Merge pull request #2 from cn-skywalker/virtual_lattice_0.15.2

Virtual lattice 0.15.2

.clang-format

@@ -84,6 +84,7 @@ PenaltyBreakTemplateDeclaration: 10
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
 PointerAlignment: Left
+QualifierAlignment: Left
 ReflowComments:  true
 SortIncludes:    true
 SortUsingDeclarations: true

.git_archival.txt

@@ -0,0 +1,3 @@
+commit: $Format:%H$
+commit-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.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 or enhancement 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) (version 15) 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/ci.yml

@@ -22,10 +22,10 @@ env:
 
 jobs:
   main:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ["3.11"]
         mpi: [n, y]
         omp: [n, y]
         dagmc: [n]
@@ -34,30 +34,30 @@ jobs:
         vectfit: [n]
 
         include:
-          - python-version: 3.6
+          - python-version: "3.12"
             omp: n
             mpi: n
-          - python-version: 3.7
+          - python-version: "3.13"
             omp: n
             mpi: n
           - dagmc: y
-            python-version: 3.8
+            python-version: "3.11"
             mpi: y
             omp: y
           - libmesh: y
-            python-version: 3.8
+            python-version: "3.11"
             mpi: y
             omp: y
           - libmesh: y
-            python-version: 3.8
+            python-version: "3.11"
             mpi: n
             omp: y
           - event: y
-            python-version: 3.8
+            python-version: "3.11"
             omp: y
             mpi: n
           - vectfit: y
-            python-version: 3.8
+            python-version: "3.11"
             omp: n
             mpi: y
     name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }},
@@ -73,62 +73,143 @@ jobs:
       EVENT: ${{ matrix.event }}
       VECTFIT: ${{ matrix.vectfit }}
       LIBMESH: ${{ matrix.libmesh }}
+      NPY_DISABLE_CPU_FEATURES: "AVX512F AVX512_SKX"
+      OPENBLAS_NUM_THREADS: 1
+      PYTEST_ADDOPTS: --cov=openmc --cov-report=lcov:coverage-python.lcov
+      # libfabric complains about fork() as a result of using Python multiprocessing.
+      # We can work around it with RDMAV_FORK_SAFE=1 in libfabric < 1.13 and with
+      # FI_EFA_FORK_SAFE=1 in more recent versions.
+      RDMAV_FORK_SAFE: 1
 
     steps:
-      - uses: actions/checkout@v2
+      - name: Setup cmake
+        uses: jwlawson/actions-setup-cmake@v2
+        with:
+          cmake-version: '3.31'
+
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Environment Variables
         run: |
-          echo "DAGMC_ROOT=$HOME/DAGMC"
           echo "OPENMC_CROSS_SECTIONS=$HOME/nndc_hdf5/cross_sections.xml" >> $GITHUB_ENV
           echo "OPENMC_ENDF_DATA=$HOME/endf-b-vii.1" >> $GITHUB_ENV
+          # get the sha of the last branch commit
+          # for push and workflow_dispatch events, use the current reference head
+          BRANCH_SHA=HEAD
+          # for a pull_request event, use the last reference of the parents of the merge commit
+          if [ "${{ github.event_name }}" == "pull_request" ]; then
+            BRANCH_SHA=$(git rev-list --parents -n 1 HEAD | rev | cut -d" " -f 1 | rev)
+          fi
+          COMMIT_MESSAGE=$(git log $BRANCH_SHA -1 --pretty=%B | tr '\n' ' ')
+          echo ${COMMIT_MESSAGE}
+          echo "COMMIT_MESSAGE=${COMMIT_MESSAGE}" >> $GITHUB_ENV
 
       - name: Apt dependencies
         shell: bash
         run: |
           sudo apt -y update
           sudo apt install -y libpng-dev \
-                              libmpich-dev \
                               libnetcdf-dev \
                               libpnetcdf-dev \
                               libhdf5-serial-dev \
-                              libhdf5-mpich-dev \
                               libeigen3-dev
+
+      - name: Optional apt dependencies for MPI
+        shell: bash
+        if: ${{ matrix.mpi == 'y' }}
+        run: |
+          sudo apt install -y libhdf5-mpich-dev \
+                              libmpich-dev
           sudo update-alternatives --set mpi /usr/bin/mpicc.mpich
           sudo update-alternatives --set mpirun /usr/bin/mpirun.mpich
           sudo update-alternatives --set mpi-x86_64-linux-gnu /usr/include/x86_64-linux-gnu/mpich
 
+      - name: Optional apt dependencies for vectfit
+        shell: bash
+        if: ${{ matrix.vectfit == 'y' }}
+        run: sudo apt install -y libblas-dev liblapack-dev
+
       - name: install
         shell: bash
         run: |
           echo "$HOME/NJOY2016/build" >> $GITHUB_PATH
           $GITHUB_WORKSPACE/tools/ci/gha-install.sh
 
+      - name: display-config
+        shell: bash
+        run: |
+          openmc -v
+
+      - name: cache-xs
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/nndc_hdf5
+            ~/endf-b-vii.1
+          key: ${{ runner.os }}-build-xs-cache
+
       - name: before
         shell: bash
         run: $GITHUB_WORKSPACE/tools/ci/gha-before-script.sh
 
       - name: test
         shell: bash
-        run: $GITHUB_WORKSPACE/tools/ci/gha-script.sh
+        run: |
+          CTEST_OUTPUT_ON_FAILURE=1 make test -C $GITHUB_WORKSPACE/build/
+          $GITHUB_WORKSPACE/tools/ci/gha-script.sh
 
-      - name: after_success
+      - name: Setup tmate debug session
+        continue-on-error: true
+        if: ${{ contains(env.COMMIT_MESSAGE, '[gha-debug]') }}
+        uses: mxschmitt/action-tmate@v3
+        timeout-minutes: 10
+
+      - name: Generate C++ coverage (gcovr)
         shell: bash
         run: |
-          cpp-coveralls -i src -i include --exclude-pattern "/usr/*" --dump cpp_cov.json
-          coveralls --merge=cpp_cov.json --service=github
+          # Produce LCOV directly from gcov data in the build tree
+          gcovr \
+            --root "$GITHUB_WORKSPACE" \
+            --object-directory "$GITHUB_WORKSPACE/build" \
+            --filter "$GITHUB_WORKSPACE/src" \
+            --filter "$GITHUB_WORKSPACE/include" \
+            --exclude "$GITHUB_WORKSPACE/src/external/.*" \
+            --exclude "$GITHUB_WORKSPACE/src/include/openmc/external/.*" \
+            --gcov-ignore-errors source_not_found \
+            --gcov-ignore-errors output_error \
+            --gcov-ignore-parse-errors suspicious_hits.warn \
+            --print-summary \
+            --lcov -o coverage-cpp.lcov || true
+
+      - name: Merge C++ and Python coverage
+        shell: bash
+        run: |
+          # Merge C++ and Python LCOV into a single file for upload
+          cat coverage-cpp.lcov coverage-python.lcov > coverage.lcov
+
+      - name: Upload coverage to Coveralls
+        if: ${{ hashFiles('coverage.lcov') != '' }}
+        uses: coverallsapp/github-action@v2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          parallel: true
+          flag-name: C++ and Python
+          path-to-lcov: coverage.lcov
 
   finish:
     needs: main
     runs-on: ubuntu-latest
     steps:
       - name: Coveralls Finished
-        uses: coverallsapp/github-action@master
+        uses: coverallsapp/github-action@v2
         with:
-          github-token: ${{ secrets.github_token }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
           parallel-finished: true

.github/workflows/dockerhub-publish-dagmc-libmesh.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:latest-dagmc-libmesh

.github/workflows/dockerhub-publish-dagmc.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:latest-dagmc

.github/workflows/dockerhub-publish-dev.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop

.github/workflows/dockerhub-publish-develop-dagmc-libmesh.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop-dagmc-libmesh

.github/workflows/dockerhub-publish-develop-dagmc.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop-dagmc

.github/workflows/dockerhub-publish-develop-libmesh.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:develop-libmesh

.github/workflows/dockerhub-publish-libmesh.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:latest-libmesh

.github/workflows/dockerhub-publish-release-dagmc-libmesh.yml

@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc-libmesh

.github/workflows/dockerhub-publish-release-dagmc.yml

@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}-dagmc

.github/workflows/dockerhub-publish-release-libmesh.yml

@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}-libmesh

.github/workflows/dockerhub-publish-release.yml

@@ -8,25 +8,25 @@ jobs:
   main:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set env
         run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:${{ env.RELEASE_VERSION }}

.github/workflows/dockerhub-publish.yml

@@ -10,20 +10,20 @@ jobs:
     steps:
       -
         name: Set up QEMU
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
       -
         name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       -
         name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v3 
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       -
         name: Build and push
         id: docker_build
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
           push: true
           tags: openmc/openmc:latest

.github/workflows/format-check.yml

@@ -0,0 +1,32 @@
+name: C++ Format Check
+
+on:
+  # allow workflow to be run manually
+  workflow_dispatch:
+
+  pull_request:
+    branches:
+      - develop
+      - master
+
+jobs:
+  cpp-linter:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - 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

.gitignore

@@ -3,6 +3,7 @@
 *.o
 *.log
 *.out
+*.pkl
 
 # Compiler python objects
 *.pyc

.gitmodules

@@ -1,9 +1,6 @@
 [submodule "vendor/pugixml"]
 	path = vendor/pugixml
 	url = https://github.com/zeux/pugixml.git
-[submodule "vendor/gsl-lite"]
-	path = vendor/gsl-lite
-	url = https://github.com/martinmoene/gsl-lite.git
 [submodule "vendor/xtensor"]
 	path = vendor/xtensor
 	url = https://github.com/xtensor-stack/xtensor.git
@@ -13,3 +10,6 @@
 [submodule "vendor/fmt"]
 	path = vendor/fmt
 	url = https://github.com/fmtlib/fmt.git
+[submodule "vendor/Catch2"]
+	path = vendor/Catch2
+	url = https://github.com/catchorg/Catch2.git

.readthedocs.yaml

@@ -1,13 +1,18 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "3.9"
-
+    python: "3.12"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow || true
 sphinx:
   configuration: docs/source/conf.py
 
 python:
   install:
-    - requirements: docs/requirements-rtd.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

CITATION.cff

@@ -0,0 +1,34 @@
+preferred-citation:
+  authors:
+  - family-names: Romano
+    given-names: Paul K.
+    orcid: "https://orcid.org/0000-0002-1147-045X"
+  - final-names: Horelik
+    given-names: Nicholas E.
+  - family-names: Herman
+    given-names: Bryan R.
+  - family-names: Nelson
+    given-names: Adam G.
+    orcid: "https://orcid.org/0000-0002-3614-0676"
+  - family-names: Forget
+    given-names: Benoit
+    orcid: "https://orcid.org/0000-0003-1459-7672"
+  - family-names: Smith
+    given-names: Kord
+  contact:
+  - family-names: Romano
+    given-names: Paul K.
+    orcid: "https://orcid.org/0000-0002-1147-045X"
+  doi: 10.1016/j.anucene.2014.07.048
+  issn: 0306-4549
+  volume: 82
+  journal: Annals of Nuclear Energy
+  publisher:
+    name: Elsevier
+  start: 90
+  end: 97
+  year: 2015
+  month: 8
+  title: "OpenMC: A state-of-the-art Monte Carlo code for research and development"
+  type: article
+  url: "https://doi.org/10.1016/j.anucene.2014.07.048"

CMakeLists.txt

@@ -1,11 +1,18 @@
-cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.16 FATAL_ERROR)
 project(openmc C CXX)
 
-# Set version numbers
-set(OPENMC_VERSION_MAJOR 0)
-set(OPENMC_VERSION_MINOR 13)
-set(OPENMC_VERSION_RELEASE 0)
-set(OPENMC_VERSION ${OPENMC_VERSION_MAJOR}.${OPENMC_VERSION_MINOR}.${OPENMC_VERSION_RELEASE})
+# Set module path
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
+
+include(GetVersionFromGit)
+
+# Output version information
+message(STATUS "OpenMC version: ${OPENMC_VERSION}")
+message(STATUS "OpenMC dev state: ${OPENMC_DEV_STATE}")
+message(STATUS "OpenMC commit hash: ${OPENMC_COMMIT_HASH}")
+message(STATUS "OpenMC commit count: ${OPENMC_COMMIT_COUNT}")
+
+# Generate version.h
 configure_file(include/openmc/version.h.in "${CMAKE_BINARY_DIR}/include/openmc/version.h" @ONLY)
 
 # Setup output directories
@@ -13,75 +20,134 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
 
-# Set module path
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
-
-# Allow user to specify <project>_ROOT variables
-if (NOT (CMAKE_VERSION VERSION_LESS 3.12))
-  cmake_policy(SET CMP0074 NEW)
+# Enable correct usage of CXX_EXTENSIONS
+if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.22)
+  cmake_policy(SET CMP0128 NEW)
 endif()
 
 #===============================================================================
 # Command line options
 #===============================================================================
 
-option(openmp   "Enable shared-memory parallelism with OpenMP"         ON)
-option(profile  "Compile with profiling flags"                         OFF)
-option(debug    "Compile with debug flags"                             OFF)
-option(optimize "Turn on all compiler optimization flags"              OFF)
-option(coverage "Compile with coverage analysis flags"                 OFF)
-option(dagmc    "Enable support for DAGMC (CAD) geometry"              OFF)
-option(libmesh  "Enable support for libMesh unstructured mesh tallies" OFF)
+option(OPENMC_USE_OPENMP      "Enable shared-memory parallelism with OpenMP"         ON)
+option(OPENMC_BUILD_TESTS     "Build tests"                                          ON)
+option(OPENMC_ENABLE_PROFILE  "Compile with profiling flags"                         OFF)
+option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags"                 OFF)
+option(OPENMC_USE_DAGMC       "Enable support for DAGMC (CAD) geometry"              OFF)
+option(OPENMC_USE_LIBMESH     "Enable support for libMesh unstructured mesh tallies" OFF)
+option(OPENMC_USE_MPI         "Enable MPI"                                           OFF)
+option(OPENMC_USE_UWUW        "Enable UWUW"                                          OFF)
+option(OPENMC_FORCE_VENDORED_LIBS "Explicitly use submodules defined in 'vendor'"    OFF)
+
+message(STATUS "OPENMC_USE_OPENMP ${OPENMC_USE_OPENMP}")
+message(STATUS "OPENMC_BUILD_TESTS ${OPENMC_BUILD_TESTS}")
+message(STATUS "OPENMC_ENABLE_PROFILE ${OPENMC_ENABLE_PROFILE}")
+message(STATUS "OPENMC_ENABLE_COVERAGE ${OPENMC_ENABLE_COVERAGE}")
+message(STATUS "OPENMC_USE_DAGMC ${OPENMC_USE_DAGMC}")
+message(STATUS "OPENMC_USE_LIBMESH ${OPENMC_USE_LIBMESH}")
+message(STATUS "OPENMC_USE_MPI ${OPENMC_USE_MPI}")
+message(STATUS "OPENMC_USE_UWUW ${OPENMC_USE_UWUW}")
+message(STATUS "OPENMC_FORCE_VENDORED_LIBS ${OPENMC_FORCE_VENDORED_LIBS}")
+
+# Warnings for deprecated options
+foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh")
+  if(DEFINED ${OLD_OPT})
+    string(TOUPPER ${OLD_OPT} OPT_UPPER)
+    if ("${OLD_OPT}" STREQUAL "profile" OR "${OLD_OPT}" STREQUAL "coverage")
+      set(NEW_OPT_PREFIX "OPENMC_ENABLE")
+    else()
+      set(NEW_OPT_PREFIX "OPENMC_USE")
+    endif()
+    message(WARNING "The OpenMC CMake option '${OLD_OPT}' has been deprecated. "
+      "Its value will be ignored. "
+      "Please use '-D${NEW_OPT_PREFIX}_${OPT_UPPER}=${${OLD_OPT}}' instead.")
+    unset(${OLD_OPT} CACHE)
+  endif()
+endforeach()
+
+foreach(OLD_BLD in ITEMS "debug" "optimize")
+  if(DEFINED ${OLD_BLD})
+    if("${OLD_BLD}" STREQUAL "debug")
+      set(BLD_VAR "Debug")
+    else()
+      set(BLD_VAR "Release")
+    endif()
+    message(WARNING "The OpenMC CMake option '${OLD_BLD}' has been deprecated. "
+      "Its value will be ignored. "
+      "OpenMC now uses the CMAKE_BUILD_TYPE variable to set the build mode. "
+      "Please use '-DCMAKE_BUILD_TYPE=${BLD_VAR}' instead.")
+    unset(${OLD_BLD} CACHE)
+  endif()
+endforeach()
+
+#===============================================================================
+# Set a default build configuration if not explicitly specified
+#===============================================================================
+
+if(NOT CMAKE_BUILD_TYPE)
+    message(STATUS "No build type selected, defaulting to RelWithDebInfo")
+    set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build" FORCE)
+endif()
+
+#===============================================================================
+# OpenMP for shared-memory parallelism (and GPU support some day!)
+#===============================================================================
+
+if(OPENMC_USE_OPENMP)
+  find_package(OpenMP REQUIRED)
+endif()
 
 #===============================================================================
 # MPI for distributed-memory parallelism
 #===============================================================================
 
-set(MPI_ENABLED FALSE)
-if(${CMAKE_CXX_COMPILER} MATCHES "(mpi[^/]*|CC)$")
-  message(STATUS "Detected MPI wrapper: ${CMAKE_CXX_COMPILER}")
-  set(MPI_ENABLED TRUE)
+if(OPENMC_USE_MPI)
+  find_package(MPI REQUIRED)
 endif()
 
+#===============================================================================
+# Helper macro for finding a dependency
+#===============================================================================
+
+macro(find_package_write_status pkg)
+  find_package(${pkg} QUIET NO_SYSTEM_ENVIRONMENT_PATH)
+  if(${pkg}_FOUND)
+    message(STATUS "Found ${pkg}: ${${pkg}_DIR} (version ${${pkg}_VERSION})")
+  else()
+    message(STATUS "Did not find ${pkg}, will use submodule instead")
+  endif()
+endmacro()
+
 #===============================================================================
 # DAGMC Geometry Support - need DAGMC/MOAB
 #===============================================================================
-if(dagmc)
+
+if(OPENMC_USE_DAGMC)
   find_package(DAGMC REQUIRED PATH_SUFFIXES lib/cmake)
   if (${DAGMC_VERSION} VERSION_LESS 3.2.0)
-    message(FATAL_ERROR "Discovered DAGMC Version: ${DAGMC_VERSION}. \
-    Please update DAGMC to version 3.2.0 or greater.")
+    message(FATAL_ERROR "Discovered DAGMC Version: ${DAGMC_VERSION}."
+      "Please update DAGMC to version 3.2.0 or greater.")
   endif()
-endif()
+  message(STATUS "Found DAGMC: ${DAGMC_DIR} (version ${DAGMC_VERSION})")
 
