Merge pull request #225 from csdechant/website-update

Website Update - AuxKernels

doc/content/source/auxkernels/AbsValueAux.md

@@ -1,20 +1,17 @@
 # AbsValueAux
 
-!alert construction title=Undocumented Class
-The AbsValueAux 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 /AuxKernels/AbsValueAux
 
 ## Overview
 
-!! Replace these lines with information regarding the AbsValueAux object.
+`AbsValueAux` returns the absolute value a coupled variable.
 
 ## Example Input File Syntax
 
-!! Describe and include an example of how to use the AbsValueAux object.
+An example of how to use `AbsValueAux` can be found in the
+test file `TM_steady.i`.
+
+!listing test/tests/TM10_circular_wg/TM_steady.i block=AuxKernels/Hphi_mag
 
 !syntax parameters /AuxKernels/AbsValueAux
 

doc/content/source/auxkernels/Current.md

@@ -1,20 +1,40 @@
 # Current
 
-!alert construction title=Undocumented Class
-The Current 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 /AuxKernels/Current
 
 ## Overview
 
-!! Replace these lines with information regarding the Current object.
+`Current` returns the electric current density of a species in logarithmic form. `Current`
+assumes the electrostatic approximation for the electric field.
+
+The electrostatic current density is defined as
+
+\begin{equation}
+J_{j} = q_{j} (\text{sign}_{j} \mu_{j} \left( \text{-} \nabla V\right) n_{j} - D_{j} \nabla (n_{j}))
+\end{equation}
+
+Where $J_{j}$ is the current density, $q_{j}$ is the charge of the species, $\text{sign}_{j}$ indicates the advection behavior ($\text{+}1$ for positively charged species and $\text{-}1$ for negatively charged species), $\mu_{j}$ is the mobility coefficient, $V$ is the potential, $n_{j}$ is the density, and $D_{j}$ is the diffusion coefficient. When converting the density to logarithmic form and applying a scaling factor of the mesh, `Current` is defined as
+
+\begin{equation}
+J_{j} = q_{j} N_{A} \left(\text{sign}_{j} \mu_{j} \frac{\text{-} \nabla (V)}{l_{c}} \exp(N_{j}) - D_{j} \exp(N_{j}) \frac{\nabla (N_{j})}{l_{c}} \right)
+\end{equation}
+
+Where $N_{j}$ is the molar density of the specie in logarithmic form, $N_{A}$ is Avogadro's number, $l_{c}$ is the scaling factor of the mesh.
+
+For the case of the where artificial diffusion is introduced to the charge specie flux, an additional term is included in the current density, such that:
+
+\begin{equation}
+J_{j,\text{ Total}} = J_{j} + q_{j} N_{A} \mu_{j} \frac{\text{-}\lVert \nabla (V) \rVert_{2}}{l_{c}} \frac{h_\text{max}}{2} \exp(N_{j}) \frac{\nabla (N_{j})}{l_{c}}
+\end{equation}
+
+Where $h_\text{max}$ is the max length of the current element.
 
 ## Example Input File Syntax
 
-!! Describe and include an example of how to use the Current object.
+An example of how to use `Current` can be found in the
+test file `Lymberopoulos_with_argon_metastables.i`.
+
+!listing test/tests/Lymberopoulos_rf_discharge/Lymberopoulos_with_argon_metastables.i block=AuxKernels/Current_em
 
 !syntax parameters /AuxKernels/Current
 

doc/content/source/auxkernels/DensityMoles.md

@@ -1,20 +1,23 @@
 # DensityMoles
 
-!alert construction title=Undocumented Class
-The DensityMoles 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 /AuxKernels/DensityMoles
 
 ## Overview
 
-!! Replace these lines with information regarding the DensityMoles object.
+`DensityMoles` converts the density value of a coupled species from a logarithmic molar density into units of #/m$^{3}$, such that:
+
+\begin{equation}
+n_{j} = N_{A} \exp(N_{j})
+\end{equation}
+
+Where $n_{j}$ is the density, $N_{j}$ is the molar density of the specie in logarithmic form, and $N_{A}$ is Avogadro's number. This is often needed due to Zapdos solving densities using a logarithmic molar formulation to help avoid negative densities and ill-conditioned matrices.
 
 ## Example Input File Syntax
 
-!! Describe and include an example of how to use the DensityMoles object.
+An example of how to use `DensityMoles` can be found in the
+test file `Lymberopoulos_with_argon_metastables.i`.
+
+!listing test/tests/Lymberopoulos_rf_discharge/Lymberopoulos_with_argon_metastables.i block=AuxKernels/em_lin
 
 !syntax parameters /AuxKernels/DensityMoles
 

doc/content/source/auxkernels/DensityNormalization.md

@@ -1,21 +1,40 @@
 # DensityNormalization
 
-!alert construction title=Undocumented Class
-The DensityNormalization 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 /AuxKernels/DensityNormalization
 
