Merge pull request #346 from dschwen/docs2_213

Add additional documentation

doc/content/source/mesh/MyTRIMMesh.md

@@ -1,15 +1,16 @@
-<!-- MOOSE Documentation Stub: Remove this when content is added. -->
-
 # MyTRIMMesh
 
-!alert construction title=Undocumented Class
-The MyTRIMMesh has not been documented, if you would like to contribute to MOOSE by
-writing documentation, please see [/generate.md]. The content contained on this page explains
-the typical 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 /Mesh/MyTRIMMesh
 
+Restricted regular orthogonal [GeneratedMesh](/GeneratedMesh.md) with equal size
+level 0 elements (no bias) and EDGE2, QUAD4, or HEX8 elements only. These
+restrictions allow the use of a custom super fast point locator to find elements
+based on spatial locations (required for fast material property lookup in the
+Binary Collision Monte Carlo stage). This mesh is also recommended for use with
+the [FourierTransform](/FourierTransform.md) user object.
+
+The use of adaptivity is fully supported.
+
 !syntax parameters /Mesh/MyTRIMMesh
 
 !syntax inputs /Mesh/MyTRIMMesh

doc/content/source/userobjects/MyTRIMRasterizer.md

@@ -7,62 +7,91 @@ provided by MooseVariables specified in parameter `var` to prepare a rasterized
 domain on which binary collision Monte Carlo is performed. Rasterization is the
 process of averaging smoothly varying compositional data over each FEM mesh element.
 
-The entries in of the `var`, `M`, and `Z` parameters are paired; we index them as $\gamma_j(\vec{r})$, $M_j$, and $Z_j$, respectively.
-Loosely speaking $\gamma_j(\vec{r})$ represents the number density of isotope $j$ at point $\vec{r}$, $M_j$ is the atomic mass, and
-$Z_j$ is the charge in units of $e$.
+The entries in of the `var`, `M`, and `Z` parameters are paired; we index them
+as $\gamma_j(\vec{r})$, $M_j$, and $Z_j$, respectively. Loosely speaking
+$\gamma_j(\vec{r})$ represents the number density of isotope $j$ at point
+$\vec{r}$, $M_j$ is the atomic mass, and $Z_j$ is the charge in units of $e$.
+
+The physical meaning of the `var` argument depends on what the user provides for
+the `site_volume` parameter. `site_volume` is a material property and can vary
+with space; it is denoted by $\Omega(\vec{r})$. MyTRIM computes the mass density
+$\rho$ of the material by:
 
-The physical meaning of the `var` argument depends on what the user provides for the
-`site_volume` parameter. `site_volume` is a material property and can vary with space;
-it is denoted by $\Omega(\vec{r})$. MyTRIM computes the mass density $\rho$ of the material by:
 \begin{equation}
   \rho = \sum\limits_{j=1}^J \frac{\gamma_j(\vec{r}) M_j}{N_A \Omega(\vec{r})},
 \end{equation}
-where $N_A$ is Avogadro's number. We identify $\gamma_j / \Omega$ as the number density $N_j$ defined
-as the number of atoms of species $j$ per unit volume. The following choices for $\Omega$ may be usage
-of the `site_volume` parameter:
 
-$\Omega = 1$: $\gamma_j = N_j$ so that the user should store number densities in the variables specified
-  in `var`.
+where $N_A$ is Avogadro's number. We identify $\gamma_j / \Omega$ as the number
+density $N_j$ defined as the number of atoms of species $j$ per unit volume. The
+following choices for $\Omega$ may be usage of the `site_volume` parameter:
+
+$\Omega = 1$: $\gamma_j = N_j$ so that the user should store number densities in
+the variables specified in `var`.
 
-$\Omega \equiv \text{compound volume, e.g. volume of UO}_2$: $\gamma_j$ should be the stoichiometric content of species $j$. Using the $\text{UO}_2$ example:
+$\Omega \equiv \text{compound volume, e.g. volume of UO}_2$: $\gamma_j$ should
+be the stoichiometric content of species $j$. Using the $\text{UO}_2$ example:
 $\gamma_U = 1$, $\gamma_O=2$.
 