-#===============================================================================
-# Check for submodules perhaps already on system
-#===============================================================================
-
-# If not found, we just pull appropriate versions from github and build them.
-find_package(fmt QUIET NO_SYSTEM_ENVIRONMENT_PATH)
-if(fmt_FOUND)
-  message(STATUS "Found fmt: ${fmt_DIR} (version ${fmt_VERSION})")
-else()
-  message(STATUS "Did not find fmt, will use submodule instead")
-endif()
-find_package(pugixml QUIET NO_SYSTEM_ENVIRONMENT_PATH)
-if(pugixml_FOUND)
-  message(STATUS "Found pugixml: ${pugixml_DIR}")
-else()
-  message(STATUS "Did not find pugixml, will use submodule instead")
+  # Check if UWUW is needed and available
+  if(OPENMC_USE_UWUW AND NOT DAGMC_BUILD_UWUW)
+    message(FATAL_ERROR "UWUW is enabled but DAGMC was not configured with UWUW.")
+  endif()
 endif()
 
 #===============================================================================
 # libMesh Unstructured Mesh Support
 #===============================================================================
-if(libmesh)
+
+if(OPENMC_USE_LIBMESH)
   find_package(LIBMESH REQUIRED)
 endif()
 
 #===============================================================================
 # libpng
 #===============================================================================
+
 find_package(PNG)
 
 #===============================================================================
@@ -102,11 +168,16 @@ if(NOT DEFINED HDF5_PREFER_PARALLEL)
 endif()
 
 find_package(HDF5 REQUIRED COMPONENTS C HL)
+
+# Remove HDF5 transitive dependencies that are system libraries
+list(FILTER HDF5_LIBRARIES EXCLUDE REGEX ".*lib(pthread|dl|m).*")
+message(STATUS "HDF5 Libraries: ${HDF5_LIBRARIES}")
+
 if(HDF5_IS_PARALLEL)
-  if(NOT MPI_ENABLED)
-    message(FATAL_ERROR "Parallel HDF5 was detected, but the detected compiler,\
-     ${CMAKE_CXX_COMPILER}, does not support MPI. An MPI-capable compiler must \
-     be used with parallel HDF5.")
+  if(NOT OPENMC_USE_MPI)
+    message(FATAL_ERROR "Parallel HDF5 was detected, but MPI was not enabled.\
+      To use parallel HDF5, OpenMC needs to be built with MPI support by passing\
+      -DOPENMC_USE_MPI=ON when calling cmake.")
   endif()
   message(STATUS "Using parallel HDF5")
 endif()
@@ -114,7 +185,7 @@ endif()
 # Version 1.12 of HDF5 deprecates the H5Oget_info_by_idx() interface.
 # Thus, we give these flags to allow usage of the old interface in newer
 # versions of HDF5.
-if(NOT (${HDF5_VERSION} VERSION_LESS 1.12.0))
+if(${HDF5_VERSION} VERSION_GREATER_EQUAL 1.12.0)
   list(APPEND cxxflags -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1)
 endif()
 
@@ -125,30 +196,13 @@ endif()
 # Skip for Visual Studio which has its own configurations through GUI
 if(NOT MSVC)
 
-if(openmp)
-  # Requires CMake 3.1+
-  find_package(OpenMP)
-  if(OPENMP_FOUND)
-    list(APPEND cxxflags ${OpenMP_CXX_FLAGS})
-    list(APPEND ldflags ${OpenMP_CXX_FLAGS})
-  endif()
-endif()
-
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-list(APPEND cxxflags -O2)
-if(debug)
-  list(REMOVE_ITEM cxxflags -O2)
-  list(APPEND cxxflags -g -O0)
-endif()
-if(profile)
+if(OPENMC_ENABLE_PROFILE)
   list(APPEND cxxflags -g -fno-omit-frame-pointer)
 endif()
-if(optimize)
-  list(REMOVE_ITEM cxxflags -O2)
-  list(APPEND cxxflags -O3)
-endif()
-if(coverage)
+
+if(OPENMC_ENABLE_COVERAGE)
   list(APPEND cxxflags --coverage)
   list(APPEND ldflags --coverage)
 endif()
@@ -162,8 +216,6 @@ endif()
 #===============================================================================
 # Update git submodules as needed
 #===============================================================================
-
-find_package(Git)
 if(GIT_FOUND AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
   option(GIT_SUBMODULE "Check submodules during build" ON)
   if(GIT_SUBMODULE)
@@ -188,42 +240,63 @@ endif()
 # pugixml library
 #===============================================================================
 
-if (NOT pugixml_FOUND)
+if(OPENMC_FORCE_VENDORED_LIBS)
   add_subdirectory(vendor/pugixml)
   set_target_properties(pugixml PROPERTIES CXX_STANDARD 14 CXX_EXTENSIONS OFF)
+else()
+  find_package_write_status(pugixml)
+  if (NOT pugixml_FOUND)
+    add_subdirectory(vendor/pugixml)
+    set_target_properties(pugixml PROPERTIES CXX_STANDARD 14 CXX_EXTENSIONS OFF)
+  endif()
 endif()
 
 #===============================================================================
 # {fmt} library
 #===============================================================================
 
-if (NOT fmt_FOUND)
+if(OPENMC_FORCE_VENDORED_LIBS)
   set(FMT_INSTALL ON CACHE BOOL "Generate the install target.")
   add_subdirectory(vendor/fmt)
+else()
+  find_package_write_status(fmt)
+  if (NOT fmt_FOUND)
+    set(FMT_INSTALL ON CACHE BOOL "Generate the install target.")
+    add_subdirectory(vendor/fmt)
+  endif()
 endif()
 
 #===============================================================================
 # xtensor header-only library
 #===============================================================================
 
-# CMake 3.13+ will complain about policy CMP0079 unless it is set explicitly
-if (NOT (CMAKE_VERSION VERSION_LESS 3.13))
-  cmake_policy(SET CMP0079 NEW)
+if(OPENMC_FORCE_VENDORED_LIBS)
+  add_subdirectory(vendor/xtl)
+  set(xtl_DIR ${CMAKE_CURRENT_BINARY_DIR}/vendor/xtl)
+  add_subdirectory(vendor/xtensor)
+else()
+  find_package_write_status(xtensor)
+  if (NOT xtensor_FOUND)
+    add_subdirectory(vendor/xtl)
+    set(xtl_DIR ${CMAKE_CURRENT_BINARY_DIR}/vendor/xtl)
+    add_subdirectory(vendor/xtensor)
+  endif()
 endif()
 
-add_subdirectory(vendor/xtl)
-set(xtl_DIR ${CMAKE_CURRENT_BINARY_DIR}/vendor/xtl)
-add_subdirectory(vendor/xtensor)
-
 #===============================================================================
-# GSL header-only library
+# Catch2 library
 #===============================================================================
 
-add_subdirectory(vendor/gsl-lite)
-
-# Make sure contract violations throw exceptions
-target_compile_definitions(gsl-lite-v1 INTERFACE GSL_THROW_ON_CONTRACT_VIOLATION)
-target_compile_definitions(gsl-lite-v1 INTERFACE gsl_CONFIG_ALLOWS_NONSTRICT_SPAN_COMPARISON=1)
+if(OPENMC_BUILD_TESTS)
+  if (OPENMC_FORCE_VENDORED_LIBS)
+    add_subdirectory(vendor/Catch2)
+  else()
+    find_package_write_status(Catch2)
+    if (NOT Catch2_FOUND)
+      add_subdirectory(vendor/Catch2)
+    endif()
+  endif()
+endif()
 
 #===============================================================================
 # RPATH information
@@ -254,18 +327,6 @@ if("${isSystemDir}" STREQUAL "-1")
   set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_FULL_LIBDIR}")
 endif()
 
-#===============================================================================
-# faddeeva library
-#===============================================================================
-
-add_library(faddeeva STATIC vendor/faddeeva/Faddeeva.cc)
-target_include_directories(faddeeva
-  PUBLIC
-    $<INSTALL_INTERFACE:include/faddeeva>
-    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/vendor/faddeeva>
-)
-target_compile_options(faddeeva PRIVATE ${cxxflags})
-
 #===============================================================================
 # libopenmc
 #===============================================================================
@@ -274,10 +335,11 @@ list(APPEND libopenmc_SOURCES
   src/bank.cpp
   src/boundary_condition.cpp
   src/bremsstrahlung.cpp
-  src/dagmc.cpp
   src/cell.cpp
+  src/chain.cpp
   src/cmfd_solver.cpp
   src/cross_sections.cpp
+  src/dagmc.cpp
   src/distribution.cpp
   src/distribution_angle.cpp
   src/distribution_energy.cpp
@@ -287,18 +349,23 @@ list(APPEND libopenmc_SOURCES
   src/endf.cpp
   src/error.cpp
   src/event.cpp
-  src/initialize.cpp
+  src/file_utils.cpp
   src/finalize.cpp
   src/geometry.cpp
   src/geometry_aux.cpp
   src/hdf5_interface.cpp
+  src/ifp.cpp
+  src/initialize.cpp
   src/lattice.cpp
   src/material.cpp
   src/math_functions.cpp
+  src/mcpl_interface.cpp
   src/mesh.cpp
   src/message_passing.cpp
   src/mgxs.cpp
   src/mgxs_interface.cpp
+  src/ncrystal_interface.cpp
+  src/ncrystal_load.cpp
   src/nuclide.cpp
   src/output.cpp
   src/particle.cpp
@@ -313,6 +380,12 @@ list(APPEND libopenmc_SOURCES
   src/progress_bar.cpp
   src/random_dist.cpp
   src/random_lcg.cpp
+  src/random_ray/random_ray_simulation.cpp
+  src/random_ray/random_ray.cpp
+  src/random_ray/flat_source_domain.cpp
+  src/random_ray/linear_source_domain.cpp
+  src/random_ray/moment_matrix.cpp
+  src/random_ray/source_region.cpp
   src/reaction.cpp
   src/reaction_product.cpp
   src/scattdata.cpp
@@ -331,20 +404,25 @@ list(APPEND libopenmc_SOURCES
   src/tallies/derivative.cpp
   src/tallies/filter.cpp
   src/tallies/filter_azimuthal.cpp
-  src/tallies/filter_cellborn.cpp
-  src/tallies/filter_cellfrom.cpp
   src/tallies/filter_cell.cpp
   src/tallies/filter_cell_instance.cpp
+  src/tallies/filter_cellborn.cpp
+  src/tallies/filter_cellfrom.cpp
+  src/tallies/filter_collision.cpp
   src/tallies/filter_delayedgroup.cpp
   src/tallies/filter_distribcell.cpp
-  src/tallies/filter_energyfunc.cpp
   src/tallies/filter_energy.cpp
-  src/tallies/filter_collision.cpp
+  src/tallies/filter_energyfunc.cpp
   src/tallies/filter_legendre.cpp
   src/tallies/filter_material.cpp
+  src/tallies/filter_materialfrom.cpp
   src/tallies/filter_mesh.cpp
+  src/tallies/filter_meshborn.cpp
+  src/tallies/filter_meshmaterial.cpp
   src/tallies/filter_meshsurface.cpp
   src/tallies/filter_mu.cpp
+  src/tallies/filter_musurface.cpp
+  src/tallies/filter_parent_nuclide.cpp
   src/tallies/filter_particle.cpp
   src/tallies/filter_polar.cpp
   src/tallies/filter_sph_harm.cpp
@@ -352,13 +430,15 @@ list(APPEND libopenmc_SOURCES
   src/tallies/filter_surface.cpp
   src/tallies/filter_time.cpp
   src/tallies/filter_universe.cpp
+  src/tallies/filter_weight.cpp
   src/tallies/filter_zernike.cpp
   src/tallies/tally.cpp
   src/tallies/tally_scoring.cpp
   src/tallies/trigger.cpp
-  src/timer.cpp
   src/thermal.cpp
+  src/timer.cpp
   src/track_output.cpp
+  src/universe.cpp
   src/urr.cpp
   src/volume_calc.cpp
   src/weight_windows.cpp
@@ -368,7 +448,8 @@ list(APPEND libopenmc_SOURCES
 
 # Add bundled external dependencies
 list(APPEND libopenmc_SOURCES
-  src/external/quartic_solver.cpp)
+  src/external/quartic_solver.cpp
+  src/external/Faddeeva.cc)
 
 # For Visual Studio compilers
 if(MSVC)
@@ -382,6 +463,8 @@ else()
   add_library(libopenmc SHARED ${libopenmc_SOURCES})
 endif()
 
+add_library(OpenMC::libopenmc ALIAS libopenmc)
+
 # Avoid vs error lnk1149 :output filename matches input filename
 if(NOT MSVC)
   set_target_properties(libopenmc PROPERTIES OUTPUT_NAME openmc)
@@ -398,39 +481,42 @@ target_include_directories(libopenmc
 target_compile_options(libopenmc PRIVATE ${cxxflags})
 
 # Add include directory for configured version file
-target_include_directories(libopenmc PRIVATE ${CMAKE_BINARY_DIR}/include)
+target_include_directories(libopenmc
+  PUBLIC $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>)
 
 if (HDF5_IS_PARALLEL)
   target_compile_definitions(libopenmc PRIVATE -DPHDF5)
 endif()
-if (MPI_ENABLED)
+if (OPENMC_USE_MPI)
   target_compile_definitions(libopenmc PUBLIC -DOPENMC_MPI)
 endif()
 
-# Set git SHA1 hash as a compile definition
-if(GIT_FOUND)
-  execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
-                  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-                  RESULT_VARIABLE GIT_SHA1_SUCCESS
-                  OUTPUT_VARIABLE GIT_SHA1
-                  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
-  if(GIT_SHA1_SUCCESS EQUAL 0)
-    target_compile_definitions(libopenmc PRIVATE -DGIT_SHA1="${GIT_SHA1}")
-  endif()
-endif()
-
 # target_link_libraries treats any arguments starting with - but not -l as
 # linker flags. Thus, we can pass both linker flags and libraries together.
 target_link_libraries(libopenmc ${ldflags} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES}
-                      pugixml faddeeva xtensor gsl-lite-v1 fmt::fmt)
+                      xtensor fmt::fmt ${CMAKE_DL_LIBS})
 
-if(dagmc)
-  target_compile_definitions(libopenmc PRIVATE DAGMC)
-  target_link_libraries(libopenmc dagmc-shared uwuw-shared)
+if(TARGET pugixml::pugixml)
+  target_link_libraries(libopenmc pugixml::pugixml)
+else()
+  target_link_libraries(libopenmc pugixml)
 endif()
 
-if(libmesh)
-  target_compile_definitions(libopenmc PRIVATE LIBMESH)
+if(OPENMC_USE_DAGMC)
+  target_compile_definitions(libopenmc PRIVATE OPENMC_DAGMC_ENABLED)
+  target_link_libraries(libopenmc dagmc-shared)
+
+  if(OPENMC_USE_UWUW)
+    target_compile_definitions(libopenmc PRIVATE OPENMC_UWUW_ENABLED)
+    target_link_libraries(libopenmc uwuw-shared)
+  endif()
+elseif(OPENMC_USE_UWUW)
+  set(OPENMC_USE_UWUW OFF)
+  message(FATAL_ERROR "DAGMC must be enabled when UWUW is enabled.")
+endif()
+
+if(OPENMC_USE_LIBMESH)
+  target_compile_definitions(libopenmc PRIVATE OPENMC_LIBMESH_ENABLED)
   target_link_libraries(libopenmc PkgConfig::LIBMESH)
 endif()
 
@@ -439,19 +525,46 @@ if (PNG_FOUND)
   target_link_libraries(libopenmc PNG::PNG)
 endif()
 
+if (OPENMC_USE_OPENMP)
+  target_link_libraries(libopenmc OpenMP::OpenMP_CXX)
+endif()
+
+if (OPENMC_USE_MPI)
+  target_link_libraries(libopenmc MPI::MPI_CXX)
+endif()
+
+if (OPENMC_BUILD_TESTS)
+  # Add cpp tests directory
+  include(CTest)
+  add_subdirectory(tests/cpp_unit_tests)
+endif()
+
+#===============================================================================
+# Log build info that this executable can report later
+#===============================================================================
+target_compile_definitions(libopenmc PRIVATE BUILD_TYPE=${CMAKE_BUILD_TYPE})
+target_compile_definitions(libopenmc PRIVATE COMPILER_ID=${CMAKE_CXX_COMPILER_ID})
+target_compile_definitions(libopenmc PRIVATE COMPILER_VERSION=${CMAKE_CXX_COMPILER_VERSION})
+if (OPENMC_ENABLE_PROFILE)
+  target_compile_definitions(libopenmc PRIVATE PROFILINGBUILD)
+endif()
+if (OPENMC_ENABLE_COVERAGE)
+  target_compile_definitions(libopenmc PRIVATE COVERAGEBUILD)
+endif()
+
 #===============================================================================
 # openmc executable
 #===============================================================================
 add_executable(openmc src/main.cpp)
+add_executable(OpenMC::openmc ALIAS openmc)
 target_compile_options(openmc PRIVATE ${cxxflags})
 target_include_directories(openmc PRIVATE ${CMAKE_BINARY_DIR}/include)
 target_link_libraries(openmc libopenmc)
 
-# Ensure C++14 standard is used. Starting with CMake 3.8, another way this could
-# be done is using the cxx_std_14 compiler feature.
-set_target_properties(
-    openmc libopenmc faddeeva
-    PROPERTIES CXX_STANDARD 14 CXX_EXTENSIONS OFF)
+# Ensure C++17 standard is used and turn off GNU extensions
+target_compile_features(openmc PUBLIC cxx_std_17)
+target_compile_features(libopenmc PUBLIC cxx_std_17)
+set_target_properties(openmc libopenmc PROPERTIES CXX_EXTENSIONS OFF)
 
 #===============================================================================
 # Python package
@@ -471,7 +584,7 @@ configure_file(cmake/OpenMCConfig.cmake.in "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIR
 configure_file(cmake/OpenMCConfigVersion.cmake.in "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfigVersion.cmake" @ONLY)
 
 set(INSTALL_CONFIGDIR ${CMAKE_INSTALL_LIBDIR}/cmake/OpenMC)
-install(TARGETS openmc libopenmc faddeeva
+install(TARGETS openmc libopenmc
   EXPORT openmc-targets
   RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
   LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
@@ -482,7 +595,6 @@ install(EXPORT openmc-targets
   NAMESPACE OpenMC::
   DESTINATION ${INSTALL_CONFIGDIR})
 
