Updating docstring for new objects and cleaning up mms test input files

closes #257

include/bcs/DielectricBCWithEffEfield.h

@@ -1,8 +1,9 @@
-//* This file is part of the MOOSE framework
-//* https://www.mooseframework.org
+//* This file is part of Zapdos, an open-source
+//* application for the simulation of plasmas
+//* https://github.com/shannon-lab/zapdos
 //*
-//* All rights reserved, see COPYRIGHT for full restrictions
-//* https://github.com/idaholab/moose/blob/master/COPYRIGHT
+//* Zapdos is powered by the MOOSE Framework
+//* https://www.mooseframework.org
 //*
 //* Licensed under LGPL 2.1, please see LICENSE for details
 //* https://www.gnu.org/licenses/lgpl-2.1.html
@@ -12,8 +13,7 @@
 #include "ADIntegratedBC.h"
 
 /**
- * Implements a simple constant Neumann BC where grad(u)=value on the boundary.
- * Uses the term produced from integrating the diffusion operator by parts.
+ *  Time integrated dielectric boundary condition
  */
 class DielectricBCWithEffEfield : public ADIntegratedBC
 {
@@ -25,51 +25,90 @@ class DielectricBCWithEffEfield : public ADIntegratedBC
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// Scaling units for the position
   Real _r_units;
 
+  /// Variable value during previous time step
   const VariableValue & _u_old;
+  /// Gradient of variable during previous time step
   const VariableGradient & _grad_u_old;
 
+  /// Electron mean energy density value
   const ADVariableValue & _mean_en;
+  /// Electron mean energy density variable
   MooseVariable & _mean_en_var;
+  /// Electron mean energy density value during previous time step 
   const VariableValue & _mean_en_old;
+  /// Electron density value
   const ADVariableValue & _em;
+  /// Electron density variable
   MooseVariable & _em_var;
+  /// Electron density value during previous time step 
   const VariableValue & _em_old;
+  /// Ion density value
   const ADVariableValue & _ip;
+  /// Ion density variable
   MooseVariable & _ip_var;
+  /// Ion density value during previous time step 
   const VariableValue & _ip_old;
 
+  /// x-component of the electric field value
   const ADVariableValue & _Ex;
+  /// x-component of the electric field variable
   MooseVariable & _Ex_var;
+  /// x-component of the electric field value during previous time step
   const VariableValue & _Ex_old;
+  /// y-component of the electric field value
   const ADVariableValue & _Ey;
+  /// y-component of the electric field variable
   MooseVariable & _Ey_var;
+  /// y-component of the electric field value during previous time step
   const VariableValue & _Ey_old;
+  /// z-component of the electric field value
   const ADVariableValue & _Ez;
+  /// z-component of the electric field variable
   MooseVariable & _Ez_var;
+  /// z-component of the electric field value during previous time step
   const VariableValue & _Ez_old;
 
+  /// Elementary charge
   const MaterialProperty<Real> & _e;
+  /// Permittivity of free space
   const ADMaterialProperty<Real> & _epsilon_0;
+  /// Avogadro's number
   const MaterialProperty<Real> & _N_A;
 
+  /// Charge sign of the ions
   const MaterialProperty<Real> & _sgnip;
+  /// Mobility coefficient of the ions
   const ADMaterialProperty<Real> & _muip;
+  /// Mass of electrons
   const MaterialProperty<Real> & _massem;
+  /// Secondary electron coefficient
   Real _user_se_coeff;
 