 ## Overview
 
-!! Replace these lines with information regarding the DensityNormalization object.
+`DensityNormalization` is similar to [`NormalizationAux`](/auxkernels/NormalizationAux.md), except it normalizes a variable in logarithmic form based on a Postprocessor value.
+
+The formulation of `DensityNormalization` is defined as
+
+\begin{equation}
+\frac{\exp(\text{variable})*\text{normal factor}}{\text{normalization}} - \text{shift}
+\end{equation}
+
+!alert warning title=Untested Class
+The DensityNormalization does not have a formalized test, yet. For this reason,
+users should be aware of unforeseen bugs when using DensityNormalization. To
+report a bug or discuss future contributions to Zapdos, please refer to the
+[Zapdos GitHub Discussions page](https://github.com/shannon-lab/zapdos/discussions).
+For standards of how to contribute to Zapdos and the MOOSE framework,
+please refer to the [MOOSE Contributing page](framework/contributing.md).
 
 ## Example Input File Syntax
 
 !! Describe and include an example of how to use the DensityNormalization object.
 
+```text
+[AuxKernels]
+  [Normalized_Electrons]
+    type = DensityNormalization
+    variable = norm_electrons
+    Density = electrons
+    normalization = max_electron
+  []
+[]
+```
+
 !syntax parameters /AuxKernels/DensityNormalization
 
 !syntax inputs /AuxKernels/DensityNormalization

doc/content/source/auxkernels/DiffusiveFlux.md

@@ -1,20 +1,34 @@
 # DiffusiveFlux
 
-!alert construction title=Undocumented Class
-The DiffusiveFlux 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 /AuxKernels/DiffusiveFlux
 
 ## Overview
 
-!! Replace these lines with information regarding the DiffusiveFlux object.
+`DiffusiveFlux` returns the diffusive flux of a species in logarithmic form.
+
+The diffusive flux is defined as
+
+\begin{equation}
+\Gamma_{\text{Diffusion}}  = \text{-}D_{j} \nabla (n_{j})
+\end{equation}
+
+Where $\Gamma_{\text{Diffusion}}$ is the diffusive flux, $D_{j}$ is the diffusion coefficient and $n_{j}$ is the density.
+When converting the density to logarithmic form and applying a scaling factor of the mesh,
+`DiffusiveFlux` is defined as
+
+\begin{equation}
+\Gamma_{\text{Diffusion}} = \text{-}D_{j} N_{A} \exp(N_{j}) \frac{\nabla (N_{j})}{l_{c}}
+\end{equation}
+
+Where $N_{j}$ is the molar density of the specie in logarithmic form, $N_{A}$ is Avogadro's
+number, $l_{c}$ is the scaling factor of the mesh.
 
 ## Example Input File Syntax
 
-!! Describe and include an example of how to use the DiffusiveFlux object.
+An example of how to use `DiffusiveFlux` can be found in the
+test file `mean_en.i`.
+
+!listing test/tests/1d_dc/mean_en.i block=AuxKernels/DiffusiveFlux_em
 
 !syntax parameters /AuxKernels/DiffusiveFlux
 

doc/content/source/auxkernels/DriftDiffusionFluxAux.md

@@ -1,21 +1,49 @@
 # DriftDiffusionFluxAux
 
-!alert construction title=Undocumented Class
-The DriftDiffusionFluxAux 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 /AuxKernels/DriftDiffusionFluxAux
 
 ## Overview
 
-!! Replace these lines with information regarding the DriftDiffusionFluxAux object.
+`DriftDiffusionFluxAux` returns the simplified drift-diffusion flux of a species. `DriftDiffusionFluxAux`
+assumes a mobility and diffusion coefficient of unity, the electrostatic approximation for the electric field, and a non-scaled version of the specie's density.
+
+The electrostatic flux is defined as
+
+\begin{equation}
+\Gamma_{j} =  \text{sign}_{j}  \left( \text{-}\nabla V\right) n_{j} - \nabla (n_{j})
+\end{equation}
+
+Where $\Gamma_{j}$ is the flux assuming drift-diffusion formulation, $\text{sign}_{j}$ indicates the advection behavior ($\text{+}1$ for positively charged species and $\text{-}1$ for negatively charged species),
+$V$ is the potential, and $n_{j}$ is the density.
+
+!alert note
+When calculating the drift-diffusion flux for scaled densities and non-unity coefficients, please refer to [`TotalFlux`](/auxkernels/TotalFlux.md).
+
+!alert warning title=Undocumented Test
+The DriftDiffusionFluxAux does not have a formalized test, yet. For this reason,
+users should be aware of unforeseen bugs when using DriftDiffusionFluxAux. To
+report bugs or discuss future contributions to Zapdos, please refer to the
+[Zapdos GitHub Discussions page](https://github.com/shannon-lab/zapdos/discussions).
+For standards of how to contribute to Zapdos and the MOOSE framework,
+please refer to the [MOOSE Contributing page](framework/contributing.md).
 
 ## Example Input File Syntax
 
 !! Describe and include an example of how to use the DriftDiffusionFluxAux object.
 
