Merge is inevitable because of new test created and test suite was changed

Merge branch 'develop' into test_surface_tallies

docs/source/capi/index.rst

@@ -0,0 +1,261 @@
+.. _capi:
+
+=====
+C API
+=====
+
+.. c:function:: void openmc_calculate_voumes()
+
+   Run a stochastic volume calculation
+
+.. c:function:: int openmc_cell_get_id(int32_t index, int32_t* id)
+
+   Get the ID of a cell
+
+   :param index: Index in the cells array
+   :type index: int32_t
+   :param id: ID of the cell
+   :type id: int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_cell_set_temperature(index index, double T, int32_t* instance)
+
+   Set the temperature of a cell.
+
+   :param index: Index in the cells array
+   :type index: int32_t
+   :param T: Temperature in Kelvin
+   :type T: double
+   :param instance: Which instance of the cell. To set the temperature for all
+                    instances, pass a null pointer.
+   :type instance: int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: void openmc_finalize()
+
+   Finalize a simulation
+
+.. c:function:: void openmc_find(double* xyz, int rtype, int32_t* id, int32_t* instance)
+
+   Determine the ID of the cell/material containing a given point
+
+   :param xyz: Cartesian coordinates
+   :type xyz: double[3]
+   :param rtype: Which ID to return (1=cell, 2=material)
+   :type rtype: int
+   :param id: ID of the cell/material found. If a material is requested and the
+              point is in a void, the ID is 0. If an error occurs, the ID is -1.
+   :type id: int32_t*
+   :param instance: If a cell is repetaed in the geometry, the instance of the
+                    cell that was found and zero otherwise.
+   :type instance: int32_t*
+
+.. c:function:: int openmc_get_cell(int32_t id, int32_t* index)
+
+   Get the index in the cells array for a cell with a given ID
+
+   :param id: ID of the cell
+   :type id: int32_t
+   :param index: Index in the cells array
+   :type index: int32_t*
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_get_keff(double k_combined[])
+
+   :param k_combined: Combined estimate of k-effective
+   :type k_combined: double[2]
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_get_nuclide(char name[], int* index)
+
+   Get the index in the nuclides array for a nuclide with a given name
+
+   :param name: Name of the nuclide
+   :type name: char[]
+   :param index: Index in the nuclides array
+   :type index: int*
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_get_tally(int32_t id, int32_t* index)
+
+   Get the index in the tallies array for a tally with a given ID
+
+   :param id: ID of the tally
+   :type id: int32_t
+   :param index: Index in the tallies array
+   :type index: int32_t*
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_get_material(int32_t id, int32_t* index)
+
+   Get the index in the materials array for a material with a given ID
+
+   :param id: ID of the material
+   :type id: int32_t
+   :param index: Index in the materials array
+   :type index: int32_t*
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: void openmc_hard_reset()
+
+   Reset tallies, timers, and pseudo-random number generator state
+
+.. c:function:: void openmc_init(int intracomm)
+
+   Initialize OpenMC
+
+   :param intracomm: MPI intracommunicator
+   :type intracomm: int
+
+.. c:function:: int openmc_load_nuclide(char name[])
+
+   Load data for a nuclide from the HDF5 data library.
+
+   :param name: Name of the nuclide.
+   :type name: char[]
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_material_add_nuclide(int32_t index, char name[], double density)
+
+   Add a nuclide to an existing material. If the nuclide already exists, the
+   density is overwritten.
+
+   :param index: Index in the materials array
+   :type index: int32_t
+   :param name: Name of the nuclide
+   :type name: char[]
+   :param density: Density in atom/b-cm
+   :type density: double
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_material_get_densities(int32_t index, int* nuclides[], double* densities[])
+
+   Get density for each nuclide in a material.
+
+   :param index: Index in the materials array
+   :type index: int32_t
+   :param nuclides: Pointer to array of nuclide indices
+   :type nuclides: int**
+   :param densities: Pointer to the array of densities
+   :type densities: double**
+   :param n: Length of the array
+   :type n: int
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_material_get_id(int32_t index, int32_t* id)
+
+   Get the ID of a material
+
+   :param index: Index in the materials array
+   :type index: int32_t
+   :param id: ID of the material
+   :type id: int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_material_set_density(int32_t index, double density)
+
+   Set the density of a material.
+
+   :param index: Index in the materials array
+   :type index: int32_t
+   :param density: Density of the material in atom/b-cm
+   :type density: double
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_material_set_densities(int32_t, n, char* name[], double density[])
+
+   :param index: Index in the materials array
+   :type index: int32_t
+   :param n: Length of name/density
+   :type n: int
+   :param name: Array of nuclide names
+   :type name: char**
+   :param density: Array of densities
+   :type density: double[]
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: int openmc_nuclide_name(int index, char* name[])
+
+   Get name of a nuclide
+
+   :param index: Index in the nuclides array
+   :type index: int
+   :param name: Name of the nuclide
+   :type name: char**
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
+.. c:function:: void openmc_plot_geometry()
+
+   Run plotting mode.
+
+.. c:function:: void openmc_reset()
+
+   Resets all tally scores
+
+.. c:function:: void openmc_run()
+
+   Run a simulation
+
+.. c:function:: int openmc_tally_get_id(int32_t index, int32_t* id)
+
+   Get the ID of a tally
+
+   :param index: Index in the tallies array
+   :type index: int32_t
+   :param id: ID of the tally
+   :type id: int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_tally_get_nuclides(int32_t index, int* nuclides[], int* n)
+
+   Get nuclides specified in a tally
+
+   :param index: Index in the tallies array
+   :type index: int32_t
+   :param nuclides: Array of nuclide indices
+   :type nuclides: int**
+   :param n: Number of nuclides
+   :type n: int*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_tally_results(int32_t index, double** ptr, int shape_[3])
+
+   Get a pointer to tally results array.
+
+   :param index: Index in the tallies array
+   :type index: int32_t
+   :param ptr: Pointer to the results array
+   :type ptr: double**
+   :param shape_: Shape of the results array
+   :type shape_: int[3]
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_tally_set_nuclides(int32_t index, int n, char* nuclides[])
+
+   Set the nuclides for a tally
+
+   :param index: Index in the tallies array
+   :type index: int32_t
+   :param n: Number of nuclides
+   :type n: int
+   :param nuclides: Array of nuclide names
+   :type nuclides: char**
+   :return: Return status (negative if an error occurred)
+   :rtype: int