+  /// Permittivity of the dielectric
   const Real & _epsilon_d;
+  /// Thickness of the dielectric
   const Real & _thickness;
+  /// Equal to 1 when the drift velocity is direct towards the wall and zero otherwise
   Real _a;
+  /// Value of "_a" during previous time step
   Real _a_old;
+  /// Value of ion flux
   ADRealVectorValue _ion_flux;
+  /// Value of ion flux during previous time step
   ADRealVectorValue _ion_flux_old;
+  /// Electron thermal velocity
   ADReal _v_thermal;
+  /// Value of electron thermal velocity during previous time step
   Real _v_thermal_old;
+  /// Electron flux
   ADRealVectorValue _em_flux;
+  /// Value of electron flux during previous time step
   ADRealVectorValue _em_flux_old;
+  /// Scaling units for the potential (V or kV)
   std::string _potential_units;
-
+  /// Scaling value for the potential
   Real _voltage_scaling;
 };

include/bcs/SakiyamaEnergySecondaryElectronWithEffEfieldBC.h

@@ -12,6 +12,10 @@
 
 #include "ADIntegratedBC.h"
 
+/**
+ *  Kinetic secondary electron for mean electron energy boundary condition 
+ *  with an effective electric field for ions
+ */
 class SakiyamaEnergySecondaryElectronWithEffEfieldBC : public ADIntegratedBC
 {
 public:
@@ -22,28 +26,36 @@ class SakiyamaEnergySecondaryElectronWithEffEfieldBC : public ADIntegratedBC
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// Scaling units for the position
   Real _r_units;
+  /// If true, secondary electron energy is equal to electron energy
   bool Te_dependent;
-
-  // Coupled variables
+  /// x-component of the electric field
   const ADVariableValue & _Ex;
+  /// y-component of the electric field
   const ADVariableValue & _Ey;
+  /// z-component of the electric field
   const ADVariableValue & _Ez;
-
+  /// Electron density
   const ADVariableValue & _em;
+  /// Ion density variables
   std::vector<MooseVariable *> _ip_var;
+  /// Ion density values
   std::vector<const ADVariableValue *> _ip;
-
+  /// Charge sign of the ions
   std::vector<const MaterialProperty<Real> *> _sgnip;
+  /// Mobility coefficient of the ions
   std::vector<const ADMaterialProperty<Real> *> _muip;
+  /// Secondary electron coefficient
   Real _se_coeff;
+  /// Custom secondary electron energy
   Real _user_se_energy;
-
+  /// Equal to 1 when the drift velocity is direct towards the wall and zero otherwise
   Real _a;
+  /// Term for secondary electron energy
   ADReal _se_energy;
+  /// Ion flux
   ADRealVectorValue _ion_flux;
-
+  /// Number of ions defined
   unsigned int _num_ions;
-  unsigned int _ip_index;
-  std::vector<unsigned int>::iterator _iter;
 };

include/bcs/SakiyamaIonAdvectionWithEffEfieldBC.h

@@ -12,6 +12,10 @@
 
 #include "ADIntegratedBC.h"
 
+/**
+ *  Kinetic advective ion boundary condition
+ *  with an effective electric field for ions
+ */
 class SakiyamaIonAdvectionWithEffEfieldBC : public ADIntegratedBC
 {
 public:
@@ -22,16 +26,18 @@ class SakiyamaIonAdvectionWithEffEfieldBC : public ADIntegratedBC
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// Scaling units for the position
   Real _r_units;
-
-  // Coupled variables
-
+  /// x-component of the electric field
   const ADVariableValue & _Ex;
+  /// y-component of the electric field
   const ADVariableValue & _Ey;
+  /// z-component of the electric field
   const ADVariableValue & _Ez;
-
+  /// Mobility coefficient
   const ADMaterialProperty<Real> & _mu;
+  /// Charge sign of the species
   const MaterialProperty<Real> & _sgn;
-
+  /// Equal to 1 when the drift velocity is direct towards the wall and zero otherwise
   Real _a;
 };

include/bcs/SakiyamaSecondaryElectronWithEffEfieldBC.h

@@ -12,6 +12,10 @@
 
 #include "ADIntegratedBC.h"
 
+/**
+ *  Kinetic secondary electron boundary condition
+ *  with an effective electric field for ions
+ */
 class SakiyamaSecondaryElectronWithEffEfieldBC : public ADIntegratedBC
 {
 public:
@@ -22,21 +26,26 @@ class SakiyamaSecondaryElectronWithEffEfieldBC : public ADIntegratedBC
 protected:
   virtual ADReal computeQpResidual() override;
 
