Merge branch 'openmc-dev:develop' into develop

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,29 @@
+---
+name: Bug report
+about: Report a bug that is preventing proper operation
+title: ''
+labels: Bugs
+assignees: ''
+
+---
+
+<!--
+If you are a user of OpenMC and are running into trouble with the code or are
+seeking general user support, we highly recommend posting on the OpenMC
+discourse forum first. GitHub issues should be used specifically for bug reports
+and feature requests.
+
+https://openmc.discourse.group/
+
+-->
+
+## Bug Description
+<!--A clear and concise description of the problem (Note: A missing feature is not a bug).-->
+
+
+## Steps to Reproduce
+<!--Steps to reproduce the behavior (input file, or modifications to an existing input file, etc.)-->
+
+
+## Environment
+<!--Operating system, OpenMC version, how OpenMC was installed, nuclear data being used, etc.-->

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Troubleshooting and User Support
+    url: https://openmc.discourse.group/
+    about: For user support and troubleshooting, please use our Discourse forum

.github/ISSUE_TEMPLATE/documentation.md

@@ -0,0 +1,10 @@
+---
+name: Documentation improvement
+about: Found something incomplete or incorrect in our documentation?
+title: ''
+labels: Documentation
+assignees: ''
+
+---
+
+<!--Describe the issue with the documentation and include a URL to the corresponding page-->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest a new feature or enhancement to existing capabilities
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Description
+<!--What is the feature or enhancement?-->
+
+
+## Alternatives
+<!--If alternative solutions have been considered, describe them here and the reasoning for the chosen solution --->
+
+
+## Compatibility
+<!--Will the enhancement change existing APIs or add something new?-->

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+<!--
+If you are a first-time contributor to OpenMC, please have a look at our
+contributing guidelines:
+https://github.com/openmc-dev/openmc/blob/develop/CONTRIBUTING.md
+-->
+
+# Description
+
+Please include a summary of the change and which issue is fixed if applicable. Please also include relevant motivation and context.
+
+Fixes # (issue)
+
+# Checklist
+
+- [ ] I have performed a self-review of my own code
+- [ ] I have run [clang-format](https://docs.openmc.org/en/latest/devguide/styleguide.html#automatic-formatting) on any C++ source files (if applicable)
+- [ ] I have followed the [style guidelines](https://docs.openmc.org/en/latest/devguide/styleguide.html#python) for Python source files (if applicable)
+- [ ] I have made corresponding changes to the documentation (if applicable)
+- [ ] I have added tests that prove my fix is effective or that my feature works (if applicable)
+<!--
+While tests will automatically be checked by CI, it is good practice to
+ensure that they pass locally first. See instructions here:
+https://docs.openmc.org/en/latest/devguide/tests.html
+-->

.github/workflows/format-check.yml

@@ -0,0 +1,25 @@
+name: C++ Format Check
+
+on: pull_request
+
+jobs:
+  cpp-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: cpp-linter/cpp-linter-action@v2
+        id: linter
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          style: file
+          files-changed-only: true
+          tidy-checks: '-*'
+          version: '15' # clang-format version
+          file-annotations: true
+          step-summary: true
+          extensions: 'cpp,h'
+
+      - name: Failure Check
+        if: steps.linter.outputs.checks-failed > 0
+        run: echo "Some files failed the formatting check! See job summary and file annotations for more info" && exit 1

docs/requirements-rtd.txt

@@ -10,3 +10,4 @@ h5py
 pandas
 uncertainties
 matplotlib
+lxml

docs/source/devguide/docbuild.rst

@@ -5,21 +5,14 @@ Building Sphinx Documentation
 =============================
 
 In order to build the documentation in the ``docs`` directory, you will need to
-have the `Sphinx <https://www.sphinx-doc.org/en/master/>`_ third-party Python
-package. The easiest way to install Sphinx is via pip:
+have the several third-party Python packages installed, including `Sphinx
+<https://www.sphinx-doc.org/en/master/>`_. To install the necessary
+prerequisites, provide the optional "docs" dependencies when installing OpenMC's
+Python API. That is, from the root directory of the OpenMC repository:
 
 .. code-block:: sh
 
-    pip install sphinx
-
-Additionally, you will need several Sphinx extensions that can be installed
-directly with pip:
-
-.. code-block:: sh
-
-    pip install sphinx-numfig
-    pip install sphinxcontrib-katex
-    pip install sphinxcontrib-svg2pdfconverter
+    python -m pip install .[docs]
 
