Merge branch 'develop' into integrator-class

Need new travis.yml to pass CI

docs/source/devguide/tests.rst

@@ -4,9 +4,6 @@
 Test Suite
 ==========
 
-Running Tests
--------------
-
 The OpenMC test suite consists of two parts, a regression test suite and a unit
 test suite. The regression test suite is based on regression or integrated
 testing where different types of input files are configured and the full OpenMC
@@ -14,27 +11,35 @@ code is executed. Results from simulations are compared with expected
 results. The unit tests are primarily intended to test individual
 functions/classes in the OpenMC Python API.
 
-The test suite relies on the third-party `pytest <https://pytest.org>`_
-package. To run either or both the regression and unit test suites, it is
-assumed that you have OpenMC fully installed, i.e., the :ref:`scripts_openmc`
-executable is available on your :envvar:`PATH` and the :mod:`openmc` Python
-module is importable. In development where it would be onerous to continually
-install OpenMC every time a small change is made, it is recommended to install
-OpenMC in development/editable mode. With setuptools, this is accomplished by
-running::
+Prerequisites
+-------------
 
-    python setup.py develop
+- The test suite relies on the third-party `pytest <https://pytest.org>`_
+  package. To run either or both the regression and unit test suites, it is
+  assumed that you have OpenMC fully installed, i.e., the :ref:`scripts_openmc`
+  executable is available on your :envvar:`PATH` and the :mod:`openmc` Python
+  module is importable. In development where it would be onerous to continually
+  install OpenMC every time a small change is made, it is recommended to install
+  OpenMC in development/editable mode. With setuptools, this is accomplished by
+  running::
 
-or using pip (recommended)::
+      python setup.py develop
 
-    pip install -e .[test]
+  or using pip (recommended)::
 
-It is also assumed that you have cross section data available that is pointed to
-by the :envvar:`OPENMC_CROSS_SECTIONS` environment variables. Furthermore, to
-run unit tests for the :mod:`openmc.data` module, it is necessary to have
-ENDF/B-VII.1 data available and pointed to by the :envvar:`OPENMC_ENDF_DATA`
-environment variable. All data sources can be obtained using the
-``tools/ci/travis-before-script.sh`` script.
+      pip install -e .[test]
+
+- The test suite requires a specific set of cross section data in order for
+  tests to pass. A download URL for the data that OpenMC expects can be found
+  within ``tools/ci/download-xs.sh``.
+- In addition to the HDF5 data, some tests rely on ENDF files. A download URL
+  for those can also be found in ``tools/ci/download-xs.sh``.
+- Some tests require `NJOY <https://www.njoy21.io/NJOY2016>`_ to preprocess
+  cross section data. The test suite assumes that you have an ``njoy``
+  executable available on your :envvar:`PATH`.
+
+Running Tests
+-------------
 
 To execute the test suite, go to the ``tests/`` directory and run::
 
@@ -46,6 +51,17 @@ installed and run::
 
     pytest --cov=../openmc --cov-report=html
 
+Generating XML Inputs
+---------------------
+
+Many of the regression tests rely on the Python API to build an appropriate
+model. However, it can sometimes be desirable to work directly with the XML
+input files rather than having to run a script in order to run the problem/test.
+To build the input files for a test without actually running the test, you can
+run::
+
+    pytest --build-inputs <name-of-test>
+
 Adding Tests to the Regression Suite
 ------------------------------------
 

docs/source/io_formats/cross_sections.rst

@@ -51,3 +51,20 @@ attributes:
   :type:
     The type of data contained in the file. Accepted values are 'neutron',
     'thermal', 'photon', and 'wmp'.
+
+.. _depletion_element:
+
+-----------------------------
+``<depletion_chain>`` Element
+-----------------------------
+
+The ``<depletion_chain>`` element indicates the location of the depletion chain file.
+This file contains information describing how nuclides decay and transmute to other
+nuclides through the depletion process. This element has a single attribute, ``path``,
+pointing to the location of the chain file.
+
+.. code-block:: xml
+
+    <depletion_chain path="/opt/data/chain_endfb7.xml"/>
+
+The structure of the depletion chain file is explained in :ref:`io_depletion_chain`.

docs/source/io_formats/depletion_results.rst

@@ -44,3 +44,10 @@ The current version of the depletion results file format is 1.0.
 **/reactions/<name>/**
 
 :Attributes: - **index** (*int*) -- Index user in results for this reaction
+
+.. note::
+
+    The reaction rates for some isotopes not originally present may
+    be non-zero, but should be negligible compared to other atoms.
+    This can be controlled by changing the
+    :class:`openmc.deplete.Operator` ``dilute_initial`` attribute.

docs/source/io_formats/materials.rst

@@ -42,8 +42,7 @@ Each ``material`` element can have the following attributes or sub-elements:
     Volume of the material in cm^3.
 
   :temperature:
-    An element with no attributes which is used to set the default temperature
-    of the material in Kelvin.
+    Temperature of the material in Kelvin.
 
     *Default*: If a material default temperature is not given and a cell
     temperature is not specified, the :ref:`global default temperature

docs/source/io_formats/source.rst

@@ -13,8 +13,9 @@ is that documented here.
 :Attributes: - **filetype** (*char[]*) -- String indicating the type of file.
 
 :Datasets:
+
            - **source_bank** (Compound type) -- Source bank information for each
              particle. The compound type has fields ``wgt``, ``xyz``, ``uvw``,
-             ``E``, and ``delayed_group``, which represent the weight, position,
-             direction, energy, energy group, and delayed_group of the source
-             particle, respectively.
+             ``E``, ``delayed_group``, and ``particle``, which represent the
+             weight, position, direction, energy, energy group, delayed group,
+             and type of the source particle, respectively.

docs/source/io_formats/summary.rst

@@ -116,6 +116,13 @@ The current version of the summary file format is 6.0.
            - **sab_names** (*char[][]*) -- Names of
              S(:math:`\alpha,\beta`) tables assigned to the material.
 
+:Attributes: - **volume** (*double[]*) -- Volume of this material [cm^3]. Only
+               present if ``volume`` supplied
+             - **temperature** (*double[]*) -- Temperature of this material [K].
+               Only present in ``temperature`` supplied
+             - **depletable** (*int[]*) -- ``1`` if the material can be depleted,
+               ``0`` otherwise. Always present
+
 **/nuclides/**
 
 :Attributes: - **n_nuclides** (*int*) -- Number of nuclides in the problem.

docs/source/pythonapi/deplete.rst

@@ -75,10 +75,24 @@ data, such as number densities and reaction rates for each material.
    :template: myclass.rst
 
    AtomNumber
+   ChainFissionHelper
+   DirectReactionRateHelper
    OperatorResult
    ReactionRates
    Results
    ResultsList
+
+
+The following classes are abstract classes that can be used to extend the
+:mod:`openmc.deplete` capabilities:
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass.rst
+
+   ReactionRateHelper
+   EnergyHelper
    TransportOperator
 
 Each of the integrator functions also relies on a number of "helper" functions

docs/source/pythonapi/model.rst

@@ -15,6 +15,7 @@ Convenience Functions
    openmc.model.hexagonal_prism
    openmc.model.rectangular_prism
    openmc.model.subdivide
+   openmc.model.pin
 
 TRISO Fuel Modeling
 -------------------