docs/source/conf.py

@@ -25,8 +25,9 @@ except ImportError:
 
 
 MOCK_MODULES = ['numpy', 'numpy.polynomial', 'numpy.polynomial.polynomial',
-                'h5py', 'pandas', 'uncertainties', 'openmoc',
-                'openmc.data.reconstruct']
+                'numpy.ctypeslib', 'scipy', 'scipy.sparse', 'scipy.interpolate',
+                'scipy.integrate', 'scipy.optimize', 'scipy.special', 'h5py',
+                'pandas', 'uncertainties', 'openmoc', 'openmc.data.reconstruct']
 sys.modules.update((mod_name, MagicMock()) for mod_name in MOCK_MODULES)
 
 import numpy as np

docs/source/index.rst

@@ -36,6 +36,7 @@ free to send a message to the User's Group `mailing list`_.
     usersguide/index
     devguide/index
     pythonapi/index
+    capi/index
     io_formats/index
     publications
     license

docs/source/io_formats/materials.rst

@@ -107,9 +107,13 @@ Each ``material`` element can have the following attributes or sub-elements:
               multi-group :ref:`energy_mode`.
 
   :sab:
-    Associates an S(a,b) table with the material. This element has one
+    Associates an S(a,b) table with the material. This element has an
     attribute/sub-element called ``name``. The ``name`` attribute
     is the name of the S(a,b) table that should be associated with the material.
+    There is also an optional ``fraction`` element which indicates what fraction
+    of the relevant nuclides will be affected by the S(a,b) table (e.g. which
+    fraction of a material is crystalline versus amorphous).  ``fraction``
+    defaults to unity.
 
     *Default*: None
 

docs/source/io_formats/settings.rst

@@ -661,6 +661,17 @@ methods like "nearest" and "interpolation" in the resolved resonance range.
 
   *Default*: False
 
+-------------------------------
+``<temperature_range>`` Element
+-------------------------------
+
+The ``<temperature_range>`` element specifies a minimum and maximum temperature
+in Kelvin above and below which cross sections should be loaded for all nuclides
+and thermal scattering tables. This can be used for multi-physics simulations
+where the temperatures might change from one iteration to the next.
+
+  *Default*: None
+
 .. _temperature_tolerance:
 
 -----------------------------------

docs/source/pythonapi/capi.rst

@@ -0,0 +1,39 @@
+---------------------------------------------------
+:data:`openmc.capi` -- Python bindings to the C API
+---------------------------------------------------
+
+.. automodule:: openmc.capi
+
+Functions
+---------
+
+.. autosummary::
+   :toctree: generated
+   :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
+
+Classes
+-------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass.rst
+
+   openmc.capi.CellView
+   openmc.capi.MaterialView
+   openmc.capi.NuclideView
+   openmc.capi.TallyView

docs/source/pythonapi/index.rst

@@ -47,5 +47,6 @@ Modules
    mgxs
    model
    data
+   capi
    examples
    openmoc

docs/source/usersguide/geometry.rst

@@ -19,7 +19,7 @@ surface is a locus of zeros of a function of Cartesian coordinates
 :math:`x,y,z`, e.g.
 
 - A plane perpendicular to the :math:`x` axis: :math:`x - x_0 = 0`
-- A cylinder perpendicular to the :math:`z` axis: :math:`(x - x_0)^2 + (y -
+- A cylinder parallel to the :math:`z` axis: :math:`(x - x_0)^2 + (y -
   y_0)^2 - R^2 = 0`
 - A sphere: :math:`(x - x_0)^2 + (y - y_0)^2 + (z - z_0)^2 - R^2 = 0`
 

docs/source/usersguide/install.rst

@@ -401,14 +401,6 @@ distributions.
       NumPy is used extensively within the Python API for its powerful
       N-dimensional array.
 
-   `h5py <http://www.h5py.org/>`_
-      h5py provides Python bindings to the HDF5 library. Since OpenMC outputs
-      various HDF5 files, h5py is needed to provide access to data within these
-      files from Python.
-
-.. admonition:: Optional
-   :class: note
-
    `SciPy <https://www.scipy.org/>`_
       SciPy's special functions, sparse matrices, and spatial data structures
       are used for several optional features in the API.
@@ -417,6 +409,14 @@ distributions.
       Pandas is used to generate tally DataFrames as demonstrated in
       :ref:`examples_pandas` example notebook.
 
+   `h5py <http://www.h5py.org/>`_
+      h5py provides Python bindings to the HDF5 library. Since OpenMC outputs
+      various HDF5 files, h5py is needed to provide access to data within these
+      files from Python.
+
+.. admonition:: Optional
+   :class: note
+
    `Matplotlib <http://matplotlib.org/>`_
       Matplotlib is used to providing plotting functionality in the API like the
       :meth:`Universe.plot` method and the :func:`openmc.plot_xs` function.