-install(DIRECTORY src/relaxng DESTINATION ${CMAKE_INSTALL_DATADIR}/openmc)
 install(FILES
   "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfig.cmake"
   "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/OpenMCConfigVersion.cmake"
@@ -491,7 +603,3 @@ install(FILES man/man1/openmc.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
 install(FILES LICENSE DESTINATION "${CMAKE_INSTALL_DOCDIR}" RENAME copyright)
 install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 install(FILES "${CMAKE_BINARY_DIR}/include/openmc/version.h" DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/openmc)
-
-# Copy headers for vendored dependencies (note that all except faddeeva are handled
-# separately since they are managed by CMake)
-install(DIRECTORY vendor/faddeeva DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})

CODEOWNERS

@@ -5,9 +5,9 @@ openmc/data/ @paulromano
 openmc/lib/ @paulromano
 
 # Depletion
-openmc/deplete/ @drewejohnson
-tests/regression_tests/deplete/ @drewejohnson
-tests/unit_tests/test_deplete_*.py @drewejohnson
+openmc/deplete/ @paulromano
+tests/regression_tests/deplete/ @paulromano
+tests/unit_tests/test_deplete_*.py @paulromano
 
 # MG-related functionality
 openmc/mgxs_library.py @nelsonag
@@ -26,6 +26,12 @@ src/dagmc.cpp @pshriwise
 tests/regression_tests/dagmc/ @pshriwise
 tests/unit_tests/dagmc/ @pshriwise
 
+# Weight windows
+openmc/weight_windows.py @pshriwise
+openmc/lib/weight_windows.py @pshriwise
+src/weight_windows.py @pshriwise
+tests/unit_tests/weightwindows/ @pshriwise
+
 # Photon transport
 openmc/data/BREMX.DAT @amandalund
 openmc/data/compton_profiles.h5 @amandalund
@@ -46,3 +52,16 @@ openmc/lib/plot.py @pshriwise
 
 # Resonance covariance
 openmc/data/resonance_covariance.py @icmeyer
+
+# Docker
+Dockerfile @shimwell
+
+# Random ray
+src/random_ray/ @jtramm
+
+# NCrystal interface
+src/ncrystal_interface.cpp @marquezj @tkittel
+src/ncrystal_load.cpp @marquezj @tkittel
+
+# MCPL interface
+src/mcpl_interface.cpp @ebknudsen

CONTRIBUTING.md

@@ -13,7 +13,7 @@ openmc@anl.gov.
 ## Resources
 
 - [GitHub Repository](https://github.com/openmc-dev/openmc)
-- [Documentation](http://docs.openmc.org/en/latest)
+- [Documentation](https://docs.openmc.org/en/latest)
 - [Discussion Forum](https://openmc.discourse.group)
 - [Slack Community](https://openmc.slack.com/signup) (If you don't see your
   domain listed, contact openmc@anl.gov)

Dockerfile

@@ -15,50 +15,53 @@
 
 # sudo docker run image_name:tag_name or ID with no tag sudo docker run ID number
 
-FROM debian:bullseye-slim
+
+# global ARG as these ARGS are used in multiple stages
+# By default one core is used to compile
+ARG compile_cores=1
 
 # By default this Dockerfile builds OpenMC without DAGMC and LIBMESH support
 ARG build_dagmc=off
 ARG build_libmesh=off
 
-# By default one core is used to compile
-ARG compile_cores=1
+FROM ubuntu:24.04 AS dependencies
+
+ARG compile_cores
+ARG build_dagmc
+ARG build_libmesh
 
 # Set default value of HOME to /root
 ENV HOME=/root
 
-# OpenMC variables
-ARG openmc_branch=master
-ENV OPENMC_REPO='https://github.com/openmc-dev/openmc'
-
 # Embree variables
-ENV EMBREE_TAG='v3.12.2'
+ENV EMBREE_TAG='v4.3.1'
 ENV EMBREE_REPO='https://github.com/embree/embree'
 ENV EMBREE_INSTALL_DIR=$HOME/EMBREE/
 
 # MOAB variables
-ENV MOAB_TAG='5.3.0'
+ENV MOAB_TAG='5.5.1'
 ENV MOAB_REPO='https://bitbucket.org/fathomteam/moab/'
 
 # Double-Down variables
-ENV DD_TAG='v1.0.0'
+ENV DD_TAG='v1.1.0'
 ENV DD_REPO='https://github.com/pshriwise/double-down'
 ENV DD_INSTALL_DIR=$HOME/Double_down
 
 # DAGMC variables
-ENV DAGMC_BRANCH='develop'
+ENV DAGMC_BRANCH='v3.2.4'
 ENV DAGMC_REPO='https://github.com/svalinn/DAGMC'
 ENV DAGMC_INSTALL_DIR=$HOME/DAGMC/
 
 # LIBMESH variables
-ENV LIBMESH_TAG='v1.6.0'
+ENV LIBMESH_TAG='v1.7.1'
 ENV LIBMESH_REPO='https://github.com/libMesh/libmesh'
 ENV LIBMESH_INSTALL_DIR=$HOME/LIBMESH
 
+# NJOY variables
+ENV NJOY_REPO='https://github.com/njoy/NJOY2016'
+
 # Setup environment variables for Docker image
-ENV CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx \
-    LD_LIBRARY_PATH=${DAGMC_INSTALL_DIR}/lib:$LD_LIBRARY_PATH \
-    OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml \
+ENV LD_LIBRARY_PATH=${DAGMC_INSTALL_DIR}/lib:$LD_LIBRARY_PATH \
     OPENMC_ENDF_DATA=/root/endf-b-vii.1 \
     DEBIAN_FRONTEND=noninteractive
 
@@ -68,23 +71,32 @@ RUN apt-get update -y && \
     apt-get install -y \
         python3-pip python-is-python3 wget git build-essential cmake \
         mpich libmpich-dev libhdf5-serial-dev libhdf5-mpich-dev \
-        libpng-dev && \
+        libpng-dev python3-venv && \
     apt-get autoremove
 
+# create virtual enviroment to avoid externally managed environment error
+RUN python3 -m venv openmc_venv
+ENV PATH=/openmc_venv/bin:$PATH
+
 # Update system-provided pip
 RUN pip install --upgrade pip
 
 # Clone and install NJOY2016
-RUN cd $HOME && git clone --depth 1 https://github.com/njoy/NJOY2016.git && \
-    cd NJOY2016 && mkdir build && cd build && \
-    cmake -Dstatic=on .. && make 2>/dev/null -j${compile_cores} install && \
-    rm -rf $HOME/NJOY2016
+RUN cd $HOME \
+    && git clone --single-branch --depth 1 ${NJOY_REPO} \
+    && cd NJOY2016 \
+    && mkdir build \
+    && cd build \
+    && cmake -Dstatic=on .. \
+    && make 2>/dev/null -j${compile_cores} install \
+    && rm -rf $HOME/NJOY2016
 
 
 RUN if [ "$build_dagmc" = "on" ]; then \
         # Install addition packages required for DAGMC
         apt-get -y install libeigen3-dev libnetcdf-dev libtbb-dev libglfw3-dev \
-        && pip install --upgrade numpy cython \
+        && pip install --upgrade numpy \
+        && pip install --no-cache-dir setuptools cython \
         # Clone and install EMBREE
         && mkdir -p $HOME/EMBREE && cd $HOME/EMBREE \
         && git clone --single-branch -b ${EMBREE_TAG} --depth 1 ${EMBREE_REPO} \
@@ -100,7 +112,8 @@ RUN if [ "$build_dagmc" = "on" ]; then \
         mkdir -p $HOME/MOAB && cd $HOME/MOAB \
         && git clone  --single-branch -b ${MOAB_TAG} --depth 1 ${MOAB_REPO} \
         && mkdir build && cd build \
-        && cmake ../moab -DENABLE_HDF5=ON \
+        && cmake ../moab -DCMAKE_BUILD_TYPE=Release \
+                      -DENABLE_HDF5=ON \
                       -DENABLE_NETCDF=ON \
                       -DBUILD_SHARED_LIBS=OFF \
                       -DENABLE_FORTRAN=OFF \
@@ -112,6 +125,7 @@ RUN if [ "$build_dagmc" = "on" ]; then \
         && make 2>/dev/null -j${compile_cores} install \
         && cd pymoab && bash install.sh \
         && python setup.py install \
+        && python -c "import pymoab" \
         && rm -rf $HOME/MOAB ; \
         # Clone and install Double-Down
         mkdir -p $HOME/Double_down && cd $HOME/Double_down \
@@ -165,43 +179,63 @@ RUN if [ "$build_libmesh" = "on" ]; then \
         && rm -rf ${LIBMESH_INSTALL_DIR}/build ${LIBMESH_INSTALL_DIR}/libmesh ; \
     fi
 
+FROM dependencies AS build
+
+ENV HOME=/root
+
+ARG openmc_branch=master
+ENV OPENMC_REPO='https://github.com/openmc-dev/openmc'
+
+ARG compile_cores
+ARG build_dagmc
+ARG build_libmesh
+
+ENV DAGMC_INSTALL_DIR=$HOME/DAGMC/
+ENV LIBMESH_INSTALL_DIR=$HOME/LIBMESH
+
 # clone and install openmc
 RUN mkdir -p ${HOME}/OpenMC && cd ${HOME}/OpenMC \
-    && git clone --shallow-submodules --recurse-submodules -b ${openmc_branch} --depth=1 ${OPENMC_REPO} \
+    && git clone --shallow-submodules --recurse-submodules --single-branch -b ${openmc_branch} ${OPENMC_REPO} \
     && mkdir build && cd build ; \
     if [ ${build_dagmc} = "on" ] && [ ${build_libmesh} = "on" ]; then \
         cmake ../openmc \
-            -Doptimize=off \
-            -Ddebug=off \
+            -DCMAKE_CXX_COMPILER=mpicxx \
+            -DOPENMC_USE_MPI=on \
             -DHDF5_PREFER_PARALLEL=on \
-            -Ddagmc=on \
-            -Dlibmesh=on \
+            -DOPENMC_USE_DAGMC=on \
+            -DOPENMC_USE_LIBMESH=on \
             -DCMAKE_PREFIX_PATH="${DAGMC_INSTALL_DIR};${LIBMESH_INSTALL_DIR}" ; \
     fi ; \
     if [ ${build_dagmc} = "on" ] && [ ${build_libmesh} = "off" ]; then \
         cmake ../openmc \
-            -Doptimize=off \
-            -Ddebug=off \
+            -DCMAKE_CXX_COMPILER=mpicxx \
+            -DOPENMC_USE_MPI=on \
             -DHDF5_PREFER_PARALLEL=on \
-            -Ddagmc=ON \
+            -DOPENMC_USE_DAGMC=ON \
             -DCMAKE_PREFIX_PATH=${DAGMC_INSTALL_DIR} ; \
     fi ; \
     if [ ${build_dagmc} = "off" ] && [ ${build_libmesh} = "on" ]; then \
         cmake ../openmc \
-            -Doptimize=off \
-            -Ddebug=off \
+            -DCMAKE_CXX_COMPILER=mpicxx \
+            -DOPENMC_USE_MPI=on \
             -DHDF5_PREFER_PARALLEL=on \
-            -Dlibmesh=on \
+            -DOPENMC_USE_LIBMESH=on \
             -DCMAKE_PREFIX_PATH=${LIBMESH_INSTALL_DIR} ; \
     fi ; \
     if [ ${build_dagmc} = "off" ] && [ ${build_libmesh} = "off" ]; then \
         cmake ../openmc \
-            -Doptimize=off \
-            -Ddebug=off \
+            -DCMAKE_CXX_COMPILER=mpicxx \
+            -DOPENMC_USE_MPI=on \
             -DHDF5_PREFER_PARALLEL=on ; \
     fi ; \
     make 2>/dev/null -j${compile_cores} install \
-    && cd ../openmc && pip install -e .[test,depletion-mpi]
+    && cd ../openmc && pip install .[test,depletion-mpi] \
+    && python -c "import openmc"
+
+FROM build AS release
+
+ENV HOME=/root
+ENV OPENMC_CROSS_SECTIONS=/root/nndc_hdf5/cross_sections.xml
 
 # Download cross sections (NNDC and WMP) and ENDF data needed by test suite
 RUN ${HOME}/OpenMC/openmc/tools/ci/download-xs.sh

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2011-2022 Massachusetts Institute of Technology, UChicago Argonne
+Copyright (c) 2011-2025 Massachusetts Institute of Technology, UChicago Argonne
 LLC, and OpenMC contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of

MANIFEST.in

@@ -8,7 +8,6 @@ include schemas.xml
 include pyproject.toml
 include pytest.ini
 include docs/source/_templates/layout.html
-include docs/sphinxext/LICENSE
 global-include *.cmake
 global-include *.cmake.in
 global-include *.rst
@@ -20,25 +19,20 @@ recursive-include docs *.svg
 recursive-include docs *.tex
 recursive-include docs *.txt
 recursive-include docs Makefile
-recursive-include examples *.h5
-recursive-include examples *.png
 recursive-include examples *.cpp
 recursive-include examples *.py
 recursive-include examples *.xml
 recursive-include include *.h
+recursive-include include *.h.in
+recursive-include include *.hh
 recursive-include man *.1
-recursive-inlcude openmc *.pyx
-recursive-include openmc *.c
-recursive-include src *.c
 recursive-include src *.cc
 recursive-include src *.cpp
-recursive-include src *.h
-recursive-include src *.hpp
 recursive-include src *.rnc
 recursive-include src *.rng
 recursive-include tests *.dat
 recursive-include tests *.h5
-recursive-inlcude tests *.h5m
+recursive-include tests *.h5m
 recursive-include tests *.py
 recursive-include tests *.xml
 recursive-include vendor CMakeLists.txt
@@ -49,6 +43,5 @@ recursive-include vendor *.hh
 recursive-include vendor *.hpp
 recursive-include vendor *.pc.in
 recursive-include vendor *.natvis
-include vendor/gsl-lite/include/gsl/gsl
 prune docs/build
 prune docs/source/pythonapi/generated/

README.md

@@ -1,10 +1,11 @@
 # OpenMC Monte Carlo Particle Transport Code
 
 [![License](https://img.shields.io/badge/license-MIT-green)](https://docs.openmc.org/en/latest/license.html)
-[![GitHub Actions build status (Linux)](https://github.com/openmc-dev/openmc/workflows/CI/badge.svg?branch=develop)](https://github.com/openmc-dev/openmc/actions?query=workflow%3ACI)
+[![GitHub Actions build status (Linux)](https://github.com/openmc-dev/openmc/actions/workflows/ci.yml/badge.svg?branch=develop)](https://github.com/openmc-dev/openmc/actions/workflows/ci.yml)
 [![Code Coverage](https://coveralls.io/repos/github/openmc-dev/openmc/badge.svg?branch=develop)](https://coveralls.io/github/openmc-dev/openmc?branch=develop)
 [![dockerhub-publish-develop-dagmc](https://github.com/openmc-dev/openmc/workflows/dockerhub-publish-develop-dagmc/badge.svg)](https://github.com/openmc-dev/openmc/actions?query=workflow%3Adockerhub-publish-develop-dagmc)
 [![dockerhub-publish-develop](https://github.com/openmc-dev/openmc/workflows/dockerhub-publish-develop/badge.svg)](https://github.com/openmc-dev/openmc/actions?query=workflow%3Adockerhub-publish-develop)
+[![conda-pacakge](https://anaconda.org/conda-forge/openmc/badges/version.svg)](https://anaconda.org/conda-forge/openmc)
 
 The OpenMC project aims to provide a fully-featured Monte Carlo particle
 transport code based on modern methods. It is a constructive solid geometry,
@@ -14,7 +15,8 @@ project started under the Computational Reactor Physics Group at MIT.
 Complete documentation on the usage of OpenMC is hosted on Read the Docs (both
 for the [latest release](https://docs.openmc.org/en/stable/) and
 [developmental](https://docs.openmc.org/en/latest/) version). If you are
-interested in the project, or would like to help and contribute, please get in touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
+interested in the project, or would like to help and contribute, please get in
+touch on the OpenMC [discussion forum](https://openmc.discourse.group/).
 
 ## Installation
 
@@ -35,20 +37,21 @@ citing the following publication:
 ## Troubleshooting
 
 If you run into problems compiling, installing, or running OpenMC, first check
-the [Troubleshooting section](https://docs.openmc.org/en/stable/usersguide/troubleshoot.html) in
-the User's Guide. If you are not able to find a solution to your problem there,
+the [Troubleshooting
+section](https://docs.openmc.org/en/stable/usersguide/troubleshoot.html) in the
+User's Guide. If you are not able to find a solution to your problem there,
 please post to the [discussion forum](https://openmc.discourse.group/).
 
 ## Reporting Bugs
 
 OpenMC is hosted on GitHub and all bugs are reported and tracked through the
-[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub. However,
-GitHub Issues should not be used for common troubleshooting purposes. If you are
-having trouble installing the code or getting your model to run properly, you
-should first send a message to the User's Group mailing list. If it turns out
-your issue really is a bug in the code, an issue will then be created on
-GitHub. If you want to request that a feature be added to the code, you may
-create an Issue on github.
+[Issues](https://github.com/openmc-dev/openmc/issues) feature on GitHub.
+However, GitHub Issues should not be used for common troubleshooting purposes.
+If you are having trouble installing the code or getting your model to run
+properly, you should first send a message to the [discussion
+forum](https://openmc.discourse.group/). If it turns out your issue really is a
+bug in the code, an issue will then be created on GitHub. If you want to request
+that a feature be added to the code, you may create an Issue on github.
 
