Fix docs

doc/conf.py

@@ -36,13 +36,13 @@
 
 # -- sphinx-multiversion configuration ---------------------------------------
 # Whitelist pattern for tags (set to None to ignore all tags)
-smv_tag_whitelist = r'^v\d[.][^12][.]\d.*$'
+smv_tag_whitelist = r'^v\d[.][^1234][.]\d$'
 
 # Whitelist pattern for branches (set to None to ignore all branches)
 smv_branch_whitelist = r'^(master)*$'
 
 # Whitelist pattern for remotes (set to None to use local branches only)
-smv_remote_whitelist = r'^(origin|upstream)$'
+smv_remote_whitelist = r'^upstream$'
 
 # Pattern for released versions
 smv_released_pattern = r'^tags/.*$'

doc/io_formats/saltproc_input.rst

@@ -72,7 +72,7 @@ Required properties are as follows: ``proc_input_file``, ``dot_input_file``, ``o
 .. _mpi_args_property:
 
 ``mpi_args``
----------------------
+------------
 
   :description:
     Arguments for running simulations on supercomputers using ``mpiexec``
@@ -93,7 +93,7 @@ Required properties are as follows: ``proc_input_file``, ``dot_input_file``, ``o
 .. _rebuild_saltproc_results_property:
 
 ``rebuild_saltproc_results``
----------------------
+----------------------------
 
   :description:
     Flag to reconstruct the ``saltproc_results.h5`` files from the stepwise
@@ -110,7 +110,7 @@ Required properties are as follows: ``proc_input_file``, ``dot_input_file``, ``o
 .. _run_without_reprocessing_property:
 
 ``run_without_reprocessing``
----------------------
+----------------------------
 
   :description:
     Flag to run SaltProc with no material reprocessing.

doc/methods/index.rst

@@ -14,6 +14,4 @@ about the SaltProc's program flow, design, mathematical background, and more.
 .. toctree::
    :maxdepth: 1
 