-$\Omega \equiv \text{average volume per atoms, i.e. } \frac{\text{volume}}{\text{number of atoms}}$: $\gamma_j$ should be the number fraction. In this case $\sum\limits_{j=1}^J \gamma_j=1$.
+$\Omega \equiv \text{average volume per atoms, i.e. }
+\frac{\text{volume}}{\text{number of atoms}}$: $\gamma_j$ should be the number
+fraction. In this case $\sum\limits_{j=1}^J \gamma_j=1$.
 
 ## Computing the PKA list
 
-Before performing damage cascades, the rasterizer computes the number of primary knock-on atoms (PKA) $n_{\text{PKA,l, M, Z}$ for each mesh element $l$, mass $M$ and atomic number $Z$ by:
+Before performing damage cascades, the rasterizer computes the number of primary
+knock-on atoms (PKA) $n_{\text{PKA,l, M, Z}$ for each mesh element $l$, mass $M$
+and atomic number $Z$ by:
+
 \begin{equation}
  n_{\text{PKA},l,M,Z} = \Delta t \sum\limits_{k=1}^K  p_k(A,Z) \int\limits_{V_l} dV R_k(\vec{r}),
 \end{equation}
-where $\Delta t$ is the current time step, $k$ indexes the `PKAGenerator` objects provided in the `pka_generator` parameter, $p_k(M,Z)$ is the probability
-that `PKAGenerator` $k$ produces a PKA with mass $M$ and atomic number $Z$, and $R_k(\vec{r})$ is the recoil rate of `PKAGenerator` $k$ that may depend on space.
-$n_{\text{PKA},l,M,Z}$ is an integer number so it is rounded to the next higher value with a probability proportional to its truncated integer complement ($1.4$ would be $2$ with a probability of $0.4$, and $1$ with a probability of $0.6$).
-The total number of PKAs is given by $n_{\text{PKA}} = \sum\limits_{l,M,Z} n_{\text{PKA},l,M,Z}$.
+
+where $\Delta t$ is the current time step, $k$ indexes the `PKAGenerator`
+objects provided in the `pka_generator` parameter, $p_k(M,Z)$ is the probability
+that `PKAGenerator` $k$ produces a PKA with mass $M$ and atomic number $Z$, and
+$R_k(\vec{r})$ is the recoil rate of `PKAGenerator` $k$ that may depend on
+space. $n_{\text{PKA},l,M,Z}$ is an integer number so it is rounded to the next
+higher value with a probability proportional to its truncated integer complement
+($1.4$ would be $2$ with a probability of $0.4$, and $1$ with a probability of
+$0.6$). The total number of PKAs is given by $n_{\text{PKA}} =
+\sum\limits_{l,M,Z} n_{\text{PKA},l,M,Z}$.
 
 ## Scaling PKA rates
 
-The rasterizer provides two parameters for modifying the number of simulated PKAs without biasing the results. The parameter `max_pka_count`
-limits the number of PKAs roughly to the provided integer number denoted by $n$. If the number of computed PKAs is smaller than or equal to `max_pka_count`, the parameter is ignored. If the
-number of PKAs is larger than `max_pka_count`, PKAs are accepted with a probability of $n/n_{\text{PKA}}$. The actual number of PKAs is usually not identical to $n$ and is denoted by $n'$.
-Any tallied result is, e.g. vacancy or interstitial densities or energy deposition, are multiplied by $n_{\text{PKA}/n'$.
+The rasterizer provides two parameters for modifying the number of simulated
+PKAs without biasing the results. The parameter `max_pka_count` limits the
+number of PKAs roughly to the provided integer number denoted by $n$. If the
+number of computed PKAs is smaller than or equal to `max_pka_count`, the
+parameter is ignored. If the number of PKAs is larger than `max_pka_count`, PKAs
+are accepted with a probability of $n/n_{\text{PKA}}$. The actual number of PKAs
+is usually not identical to $n$ and is denoted by $n'$. Any tallied result is,
+e.g. vacancy or interstitial densities or energy deposition, are multiplied by
+$n_{\text{PKA}/n'$.
 
