real>> & _saturation;
-  const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions;
   const MaterialProperty<Real> & _porosity_old;
+
+  /// Fluid density
+  const ADMaterialProperty<std::vector<Real>> & _density;
   const MaterialProperty<std::vector<Real>> & _density_old;
+
+  /// Fluid phase saturation
+  const ADMaterialProperty<std::vector<Real>> & _saturation;
   const MaterialProperty<std::vector<Real>> & _saturation_old;
+
+  /// Mass fraction of fluid components in fluid phases
+  const ADMaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions;
   const MaterialProperty<std::vector<std::vector<Real>>> & _mass_fractions_old;
 };