Merge remote-tracking branch 'origin/develop' into transfer-rates-nuc…

…lides

.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
+-->

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/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/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.
 
 **/**
 

docs/source/quickinstall.rst

@@ -157,7 +157,7 @@ distribution/repository, run:
 
 .. code-block:: sh
 
-    pip install .
+    python -m pip install .
 
 If you want to build a parallel version of OpenMC (using OpenMP or MPI),
 directions can be found in the :ref:`detailed installation instructions

docs/source/usersguide/basics.rst

@@ -83,12 +83,12 @@ Creating Input Files
 .. currentmodule:: openmc
 
 The most rudimentary option for creating input files is to simply write them
-from scratch using the :ref:`XML format specifications
-<io_file_formats_input>`. This approach will feel familiar to users of other
-Monte Carlo codes such as MCNP and Serpent, with the added bonus that the XML
-formats feel much more "readable". Alternatively, input files can be generated
-using OpenMC's :ref:`Python API <pythonapi>`, which is introduced in the
-following section.
+from scratch using the :ref:`XML format specifications <io_file_formats_input>`.
+This approach will feel familiar to users of other Monte Carlo codes such as
+MCNP and Serpent, with the added bonus that the XML formats feel much more
+"readable". However, it is strongly recommended to generate input files using
+OpenMC's :ref:`Python API <pythonapi>`, which is introduced in the following
+section.
 
 ----------
 Python API
@@ -178,14 +178,3 @@ energy  electronvolt eV
 time    second       s
 ======= ============ ======
 
-------------------------------------
-ERSN-OpenMC Graphical User Interface
-------------------------------------
-
-A third-party Java-based user-friendly graphical user interface for creating XML
-input files called ERSN-OpenMC_ is developed and maintained by members of the
-Radiation and Nuclear Systems Group at the Faculty of Sciences Tetouan, Morocco.
-The GUI also allows one to automatically download prerequisites for installing and
-running OpenMC.
-
-.. _ERSN-OpenMC: https://github.com/EL-Bakkali-Jaafar/ERSN-OpenMC

docs/source/usersguide/install.rst

@@ -488,13 +488,13 @@ OpenMC locally by specifying an install prefix when running cmake:
 The ``CMAKE_INSTALL_PREFIX`` variable can be changed to any path for which you
 have write-access.
 
-Compiling on Windows 10
------------------------
+Compiling on Windows
+--------------------
 
-Recent versions of Windows 10 include a subsystem for Linux that allows one to
-run Bash within Ubuntu running in Windows. First, follow the installation guide
-`here <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_ to get Bash
-on Ubuntu on Windows setup. Once you are within bash, obtain the necessary
+Recent versions of Windows include a subsystem for Linux that allows one to run
+Bash within Ubuntu running in Windows. First, follow the installation guide
+`here <https://learn.microsoft.com/en-us/windows/wsl/install>`_ to get Bash on
+Ubuntu on Windows set up. Once you are within bash, obtain the necessary
 :ref:`prerequisites <prerequisites>` via ``apt``. Finally, follow the
 :ref:`instructions for compiling on linux <compile_linux>`.
 
@@ -522,7 +522,7 @@ distribution/repository, run:
 
 .. code-block:: sh
 
-    pip install .
+    python -m pip install .
 
 pip will first check that all :ref:`required third-party packages
 <usersguide_python_prereqs>` have been installed, and if they are not present,
@@ -608,15 +608,15 @@ for OpenMC. Thus, the install process would proceed as follows:
     make install
 
     cd ..
-    MPICC=<path to mpicc> pip install mpi4py
-    HDF5_DIR=<path to HDF5> pip install --no-binary=h5py h5py
+    MPICC=<path to mpicc> python -m pip install mpi4py
+    HDF5_DIR=<path to HDF5> python -m pip install --no-binary=h5py h5py
 
 If you are using parallel HDF5, you'll also need to make sure the right MPI
 wrapper is used when installing h5py:
 
 .. code-block:: sh
 
-    CC=<path to mpicc> HDF5_MPI=ON HDF5_DIR=<path to HDF5> pip install --no-binary=h5py h5py
+    CC=<path to mpicc> HDF5_MPI=ON HDF5_DIR=<path to HDF5> python -m pip install --no-binary=h5py h5py
 
 .. _Conda: https://conda.io/en/latest/
 .. _pip: https://pip.pypa.io/en/stable/

openmc/deplete/abc.py

@@ -274,8 +274,7 @@ def divide_by_atoms(self, number):
         Parameters
         ----------
         number : iterable of float
-            Number density [atoms/b-cm] of each nuclide tracked in the
-            calculation.
+            Number of each nuclide in [atom] tracked in the calculation.
 