-The parameter `recoil_rate_scaling` is a real number that is multiplied to the recoil rate $R_k(\vec{r})$. All tallied results are divided by `recoil_rate_scaling`.
+The parameter `recoil_rate_scaling` is a real number that is multiplied to the
+recoil rate $R_k(\vec{r})$. All tallied results are divided by
+`recoil_rate_scaling`.
 
 ## Recombination
 
-A simple model for recombination *within* damage cascades is currently implemented. A vacancy-interstitial pair is annihilated if their distance
-is less than `r_rec`. Note that `r_rec` must be given in Angstrom. Recombination within damage cascades typically occurs within thermal spike areas
-where sufficient energy has been deposited to displace virtually all contained atoms. In thermal spike areas the atoms are effectively in a liquid state.
-Recrystallization takes place when energy has been dissipated from the thermal spike area and most Frenkel pairs annihilate. Surviving Frenkel pairs
-have usually been transported out of the melted zone through collision sequences along closely packed directions. The current recombination model
-does not accurately describe this physics.
+A simple model for recombination *within* damage cascades is currently
+implemented. A vacancy-interstitial pair is annihilated if their distance is
+less than `r_rec`. Note that `r_rec` must be given in Angstrom. Recombination
+within damage cascades typically occurs within thermal spike areas where
+sufficient energy has been deposited to displace virtually all contained atoms.
+In thermal spike areas the atoms are effectively in a liquid state.
+Recrystallization takes place when energy has been dissipated from the thermal
+spike area and most Frenkel pairs annihilate. Surviving Frenkel pairs have
+usually been transported out of the melted zone through collision sequences
+along closely packed directions. The current recombination model does not
+accurately describe this physics.
 
 ## Periodic variables
 
-If all variables in the `var` parameters are auxiliary variables, the rasterizer has to be made
-aware of periodic boundaries. The user needs to provide a nonlinear variable that the desired periodic
-variable apply to in the `periodic_var` parameter.
+If all variables in the `var` parameters are auxiliary variables, the rasterizer
+has to be made aware of periodic boundaries. The user needs to provide a
+nonlinear variable that the desired periodic variable apply to in the
+`periodic_var` parameter.
 
 !syntax parameters /UserObjects/MyTRIMRasterizer
 

doc/content/source/userobjects/PKAConstant.md

@@ -1,15 +1,10 @@
-<!-- MOOSE Documentation Stub: Remove this when content is added. -->
-
 # PKAConstant
 
-!alert construction title=Undocumented Class
-The PKAConstant has not been documented, if you would like to contribute to MOOSE by
-writing documentation, please see [/generate.md]. The content contained on this page explains
-the typical 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 /UserObjects/PKAConstant
 
+This generator will place PKAs uniformly in the domain with a random direction.
+The mass, charge, and energy are constants given by the user.
+
 !syntax parameters /UserObjects/PKAConstant
 
 !syntax inputs /UserObjects/PKAConstant

doc/content/source/userobjects/PKAFissionFragmentEmpirical.md

@@ -1,15 +1,10 @@
-<!-- MOOSE Documentation Stub: Remove this when content is added. -->
-
 # PKAFissionFragmentEmpirical
 
-!alert construction title=Undocumented Class
-The PKAFissionFragmentEmpirical has not been documented, if you would like to contribute to MOOSE by
-writing documentation, please see [/generate.md]. The content contained on this page explains
-the typical 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 /UserObjects/PKAFissionFragmentEmpirical
 
+Samples an empirical distribution using the MyTRIM MassInverter and EnergyInverter.
+These distributions are parameterized from `insert citation here`.
+
 !syntax parameters /UserObjects/PKAFissionFragmentEmpirical
 
 !syntax inputs /UserObjects/PKAFissionFragmentEmpirical

doc/content/source/userobjects/PKAFissionFragmentNeutronics.md

@@ -12,46 +12,63 @@ It is computed by:
 F_i(\vec{r}, \vec{\rho}) = \sum\limits_{g=1}^G N_i(\vec{r},\vec{\rho})\sigma_{f,g,i} \phi_g(\vec{r}),
 \end{equation}
 