-   coupling
    reprocessing
-   geometry_switching

doc/methods/reprocessing.rst

@@ -3,4 +3,163 @@
 Reprocessing Methods
 ====================
 
-Coming soon!
+SaltProc models separations and feeds using three different data structures:
+
+Material flows
+--------------
+A material flow represents a material with a given
+volume :math:`V`, density :math:`\rho`, temperature :math:`T`, and nuclide composition :math:`\mathbf{N}` flowing in or out
+of a processing component.
+It can also include information such as void fraction. :class:`saltproc.Materialflow`
+objects contain the prior mentioned quantities as attributes, as well as
+methods to perform the following:
+
+1. Add two :class:`saltproc.Materialflow` objects together
+
+   a. The mass of the sum is :math:`m_{1+2} = m_{1} + m_{2}`
+
+   b. The composition of the sum is :math:`\mathbf{N}_{1+2} = \frac{\mathbf{N}_{1} * m_{1} + \mathbf{N}_{2} * m_{2}}{m_{1} + m_{2}}`
+
+   c. The temperature and density are assumed to be equal to the first :class:`saltproc.Materialflow` object
+
+2. Scale a :class:`saltproc.Materialflow` object by a constant, specifically the mass and volume of the :class:`saltproc.Materialflow` object.
+
+:class:`saltproc.Materialflow`. objects are used to store information about
+materials in reprocessing as well as materials being fed into the system.
+
+Processes
+.........
+A process is an abstraction of chemical separation, extraction, or some
+other removal. Two processes commonly used in \Gls{msr}s include
+extracting metals using gas sparging and filtering. In SaltProc,
+:class:`saltproc.Process` objects contain data and functions to perform their
+associated processing task. At a minimum, a :class:`saltproc.Process` object includes
+the following
+
+1. A mass flow rate, :math:`\dot{m}`, which specifies the mass of fuel salt a process can operate on per unit time
+2. An extraction efficiency, :math:`\epsilon`, for target element(s)
+3. A method to apply the process on a :class:`saltproc.Materialflow` object
+
+Graphs
+......
+A graph is a mathematical object that connects *nodes*
+with *edges*. More formally,
+a graph is a pair of sets, :math:`(V, E)`, where
+
+- :math:`V` is a set whose elements are called nodes
+- :math:`E` is a set whose elements are pairs of elements in :math:`V`
+
+A directed graph is a graph in which the elements are ordered pairs of elements
+in :math:`V`. This gives the edges a direction. SaltProc uses directed graphs to
+model the order and path in which processes operate on materials.
+
+Processes and feeds are defined in one JSON input file, and the graph linking
+processes is defined in a DOT file. The process graph must be directed and
+acyclic in order to work with SaltProc. At runtime,
+SaltProc reads this input file to create :class:`saltproc.Process` objects for each item
+in the file. Every process file must have at least a :class:`core_outlet` and
+:class:`core_inlet` Process.
+
+Material reprocessing
+---------------------
+
+Recall that SaltProc uses a *batchwise* reprocessing scheme.
+Let :math:`\mathbf{n}(t)^{j}` denote the nuclide mass vector for depletable material
+:math:`j` as a function of time. For each depletable material :math:`j`, the depletion
+solver numerically integrates the equation
+
+.. math::
+
+    \frac{d\mathbf{n}^{j}(t)}{dt} = \mathbf{A}(\mathbf{n}^{j}(t), t)
+
+from time :math:`i` to time :math:`i+1` to get :math:`\mathbf{n}^{j}(i+1)`, where :math:`A` is the
+depletion matrix. This sequence is called a **depletion step**.
+
+Now, let the mass and volume of depletable material :math:`j` be
+:math:`m^{j}` and :math:`V^{j}` respectively. Let the mass flow rate of process :math:`p` be
+:math:`\dot{m}_{p}`. At the end of each depletion step, SaltProc constructs process
+paths from the process graph defined in the DOT file, and sequentially applies
+each process :math:`p` in each path :math:`r` to the relevant materials to obtain through
+and waste streams for each material. SaltProc tracks the mass and nuclide vector for both through and waste streams. For through
+streams, SaltProc also tracks the volume and mass flow rate. For every node
+:math:`p\in[0,l]` where :math:`0` represents the core outlet and :math:`l` represents the core
+inlet, in the path :math:`r`, for the through streams we have
+
+.. math::
+
+    \mathbf{n}^{j}_{\text{through, }p,r} = \mathbf{n}^{j}_{\text{through, }p-1,r} (1 - \pmb{\epsilon}^{j}_{p,r})
+
+.. math::
+
+    m^{j}_{\text{through, } p,r} = \alpha_{p} m^{j}_{\text{through, }p-1,r} - m^{j}_{\text{waste, }p,r}
+
+.. math::
+
+    V^{j}_{\text{through, }p,r} = \alpha_{p}V^{j}_{\text{through, }p-1,r}
+
+where 
+
+.. math::
+
+    \alpha_{p,r} = \frac{\dot{m}_{p,r}}{\dot{m}_{\text{outlet}}}
+
+and the initial conditions are 
+
+.. math::
+
+    \mathbf{n}^{j}_{\text{through, }0,r} = \mathbf{n}^{j}(i+1)
+
+.. math::
+
+    m^{j}_{\text{through, }0,r} = \rho^{j}(i+1)V^{j}(i+1)
+
+.. math::
+
+    V^{j}_{\text{through, }0,r} = V^{j}(i+1)
+
+Similarly, for the waste streams, we have
+
+.. math::
+
+    \mathbf{n}^{j}_{\text{waste, }p,r} = \mathbf{n}^{j}_{\text{through, }p-1,r} \cdot \pmb{\epsilon}^{j}_{p,r}
+
+.. math::
+
+    m^{j}_{\text{waste, }p,r} = \alpha_{p,r} m^{j}_{\text{through, }p-1,r} \langle\mathbf{1},\mathbf{n}^{j}_{\text{waste, }p,r}\rangle
+
+
+SaltProc does not currently track the volume and mass flow rate of waste streams.
+In practice, since it is extremely resource intensive to separate individual
+isotopes, SaltProc only allows extraction efficiencies to be defined for
+elements. Additionally, any chemical processing would only act on elements, so there is little point in having isotope specific extration efficiencies. So, for any isotope :math:`a` of xenon,
+:math:`\epsilon_{\ce{^{a}Xe}} = \epsilon_{\ce{^{a^{\prime}}Xe}}`  where
+:math:`a^{\prime} \in \text{isotopes of Xe}`
+
+After the recursive computation, SaltProc sums through and waste streams over all
+paths to get the total through stream at the inlet, and the total waste stream at
+the inlet which represents all material removed during reprocessing. In practice,
+we are working with nuclide mass fractions, not total masses, so in the program
+there is an expansion and then normalization of the vectors:
+
+.. math::
+
+    \mathbf{n}^{j}_\text{through, inlet, net} = \frac{\sum_{r} m^{j}_{\text{through, inlet, }r} \mathbf{n}^{j}_{\text{through, inlet, }r}}{\sum_{r} m^{j}_{\text{through, inlet, }r}}
+
+.. math::
+
+    \mathbf{n}^{j}_{\text{waste, inlet, net}} = \frac{\sum_{r} m^{j}_{\text{waste, inlet, }r} \mathbf{n}^{j}_{\text{waste, inlet, }r}}{m^{j}_{\text{waste, inlet, }r}}
+
+Before running the next depletion step, for any material that has an associated
+feed material defined, SaltProc will add an amount of the feed material
+equivalent to the removed mass so that the mass of fuel salt undergoing depletion
+remains constant. For feed :math:`j'` corresponding to material :math:`j`, we have
+
+.. math::
+
+    \mathbf{n}^{j}_\text{filled} = \frac{m^{j}_{\text{through, }l}\mathbf{n}^{j}_\text{through, inlet, net} +  m^{j}_{\text{removed}}\mathbf{n}^{j'}}{m^{j}_{\text{through, }0}}
+
+where 
+
+.. math::
+
+    m^{j}_\text{removed} = m^{j}_{\text{through, }0} - m^{j}_{\text{through, }l}