 ## License
 

cmake/Modules/FindLIBMESH.cmake

@@ -14,8 +14,8 @@ if(DEFINED ENV{METHOD})
   message(STATUS "Using environment variable METHOD to determine libMesh build: ${LIBMESH_PC_FILE}")
 endif()
 
-include(FindPkgConfig)
-set(ENV{PKG_CONFIG_PATH} "$ENV{PKG_CONFIG_PATH}:${LIBMESH_PC}")
-set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH True)
-pkg_check_modules(LIBMESH REQUIRED ${LIBMESH_PC_FILE}>=1.6.0 IMPORTED_TARGET)
-pkg_get_variable(LIBMESH_PREFIX ${LIBMESH_PC_FILE} prefix)
+find_package(PkgConfig REQUIRED)
+
+set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH TRUE)
+pkg_check_modules(LIBMESH REQUIRED ${LIBMESH_PC_FILE}>=1.7.0 IMPORTED_TARGET)
+pkg_get_variable(LIBMESH_PREFIX ${LIBMESH_PC_FILE} prefix)

cmake/Modules/GetVersionFromGit.cmake

@@ -0,0 +1,120 @@
+# GetVersionFromGit.cmake
+# Standalone script to retrieve versioning information from Git or .git_archival.txt.
+# Customizable for any project by setting variables before including this file.
+
+# Configurable variables:
+#   - VERSION_PREFIX: Prefix for version tags (default: "v").
+#   - VERSION_SUFFIX: Suffix for version tags (default: "[~+-]([a-zA-Z0-9]+)").
+#   - VERSION_REGEX: Regex to extract version (default: "(?[0-9]+\\.[0-9]+\\.[0-9]+)").
+#   - ARCHIVAL_FILE: Path to .git_archival.txt (default: "${CMAKE_SOURCE_DIR}/.git_archival.txt").
+#   - DESCRIBE_NAME_KEY: Key for describe name in .git_archival.txt (default: "describe-name: ").
+#   - COMMIT_HASH_KEY: Key for commit hash in .git_archival.txt (default: "commit: ").
+
+# Default Format Example:
+#   1.2.3 v1.2.3 v1.2.3-rc1
+
+set(VERSION_PREFIX "v" CACHE STRING "Prefix used in version tags")
+set(VERSION_SUFFIX "[~+-]([a-zA-Z0-9]+)" CACHE STRING "Suffix used in version tags")
+set(VERSION_REGEX "?([0-9]+\\.[0-9]+\\.[0-9]+)" CACHE STRING "Regex for extracting version")
+set(ARCHIVAL_FILE "${CMAKE_SOURCE_DIR}/.git_archival.txt" CACHE STRING "Path to .git_archival.txt")
+set(DESCRIBE_NAME_KEY "describe-name: " CACHE STRING "Key for describe name in .git_archival.txt")
+set(COMMIT_HASH_KEY "commit: " CACHE STRING "Key for commit hash in .git_archival.txt")
+
+
+# Combine prefix and regex
+set(VERSION_REGEX_WITH_PREFIX "^${VERSION_PREFIX}${VERSION_REGEX}")
+
+# Find Git
+find_package(Git)
+
+# Attempt to retrieve version from Git
+if(EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
+    message(STATUS "Using git describe for versioning")
+
+    # Extract the version string
+    execute_process(
+        COMMAND git describe --tags --dirty
+        WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+        OUTPUT_VARIABLE VERSION_STRING
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+        ERROR_QUIET
+    )
+
+    # If no tags are found, set version to 0 and show a warning
+    if(VERSION_STRING STREQUAL "")
+        set(VERSION_STRING "0.0.0")
+        message(WARNING 
+            "No git tags found. Version set to 0.0.0.\n"
+            "Run 'git fetch --tags' to ensure proper versioning.\n"
+            "For more information, see OpenMC developer documentation."
+        )
+    endif()
+
+    # Extract the commit hash
+    execute_process(
+        COMMAND git rev-parse HEAD
+        WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+        OUTPUT_VARIABLE COMMIT_HASH
+        OUTPUT_STRIP_TRAILING_WHITESPACE
+    )
+else()
+    message(STATUS "Using archival file for versioning: ${ARCHIVAL_FILE}")
+    if(EXISTS "${ARCHIVAL_FILE}")
+        file(READ "${ARCHIVAL_FILE}" ARCHIVAL_CONTENT)
+
+        # Extract the describe-name line
+        string(REGEX MATCH "${DESCRIBE_NAME_KEY}([^\\n]+)" VERSION_STRING "${ARCHIVAL_CONTENT}")
+        if(VERSION_STRING MATCHES "${DESCRIBE_NAME_KEY}(.*)")
+            set(VERSION_STRING "${CMAKE_MATCH_1}")
+        else()
+            message(FATAL_ERROR "Could not extract version from ${ARCHIVAL_FILE}")
+        endif()
+
+        # Extract the commit hash
+        string(REGEX MATCH "${COMMIT_HASH_KEY}([a-f0-9]+)" COMMIT_HASH "${ARCHIVAL_CONTENT}")
+        if(COMMIT_HASH MATCHES "${COMMIT_HASH_KEY}([a-f0-9]+)")
+            set(COMMIT_HASH "${CMAKE_MATCH_1}")
+        else()
+            message(FATAL_ERROR "Could not extract commit hash from ${ARCHIVAL_FILE}")
+        endif()
+    else()
+        message(FATAL_ERROR "Neither git describe nor ${ARCHIVAL_FILE} is available for versioning.")
+    endif()
+endif()
+
+# Ensure version string format
+if(VERSION_STRING MATCHES "${VERSION_REGEX_WITH_PREFIX}")
+    set(VERSION_NO_SUFFIX "${CMAKE_MATCH_1}")
+else()
+    message(FATAL_ERROR "Invalid version format: Missing base version in ${VERSION_STRING}")
+endif()
+
+# Check for development state
+if(VERSION_STRING MATCHES "-([0-9]+)-g([0-9a-f]+)")
+    set(DEV_STATE "true")
+    set(COMMIT_COUNT "${CMAKE_MATCH_1}")
+    string(REGEX REPLACE "-([0-9]+)-g([0-9a-f]+)" "" VERSION_WITHOUT_META "${VERSION_STRING}")
+else()
+    set(DEV_STATE "false")
+    set(VERSION_WITHOUT_META "${VERSION_STRING}")
+endif()
+
+# Split and set version components
+string(REPLACE "." ";" VERSION_LIST "${VERSION_NO_SUFFIX}")
+list(GET VERSION_LIST 0 VERSION_MAJOR)
+list(GET VERSION_LIST 1 VERSION_MINOR)
+list(GET VERSION_LIST 2 VERSION_PATCH)
+
+# Increment patch number for dev versions
+if(DEV_STATE)
+    math(EXPR VERSION_PATCH "${VERSION_PATCH} + 1")
+endif()
+
+# Export variables
+set(OPENMC_VERSION_MAJOR "${VERSION_MAJOR}")
+set(OPENMC_VERSION_MINOR "${VERSION_MINOR}")
+set(OPENMC_VERSION_PATCH "${VERSION_PATCH}")
+set(OPENMC_VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
+set(OPENMC_COMMIT_HASH "${COMMIT_HASH}")
+set(OPENMC_DEV_STATE "${DEV_STATE}")
+set(OPENMC_COMMIT_COUNT "${COMMIT_COUNT}")

cmake/OpenMCConfig.cmake.in

@@ -1,19 +1,21 @@
 get_filename_component(OpenMC_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" DIRECTORY)
 
-find_package(fmt REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../fmt)
-find_package(gsl-lite REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../gsl-lite)
-find_package(pugixml REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../pugixml)
-find_package(xtl REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtl)
-find_package(xtensor REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtensor)
-if(@dagmc@)
+# Compute the install prefix from this file's location
+get_filename_component(_OPENMC_PREFIX "${OpenMC_CMAKE_DIR}/../../.." ABSOLUTE)
+
+find_package(fmt CONFIG REQUIRED HINTS ${_OPENMC_PREFIX})
+find_package(pugixml CONFIG REQUIRED HINTS ${_OPENMC_PREFIX})
+find_package(xtl CONFIG REQUIRED HINTS ${_OPENMC_PREFIX})
+find_package(xtensor CONFIG REQUIRED HINTS ${_OPENMC_PREFIX})
+if(@OPENMC_USE_DAGMC@)
   find_package(DAGMC REQUIRED HINTS @DAGMC_DIR@)
 endif()
 
-if(@libmesh@)
+if(@OPENMC_USE_LIBMESH@)
   include(FindPkgConfig)
   list(APPEND CMAKE_PREFIX_PATH @LIBMESH_PREFIX@)
   set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH True)
-  pkg_check_modules(LIBMESH REQUIRED @LIBMESH_PC_FILE@>=1.6.0 IMPORTED_TARGET)
+  pkg_check_modules(LIBMESH REQUIRED @LIBMESH_PC_FILE@>=1.7.0 IMPORTED_TARGET)
 endif()
 
 find_package(PNG)
@@ -21,3 +23,15 @@ find_package(PNG)
 if(NOT TARGET OpenMC::libopenmc)
   include("${OpenMC_CMAKE_DIR}/OpenMCTargets.cmake")
 endif()
+
+if(@OPENMC_USE_MPI@)
+  find_package(MPI REQUIRED)
+endif()
+
+if(@OPENMC_USE_OPENMP@)
+  find_package(OpenMP REQUIRED)
+endif()
+
+if(@OPENMC_USE_UWUW@ AND NOT ${DAGMC_BUILD_UWUW})
+  message(FATAL_ERROR "UWUW is enabled in OpenMC but the DAGMC installation discovered was not configured with UWUW.")
+endif()

docs/requirements-rtd.txt

@@ -1,11 +0,0 @@
-sphinx==4.3.0
-sphinx-numfig
-jupyter
-sphinxcontrib-katex
-sphinxcontrib-svg2pdfconverter
-numpy
-scipy
-h5py
-pandas
-uncertainties
-matplotlib

docs/source/capi/index.rst

@@ -84,6 +84,17 @@ Functions
    :return: Return status (negative if an error occurred)
    :rtype: int
 
+.. c:function:: int openmc_cell_get_density(int32_t index, const int32_t* instance, double* density)
+
+   Get the density of a cell
+
+   :param int32_t index: Index in the cells array
+   :param int32_t* instance: Which instance of the cell. If a null pointer is passed, the density
+                             multiplier of the first instance is returned.
+   :param double* density: Density of the cell in [g/cm3]
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
 .. c:function:: int openmc_cell_set_fill(int32_t index, int type, int32_t n, const int32_t* indices)
 
    Set the fill for a cell
@@ -113,8 +124,22 @@ Functions
    :param double T: Temperature in Kelvin
    :param instance: Which instance of the cell. To set the temperature for all
                     instances, pass a null pointer.
-   :param set_contained: If the cell is not filled by a material, whether to set the temperatures
-                         of all filled cells
+   :param bool set_contained: If the cell is not filled by a material, whether
+                              to set the temperatures of all filled cells
+   :type instance: const int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_cell_set_density(index index, double density, const int32_t* instance, bool set_contained)
+
+   Set the density of a cell.
+
+   :param int32_t index: Index in the cells array
+   :param double density: Density of the cell in [g/cm3]
+   :param instance: Which instance of the cell. To set the density multiplier for all
+                    instances, pass a null pointer.
+   :param bool set_contained: If the cell is not filled by a material, whether
+                              to set the density multiplier of all filled cells
    :type instance: const int32_t*
    :return: Return status (negative if an error occurred)
    :rtype: int
@@ -355,7 +380,7 @@ Functions
    Get density of a material.
 
    :param int32_t index: Index in the materials array
-   :param double* denity: Pointer to a density
+   :param double* density: Pointer to a density
    :return: Return status (negative if an error occurs)
    :rtype: int
 
@@ -420,6 +445,16 @@ Functions
    :return: Return status (negative if an error occurred)
    :rtype: int
 
+.. c:function:: int openmc_mesh_filter_get_mesh(int32_t index, int32_t* index_mesh)
+
+   Get the mesh for a mesh filter
+
+   :param int32_t index: Index in the filters array
+   :param index_mesh: Index in the meshes array
+   :type index_mesh: int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
 .. c:function:: int openmc_mesh_filter_set_mesh(int32_t index, int32_t index_mesh)
 
    Set the mesh for a mesh filter
@@ -429,6 +464,98 @@ Functions
    :return: Return status (negative if an error occurred)
    :rtype: int
 
+.. c:function:: int openmc_mesh_filter_get_translation(int32_t index, double translation[3])
+
+   Get the 3-D translation coordinates for a mesh filter
+
+   :param int32_t index: Index in the filters array
+   :param double[3] translation: 3-D translation coordinates
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_mesh_filter_set_translation(int32_t index, double translation[3])
+
+   Set the 3-D translation coordinates for a mesh filter
+
+   :param int32_t index: Index in the filters array
+   :param double[3] translation: 3-D translation coordinates
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshborn_filter_get_mesh(int32_t index, int32_t* index_mesh)
+
+   Get the mesh for a meshborn filter
+
+   :param int32_t index: Index in the filters array
+   :param index_mesh: Index in the meshes array
+   :type index_mesh: int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshborn_filter_set_mesh(int32_t index, int32_t index_mesh)
+
+   Set the mesh for a meshborn filter
+
+   :param int32_t index: Index in the filters array
+   :param int32_t index_mesh: Index in the meshes array
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshborn_filter_get_translation(int32_t index, double translation[3])
+
+   Get the 3-D translation coordinates for a meshborn filter
+
+   :param int32_t index: Index in the filters array
+   :param double[3] translation: 3-D translation coordinates
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshborn_filter_set_translation(int32_t index, double translation[3])
+
+   Set the 3-D translation coordinates for a meshborn filter
+
+   :param int32_t index: Index in the filters array
+   :param double[3] translation: 3-D translation coordinates
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshsurface_filter_get_mesh(int32_t index, int32_t* index_mesh)
+
+   Get the mesh for a mesh surface filter
+
+   :param int32_t index: Index in the filters array
+   :param index_mesh: Index in the meshes array
+   :type index_mesh: int32_t*
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshsurface_filter_set_mesh(int32_t index, int32_t index_mesh)
+
+   Set the mesh for a mesh surface filter
+
+   :param int32_t index: Index in the filters array
+   :param int32_t index_mesh: Index in the meshes array
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshsurface_filter_get_translation(int32_t index, double translation[3])
+
+   Get the 3-D translation coordinates for a mesh surface filter
+
+   :param int32_t index: Index in the filters array
+   :param double[3] translation: 3-D translation coordinates
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
+.. c:function:: int openmc_meshsurface_filter_set_translation(int32_t index, double translation[3])
+
+   Set the 3-D translation coordinates for a mesh surface filter
+
+   :param int32_t index: Index in the filters array
+   :param double[3] translation: 3-D translation coordinates
+   :return: Return status (negative if an error occurred)
+   :rtype: int
+
 .. c:function:: int openmc_next_batch()
 
    Simulate next batch of particles. Must be called after openmc_simulation_init().
@@ -460,6 +587,13 @@ Functions
    :return: Return status (negative if an error occurs)
    :rtype: int
 
+.. c:function:: int openmc_remove_tally(int32_t index);
+
+   Given an index of a tally, remove it from the tallies array
+   :param int index: Index in tallies array
+   :return: Return status (negative if an error occurs)
+   :rtype: int
+
 .. c:function:: int openmc_run()
 
    Run a simulation

docs/source/conf.py

@@ -52,7 +52,7 @@ if not on_rtd:
 templates_path = ['_templates']
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = {'.rst': 'restructuredtext'}
 
 # The encoding of source files.
 #source_encoding = 'utf-8'
@@ -62,16 +62,17 @@ master_doc = 'index'
 
 # General information about the project.
 project = 'OpenMC'
-copyright = '2011-2022, Massachusetts Institute of Technology, UChicago Argonne LLC, and OpenMC contributors'
+copyright = '2011-2025, Massachusetts Institute of Technology, UChicago Argonne LLC, and OpenMC contributors'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# The short X.Y version.
-version = "0.13"
+
+import openmc
+
 # The full version, including alpha/beta/rc tags.
-release = "0.13.0"
+version = release = openmc.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -120,10 +121,8 @@ pygments_style = 'tango'
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages
-if not on_rtd:
-    import sphinx_rtd_theme
-    html_theme = 'sphinx_rtd_theme'
-    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+html_theme = 'sphinx_rtd_theme'
+html_baseurl = "https://docs.openmc.org/en/stable/"
 
 html_logo = '_images/openmc_logo.png'
 
@@ -215,6 +214,7 @@ latex_elements = {
 \setcounter{tocdepth}{2}
 \numberwithin{equation}{section}
 \DeclareUnicodeCharacter{03B1}{$\alpha$}
+\DeclareUnicodeCharacter{03C0}{$\pi$}
 """,
 'printindex': r""
 }
@@ -246,7 +246,7 @@ napoleon_use_ivar = True
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
-    'matplotlib': ('https://matplotlib.org/', None)
+    'matplotlib': ('https://matplotlib.org/stable/', None)
 }

docs/source/devguide/contributing.rst

@@ -109,7 +109,7 @@ Leadership Team
 The TC consists of the following individuals:
 
 - `Paul Romano <https://github.com/paulromano>`_
-- `Sterling Harper <https://github.com/smharper>`_
+- `Patrick Shriwise <https://github.com/pshriwise>`_
 - `Adam Nelson <https://github.com/nelsonag>`_
 - `Benoit Forget <https://github.com/bforget>`_
 

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/docker.rst

@@ -45,12 +45,11 @@ Now you can run the following to create a `Docker container`_ called
 This command will open an interactive shell running from within the
 Docker container where you have access to use OpenMC.
 
-.. note:: The ``docker run`` command supports many
-          `options <https://docs.docker.com/engine/reference/commandline/run/>`_
+.. note:: The ``docker run`` command supports many options_
           for spawning containers -- including `mounting volumes`_ from the
           host filesystem -- which many users will find useful.
 
-.. _Docker image: https://docs.docker.com/engine/reference/commandline/images/
+.. _Docker image: https://docs.docker.com/get-started/docker-concepts/the-basics/what-is-an-image/
 .. _Docker container: https://www.docker.com/resources/what-container
-.. _options: https://docs.docker.com/engine/reference/commandline/run/
-.. _mounting volumes: https://docs.docker.com/storage/volumes/
+.. _options: https://docs.docker.com/reference/cli/docker/container/run/
+.. _mounting volumes: https://docs.docker.com/engine/storage/volumes/

docs/source/devguide/index.rst

@@ -15,6 +15,7 @@ other related topics.
     contributing
     workflow
     styleguide
+    policies
     tests
     user-input
     docbuild

docs/source/devguide/policies.rst

@@ -0,0 +1,35 @@
+.. _devguide_policies:
+
+========
+Policies
+========
+
+---------------------
+Python Version Policy
+---------------------
+
+OpenMC follows the Scientific Python Ecosystem Coordination guidelines `SPEC 0
+<https://scientific-python.org/specs/spec-0000/>`_ on minimum supported
+versions, which recommends that support for Python versions be dropped 3 years
+after their initial release.
+
+-------------------
+C++ Standard Policy
+-------------------
+
+C++ code in OpenMC must conform to the most recent C++ standard that is fully
+supported in the `version of the gcc compiler
+<https://gcc.gnu.org/projects/cxx-status.html>`_ that is distributed with the
+oldest version of Ubuntu that is still within its `standard support period
+<https://ubuntu.com/about/release-cycle>`_. Ubuntu 20.04 LTS will be supported
+through April 2025 and is distributed with gcc 9.3.0, which fully supports the
+C++17 standard.
+
+--------------------
+CMake Version Policy
+--------------------
+
+Similar to the C++ standard policy, the minimum supported version of CMake
+corresponds to whatever version is distributed with the oldest version of Ubuntu
+still within its standard support period. Ubuntu 20.04 LTS is distributed with
+CMake 3.16.

docs/source/devguide/styleguide.rst

@@ -29,6 +29,10 @@ whenever a file is saved. For example, `Visual Studio Code
 <https://code.visualstudio.com/docs/cpp/cpp-ide#_code-formatting>`_ includes
 support for running clang-format.
 