-where $\vec{r}$ is the location in the macroscopic, neutronics domain and $\vec{\rho}$
-is the location in the microscopic domain. These two locations are separated because their
-scale is significantly separated by 3-4 orders of magnitude. Changes with $\vec{r}$ are
-understood to be smooth changes of the average composition of the microscopic domain (orders of centimeters), while changes with $\vec{\rho}$ captures compositional changes between grains on the microscopic domain, i.e. on the orders of micro-meters. The notation of separating the spatial dependence into two scales follows homogenization theory. $N_i$ is the number density of isotope $i$, $\sigma_{f,g,i}$ is the microscopic fission cross section of isotope $i$ in group $g$, and $\phi_g$ is the scalar flux in group $g$.
+where $\vec{r}$ is the location in the macroscopic, neutronics domain and
+$\vec{\rho}$ is the location in the microscopic domain. These two locations are
+separated because their scale is significantly separated by 3-4 orders of
+magnitude. Changes with $\vec{r}$ are understood to be smooth changes of the
+average composition of the microscopic domain (orders of centimeters), while
+changes with $\vec{\rho}$ captures compositional changes between grains on the
+microscopic domain, i.e. on the orders of micro-meters. The notation of
+separating the spatial dependence into two scales follows homogenization theory.
+$N_i$ is the number density of isotope $i$, $\sigma_{f,g,i}$ is the microscopic
+fission cross section of isotope $i$ in group $g$, and $\phi_g$ is the scalar
+flux in group $g$.
 
 Denoting the microscopic domain as $\Theta_m$ located at $\vec{r}_m$, we can define a slowly varying average of the number densities:
 
 \begin{equation}
   N_i(\vec{r}) = \frac{1}{\Theta_m} \int_{\Theta_m} N_i(\vec{r},\vec{\rho}) d\vec{\rho}.
 \end{equation}
 
-$N_i(\vec{r})$ is the number density provided to neutronics calculations. The nuclide fission rates computed by the neutronics calculation is consequently the slowly varying average
-given by:
+$N_i(\vec{r})$ is the number density provided to neutronics calculations. The
+nuclide fission rates computed by the neutronics calculation is consequently the
+slowly varying average given by:
 
 \begin{equation}
 F_i (\vec{r}) = \sum\limits_{g=1}^G N_i(\vec{r})\sigma_{f,g,i}.
 \end{equation}
 
-The `PKAFissionFragmentNeutronics` accepts the values of $F_i (\vec{r}_m)$ as the `partial_reaction_rates` parameter.
-The fission rate density in the microscopic domain is computed by:
+The `PKAFissionFragmentNeutronics` accepts the values of $F_i (\vec{r}_m)$ as
+the `partial_reaction_rates` parameter. The fission rate density in the
+microscopic domain is computed by:
+
 \begin{equation}
   F_i (\vec{r}_m, \vec{\rho}) = \frac{N_i(\vec{r}_m, \vec{\rho})}{N_i(\vec{r}_m)} F_i(\vec{r}_m),
 \end{equation}  
-where $N_i(\vec{r}_m, \vec{\rho}) = \gamma_i(\vec{\rho}) / \Omega(\vec{\rho})$, $\Omega(\vec{\rho})$ is the site volume
-that is provided to the `MyTRIMRasterizer` and $\gamma_i$ is the $i$-th variable provided to the `MyTRIMRasterizer's` `var`
-parameter. Hence, we have:
+
+where $N_i(\vec{r}_m, \vec{\rho}) = \gamma_i(\vec{\rho}) / \Omega(\vec{\rho})$,
+$\Omega(\vec{\rho})$ is the site volume that is provided to the
+`MyTRIMRasterizer` and $\gamma_i$ is the $i$-th variable provided to the
+`MyTRIMRasterizer's` `var` parameter. Hence, we have:
+
 \begin{equation}
   F_i (\vec{r}_m, \vec{\rho}) = \frac{\gamma_i(\vec{\rho})}{\Omega(\vec{r}) N_i(\vec{r}_m)} F_i(\vec{r}_m),
 \end{equation}  
 
-`PKAFissionFragmentNeutronics` accepts the values of $N_i(\vec{r}_m)$ in the `averaged_number_densities` parameter.
+`PKAFissionFragmentNeutronics` accepts the values of $N_i(\vec{r}_m)$ in the
+`averaged_number_densities` parameter.
 