 -----------------------------------
 Building Documentation as a Webpage

docs/source/devguide/tests.rst

@@ -23,11 +23,7 @@ Prerequisites
   OpenMC in development/editable mode. With setuptools, this is accomplished by
   running::
 
-      python setup.py develop
-
-  or using pip (recommended)::
-
-      pip install -e .[test]
+      python -m 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
@@ -83,13 +79,13 @@ does not exist run::
 
     touch test_<name-of-header-file>.cpp
 
-The file must be added to the CMake build system in 
-``tests/cpp_unit_tests/CMakeLists.txt``. ``test_<name-of-header-file>`` should 
-be added to ``TEST_NAMES``. 
+The file must be added to the CMake build system in
+``tests/cpp_unit_tests/CMakeLists.txt``. ``test_<name-of-header-file>`` should
+be added to ``TEST_NAMES``.
 
-To add a test case to ``test_<name-of-header-file>.cpp`` ensure 
-``catch2/catch_test_macros.hpp`` is included. A unit test can then be added 
-using the ``TEST_CASE`` macro and the ``REQUIRE`` assertion from Catch2. 
+To add a test case to ``test_<name-of-header-file>.cpp`` ensure
+``catch2/catch_test_macros.hpp`` is included. A unit test can then be added
+using the ``TEST_CASE`` macro and the ``REQUIRE`` assertion from Catch2.
 
 Adding Tests to the Regression Suite
 ------------------------------------

docs/source/devguide/workflow.rst

@@ -116,7 +116,7 @@ pip_. From the root directory of the OpenMC repository, run:
 
 .. code-block:: sh
 
-    pip install -e .[test]
+    python -m pip install -e .[test]
 
 This installs the OpenMC Python package in `"editable" mode
 <https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs>`_ so that 1)

docs/source/io_formats/depletion_results.rst

@@ -47,10 +47,3 @@ The current version of the depletion results file format is 1.1.
 **/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/index.rst

@@ -51,3 +51,4 @@ Output Files
    track
    voxel
    volume
+   weight_windows

docs/source/io_formats/particle_restart.rst

@@ -26,6 +26,8 @@ The current version of the particle restart file format is 2.0.
            - **run_mode** (*char[]*) -- Run mode used, either 'fixed source',
              'eigenvalue', or 'particle restart'.
            - **id** (*int8_t*) -- Unique identifier of the particle.
+           - **type** (*int*) -- Particle type (0=neutron, 1=photon, 2=electron,
+             3=positron)
            - **weight** (*double*) -- Weight of the particle.
            - **energy** (*double*) -- Energy of the particle in eV for
              continuous-energy mode, or the energy group of the particle for

docs/source/io_formats/settings.rst

@@ -449,24 +449,27 @@ attributes/sub-elements:
 
     *Default*: 1.0
 
+  :type:
+    Indicator of source type. One of ``independent``, ``file``, or ``compiled``.
+
   :particle:
     The source particle type, either ``neutron`` or ``photon``.
 
     *Default*: neutron
 
   :file:
-    If this attribute is given, it indicates that the source is to be read from
-    a binary source file whose path is given by the value of this element. Note,
-    the number of source sites needs to be the same as the number of particles
-    simulated in a fission source generation.
+    If this attribute is given, it indicates that the source type is ``file``,
+    meaning particles are to be read from a binary source file whose path is
+    given by the value of this element.
 
     *Default*: None
 
   :library:
-    If this attribute is given, it indicates that the source is to be
-    instantiated from an externally compiled source function. This source can be
-    as complex as is required to define the source for your problem. The library
-    has a few basic requirements:
+    If this attribute is given, it indicates that the source type is
+    ``compiled``, meaning that particles are instantiated from an externally
+    compiled source function. This source can be completely customized as needed
+    to define the source for your problem. The library has a few basic
+    requirements:
 
     * It must contain a class that inherits from ``openmc::Source``;
     * The class must implement a function called ``sample()``;
@@ -476,14 +479,12 @@ attributes/sub-elements:
 
     More documentation on how to build sources can be found in :ref:`custom_source`.
 