+  /// Scaling units for the position
   Real _r_units;
-
-  // Coupled variables
-
+  /// x-component of the electric field
   const ADVariableValue & _Ex;
+  /// y-component of the electric field
   const ADVariableValue & _Ey;
+  /// z-component of the electric field
   const ADVariableValue & _Ez;
+  /// Ion density values
   std::vector<const ADVariableValue *> _ip;
-
+  /// Equal to 1 when the drift velocity is direct towards the wall and zero otherwise
   Real _a;
+  /// Ion flux
   ADRealVectorValue _ion_flux;
+  /// Secondary electron coefficient
   Real _user_se_coeff;
-
+   /// Charge sign of the ions
   std::vector<const MaterialProperty<Real> *> _sgnip;
+  /// Mobility coefficient of the ions
   std::vector<const ADMaterialProperty<Real> *> _muip;
-
+  /// Number of ions defined
   unsigned int _num_ions;
 };

include/kernels/EffectiveEField.h

@@ -12,6 +12,9 @@
 
 #include "ADKernel.h"
 
+/**
+ *  Supplies the source term of the time derivative calculation of the effective electric field for ions
+ */
 class EffectiveEField : public ADKernel
 {
 public:
@@ -20,15 +23,15 @@ class EffectiveEField : public ADKernel
   EffectiveEField(const InputParameters & parameters);
 
 protected:
-  // virtual ADRealVectorValue precomputeQpResidual() override;
   virtual ADReal computeQpResidual();
 
-  //  // using ADKernelGrad::getPostprocessorValue;
-
 private:
   /// Position units
   const Real _r_units;
+  /// Momentum-transfer frequency of ions
   const Real _nu;
+  /// Component of the electric field
   unsigned _component;
+  /// Electric field provided as a material property
   const ADMaterialProperty<RealVectorValue> & _electric_field;
 };

include/kernels/EffectiveEFieldAdvection.h

@@ -12,6 +12,10 @@
 
 #include "ADKernel.h"
 
+/*
+ *  Effective electric field driven advection term. The effective electric 
+ *  field is supplied as scalar components of the field
+ */
 class EffectiveEFieldAdvection : public ADKernel
 {
 public:
@@ -20,20 +24,20 @@ class EffectiveEFieldAdvection : public ADKernel
   EffectiveEFieldAdvection(const InputParameters & parameters);
 
 protected:
-  // virtual ADRealVectorValue precomputeQpResidual() override;
   virtual ADReal computeQpResidual();
 
-  //  // using ADKernelGrad::getPostprocessorValue;
-
 private:
   /// Position units
   const Real _r_units;
 
-  /// The diffusion coefficient (either constant or mixture-averaged)
+  /// Mobility coefficient
   const ADMaterialProperty<Real> & _mu;
+  /// Charge sign of the species
   const MaterialProperty<Real> & _sign;
-
+  /// x-component of the electric field
   const ADVariableValue & _u_Efield;
+  /// y-component of the electric field
   const ADVariableValue & _v_Efield;
+  /// z-component of the electric field
   const ADVariableValue & _w_Efield;
 };

include/kernels/ThermalConductivityDiffusion.h

@@ -12,6 +12,11 @@
 
 #include "ADKernel.h"
 
+/**
+ *  Electron energy diffusion term
+ *  that assumes a thermal conductivity of
+ *  K = 3/2 D_e n_e
+ */
 class ThermalConductivityDiffusion : public ADKernel
 {
 public:
@@ -23,11 +28,15 @@ class ThermalConductivityDiffusion : public ADKernel
   virtual ADReal computeQpResidual() override;
 
 private:
+
+  /// Position units
   Real _r_units;
+  /// Coefficient relating diffusion coefficient * density to thermal conductivity
   Real _coeff;
-
+  /// Diffusion coefficient
   const ADMaterialProperty<Real> & _diffem;
-
+  /// Electron density
   const ADVariableValue & _em;
+  /// Gradient of electron density
   const ADVariableGradient & _grad_em;
 };