-The expected number of fissions in a mesh element with index $j$ and volume $V_j$ is given by:
+The expected number of fissions in a mesh element with index $j$ and volume
+$V_j$ is given by:
 
 \begin{equation}
 C_i = \Delta t \int_{V_j} F_i (\vec{r}_m, \vec{\rho})  d\vec{\rho}.
 \end{equation}
 
-Non-integer results are rounded up with a probability of the $C_i - \text{int}(C_i)$; otherwise
-rounded down. Two PKAs are created from each fission event. The algorithm for sampling their type, energy, and direction of motion is described in [cite:SchunertTREATHeatSource].
+Non-integer results are rounded up with a probability of the $C_i -
+\text{int}(C_i)$; otherwise rounded down. Two PKAs are created from each fission
+event. The algorithm for sampling their type, energy, and direction of motion is
+described in [cite:SchunertTREATHeatSource].
 
 !syntax parameters /UserObjects/PKAFissionFragmentNeutronics
 

doc/content/source/userobjects/PKAFixedPointGenerator.md

@@ -1,15 +1,16 @@
-<!-- MOOSE Documentation Stub: Remove this when content is added. -->
-
 # PKAFixedPointGenerator
 
-!alert construction title=Undocumented Class
-The PKAFixedPointGenerator has not been documented, if you would like to contribute to MOOSE by
-writing documentation, please see [/generate.md]. The content contained on this page explains
-the typical 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 /UserObjects/PKAFixedPointGenerator
 
+Launches a given *number* of PKAs from a specified point. Each PKA is assigned a
+random direction. For a generator with a uniform spatial distribution see
+[PKAConstant](/PKAConstant.md).
+
+!alert note
+The number of PKAs inserted by this generator is *independent* of the simulation timestep!
+
+For a generator with a specified PKA direction see [PKAGun](/PKAGun.md).
+
 !syntax parameters /UserObjects/PKAFixedPointGenerator
 
 !syntax inputs /UserObjects/PKAFixedPointGenerator

doc/content/source/userobjects/PKAFunction.md

@@ -1,15 +1,11 @@
-<!-- MOOSE Documentation Stub: Remove this when content is added. -->
-
 # PKAFunction
 
-!alert construction title=Undocumented Class
-The PKAFunction has not been documented, if you would like to contribute to MOOSE by
-writing documentation, please see [/generate.md]. The content contained on this page explains
-the typical 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 /UserObjects/PKAFunction
 
+This generator performs similarly to [PKkAConstant](/PKAConstant.md), except
+that each parameter can be a MOOOSE Function. Currently only the time variable
+`t` can be used in the function expressions.
+
 !syntax parameters /UserObjects/PKAFunction
 
 !syntax inputs /UserObjects/PKAFunction

doc/content/source/userobjects/PKAGeneratorAlphaDecay.md

@@ -1,13 +1,5 @@
-<!-- MOOSE Documentation Stub: Remove this when content is added. -->
-
 # PKAGeneratorAlphaDecay
 
-!alert construction title=Undocumented Class
-The PKAGeneratorAlphaDecay has not been documented, if you would like to contribute to MOOSE by
-writing documentation, please see [/generate.md]. The content contained on this page explains
-the typical 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 /UserObjects/PKAGeneratorAlphaDecay
 
 !syntax parameters /UserObjects/PKAGeneratorAlphaDecay

doc/content/source/userobjects/PKAGeneratorRecoil.md

@@ -1,15 +1,12 @@
-<!-- MOOSE Documentation Stub: Remove this when content is added. -->
-
 # PKAGeneratorRecoil
 
-!alert construction title=Undocumented Class
-The PKAGeneratorRecoil has not been documented, if you would like to contribute to MOOSE by
-writing documentation, please see [/generate.md]. The content contained on this page explains
-the typical 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 /UserObjects/PKAGeneratorRecoil
 
+This generator will receive a multidimensional probability distribution from a
+[MultiAppNeutronicsSpectrumTransfer](/MultiAppNeutronicsSpectrumTransfer.md).
+This probability distribution is sampled to insert PKAs with the right mass,
+energy, and direction distribution.
+
 !syntax parameters /UserObjects/PKAGeneratorRecoil
 
 !syntax inputs /UserObjects/PKAGeneratorRecoil