         Returns
         -------

openmc/deplete/helpers.py

@@ -26,6 +26,7 @@
     "ConstantFissionYieldHelper", "FissionYieldCutoffHelper",
     "AveragedFissionYieldHelper", "FluxCollapseHelper")
 
+
 class TalliedFissionYieldHelper(FissionYieldHelper):
     """Abstract class for computing fission yields with tallies
 
@@ -159,22 +160,23 @@ def nuclides(self, nuclides):
     def generate_tallies(self, materials, scores):
         """Produce one-group reaction rate tally
 
-        Uses the :mod:`openmc.lib` to generate a tally
-        of relevant reactions across all burnable materials.
+        Uses the :mod:`openmc.lib` to generate a tally of relevant reactions
+        across all burnable materials.
 
         Parameters
         ----------
-        materials : iterable of :class:`openmc.Material`
-            Burnable materials in the problem. Used to
-            construct a :class:`openmc.MaterialFilter`
+        materials : iterable of :class:`openmc.lib.Material`
+            Burnable materials in the problem. Used to construct a
+            :class:`openmc.lib.MaterialFilter`
         scores : iterable of str
-            Reaction identifiers, e.g. ``"(n, fission)"``,
-            ``"(n, gamma)"``, needed for the reaction rate tally.
+            Reaction identifiers, e.g. ``"(n, fission)"``, ``"(n, gamma)"``,
+            needed for the reaction rate tally.
         """
         self._rate_tally = Tally()
         self._rate_tally.writable = False
         self._rate_tally.scores = scores
         self._rate_tally.filters = [MaterialFilter(materials)]
+        self._rate_tally.multiply_density = False
         self._rate_tally_means_cache = None
 
     @property
@@ -194,7 +196,7 @@ def reset_tally_means(self):
         """
         self._rate_tally_means_cache = None
 
-    def get_material_rates(self, mat_id, nuc_index, react_index):
+    def get_material_rates(self, mat_id, nuc_index, rx_index):
         """Return an array of reaction rates for a material
 
         Parameters
@@ -204,7 +206,7 @@ def get_material_rates(self, mat_id, nuc_index, react_index):
         nuc_index : iterable of int
             Index for each nuclide in :attr:`nuclides` in the
             desired reaction rate matrix
-        react_index : iterable of int
+        rx_index : iterable of int
             Index for each reaction scored in the tally
 
         Returns
@@ -215,9 +217,8 @@ def get_material_rates(self, mat_id, nuc_index, react_index):
         """
         self._results_cache.fill(0.0)
         full_tally_res = self.rate_tally_means[mat_id]
-        for i_tally, (i_nuc, i_react) in enumerate(
-                product(nuc_index, react_index)):
-            self._results_cache[i_nuc, i_react] = full_tally_res[i_tally]
+        for i_tally, (i_nuc, i_rx) in enumerate(product(nuc_index, rx_index)):
+            self._results_cache[i_nuc, i_rx] = full_tally_res[i_tally]
 
         return self._results_cache
 
@@ -304,6 +305,7 @@ def generate_tallies(self, materials, scores):
             self._rate_tally.writable = False
             self._rate_tally.scores = self._reactions_direct
             self._rate_tally.filters = [MaterialFilter(materials)]
+            self._rate_tally.multiply_density = False
             self._rate_tally_means_cache = None
             if self._nuclides_direct is not None:
                 # check if any direct tally nuclides are requested that are not
@@ -375,13 +377,7 @@ def get_material_rates(self, mat_index, nuc_index, react_index):
 
         mat = self._materials[mat_index]
 
-        # Build nucname: density mapping to enable O(1) lookup in loop below
-        densities = dict(zip(mat.nuclides, mat.densities))
-
         for name, i_nuc in zip(self.nuclides, nuc_index):
-            # Determine density of nuclide
-            density = densities[name]
-
             for mt, score, i_rx in zip(self._mts, self._scores, react_index):
                 if score in self._reactions_direct and name in nuclides_direct:
                     # Determine index in rx_rates
@@ -396,8 +392,7 @@ def get_material_rates(self, mat_index, nuc_index, react_index):
                     rate_per_nuc = nuc.collapse_rate(
                         mt, mat.temperature, self._energies, flux)
 
-                    # Multiply by density to get absolute reaction rate
-                    self._results_cache[i_nuc, i_rx] = rate_per_nuc * density
+                    self._results_cache[i_nuc, i_rx] = rate_per_nuc
 
         return self._results_cache