+.. note::
+    OpenMC's CI uses `clang-format` version 15. A different version of `clang-format`
+    may produce different line changes and as a result fail the CI test.
+
 Miscellaneous
 -------------
 
@@ -36,14 +40,15 @@ Follow the `C++ Core Guidelines`_ except when they conflict with another
 guideline listed here. For convenience, many important guidelines from that
 list are repeated here.
 
-Conform to the C++14 standard.
+Conform to the C++17 standard.
 
 Always use C++-style comments (``//``) as opposed to C-style (``/**/``). (It
 is more difficult to comment out a large section of code that uses C-style
 comments.)
 
 Do not use C-style casting. Always use the C++-style casts ``static_cast``,
-``const_cast``, or ``reinterpret_cast``. (See `ES.49 <http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#es49-if-you-must-use-a-cast-use-a-named-cast>`_)
+``const_cast``, or ``reinterpret_cast``. (See `ES.49
+<https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#es49-if-you-must-use-a-cast-use-a-named-cast>`_)
 
 Source Files
 ------------
@@ -51,7 +56,7 @@ Source Files
 Use a ``.cpp`` suffix for code files and ``.h`` for header files.
 
 Header files should always use include guards with the following style (See
-`SF.8 <http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#sf8-use-include-guards-for-all-h-files>`_):
+`SF.8 <https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#Rs-guards>`_):
 
 .. code-block:: C++
 
@@ -142,7 +147,7 @@ Style for Python code should follow PEP8_.
 
 Docstrings for functions and methods should follow numpydoc_ style.
 
-Python code should work with Python 3.6+.
+Python code should work with Python 3.8+.
 
 Use of third-party Python packages should be limited to numpy_, scipy_,
 matplotlib_, pandas_, and h5py_. Use of other third-party packages must be
@@ -152,11 +157,11 @@ Prefer pathlib_ when working with filesystem paths over functions in the os_
 module or other standard-library modules. Functions that accept arguments that
 represent a filesystem path should work with both strings and Path_ objects.
 
-.. _C++ Core Guidelines: http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
-.. _PEP8: https://www.python.org/dev/peps/pep-0008/
+.. _C++ Core Guidelines: https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
+.. _PEP8: https://peps.python.org/pep-0008/
 .. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html
 .. _numpy: https://numpy.org/
-.. _scipy: https://www.scipy.org/
+.. _scipy: https://scipy.org/
 .. _matplotlib: https://matplotlib.org/
 .. _pandas: https://pandas.pydata.org/
 .. _h5py: https://www.h5py.org/

docs/source/devguide/tests.rst

@@ -23,17 +23,17 @@ 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
-  within ``tools/ci/download-xs.sh``.
+  within ``tools/ci/download-xs.sh``. Once the tarball is downloaded and
+  unpacked, set the :envvar:`OPENMC_CROSS_SECTIONS` environment variable to the
+  path of the ``cross_sections.xml`` file within the unpacked data.
 - 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``.
+  for those can also be found in ``tools/ci/download-xs.sh``. Once the tarball
+  is downloaded and unpacked, set the :envvar:`OPENMC_ENDF_DATA` environment
+  variable to the top-level directory of the unpacked tarball.
 - 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`.
@@ -41,7 +41,7 @@ Prerequisites
 Running Tests
 -------------
 
-To execute the test suite, go to the ``tests/`` directory and run::
+To execute the Python test suite, go to the ``tests/`` directory and run::
 
     pytest
 
@@ -51,6 +51,63 @@ installed and run::
 
     pytest --cov=../openmc --cov-report=html
 
+To execute the C++ test suite, go to your build directory and run::
+
+    ctest
+
+If you want to view testing output on failure run::
+
+    ctest --output-on-failure
+
+Possible Reasons for Test Failures
+----------------------------------
+
+You may find that when you run the test suite, not everything passes. First,
+make sure you have satisfied all the prerequisites above. After you have done
+that, consider the following:
+
+- When building OpenMC, make sure you run CMake with
+  ``-DCMAKE_BUILD_TYPE=Debug``. Building with a release build will result in
+  some test failures due to differences in which compiler optimizations are
+  used.
+- Because tallies involve the sum of many floating point numbers, the
+  non-associativity of floating point numbers can result in different answers
+  especially when the number of threads is high (different order of operations).
+  Thus, if you are running on a CPU with many cores, you may need to limit the
+  number of OpenMP threads used. It is recommended to set the
+  :envvar:`OMP_NUM_THREADS` environment variable to 2.
+- Recent versions of NumPy use instruction dispatch that may generate different
+  results depending the particular ISA that you are running on. To avoid issues,
+  you may need to disable AVX512 instructions. This can be done by setting the
+  :envvar:`NPY_DISABLE_CPU_FEATURES` environment variable to "AVX512F
+  AVX512_SKX". When NumPy/SciPy are built against OpenBLAS, you may also need to
+  limit the number of threads that OpenBLAS uses internally; this can be done by
+  setting the :envvar:`OPENBLAS_NUM_THREADS` environment variable to 1.
+
+Debugging Tests in CI
+---------------------
+
+Tests can be debugged in CI using a feature called 
+`tmate <https://github.com/mxschmitt/action-tmate?tab=readme-ov-file#debug-your-github-actions-by-using-tmate>`_. 
+CI debugging can be
+enabled by including "[gha-debug]" in the commit message. When the test fails, a
+link similar to the one shown below will be provided in the GitHub Actions
+output after failure occurs. Logging into the provided link will allow you to
+debug the test in the CI environment. The following is an example of the output
+shown in the CI log that provides the link to the tmate session:
+
+.. code-block:: text
+   :linenos:
+
+   Created new session successfully
+   ssh 2VcykjU7vNdvAzEjQcc839GM2@nyc1.tmate.io
+   https://tmate.io/t/2VcykjU7vNdvAzEjQcc839GM2
+   Entering main loop
+   Web shell: https://tmate.io/t/2VcykjU7vNdvAzEjQcc839GM2
+   SSH: ssh 2VcykjU7vNdvAzEjQcc839GM2@nyc1.tmate.io
+   ...
+
+
 Generating XML Inputs
 ---------------------
 
@@ -62,6 +119,23 @@ run::
 
     pytest --build-inputs <name-of-test>
 
+Adding C++ Unit Tests
+---------------------
+
+The C++ test suite uses Catch2 integrated with CTest. Each header file should
+have a corresponding test file in ``tests/cpp_unit_tests/``. If the test file
+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``.
+
+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
 ------------------------------------
 
@@ -84,6 +158,12 @@ following files to your new test directory:
       compiler options during openmc configuration and build (e.g., no MPI, no
       debug/optimization).
 
+For tests using the Python API, both the **inputs_true.dat** and
+**results_true.dat** files can be generated automatically in the correct format
+via::
+
+    pytest --update <name-of-test>
+
 In addition to this description, please see the various types of tests that are
 already included in the test suite to see how to create them. If all is
 implemented correctly, the new test will automatically be discovered by pytest.

docs/source/devguide/user-input.rst

@@ -49,23 +49,12 @@ following steps should be followed to make changes to user input:
    written out to the statepoint or summary files and that the
    :class:`openmc.StatePoint` and :class:`openmc.Summary` classes read them in.
 
-7. Finally, a set of `RELAX NG`_ schemas exists that enables validation of input
-   files. You should modify the RELAX NG schema for the file you changed. The
-   easiest way to do this is to change the `compact syntax`_ file
-   (e.g. ``src/relaxng/geometry.rnc``) and then convert it to regular XML syntax
-   using trang_::
-
-       trang geometry.rnc geometry.rng
-
 For most user input additions and changes, it is simple enough to follow a
 "monkey see, monkey do" approach. When in doubt, contact your nearest OpenMC
 developer or send a message to the `developers mailing list`_.
 
 
 .. _property attribute: https://docs.python.org/3.6/library/functions.html#property
-.. _XML Schema Part 2: http://www.w3.org/TR/xmlschema-2/
-.. _boolean: http://www.w3.org/TR/xmlschema-2/#boolean
-.. _RELAX NG: https://relaxng.org/
-.. _compact syntax: https://relaxng.org/compact-tutorial-20030326.html
-.. _trang: https://relaxng.org/jclark/trang.html
+.. _XML Schema Part 2: https://www.w3.org/TR/xmlschema-2/
+.. _boolean: https://www.w3.org/TR/xmlschema-2/#boolean
 .. _developers mailing list: https://groups.google.com/forum/?fromgroups=#!forum/openmc-dev

docs/source/devguide/workflow.rst

@@ -4,7 +4,7 @@
 Development Workflow
 ====================
 
-Anyone wishing to make contributions to OpenMC should be fully acquianted and
+Anyone wishing to make contributions to OpenMC should be fully acquainted and
 comfortable working with git_ and GitHub_. We assume here that you have git
 installed on your system, have a GitHub account, and have setup SSH keys to be
 able to create/push to repositories on GitHub.
@@ -81,7 +81,7 @@ features and bug fixes. The general steps for contributing are as follows:
    openmc-dev/openmc as the target.
 
    At a minimum, you should describe what the changes you've made are and why
-   you are making them. If the changes are related to an oustanding issue, make
+   you are making them. If the changes are related to an outstanding issue, make
    sure it is cross-referenced.
 
 5. A committer will review your pull request based on the criteria
@@ -91,6 +91,30 @@ features and bug fixes. The general steps for contributing are as follows:
 6. After the pull request has been thoroughly vetted, it is merged back into the
    *develop* branch of openmc-dev/openmc.
 
+Setting Up Upstream Tracking (Required for Versioning)
+------------------------------------------------------
+
+By default, your fork **does not** include tags from the upstream OpenMC repository.  
+OpenMC relies on `git describe --tags` for versioning in source builds, and missing tags can lead  
+to incorrect version detection (i.e., ``0.0.0``). To ensure proper versioning, follow these steps:
+
+1. **Add the Upstream Repository**  
+   This allows you to fetch updates from the main OpenMC repository.
+
+   .. code-block:: sh
+
+       git remote add upstream https://github.com/openmc-dev/openmc.git
+
+2. **Fetch and Push Tags**  
+   Retrieve tags from the upstream repository and update your fork:
+
+   .. code-block:: sh
+
+       git fetch --tags upstream
+       git push --tags origin
+
+This ensures that both your **local** and **remote** fork have the correct versioning information.
+
 Private Development
 -------------------
 
@@ -116,20 +140,20 @@ 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/reference/pip_install/#editable-installs>`_ so
-that 1) it can be imported from a Python interpreter and 2) any changes made are
+<https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs>`_ so that 1)
+it can be imported from a Python interpreter and 2) any changes made are
 immediately reflected in the installed version (that is, you don't need to keep
 reinstalling it). While the same effect can be achieved using the
 :envvar:`PYTHONPATH` environment variable, this is generally discouraged as it
 can interfere with virtual environments.
 
-.. _git: http://git-scm.com/
+.. _git: https://git-scm.com/
 .. _GitHub: https://github.com/
 .. _git flow: https://nvie.com/git-model
-.. _valgrind: https://www.valgrind.org/
+.. _valgrind: https://valgrind.org/
 .. _style guide: https://docs.openmc.org/en/latest/devguide/styleguide.html
 .. _pull request: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests
 .. _openmc-dev/openmc: https://github.com/openmc-dev/openmc

docs/source/index.rst

@@ -12,7 +12,7 @@ files produced by NJOY. Parallelism is enabled via a hybrid MPI and OpenMP
 programming model.
 
 OpenMC was originally developed by members of the `Computational Reactor Physics
-Group <http://crpg.mit.edu>`_ at the `Massachusetts Institute of Technology
+Group <https://crpg.mit.edu>`_ at the `Massachusetts Institute of Technology
 <https://web.mit.edu>`_ starting in 2011. Various universities, laboratories,
 and other organizations now contribute to the development of OpenMC. For more
 information on OpenMC, feel free to post a message on the `OpenMC Discourse

docs/source/io_formats/depletion_chain.rst

@@ -56,6 +56,27 @@ attributes:
 
 .. _io_chain_reaction:
 
+--------------------
+``<source>`` Element
+--------------------
+
+The ``<source>`` element represents photon and electron sources associated with
+the decay of a nuclide and contains information to construct an
+:class:`openmc.stats.Univariate` object that represents this emission as an
+energy distribution. This element has the following attributes:
+
+  :type:
+    The type of :class:`openmc.stats.Univariate` source term.
+
+  :particle:
+    The type of particle emitted, e.g., 'photon' or 'electron'
+
+  :parameters:
+    The parameters of the source term, e.g., for a
+    :class:`openmc.stats.Discrete` source, the energies (in [eV]) at which the
+    particles are emitted and their relative intensities in [Bq/atom] (in other
+    words, decay constants).
+
 ----------------------
 ``<reaction>`` Element
 ----------------------

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/geometry.rst

@@ -48,7 +48,7 @@ Each ``<surface>`` element can have the following attributes or sub-elements:
 
   :periodic_surface_id:
      If a periodic boundary condition is applied, this attribute identifies the
-     ``id`` of the corresponding periodic sufrace.
+     ``id`` of the corresponding periodic surface.
 
 The following quadratic surfaces can be modeled:
 
@@ -219,6 +219,30 @@ Each ``<cell>`` element can have the following attributes or sub-elements:
 
     *Default*: None
 
+  :triso_particle:
+    If the cell is filled with a TRISO particle,  use this element to mark it.
+
+    .. note:: Only cells with spherical area can be marked.
+
+    *Default*: false
+
+  :virtual_lattice:
+    If the cell is filled with a matrix containing the TRISO particle,  use this
+    element to mark it. This can accelerate the search speed of neutrons in the 
+    region containing a large number of TRISO particles.
+
+    *Default*: false
+  
+  :shape:
+    If the virtual_lattice is True. This element specifies the shape of the
+    lattice.
+
+    .. note:: The shape of the lattice must be specified if the virtual_lattice
+              is True. Related methods can be referred to Liang, J., Li, R., Liu, Z., 
+              2024. Virtual lattice method for efficient Monte Carlo transport simulation
+              of dispersion nuclear fuels. Computer Physics Communications 295, 108985. 
+              https://doi.org/10.1016/j.cpc.2023.108985
+
 
 ---------------------
 ``<lattice>`` Element
@@ -407,13 +431,33 @@ Each ``<dagmc_universe>`` element can have the following attributes or sub-eleme
 
     *Default*: None
 
+  :material_overrides:
+    This element contains information on material overrides to be applied to the
+    DAGMC universe. It has the following attributes and sub-elements:
 
-  .. note:: A geometry.xml file containing only a DAGMC model for a file named `dagmc.h5m` (no CSG)
-            looks as follows
+    :cell:
+      Material override information for a single cell. It contains the following
+      attributes and sub-elements:
 
-            .. code-block:: xml
+      :id:
+        The cell ID in the DAGMC geometry for which the material override will
+        apply.
 
-              <?xml version='1.0' encoding='utf-8'?>
-              <geometry>
-                <dagmc_universe filename="dagmc.h5m" id="1" />
-              </geometry>
+      :materials:
+        A list of material IDs that will apply to instances of the cell. If the
+        list contains only one ID, it will replace the original material
+        assignment of all instances of the DAGMC cell. If the list contains more
+        than one material, each material ID of the list will be assigned to the
+        various instances of the DAGMC cell.
+
+    *Default*: None
+
+.. note:: A geometry.xml file containing only a DAGMC model for a file named
+          `dagmc.h5m` (no CSG) looks as follows:
+
+    .. code-block:: xml
+
+        <?xml version='1.0' encoding='utf-8'?>
+        <geometry>
+          <dagmc_universe filename="dagmc.h5m" id="1" />
+        </geometry>

docs/source/io_formats/index.rst

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

docs/source/io_formats/nuclear_data.rst

@@ -339,6 +339,16 @@ Incoherent elastic scattering
               [eV\ :math:`^{-1}`].
 :Attributes: - **type** (*char[]*) -- 'IncoherentElastic'
 
+Sum of functions
+----------------
+
+:Object type: Group
+:Attributes: - **type** (*char[]*) -- "Sum"
+             - **n** (*int*) -- Number of functions
+:Datasets:
+           - ***func_<i>** (:ref:`function <1d_functions>`) -- Dataset for the
+             i-th function (indexing starts at 1)
+
 .. _angle_energy:
 
 --------------------------
@@ -501,6 +511,19 @@ equiprobable bins.
            - **skewed** (*int8_t*) -- Whether discrete angles are equi-probable
              (0) or have a skewed distribution (1).
 
+Mixed Elastic
+-------------
+
+This angle-energy distribution is used when an evaluation specifies both
+coherent and incoherent elastic thermal neutron scattering.
+
+:Object type: Group
+:Attributes: - **type** (*char[]*) -- "mixed_elastic"
+:Groups: - **coherent** -- Distribution for coherent elastic scattering. The
+           format is given in :ref:`angle_energy`.
+         - **incoherent** -- Distribution for incoherent elastic scattering.
+           The format is given in :ref:`angle_energy`.
+
 .. _energy_distribution:
 
 --------------------

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/plots.rst

@@ -7,13 +7,18 @@ Geometry Plotting Specification -- plots.xml
 Basic plotting capabilities are available in OpenMC by creating a plots.xml file
 and subsequently running with the ``--plot`` command-line flag. The root element
 of the plots.xml is simply ``<plots>`` and any number output plots can be
-defined with ``<plot>`` sub-elements.  Two plot types are currently implemented
+defined with ``<plot>`` sub-elements.  Four plot types are currently implemented
 in openMC:
 
 * ``slice``  2D pixel plot along one of the major axes. Produces a PNG image
   file.
 * ``voxel``  3D voxel data dump. Produces an HDF5 file containing voxel xyz
   position and cell or material id.
+* ``wireframe_raytrace``  2D pixel plot of a three-dimensional view of a
+  geometry using wireframes around cells or materials and coloring by depth
+  through each material.
+* ``solid_raytrace``  2D pixel plot of a three-dimensional view of a geometry
+  with solid colored surfaces of a set of cells or materials.
 
