Merge branch 'develop' into photon-alund

docs/source/pythonapi/base.rst

@@ -91,18 +91,6 @@ Many of the above classes are derived from several abstract classes:
    openmc.Region
    openmc.Lattice
 
-Two helper function are also available to create rectangular and hexagonal
-prisms defined by the intersection of four and six surface half-spaces,
-respectively.
-
-.. autosummary::
-   :toctree: generated
-   :nosignatures:
-   :template: myfunction.rst
-
-   openmc.get_hexagonal_prism
-   openmc.get_rectangular_prism
-
 .. _pythonapi_tallies:
 
 Constructing Tallies

docs/source/pythonapi/capi.rst

@@ -1,6 +1,6 @@
----------------------------------------------------
-:data:`openmc.capi` -- Python bindings to the C API
----------------------------------------------------
+--------------------------------------------------
+:mod:`openmc.capi` -- Python bindings to the C API
+--------------------------------------------------
 
 .. automodule:: openmc.capi
 
@@ -12,18 +12,25 @@ Functions
    :nosignatures:
    :template: myfunction.rst
 
-   openmc.capi.calculate_volumes
-   openmc.capi.finalize
-   openmc.capi.find_cell
-   openmc.capi.find_material
-   openmc.capi.hard_reset
-   openmc.capi.init
-   openmc.capi.keff
-   openmc.capi.load_nuclide
-   openmc.capi.plot_geometry
-   openmc.capi.reset
-   openmc.capi.run
-   openmc.capi.run_in_memory
+   calculate_volumes
+   finalize
+   find_cell
+   find_material
+   hard_reset
+   init
+   iter_batches
+   keff
+   load_nuclide
+   next_batch
+   num_realizations
+   plot_geometry
+   reset
+   run
+   run_in_memory
+   simulation_init
+   simulation_finalize
+   source_bank
+   statepoint_write
 
 Classes
 -------
@@ -33,9 +40,9 @@ Classes
    :nosignatures:
    :template: myclass.rst
 
-   openmc.capi.Cell
-   openmc.capi.EnergyFilter
-   openmc.capi.MaterialFilter
-   openmc.capi.Material
-   openmc.capi.Nuclide
-   openmc.capi.Tally
+   Cell
+   EnergyFilter
+   MaterialFilter
+   Material
+   Nuclide
+   Tally

docs/source/pythonapi/data.rst

@@ -35,9 +35,12 @@ Core Functions
     :template: myfunction.rst
 
     openmc.data.atomic_mass
+    openmc.data.gnd_name
     openmc.data.linearize
     openmc.data.thin
+    openmc.data.water_density
     openmc.data.write_compact_458_library
+    openmc.data.zam
 
 Angle-Energy Distributions
 --------------------------

docs/source/pythonapi/deplete.rst

@@ -0,0 +1,85 @@
+.. _pythonapi_deplete:
+
+----------------------------------
+:mod:`openmc.deplete` -- Depletion
+----------------------------------
+
+.. module:: openmc.deplete
+
+Two functions are provided that implement different time-integration algorithms
+for depletion calculations.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   integrator.predictor
+   integrator.cecm
+
+Each of these functions expects a "transport operator" to be passed. An operator
+specific to OpenMC is available using the following class:
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass.rst
+
+   Operator
+
+When running in parallel using `mpi4py <http://mpi4py.scipy.org>`_, the MPI
+intercommunicator used can be changed by modifying the following module
+variable. If it is not explicitly modified, it defaults to
+``mpi4py.MPI.COMM_WORLD``.
+
+.. data:: comm
+
+   MPI intercommunicator used to call OpenMC library
+
+   :type: mpi4py.MPI.Comm
+
+Internal Classes and Functions
+------------------------------
+
+During a depletion calculation, the depletion chain, reaction rates, and number
+densities are managed through a series of internal classes that are not normally
+visible to a user. However, should you find yourself wondering about these
+classes (e.g., if you want to know what decay modes or reactions are present in
+a depletion chain), they are documented here. The following classes store data
+for a depletion chain:
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass.rst
+
+   Chain
+   DecayTuple
+   Nuclide
+   ReactionTuple
+
+The following classes are used during a depletion simulation and store auxiliary
+data, such as number densities and reaction rates for each material.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass.rst
+
+   AtomNumber
+   OperatorResult
+   ReactionRates
+   Results
+   ResultsList
+   TransportOperator
+
+Each of the integrator functions also relies on a number of "helper" functions
+as follows:
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   integrator.CRAM16
+   integrator.CRAM48

docs/source/pythonapi/index.rst

@@ -15,14 +15,15 @@ there are many substantial benefits to using the Python API, including:
 - The ability to define dimensions using variables.
 - Availability of standard-library modules for working with files.
 - An entire ecosystem of third-party packages for scientific computing.
-- Ability to create materials based on natural elements or uranium enrichment
 - Automated multi-group cross section generation (:mod:`openmc.mgxs`)
+- A fully-featured nuclear data interface (:mod:`openmc.data`)
+- Depletion capability (:mod:`openmc.deplete`)
 - Convenience functions (e.g., a function returning a hexagonal region)
 - Ability to plot individual universes as geometry is being created
 - A :math:`k_\text{eff}` search function (:func:`openmc.search_for_keff`)
 - Random sphere packing for generating TRISO particle locations
   (:func:`openmc.model.pack_trisos`)
-- A fully-featured nuclear data interface (:mod:`openmc.data`)
+- Ability to create materials based on natural elements or uranium enrichment
 
 For those new to Python, there are many good tutorials available online. We
 recommend going through the modules from `Codecademy
@@ -40,13 +41,14 @@ Modules
 -------
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    base
-   stats
-   mgxs
    model
+   examples
+   deplete
+   mgxs
+   stats
    data
    capi
-   examples
    openmoc

docs/source/pythonapi/model.rst

@@ -2,6 +2,19 @@
 :mod:`openmc.model` -- Model Building
 -------------------------------------
 
+Convenience Functions
+---------------------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   openmc.model.borated_water
+   openmc.model.get_hexagonal_prism
+   openmc.model.get_rectangular_prism
+   openmc.model.subdivide
+
 TRISO Fuel Modeling
 -------------------