+```text
+[AuxKernels]
+  [Electron_Flux]
+    type = DriftDiffusionFluxAux
+    variable = electron_flux
+    u = electrons
+    potential =  potential
+    positive_charge = false
+    component = 0
+  []
+[]
+```
+
 !syntax parameters /AuxKernels/DriftDiffusionFluxAux
 
 !syntax inputs /AuxKernels/DriftDiffusionFluxAux

doc/content/source/auxkernels/EFieldAdvAux.md

@@ -1,20 +1,34 @@
 # EFieldAdvAux
 
-!alert construction title=Undocumented Class
-The EFieldAdvAux 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 /AuxKernels/EFieldAdvAux
 
 ## Overview
 
-!! Replace these lines with information regarding the EFieldAdvAux object.
+`EFieldAdvAux` returns electric field driven advective flux of defined species in logarithmic form. `EFieldAdvAux`
+assumes the electrostatic approximation for the electric field.
+
+The advective flux is defined as
+
+\begin{equation}
+\Gamma_{\text{Advection}}  = \text{sign}_{j} \mu_{j} \left( \text{-} \nabla V\right) n_{j}
+\end{equation}
+
+Where $\Gamma_{\text{Advection}}$ is the advective flux, $\text{sign}_{j}$ indicates the advection behavior ($\text{+}1$ for positively charged species and $\text{-}1$ for negatively charged species), $\mu_{j}$ is the mobility coefficient, $V$ is the potential, and $n_{j}$ is the density. When converting the density to logarithmic form and applying a scaling factor of the mesh,
+`EFieldAdvAux` is defined as
+
+\begin{equation}
+\Gamma_{\text{Advection}}  = N_{A} \text{sign}_{j} \mu_{j} \frac{\text{-} \nabla (V)}{l_{c}} \exp(N_{j})
+\end{equation}
+
+Where $N_{j}$ is the molar density of the specie in logarithmic form, $N_{A}$ is Avogadro's
+number, $l_{c}$ is the scaling factor of the mesh.
 
 ## Example Input File Syntax
 
-!! Describe and include an example of how to use the EFieldAdvAux object.
+An example of how to use `EFieldAdvAux` can be found in the
+test file `mean_en.i`.
+
+!listing test/tests/1d_dc/mean_en.i block=AuxKernels/EFieldAdvAux_em
 
 !syntax parameters /AuxKernels/EFieldAdvAux
 

doc/content/source/auxkernels/Efield.md

@@ -1,20 +1,26 @@
 # Efield
 
-!alert construction title=Undocumented Class
-The Efield 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 /AuxKernels/Efield
 
 ## Overview
 
-!! Replace these lines with information regarding the Efield object.
+`Efield` returns a component of the electrostatic electric field.
+
+The formulation of `Efield` is defined as
+
+\begin{equation}
+E_{\text{comp.}} = \frac{\text{-} \nabla_{\text{comp.}} (V) \ V_{c}}{l_{c}}
+\end{equation}
+
+Where $E_{\text{comp.}}$ is a component of the electric field, $V$ is the potential, $V_{c}$ is the
+scaling factor of the potential , and $l_{c}$ is the scaling factor of the mesh.
 
 ## Example Input File Syntax
 
-!! Describe and include an example of how to use the Efield object.
+An example of how to use `Efield` can be found in the
+test file `Lymberopoulos_with_argon_metastables.i`.
+
+!listing test/tests/Lymberopoulos_rf_discharge/Lymberopoulos_with_argon_metastables.i block=AuxKernels/Efield_calc
 
 !syntax parameters /AuxKernels/Efield
 

doc/content/source/auxkernels/ElectronTemperature.md

@@ -1,20 +1,35 @@
 # ElectronTemperature
 
-!alert construction title=Undocumented Class
-The ElectronTemperature 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 /AuxKernels/ElectronTemperature
 
 ## Overview
 
-!! Replace these lines with information regarding the ElectronTemperature object.
+`ElectronTemperature` returns the electron temperature.
+
+The electron temperature is defined as
+
+\begin{equation}
+T_{e} = \frac{2}{3} \frac{n_{\varepsilon}}{n_{e}}
+\end{equation}
+
+Where $T_{e}$ is the electron temperature, $n_{\varepsilon}$ is the mean energy density
+of the electrons, and $n_{e}$ is the electron density.
+When converting the density to logarithmic form,
+`ElectronTemperature` is defined as
+
+\begin{equation}
+T_{e} = \frac{2}{3} \exp(N_{\varepsilon} - N_{e})
+\end{equation}
+
+Where $N_{\varepsilon}$ is the electron mean energy density in logarithmic form
+and $N_{e}$ is the electron density in logarithmic form.
 
 ## Example Input File Syntax
 
-!! Describe and include an example of how to use the ElectronTemperature object.
+An example of how to use `ElectronTemperature` can be found in the
+test file `Lymberopoulos_with_argon_metastables.i`.
+
+!listing test/tests/Lymberopoulos_rf_discharge/Lymberopoulos_with_argon_metastables.i block=AuxKernels/Te
 
 !syntax parameters /AuxKernels/ElectronTemperature