 
 ------------------
@@ -66,21 +71,22 @@ sub-elements:
     *Default*: None - Required entry
 
   :type:
-    Keyword for type of plot to be produced. Currently only "slice" and "voxel"
-    plots are implemented. The "slice" plot type creates 2D pixel maps saved in
-    the PNG file format. The "voxel" plot type produces a binary datafile
-    containing voxel grid positioning and the cell or material (specified by the
-    ``color`` tag) at the center of each voxel. Voxel plot files can be
-    processed into VTK files using the :ref:`scripts_voxel` script provided with
-    OpenMC and subsequently viewed with a 3D viewer such as VISIT or Paraview.
-    See the :ref:`io_voxel` for information about the datafile structure.
+    Keyword for type of plot to be produced. Currently "slice", "voxel",
+    "wireframe_raytrace", and "solid_raytrace" plots are implemented. The
+    "slice" plot type creates 2D pixel maps saved in the PNG file format. The
+    "voxel" plot type produces a binary datafile containing voxel grid
+    positioning and the cell or material (specified by the ``color`` tag) at the
+    center of each voxel. Voxel plot files can be processed into VTK files using
+    the :func:`openmc.voxel_to_vtk` function and subsequently viewed with a 3D
+    viewer such as VISIT or Paraview. See :ref:`io_voxel` for information about
+    the datafile structure.
 
     .. note:: High-resolution voxel files produced by OpenMC can be quite large,
               but the equivalent VTK files will be significantly smaller.
 
     *Default*: "slice"
 
-``<plot>`` elements of ``type`` "slice" and "voxel" must contain the ``pixels``
+All ``<plot>`` elements must contain the ``pixels``
 attribute or sub-element:
 
   :pixels:
@@ -96,7 +102,7 @@ attribute or sub-element:
                  ``width``/``pixels`` along that basis direction may not appear
                  in the plot.
 
-    *Default*: None - Required entry for "slice" and "voxel" plots
+    *Default*: None - Required entry for all plots
 
 ``<plot>`` elements of ``type`` "slice" can also contain the following
 attributes or sub-elements.  These are not used in "voxel" plots:
@@ -125,6 +131,11 @@ attributes or sub-elements.  These are not used in "voxel" plots:
       Specifies the custom color for the cell or material. Should be 3 integers
       separated by spaces.
 
+    :xs:
+      The attenuation coefficient for volume rendering of color in units of
+      inverse centimeters. Zero corresponds to transparency. Only for plot type
+      "wireframe_raytrace".
+
     As an example, if your plot is colored by material and you want material 23
     to be blue, the corresponding ``color`` element would look like:
 
@@ -151,6 +162,18 @@ attributes or sub-elements.  These are not used in "voxel" plots:
 
     *Default*: 255 255 255 (white)
 
+  :show_overlaps:
+    Indicates whether overlapping regions of different cells are shown.
+
+    *Default*: None
+
+  :overlap_color:
+    Specifies the RGB color of overlapping regions of different cells. Does not
+    do anything if ``show_overlaps`` is "false" or not specified. Should be 3
+    integers separated by spaces.
+
+    *Default*: 255 0 0 (red)
+
   :meshlines:
     The ``meshlines`` sub-element allows for plotting the boundaries of a
     regular mesh on top of a plot. Only one ``meshlines`` element is allowed per
@@ -179,3 +202,80 @@ attributes or sub-elements.  These are not used in "voxel" plots:
       *Default*: 0 0 0 (black)
 
     *Default*: None
+
+``<plot>`` elements of ``type`` "wireframe_raytrace" or "solid_raytrace" can contain the
+following attributes or sub-elements.
+
+  :camera_position:
+    Location in 3D Cartesian space the camera is at.
+
+
+    *Default*: None - Required for all ``wireframe_raytrace`` or
+    ``solid_raytrace`` plots
+
+  :look_at:
+    Location in 3D Cartesian space the camera is looking at.
+
+
+    *Default*: None - Required for all ``wireframe_raytrace`` or
+    ``solid_raytrace`` plots
+
+  :field_of_view:
+    The horizontal field of view in degrees. Defaults to roughly the same value
+    as for the human eye.
+
+    *Default*: 70
+
+  :orthographic_width:
+    If set to a nonzero value, an orthographic rather than perspective
+    projection for the camera is employed. An orthographic projection puts out
+    parallel rays from the camera of a width prescribed here in the horizontal
+    direction, with the width in the vertical direction decided by the pixel
+    aspect ratio.
+
+    *Default*: 0
+
+``<plot>`` elements of ``type`` "solid_raytrace" can contain the following attributes or
+sub-elements.
+
+  :opaque_ids:
+    List of integer IDs of cells or materials to be treated as visible in the
+    plot. Whether the integers are interpreted as cell or material IDs depends
+    on ``color_by``.
+
+    *Default*: None - Required for all phong plots
+
+  :light_position:
+    Location in 3D Cartesian space of the light.
+
+
+    *Default*: Same location as ``camera_position``
+
+  :diffuse_fraction:
+    Fraction of light originating from non-directional sources. If set to one,
+    the coloring is not influenced by surface curvature, and no shadows appear.
+    If set to zero, only regions illuminated by the light are not black.
+
+
+    *Default*: 0.1
+
+``<plot>`` elements of ``type`` "wireframe_raytrace" can contain the following
+attributes or sub-elements.
+
+  :wireframe_color:
+    RGB value of the wireframe's color
+
+    *Default*: 0, 0, 0 (black)
+
+  :wireframe_thickness:
+    Integer number of pixels that the wireframe takes up. The value is a radius
+    of the wireframe. Setting to zero removes any wireframing.
+
+    *Default*: 0
+
+  :wireframe_ids:
+    Integer IDs of cells or materials of regions to draw wireframes around.
+    Whether the integers are interpreted as cell or material IDs depends on
+    ``color_by``.
+
+    *Default*: None

docs/source/io_formats/properties.rst

@@ -4,7 +4,7 @@
 Properties File Format
 ======================
 
-The current version of the properties file format is 1.0.
+The current version of the properties file format is 1.1.
 
 **/**
 
@@ -25,6 +25,7 @@ The current version of the properties file format is 1.0.
 **/geometry/cells/cell <uid>/**
 
 :Datasets: - **temperature** (*double[]*) -- Temperature of the cell in [K].
+           - **density** (*double[]*) -- Density of the cell in [g/cm3].
 
 **/materials/**
 

docs/source/io_formats/settings.rst

@@ -32,6 +32,17 @@ standard deviation.
 
   *Default*: false
 
+-------------------------------------
+``<create_delayed_neutrons>`` Element
+-------------------------------------
+
+The ``<create_delayed_neutrons>`` element indicates whether delayed neutrons
+are created in fission. If this element is set to "true", delayed neutrons
+will be created in fission events; otherwise only prompt neutrons will be
+created.
+
+  *Default*: true
+
 -------------------------------------
 ``<create_fission_neutrons>`` Element
 -------------------------------------
@@ -49,13 +60,15 @@ fission.
 ``<cutoff>`` Element
 --------------------
 
-The ``<cutoff>`` element indicates two kinds of cutoffs. The first is the weight
-cutoff used below which particles undergo Russian roulette. Surviving particles
-are assigned a user-determined weight. Note that weight cutoffs and Russian
-rouletting are not turned on by default. The second is the energy cutoff which
-is used to kill particles under certain energy. The energy cutoff should not be
-used unless you know particles under the energy are of no importance to results
-you care. This element has the following attributes/sub-elements:
+The ``<cutoff>`` element indicates three kinds of cutoffs. The first is the
+weight cutoff used below which particles undergo Russian roulette. Surviving
+particles are assigned a user-determined weight. Note that weight cutoffs and
+Russian rouletting are not turned on by default. The second is the energy cutoff
+which is used to kill particles under certain energy. The energy cutoff should
+not be used unless you know particles under the energy are of no importance to
+results you care. The third is the time cutoff used to kill particles whose time
+exceeds a specific cutoff. Particles will be killed exactly at the specified
+time.
 
   :weight:
     The weight below which particles undergo Russian roulette.
@@ -68,6 +81,13 @@ you care. This element has the following attributes/sub-elements:
 
     *Default*: 1.0
 
+  :survival_normalization:
+    If this element is set to "true", this will enable the use of survival
+    biasing source normalization, whereby the weight parameters, weight and
+    weight_avg, are multiplied per history by the start weight of said history.
+
+    *Default*: false
+
   :energy_neutron:
     The energy under which neutrons will be killed.
 
@@ -88,6 +108,26 @@ you care. This element has the following attributes/sub-elements:
 
     *Default*: 0.0
 
+  :time_neutron
+    The time above which neutrons will be killed.
+
+    *Default*: Infinity
+
+  :time_photon
+    The time above which photons will be killed.
+
+    *Default*: Infinity
+
+  :time_electron
+    The time above which electrons will be killed.
+
+    *Default*: Infinity
+
+  :time_positron
+    The time above which positorns will be killed.
+
+    *Default*: Infinity
+
 ----------------------------
 ``<delayed_photon_scaling>``
 ----------------------------
@@ -138,6 +178,16 @@ history-based parallelism.
 
   *Default*: false
 
+--------------------------------
+``<free_gas_threshold>`` Element
+--------------------------------
+
+The ``<free_gas_threshold>`` element specifies the energy multiplier, expressed
+in units of :math:`kT`, that determines when the free gas scattering approach is
+used for elastic scattering. Values must be positive.
+
+  *Default*: 400.0
+
 -----------------------------------
 ``<generations_per_batch>`` Element
 -----------------------------------
@@ -205,7 +255,7 @@ based on the recommended value in LA-UR-14-24530_.
 
   .. note:: This element is not used in the multi-group :ref:`energy_mode`.
 
-.. _LA-UR-14-24530: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-14-24530.pdf
+.. _LA-UR-14-24530: https://mcnp.lanl.gov/pdf_files/TechReport_2014_LANL_LA-UR-14-24530_Brown.pdf
 
 ---------------------------
 ``<material_cell_offsets>``
@@ -219,19 +269,45 @@ to false.
 
   *Default*: true
 
-----------------------------------------
-``<max_particles_in_flight>`` Element
-----------------------------------------
+--------------------------------
+``<max_lost_particles>`` Element
+--------------------------------
 
-This element indicates the number of neutrons to run in flight concurrently
+This element indicates the maximum number of lost particles.
+
+  *Default*: 10
+
+------------------------------------
+``<rel_max_lost_particles>`` Element
+------------------------------------
+
+
+This element indicates the maximum number of lost particles, relative to the
+total number of particles.
+
+  *Default*: 1.0e-6
+
+-------------------------------------
+``<max_particles_in_flight>`` Element
+-------------------------------------
+
+This element indicates the number of particles to run in flight concurrently
 when using event-based parallelism. A higher value uses more memory, but
 may be more efficient computationally.
 
   *Default*: 100000
 
----------------------------
+---------------------------------
+``<max_particle_events>`` Element
+---------------------------------
+
+This element indicates the maximum number of events a particle can undergo.
+
+  *Default*: 1000000
+
+-----------------------
 ``<max_order>`` Element
----------------------------
+-----------------------
 
 The ``<max_order>`` element allows the user to set a maximum scattering order
 to apply to every nuclide/material in the problem.  That is, if the data
@@ -243,6 +319,23 @@ then, OpenMC will only use up to the :math:`P_1` data.
   .. note:: This element is not used in the continuous-energy
     :ref:`energy_mode`.
 
+--------------------------------
+``<max_history_splits>`` Element
+--------------------------------
+
+The ``<max_history_splits>`` element indicates the number of times a particle can split during a history.
+
+  *Default*: 1000
+
+--------------------------------------
+``<max_write_lost_particles>`` Element
+--------------------------------------
+
+This ``<max_write_lost_particles>`` element indicates the maximum number of
+particle restart files (per MPI process) to write for lost particles.
+
+  *Default*: None
+
 .. _mesh_element:
 
 ------------------
@@ -334,6 +427,15 @@ either "false" or "true".
 
   *Default*: false
 
+-----------------------
+``<plot_seed>`` Element
+-----------------------
+
+The ``<plot_seed>`` element is used to set the seed for the pseudorandom number
+generator during generation of colors in plots.
+
+  *Default*: 1
+
 ---------------------
 ``<ptables>`` Element
 ---------------------
@@ -346,6 +448,64 @@ or sub-elements and can be set to either "false" or "true".
 
   .. note:: This element is not used in the multi-group :ref:`energy_mode`.
 
+------------------------
+``<random_ray>`` Element
+------------------------
+
+The ``<random_ray>`` element enables random ray mode and contains a number of
+settings relevant to the solver. Tips for selecting these parameters can be
+found in the :ref:`random ray user guide <random_ray>`.
+
+  :distance_inactive:
+    The inactive ray length (dead zone length) in [cm].
+
+    *Default*: None
+
+  :distance_active:
+    The active ray length in [cm].
+
+    *Default*: None
+
+  :source:
+    Specifies the starting ray distribution, and follows the format for
+    :ref:`source_element`. It must be uniform in space and angle and cover the
+    full domain. It does not represent a physical neutron or photon source -- it
+    is only used to sample integrating ray starting locations and directions.
+
+    *Default*: None
+
+  :sample_method:
+    Specifies the method for sampling the starting ray distribution. This
+    element can be set to "prng" or "halton".
+
+    *Default*: prng
+
+  :source_region_meshes:
+    Relates meshes to spatial domains for subdividing source regions with each domain.
+
+    :mesh:
+      Contains an ``id`` attribute and one or more ``<domain>`` sub-elements.
+
+      :id:
+        The unique identifier for the mesh.
+
+      :domain:
+        Each domain element has an ``id`` attribute and a ``type`` attribute.
+
+        :id:
+          The unique identifier for the domain.
+
+        :type:
+          The type of the domain. Can be ``material``, ``cell``, or ``universe``.
+
+  :diagonal_stabilization_rho:
+    The rho factor for use with diagonal stabilization. This technique is
+    applied when negative diagonal (in-group) elements are detected in
+    the scattering matrix of input MGXS data, which is a common feature
+    of transport corrected MGXS data.
+
+    *Default*: 1.0
+
 ----------------------------------
 ``<resonance_scattering>`` Element
 ----------------------------------
@@ -421,6 +581,17 @@ pseudo-random number generator.
 
   *Default*: 1
 
+--------------------
+``<stride>`` Element
+--------------------
+
+The ``stride`` element is used to specify how many random numbers are allocated
+for each source particle history.
+
+  *Default*: 152,917
+
+.. _source_element:
+
 --------------------
 ``<source>`` Element
 --------------------
@@ -438,24 +609,29 @@ attributes/sub-elements:
 
     *Default*: 1.0
 
+  :type:
+    Indicator of source type. One of ``independent``, ``file``, ``compiled``, or
+    ``mesh``. The type of the source will be determined by this attribute if it
+    is present.
+
   :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()``;
@@ -463,16 +639,15 @@ attributes/sub-elements:
       as a unique pointer. This function can be used to pass parameters through to
       the source from the XML, if needed.
 
-    More documentation on how to build sources can be found in :ref:`custom_source`.
-
-    *Default*: None
+    More documentation on how to build sources can be found in
+    :ref:`compiled_source`.
 
   :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_compiled_source`.
 
   :space:
     An element specifying the spatial distribution of source sites. This element
@@ -480,19 +655,37 @@ attributes/sub-elements:
 
     :type:
       The type of spatial distribution. Valid options are "box", "fission",
-      "point", "cartesian", "cylindrical", and "spherical". A "box" spatial
-      distribution has coordinates sampled uniformly in a parallelepiped. A
-      "fission" spatial distribution samples locations from a "box"
+      "point", "cartesian", "cylindrical", "spherical", "mesh", and "cloud".
+
+      A "box" spatial distribution has coordinates sampled uniformly in a
+      parallelepiped.
+
+      A "fission" spatial distribution samples locations from a "box"
       distribution but only locations in fissionable materials are accepted.
+
       A "point" spatial distribution has coordinates specified by a triplet.
+
       A "cartesian" spatial distribution specifies independent distributions of
-      x-, y-, and z-coordinates. A "cylindrical" spatial distribution specifies
-      independent distributions of r-, phi-, and z-coordinates where phi is the
-      azimuthal angle and the origin for the cylindrical coordinate system is
-      specified by origin. A "spherical" spatial distribution specifies
-      independent distributions of r-, theta-, and phi-coordinates where theta
-      is the angle with respect to the z-axis, phi is the azimuthal angle, and
-      the sphere is centered on the coordinate (x0,y0,z0).
+      x-, y-, and z-coordinates.
+
+      A "cylindrical" spatial distribution specifies independent distributions
+      of r-, phi-, and z-coordinates where phi is the azimuthal angle and the
+      origin for the cylindrical coordinate system is specified by origin.
+
+      A "spherical" spatial distribution specifies independent distributions of
+      r-, cos_theta-, and phi-coordinates where cos_theta is the cosine of the
+      angle with respect to the z-axis, phi is the azimuthal angle, and the
+      sphere is centered on the coordinate (x0,y0,z0).
+
+      A "mesh" spatial distribution samples source sites from a mesh element
+      based on the relative strengths provided in the node. Source locations
+      within an element are sampled isotropically. If no strengths are provided,
+      the space within the mesh is uniformly sampled.
+
+      A "cloud" spatial distribution samples source sites from a list of spatial
+      positions provided in the node, based on the relative strengths provided
+      in the node. If no strengths are provided, the positions are uniformly
+      sampled.
 
       *Default*: None
 
@@ -559,6 +752,26 @@ attributes/sub-elements:
       For "cylindrical and "spherical" distributions, this element specifies
       the coordinates for the origin of the coordinate system.
 