-    *Default*: None
-
   :parameters:
-    If this attribute is given, it provides the parameters to pass through to the
-    class generated using the ``library`` parameter . More documentation on how to
-    build parametrized sources can be found in :ref:`parameterized_custom_source`.
-
-    *Default*: None
+    If this attribute is given, it indicated that the source type is
+    ``compiled``. Its value provides the parameters to pass through to the class
+    generated using the ``library`` parameter. More documentation on how to
+    build parametrized sources can be found in
+    :ref:`parameterized_custom_source`.
 
   :space:
     An element specifying the spatial distribution of source sites. This element
@@ -1066,7 +1067,7 @@ sub-elements/attributes:
   :particle_type:
     The particle that the weight windows will apply to (e.g., 'neutron')
 
-    *Default*: None
+    *Default*: 'neutron'
 
   :energy_bins:
     Monotonically increasing list of bounding energies in [eV] to be used for
@@ -1104,3 +1105,74 @@ sub-elements/attributes:
     Threshold below which particles will be terminated
 
     *Default*: :math:`10^{-38}`
+
+--------------------------------------
+``<weight_window_generator>`` Element
+--------------------------------------
+
+The ``<weight_window_generator>`` element provides information for creating a set of
+mesh-based weight windows.
+
+  :mesh:
+    ID of a mesh that is to be used for the weight windows spatial bins
+
+    *Default*: None
+
+  :energy_bounds:
+    The weight window energy bounds. If not present, the max/min energy of the
+    cross section data is applied as a single energy bin.
+
+    *Default*: None
+
+  :particle_type:
+    The particle that the weight windows will apply to (e.g., 'neutron')
+
+    *Default*: neutron
+
+  :max_realizations:
+    The number of tally realizations after which the weight windows will stop updating.
+
+    *Default*: 1
+
+  :update_interval:
+    The number of tally realizations between weight window updates.
+
+    *Default*: 1
+
+  :on_the_fly:
+    Controls whether or not the tally results are reset after a weight window update.
+
+    *Default*: true
+
+  :method:
+    Method used to update weight window values (currently only 'magic' is supported)
+
+    *Default*: magic
+
+  :update_parameters:
+    Method-specific update parameters used when generating/updating weight windows.
+
+    For MAGIC:
+
+      :value:
+        The type of tally value to use when creating weight windows (one of 'mean' or 'rel_err')
+
+        *Default*: 'mean'
+
+      :threshold:
+        The relative error threshold above which tally results will be ignored.
+
+        *Default*: 1.0
+
+      :ratio:
+        The ratio of the lower to upper weight window bounds.
+
+        *Default*: 5.0
+
+--------------------------------------
+``<weight_windows_file>`` Element
+--------------------------------------
+
+  The ``weight_windows_file`` element has no attributes and contains the path to
+  a weight windows HDF5 file to load during simulation initialization.
+

docs/source/io_formats/statepoint.rst

@@ -4,7 +4,7 @@
 State Point File Format
 =======================
 
-The current version of the statepoint file format is 17.0.
+The current version of the statepoint file format is 18.1.
 
 **/**
 
@@ -68,6 +68,8 @@ The current version of the statepoint file format is 17.0.
 :Attributes: - **n_meshes** (*int*) -- Number of meshes in the problem.
              - **ids** (*int[]*) -- User-defined unique ID of each mesh.
 
+.. _mesh-spec-hdf5:
+
 **/tallies/meshes/mesh <uid>/**
 
 :Datasets: - **type** (*char[]*) -- Type of mesh.
@@ -139,6 +141,8 @@ The current version of the statepoint file format is 17.0.
              - **internal** (*int*) -- Flag indicating the presence of tally
                data (0) or absence of tally data (1). All user defined
                tallies will have a value of 0 unless otherwise instructed.
+             - **multiply_density** (*int*) -- Flag indicating whether reaction
+               rates should be multiplied by atom density (1) or not (0).
 
 :Datasets: - **n_realizations** (*int*) -- Number of realizations.
            - **n_filters** (*int*) -- Number of filters used.

docs/source/io_formats/tallies.rst

@@ -69,6 +69,12 @@ The ``<tally>`` element accepts the following sub-elements:
     list of valid scores can be found in the :ref:`user's guide
     <usersguide_scores>`.
 
+  :multiply_density:
+    A boolean that indicates whether reaction rate scores should be computed by
+    multiplying by the atom density of a nuclide present in a material.
+
+    *Default*: true
+
   :trigger:
     Precision trigger applied to all filter bins and nuclides for this tally.
     It must specify the trigger's type, threshold and scores to which it will