+    :mesh_id:
+      For "mesh" spatial distributions, this element specifies which mesh ID to
+      use for the geometric description of the mesh.
+
+    :coords:
+      For "cloud" distributions, this element specifies a list of coordinates
+      for each of the points in the cloud.
+
+    :strengths:
+      For "mesh" and "cloud" spatial distributions, this element specifies the
+      relative source strength of each mesh element or each point in the cloud.
+
+    :volume_normalized:
+      For "mesh" spatial distrubtions, this optional boolean element specifies
+      whether the vector of relative strengths should be multiplied by the mesh
+      element volume. This is most common if the strengths represent a source
+      per unit volume.
+
+      *Default*: false
+
   :angle:
     An element specifying the angular distribution of source sites. This element
     has the following attributes:
@@ -606,6 +819,47 @@ attributes/sub-elements:
 
     *Default*: false
 
+  :mesh:
+    For mesh sources, this indicates the ID of the corresponding mesh.
+
+  :source:
+    For mesh sources, this sub-element specifies the source for an individual
+    mesh element and follows the format for :ref:`source_element`. The number of
+    ``<source>`` sub-elements should correspond to the number of mesh elements.
+
+  :constraints:
+    This sub-element indicates the presence of constraints on sampled source
+    sites (see :ref:`usersguide_source_constraints` for details). It may have
+    the following sub-elements:
+
+    :domain_ids:
+      The unique IDs of domains for which source sites must be within.
+
+      *Default*: None
+
+    :domain_type:
+      The type of each domain for source rejection ("cell", "material", or
+      "universe").
+
+      *Default*: None
+
+    :fissionable:
+      A boolean indicating whether source sites must be sampled within a
+      material that is fissionable in order to be accepted.
+
+    :time_bounds:
+      A pair of times in [s] indicating the lower and upper bound for a time
+      interval that source particles must be within.
+
+    :energy_bounds:
+      A pair of energies in [eV] indicating the lower and upper bound for an
+      energy interval that source particles must be within.
+
+    :rejection_strategy:
+      Either "resample", indicating that source sites should be resampled when
+      one is rejected, or "kill", indicating that a rejected source site is
+      assigned zero weight.
+
 .. _univariate:
 
 Univariate Probability Distributions
@@ -673,6 +927,16 @@ variable and whose sub-elements/attributes are as follows:
   :dist:
     This sub-element of a ``pair`` element provides information on the corresponding univariate distribution.
 
+---------------------------------------
+``<source_rejection_fraction>`` Element
+---------------------------------------
+
+The ``<source_rejection_fraction>`` element specifies the minimum fraction of
+external source sites that must be accepted when applying rejection sampling
+based on constraints.
+
+   *Default*: 0.05
+
 -------------------------
 ``<state_point>`` Element
 -------------------------
@@ -731,27 +995,39 @@ attributes/sub-elements:
 
     *Default*: false
 
----------------------------
-``<surf_src_read>`` Element
----------------------------
+  :mcpl:
+    If this element is set to "true", the source point file containing the
+    source bank will be written as an MCPL_ file name ``source.mcpl`` instead of
+    an HDF5 file. This option is only applicable if the ``<separate>`` element
+    is set to true.
 
-The ``<surf_src_read>`` element specifies a surface source file for OpenMC to
-read source bank for initializing histories.
-This element has the following attributes/sub-elements:
+    *Default*: false
+
+------------------------------
+``<surf_source_read>`` Element
+------------------------------
+
+The ``<surf_source_read>`` element specifies a surface source file for OpenMC to
+read source bank for initializing histories. This element has the following
+attributes/sub-elements:
 
   :path:
     Absolute or relative path to a surface source file to read in source bank.
 
     *Default*: ``surface_source.h5`` in current working directory
 
-----------------------------
-``<surf_src_write>`` Element
-----------------------------
+-------------------------------
+``<surf_source_write>`` Element
+-------------------------------
 
-The ``<surf_src_write>`` element triggers OpenMC to bank particles crossing
+The ``<surf_source_write>`` element triggers OpenMC to bank particles crossing
 certain surfaces and write out the source bank in a separate file called
-``surface_source.h5``.
-This element has the following attributes/sub-elements:
+``surface_source.h5``. One or multiple surface IDs and one cell ID can be used
+to select the surfaces of interest. If no surface IDs are declared, every surface
+of the model is eligible to bank particles. In that case, a cell ID (using
+either the ``cell``, ``cellfrom`` or ``cellto`` attributes) can be used to select
+every surface of a specific cell. This element has the following
+attributes/sub-elements:
 
   :surface_ids:
     A list of integers separated by spaces indicating the unique IDs of surfaces
@@ -767,6 +1043,53 @@ This element has the following attributes/sub-elements:
 
     *Default*: None
 
+  :max_source_files:
+    An integer value indicating the number of surface source files to be written
+    containing the maximum number of particles each. The surface source bank
+    will be cleared in simulation memory each time a surface source file is
+    written. By default a ``surface_source.h5`` file will be created when the
+    maximum number of saved particles is reached.
+
+    *Default*: 1
+
+  :mcpl:
+    An optional boolean which indicates if the banked particles should be
+    written to a file in the MCPL_-format instead of the native HDF5-based
+    format. If activated the output file name is changed to
+    ``surface_source.mcpl``.
+
+    *Default*: false
+
+    .. _MCPL: https://mctools.github.io/mcpl/mcpl.pdf
+
+  :cell:
+    An integer representing the cell ID used to determine if particles crossing
+    identified surfaces are to be banked. Particles coming from or going to this
+    declared cell will be banked if they cross the identified surfaces.
+
+    *Default*: None
+
+  :cellfrom:
+    An integer representing the cell ID used to determine if particles crossing
+    identified surfaces are to be banked. Particles coming from this declared
+    cell will be banked if they cross the identified surfaces.
+
+    *Default*: None
+
+  :cellto:
+    An integer representing the cell ID used to determine if particles crossing
+    identified surfaces are to be banked. Particles going to this declared cell
+    will be banked if they cross the identified surfaces.
+
+    *Default*: None
+
+.. note:: The ``cell``, ``cellfrom`` and ``cellto`` attributes cannot be
+          used simultaneously.
+
+.. note:: Surfaces with boundary conditions that are not "transmission" or "vacuum"
+          are not eligible to store any particles when using ``cell``, ``cellfrom``
+          or ``cellto`` attributes. It is recommended to use surface IDs instead.
+
 ------------------------------
 ``<survival_biasing>`` Element
 ------------------------------
@@ -832,7 +1155,9 @@ cell, the nearest temperature at which cross sections are given is to be
 applied, within a given tolerance (see :ref:`temperature_tolerance`). A value of
 "interpolation" indicates that cross sections are to be linear-linear
 interpolated between temperatures at which nuclear data are present (see
-:ref:`temperature_treatment`).
+:ref:`temperature_treatment`). With the "interpolation" method, temperatures
+outside of the bounds of the nuclear data may be accepted, provided they still
+fall within the tolerance (see :ref:`temperature_tolerance`).
 
   *Default*: "nearest"
 
@@ -871,7 +1196,12 @@ The ``<temperature_tolerance>`` element specifies a tolerance in Kelvin that is
 to be applied when the "nearest" temperature method is used. For example, if a
 cell temperature is 340 K and the tolerance is 15 K, then the closest
 temperature in the range of 325 K to 355 K will be used to evaluate cross
-sections.
+sections. If the ``<temperature_method>`` is "interpolation", the tolerance
+specified applies to cell temperatures outside of the data bounds. For example,
+if a cell is specified at 695K, a tolerance of 15K and data is only available
+at 700K and 1000K, the cell's cross sections will be evaluated at 700K, since
+the desired temperature of 695K is within the tolerance of the actual data
+despite not being bounded on both sides.
 
   *Default*: 10 K
 
@@ -986,8 +1316,14 @@ The ``<volume_calc>`` element indicates that a stochastic volume calculation
 should be run at the beginning of the simulation. This element has the following
 sub-elements/attributes:
 
-  :cells:
-    The unique IDs of cells for which the volume should be estimated.
+  :domain_type:
+    The type of each domain for the volume calculation ("cell", "material", or
+    "universe").
+
+    *Default*: None
+
+  :domain_ids:
+    The unique IDs of domains for which the volume should be estimated.
 
     *Default*: None
 
@@ -997,16 +1333,41 @@ sub-elements/attributes:
     *Default*: None
 
   :lower_left:
-     The lower-left Cartesian coordinates of a bounding box that is used to
-     sample points within.
+    The lower-left Cartesian coordinates of a bounding box that is used to
+    sample points within.
 
-     *Default*: None
+    *Default*: None
 
   :upper_right:
-     The upper-right Cartesian coordinates of a bounding box that is used to
-     sample points within.
+    The upper-right Cartesian coordinates of a bounding box that is used to
+    sample points within.
 
-     *Default*: None
+    *Default*: None
+
+  :threshold:
+    Presence of a ``<threshold>`` sub-element indicates that the volume
+    calculation will be halted based on a threshold on the error. It has the
+    following sub-elements/attributes:
+
+    :type:
+      The type of the trigger. Accepted options are "variance", "std_dev",
+      and "rel_err".
+
+      :variance:
+        Variance of the mean, :math:`\sigma^2`
+
+      :std_dev:
+        Standard deviation of the mean, :math:`\sigma`
+
+      :rel_err:
+        Relative error of the mean, :math:`\frac{\sigma}{\mu}`
+
+      *Default*: None
+
+    :threshold:
+      The trigger's convergence criterion for the given type.
+
+      *Default*: None
 
 ----------------------------
 ``<weight_windows>`` Element
@@ -1027,7 +1388,7 @@ 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
@@ -1065,3 +1426,92 @@ 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 (one of 'magic' or 'fw_cadis')
+
+    *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_window_checkpoints>`` Element
+---------------------------------------
+
+The ``<weight_window_checkpoints>`` element indicates the checkpoints for weight
+window split/roulette (surface, collision or both). This element has the
+following sub-elements/attributes:
+
+  :surface:
+    If set to "true", weight window checks will be performed at surface
+    crossings.
+
+    *Default*: False
+
+  :collision:
+    If set to "true", weight window checks will be performed at collisions.
+
+    *Default*: True
+
+--------------------------------------
+``<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.
 
 **/**
 
@@ -23,6 +23,7 @@ The current version of the statepoint file format is 17.0.
                bank is present (1) or not (0).
 
 :Datasets: - **seed** (*int8_t*) -- Pseudo-random number generator seed.
+           - **stride** (*uint64_t*) -- Pseudo-random number generator stride.
            - **energy_mode** (*char[]*) -- Energy mode of the run, either
              'continuous-energy' or 'multi-group'.
            - **run_mode** (*char[]*) -- Run mode used, either 'eigenvalue' or
@@ -68,20 +69,44 @@ 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.
+:Attributes: - **id** (*int*) -- ID of the mesh
+
+:Datasets: - **name** (*char[]*) -- Name of the mesh.
+           - **type** (*char[]*) -- Type of mesh.
            - **dimension** (*int*) -- Number of mesh cells in each dimension.
-           - **lower_left** (*double[]*) -- Coordinates of lower-left corner of
-             mesh.
-           - **upper_right** (*double[]*) -- Coordinates of upper-right corner
-             of mesh.
-           - **width** (*double[]*) -- Width of each mesh cell in each
-             dimension.
+           - **Regular Mesh Only:**
+              - **lower_left** (*double[]*) -- Coordinates of lower-left corner of
+                mesh.
+              - **upper_right** (*double[]*) -- Coordinates of upper-right corner
+                of mesh.
+              - **width** (*double[]*) -- Width of each mesh cell in each
+                dimension.
+           - **Rectilinear Mesh Only:**
+              - **x_grid** (*double[]*) -- Mesh divisions along the x-axis.
+              - **y_grid** (*double[]*) -- Mesh divisions along the y-axis.
+              - **z_grid** (*double[]*) -- Mesh divisions along the z-axis.
+           - **Cylindrical & Spherical Mesh Only:**
+              - **r_grid** (*double[]*) -- The mesh divisions along the r-axis.
+              - **phi_grid** (*double[]*) -- The mesh divisions along the phi-axis.
+              - **origin** (*double[]*) -- The origin in cartesian coordinates.
+           - **Spherical Mesh Only:**
+              - **theta_grid** (*double[]*) -- The mesh divisions along the theta-axis.
            - **Unstructured Mesh Only:**
+              - **filename** (*char[]*) -- Name of the mesh file.
+              - **library** (*char[]*) -- Mesh library used to represent the
+                                          mesh ("moab" or "libmesh").
+              - **length_multiplier** (*double*) Scaling factor applied to the mesh.
+              - **options** (*char[]*) -- Special options that control spatial
+                                          search data structures used.
               - **volumes** (*double[]*) -- Volume of each mesh cell.
-              - **centroids** (*double[]*) -- Location of the mesh cell
-                centroids.
+              - **vertices** (*double[]*) -- x, y, z values of the mesh vertices.
+              - **connectivity** (*int[]*) -- Connectivity array for the mesh
+                cells.
+              - **element_types** (*int[]*) -- Mesh element types.
 
 **/tallies/filters/**
 
@@ -103,6 +128,10 @@ The current version of the statepoint file format is 17.0.
            - **y** (*double[]*) -- Interpolant values for energyfunction
              interpolation. Only used for 'energyfunction' filters.
 
+             :Attributes:
+                          - **interpolation** (*int*) -- Interpolation type. Only used for
+                            'energyfunction' filters.
+
 **/tallies/derivatives/derivative <id>/**
 
 :Datasets: - **independent variable** (*char[]*) -- Independent variable of
@@ -118,6 +147,8 @@ 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.
@@ -149,7 +180,7 @@ All values are given in seconds and are measured on the master process.
              finalization.
            - **transport** (*double*) -- Time spent transporting particles.
            - **inactive batches** (*double*) -- Time spent in the inactive
-             batches (including non-transport activities like communcating
+             batches (including non-transport activities like communicating
              sites).
            - **active batches** (*double*) -- Time spent in the active batches
              (including non-transport activities like communicating sites).

docs/source/io_formats/summary.rst

@@ -4,7 +4,7 @@
 Summary File Format
 ===================
 
-The current version of the summary file format is 6.0.
+The current version of the summary file format is 6.1.
 
 **/**
 
@@ -38,6 +38,7 @@ The current version of the summary file format is 6.0.
              is an array if the cell uses distributed materials, otherwise it is
              a scalar.
            - **temperature** (*double[]*) -- Temperature of the cell in Kelvin.
+           - **density** (*double[]*) -- Density of the cell in [g/cm3].
            - **translation** (*double[3]*) -- Translation applied to the fill
              universe. This dataset is present only if fill_type is set to
              'universe'.
@@ -60,9 +61,11 @@ The current version of the summary file format is 6.0.
            - **coefficients** (*double[]*) -- Array of coefficients that define
              the surface. See :ref:`surface_element` for what coefficients are
              defined for each surface type.
-           - **boundary_condition** (*char[]*) -- Boundary condition applied to
-             the surface. Can be 'transmission', 'vacuum', 'reflective', or
-             'periodic'.
+           - **boundary_type** (*char[]*) -- Boundary condition applied to
+             the surface. Can be 'transmission', 'vacuum', 'reflective',
+             'periodic', or 'white'.
+           - **albedo** (*double*) -- Boundary albedo as a positive multiplier
+             of particle weight. If absent, it is assumed to be 1.0.
            - **geom_type** (*char[]*) -- Type of geometry used to create the cell.
              Either 'csg' or 'dagmc'.
 

docs/source/io_formats/tallies.rst

@@ -40,15 +40,15 @@ The ``<tally>`` element accepts the following sub-elements:
 
   :nuclides:
     If specified, the scores listed will be for particular nuclides, not the
-    summation of reactions from all nuclides. The format for nuclides should be
-    [Atomic symbol]-[Mass number], e.g. "U-235". The reaction rate for all
+    summation of reactions from all nuclides. Nuclides are expressed using the
+    GNDS naming convention, e.g. "U235" or "Am242_m1". The reaction rate for all
     nuclides can be obtained with "total". For example, to obtain the reaction
-    rates for U-235, Pu-239, and all nuclides in a material, this element should
+    rates for U235, Pu239, and all nuclides in a material, this element should
     be:
 
     .. code-block:: xml
 
-        <nuclides>U-235 Pu-239 total</nuclides>
+        <nuclides>U235 Pu239 total</nuclides>
 
     *Default*: total
 
@@ -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
@@ -94,6 +100,18 @@ The ``<tally>`` element accepts the following sub-elements:
 
      *Default*: None
 
+   :ignore_zeros:
+     Whether to allow zero tally bins to be ignored when assessing the
+     convergece of the precision trigger. If True, only nonzero tally scores
+     will be compared to the trigger's threshold.
+
+     .. note:: The ``ignore_zeros`` option can cause the tally trigger to fire
+               prematurely if there are no hits in any bins at the first
+               evalulation. It is the user's responsibility to specify enough
+               particles per batch to get a nonzero score in at least one bin.
+
+     *Default*: False
+
    :scores:
      The score(s) in this tally to which the trigger should be applied.
 
@@ -311,6 +329,11 @@ If a mesh is desired as a filter for a tally, it must be specified in a separate
 element with the tag name ``<mesh>``. This element has the following
 attributes/sub-elements:
 
+  :name:
+    An optional string name to identify the mesh in output files.
+
+    *Default*: ""
+
   :type:
     The type of mesh. This can be either "regular", "rectilinear",
     "cylindrical", "spherical", or "unstructured".
@@ -351,10 +374,17 @@ attributes/sub-elements:
   :theta_grid:
     The mesh divisions along the theta-axis. (For spherical mesh only.)
 
+  :origin:
+    The origin in cartesian coordinates. (For cylindrical and spherical meshes only.)
+
   :library:
     The mesh library used to represent an unstructured mesh. This can be either
     "moab" or "libmesh". (For unstructured mesh only.)
 
+  :options:
+    Special options that control spatial search data structures used. (For
+    unstructured mesh using MOAB only)
+
   :filename:
     The name of the mesh file to be loaded at runtime. (For unstructured mesh
     only.)

docs/source/io_formats/track.rst

@@ -4,18 +4,34 @@
 Track File Format
 =================
 
-The current revision of the particle track file format is 2.0.
+The current revision of the particle track file format is 3.0.
 
 **/**
 
 :Attributes: - **filetype** (*char[]*) -- String indicating the type of file.
              - **version** (*int[2]*) -- Major and minor version of the track
                file format.
-             - **n_particles** (*int*) -- Number of particles for which tracks
-               are recorded.
-             - **n_coords** (*int[]*) -- Number of coordinates for each
-               particle.
 
 :Datasets:
-           - **coordinates_<i>** (*double[][3]*) -- (x,y,z) coordinates for the
-             *i*-th particle.
+           - **track_<b>_<g>_<p>** (Compound type) -- Particle track information
+             for source particle in batch *b*, generation *g*, and particle
+             number *p*. particle. The compound type has fields ``r``, ``u``,
+             ``E``, ``time``, ``wgt``, ``cell_id``, ``cell_instance``, and
+             ``material_id``, which represent the position (each coordinate in
+             [cm]), direction, energy in [eV], time in [s], weight, cell ID,
+             cell instance, and material ID, respectively. When the particle is
+             present in a cell with no material assigned, the material ID is
+             given as -1. Note that this array contains information for one or
+             more primary/secondary particles originating. The starting index
+             for each primary/secondary particle is given by the ``offsets``
+             attribute.
+
+             :Attributes: - **n_particles** (*int*) -- Number of
+                            primary/secondary particles for the source history.
+                          - **offsets** (*int[]*) Offset (starting index) into
+                            the array for each primary/secondary particle. The
+                            last offset should match the total size of the
+                            array.
+                          - **particles** (*int[]*) -- Particle type for each
+                            primary/secondary particle (0=neutron, 1=photon,
+                            2=electron, 3=positron).

docs/source/io_formats/weight_windows.rst

@@ -0,0 +1,39 @@
+.. _io_weight_windows:
+
+====================
+Weight Window Format
+====================
+
+The current revision of the weight window file format is 1.0.
+
+**/**
+
+:Attributes: - **filetype** (*char[]*) -- String indicating the type of file.
+             - **version** (*int[2]*) -- Major and minor version of the weight
+               window file format.
+
+**/weight_windows/**
+
+:Attributes: - **n_weight_windows** (*int*) -- Number of weight window objects in the file.
+             - **ids** (*int[]*) -- Unique IDs of weight window objects in the file.
+
+**/weight_windows/weight_windows_<uid>/**
+
+:Datasets: - **mesh** (*int*) -- ID of the mesh associated with the weight window object.
+           - **particle_type** (*char[]*)  -- Particle type to which the weight windows apply.
+           - **energy_bounds** (*double[]*) -- Energy bounds of the weight windows in [eV]
+           - **lower_ww_bounds** (*double[]*) -- Weight window lower bounds.
+           - **upper_ww_bounds** (*double[]*) -- Weight window upper bounds.
+           - **survival_ratio** (*double*) -- Weight window survival ratio.
+           - **max_lower_bound_ratio** (*double*) -- Maximum particle weight to lower weight window bound ratio.
+           - **max_split** (*int*) -- Maximum number of splits per weight window check.
+           - **weight_cutoff** (*double*) -- Particle weight cutoff.
+
+**/meshes/**
+
+:Attributes: - **n_meshes** (*int*) -- Number of meshes in the file.
+             - **ids** (*int[]*) -- User-defined unique ID of each mesh.
+
+**/meshes/mesh <uid>/**
+
+Please see the section on **/tallies/meshes/** in the :doc:`statepoint`.

docs/source/license.rst

@@ -4,7 +4,7 @@
 License Agreement
 =================
 
-Copyright © 2011-2022 Massachusetts Institute of Technology, UChicago Argonne
+Copyright © 2011-2025 Massachusetts Institute of Technology, UChicago Argonne
 LLC, and OpenMC contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of

docs/source/methods/charged_particles_physics.rst

@@ -0,0 +1,362 @@
+.. _methods_charged_particle_physics:
+
+========================
+Charged Particle Physics
+========================
+
+OpenMC neglects the spatial transport of charged particles (electrons and
+positrons), assuming they deposit all their energy locally and produce
+bremsstrahlung photons at their birth location. This approximation, called
+thick-target bremsstrahlung (TTB) approximation is justified by the fact that
+charged particles have much shorter stopping ranges compared to neutrons and
+photons, especially in high-density materials.
+
+-----------------------------
+Charged Particle Interactions
+-----------------------------
+
+Bremsstrahlung
+--------------
+
+When a charged particle is decelerated in the field of an atom, some of its
+kinetic energy is converted into electromagnetic radiation known as
+bremsstrahlung, or 'braking radiation'. In each event, an electron or positron
+with kinetic energy :math:`T` generates a photon with an energy :math:`E`
+between :math:`0` and :math:`T`. Bremsstrahlung is described by a cross section
+that is differential in photon energy, in the direction of the emitted photon,
+and in the final direction of the charged particle. However, in Monte Carlo
+simulations it is typical to integrate over the angular variables to obtain a
+single differential cross section with respect to photon energy, which is often
+expressed in the form
+
+.. math::
+    :label: bremsstrahlung-dcs
+
+    \frac{d\sigma_{\text{br}}}{dE} = \frac{Z^2}{\beta^2} \frac{1}{E}
+    \chi(Z, T, \kappa),
+
+where :math:`\kappa = E/T` is the reduced photon energy and :math:`\chi(Z, T,
+\kappa)` is the scaled bremsstrahlung cross section, which is experimentally
+measured.
+
+Because electrons are attracted to atomic nuclei whereas positrons are
+repulsed, the cross section for positrons is smaller, though it approaches that
+of electrons in the high energy limit. To obtain the positron cross section, we
+multiply :eq:`bremsstrahlung-dcs` by the :math:`\kappa`-independent factor used
+in Salvat_,
+
+.. math::
+    :label: positron-factor
+
+    \begin{aligned}
+    F_{\text{p}}(Z,T) =
+    & 1 - \text{exp}(-1.2359\times 10^{-1}t + 6.1274\times 10^{-2}t^2 - 3.1516\times 10^{-2}t^3 \\
+    & + 7.7446\times 10^{-3}t^4 - 1.0595\times 10^{-3}t^5 + 7.0568\times 10^{-5}t^6 \\
+    & - 1.8080\times 10^{-6}t^7),
+    \end{aligned}
+
+where
+
+.. math::
+    :label: positron-factor-t
+
+    t = \ln\left(1 + \frac{10^6}{Z^2}\frac{T}{\text{m}_\text{e}c^2} \right).
+
+:math:`F_{\text{p}}(Z,T)` is the ratio of the radiative stopping powers for
+positrons and electrons. Stopping power describes the average energy loss per
+unit path length of a charged particle as it passes through matter:
+
+.. math::
+    :label: stopping-power
+
+    -\frac{dT}{ds} = n \int E \frac{d\sigma}{dE} dE \equiv S(T),
+
+where :math:`n` is the number density of the material and :math:`d\sigma/dE` is
+the cross section differential in energy loss. The total stopping power
+:math:`S(T)` can be separated into two components: the radiative stopping
+power :math:`S_{\text{rad}}(T)`, which refers to energy loss due to
+bremsstrahlung, and the collision stopping power :math:`S_{\text{col}}(T)`,
+which refers to the energy loss due to inelastic collisions with bound
+electrons in the material that result in ionization and excitation. The
+radiative stopping power for electrons is given by
+
+.. math::
+    :label: radiative-stopping-power
+
+    S_{\text{rad}}(T) = n \frac{Z^2}{\beta^2} T \int_0^1 \chi(Z,T,\kappa)
+    d\kappa.
+
+
+To obtain the radiative stopping power for positrons,
+:eq:`radiative-stopping-power`  is multiplied by :eq:`positron-factor`.
+
+While the models for photon interactions with matter described above can safely
+assume interactions occur with free atoms, sampling the target atom based on
+the macroscopic cross sections, molecular effects cannot necessarily be
+disregarded for charged particle treatment. For compounds and mixtures, the
+bremsstrahlung cross section is calculated using Bragg's additivity rule as
+
+.. math::
+    :label: material-bremsstrahlung-dcs
+
+    \frac{d\sigma_{\text{br}}}{dE} = \frac{1}{\beta^2 E} \sum_i \gamma_i Z^2_i
+    \chi(Z_i, T, \kappa),
+
+where the sum is over the constituent elements and :math:`\gamma_i` is the
+atomic fraction of the :math:`i`-th element. Similarly, the radiative stopping
+power is calculated using Bragg's additivity rule as
+
+.. math::
+    :label: material-radiative-stopping-power
+
+    S_{\text{rad}}(T) = \sum_i w_i S_{\text{rad},i}(T),
+
+where :math:`w_i` is the mass fraction of the :math:`i`-th element and
+:math:`S_{\text{rad},i}(T)` is found for element :math:`i` using
+:eq:`radiative-stopping-power`. The collision stopping power, however, is a
+function of certain quantities such as the mean excitation energy :math:`I` and
+the density effect correction :math:`\delta_F` that depend on molecular
+properties. These quantities cannot simply be summed over constituent elements
+in a compound, but should instead be calculated for the material. The Bethe
+formula can be used to find the collision stopping power of the material:
+
+.. math::
+    :label: material-collision-stopping-power
+
+    S_{\text{col}}(T) = \frac{2 \pi r_e^2 m_e c^2}{\beta^2} N_A \frac{Z}{A_M}
+    [\ln(T^2/I^2) + \ln(1 + \tau/2) + F(\tau) - \delta_F(T)],
+
+where :math:`N_A` is Avogadro's number, :math:`A_M` is the molar mass,
+:math:`\tau = T/m_e`, and :math:`F(\tau)` depends on the particle type. For
+electrons,
+
+.. math::
+    :label: F-electron
+
+    F_{-}(\tau) = (1 - \beta^2)[1 + \tau^2/8 - (2\tau + 1) \ln2],
+
+while for positrons
+
+.. math::
+    :label: F-positron
+
+    F_{+}(\tau) = 2\ln2 - (\beta^2/12)[23 + 14/(\tau + 2) + 10/(\tau + 2)^2 +
+    4/(\tau + 2)^3].
+
+The density effect correction :math:`\delta_F` takes into account the reduction
+of the collision stopping power due to the polarization of the material the
+charged particle is passing through by the electric field of the particle.
+It can be evaluated using the method described by Sternheimer_, where the
+equation for :math:`\delta_F` is
+
+.. math::
+    :label: density-effect-correction
+
+    \delta_F(\beta) = \sum_{i=1}^n f_i \ln[(l_i^2 + l^2)/l_i^2] -
+    l^2(1-\beta^2).
+
+Here, :math:`f_i` is the oscillator strength of the :math:`i`-th transition,
+given by :math:`f_i = n_i/Z`, where :math:`n_i` is the number of electrons in
+the :math:`i`-th subshell. The frequency :math:`l` is the solution of the
+equation
+
+.. math::
+    :label: density-effect-l
+
+    \frac{1}{\beta^2} - 1 = \sum_{i=1}^{n} \frac{f_i}{\bar{\nu}_i^2 + l^2},
+
+where :math:`\bar{v}_i` is defined as
+
+.. math::
+    :label: density-effect-nubar
+
+    \bar{\nu}_i = h\nu_i \rho / h\nu_p.
+
+The plasma energy :math:`h\nu_p` of the medium is given by
+
+.. math::
+    :label: plasma-frequency
+
+    h\nu_p = \sqrt{\frac{(hc)^2 r_e \rho_m N_A Z}{\pi A}},
+
+where :math:`A` is the atomic weight and :math:`\rho_m` is the density of the
+material. In :eq:`density-effect-nubar`, :math:`h\nu_i` is the oscillator
+energy, and :math:`\rho` is an adjustment factor introduced to give agreement
+between the experimental values of the oscillator energies and the mean
+excitation energy. The :math:`l_i` in :eq:`density-effect-correction` are
+defined as
+
+.. math::
+    :label: density-effect-li
+
+    \begin{aligned}
+    l_i &= (\bar{\nu}_i^2 + 2/3f_i)^{1/2} ~~~~&\text{for}~~ \bar{\nu}_i > 0 \\
+    l_n &= f_n^{1/2} ~~~~&\text{for}~~ \bar{\nu}_n = 0,
+    \end{aligned}
+
+where the second case applies to conduction electrons. For a conductor,
+:math:`f_n` is given by :math:`n_c/Z`, where :math:`n_c` is the effective
+number of conduction electrons, and :math:`v_n = 0`. The adjustment factor
+:math:`\rho` is determined using the equation for the mean excitation energy:
+
+.. math::
+    :label: mean-excitation-energy
+
+    \ln I = \sum_{i=1}^{n-1} f_i \ln[(h\nu_i\rho)^2 + 2/3f_i(h\nu_p)^2]^{1/2} +
+    f_n \ln (h\nu_pf_n^{1/2}).
+
+.. _ttb:
+
+
+Thick-Target Bremsstrahlung Approximation
++++++++++++++++++++++++++++++++++++++++++
+
+Since charged particles lose their energy on a much shorter distance scale than
+neutral particles, not much error should be introduced by neglecting to
+transport electrons. However, the bremsstrahlung emitted from high energy
+electrons and positrons can travel far from the interaction site. Thus, even
+without a full electron transport mode it is necessary to model bremsstrahlung.
+We use a thick-target bremsstrahlung (TTB) approximation based on the models in
+Salvat_ and Kaltiaisenaho_ for generating bremsstrahlung photons, which assumes
+the charged particle loses all its energy in a single homogeneous material
+region.
+
+To model bremsstrahlung using the TTB approximation, we need to know the number
+of photons emitted by the charged particle and the energy distribution of the
+photons. These quantities can be calculated using the continuous slowing down
+approximation (CSDA). The CSDA assumes charged particles lose energy
+continuously along their trajectory with a rate of energy loss equal to the
+total stopping power, ignoring fluctuations in the energy loss. The
+approximation is useful for expressing average quantities that describe how
+charged particles slow down in matter. For example, the CSDA range approximates
+the average path length a charged particle travels as it slows to rest:
+
+.. math::
+    :label: csda-range
+
+    R(T) = \int^T_0 \frac{dT'}{S(T')}.
+
+Actual path lengths will fluctuate around :math:`R(T)`. The average number of
+photons emitted per unit path length is given by the inverse bremsstrahlung
+mean free path:
+
+.. math::
+    :label: inverse-bremsstrahlung-mfp
+
+    \lambda_{\text{br}}^{-1}(T,E_{\text{cut}})
+    = n\int_{E_{\text{cut}}}^T\frac{d\sigma_{\text{br}}}{dE}dE
+    = n\frac{Z^2}{\beta^2}\int_{\kappa_{\text{cut}}}^1\frac{1}{\kappa}
+    \chi(Z,T,\kappa)d\kappa.
+
+The lower limit of the integral in :eq:`inverse-bremsstrahlung-mfp` is non-zero
+because the bremsstrahlung differential cross section diverges for small photon
+energies but is finite for photon energies above some cutoff energy
+:math:`E_{\text{cut}}`. The mean free path
+:math:`\lambda_{\text{br}}^{-1}(T,E_{\text{cut}})` is used to calculate the
+photon number yield, defined as the average number of photons emitted with
+energy greater than :math:`E_{\text{cut}}` as the charged particle slows down
+from energy :math:`T` to :math:`E_{\text{cut}}`. The photon number yield is
+given by
+
+.. math::
+    :label: photon-number-yield
+
+    Y(T,E_{\text{cut}}) = \int^{R(T)}_{R(E_{\text{cut}})}
+    \lambda_{\text{br}}^{-1}(T',E_{\text{cut}})ds = \int_{E_{\text{cut}}}^T
+    \frac{\lambda_{\text{br}}^{-1}(T',E_{\text{cut}})}{S(T')}dT'.
+
+:math:`Y(T,E_{\text{cut}})` can be used to construct the energy spectrum of
+bremsstrahlung photons: the number of photons created with energy between
+:math:`E_1` and :math:`E_2` by a charged particle with initial kinetic energy
+:math:`T` as it comes to rest is given by :math:`Y(T,E_1) - Y(T,E_2)`.
+
+To simulate the emission of bremsstrahlung photons, the total stopping power
+and bremsstrahlung differential cross section for positrons and electrons must
+be calculated for a given material using :eq:`material-bremsstrahlung-dcs` and
+:eq:`material-radiative-stopping-power`. These quantities are used to build the
+tabulated bremsstrahlung energy PDF and CDF for that material for each incident
+energy :math:`T_k` on the energy grid. The following algorithm is then applied
+to sample the photon energies:
+
+1. For an incident charged particle with energy :math:`T`, sample the number of
+   emitted photons as
+
+   .. math::
+
+       N = \lfloor Y(T,E_{\text{cut}}) + \xi_1 \rfloor.
+
+2. Rather than interpolate the PDF between indices :math:`k` and :math:`k+1`
+   for which :math:`T_k < T < T_{k+1}`, which is computationally expensive, use
+   the composition method and sample from the PDF at either :math:`k` or
+   :math:`k+1`. Using linear interpolation on a logarithmic scale, the PDF can
+   be expressed as
+
+   .. math::
+
+       p_{\text{br}}(T,E) = \pi_k p_{\text{br}}(T_k,E) + \pi_{k+1}
+       p_{\text{br}}(T_{k+1},E),
+
+   where the interpolation weights are
+
+   .. math::
+
+       \pi_k = \frac{\ln T_{k+1} - \ln T}{\ln T_{k+1} - \ln T_k},~~~
+       \pi_{k+1} = \frac{\ln T - \ln T_k}{\ln T_{k+1} - \ln T_k}.
+
+   Sample either the index :math:`i = k` or :math:`i = k+1` according to the
+   point probabilities :math:`\pi_{k}` and :math:`\pi_{k+1}`.
+
+3. Determine the maximum value of the CDF :math:`P_{\text{br,max}}`.
+
+3. Sample the photon energies using the inverse transform method with the
+   tabulated CDF :math:`P_{\text{br}}(T_i, E)` i.e.,
+
+   .. math::
+
+       E = E_j \left[ (1 + a_j) \frac{\xi_2 P_{\text{br,max}} -
+       P_{\text{br}}(T_i, E_j)} {E_j p_{\text{br}}(T_i, E_j)} + 1
+       \right]^{\frac{1}{1 + a_j}}
+
+   where the interpolation factor :math:`a_j` is given by
+
+   .. math::
+
+       a_j = \frac{\ln p_{\text{br}}(T_i,E_{j+1}) - \ln p_{\text{br}}(T_i,E_j)}
+       {\ln E_{j+1} - \ln E_j}
+
+   and :math:`P_{\text{br}}(T_i, E_j) \le \xi_2 P_{\text{br,max}} \le
+   P_{\text{br}}(T_i, E_{j+1})`.
+
+We ignore the range of the electron or positron, i.e., the bremsstrahlung
+photons are produced in the same location that the charged particle was
+created. The direction of the photons is assumed to be the same as the
+direction of the incident charged particle, which is a reasonable approximation
+at higher energies when the bremsstrahlung radiation is emitted at small
+angles.
+
+
+Electron-Positron Annihilation
+------------------------------
+
+When a positron collides with an electron, both particles are annihilated and
+generally two photons with equal energy are created. If the kinetic energy of
+the positron is high enough, the two photons can have different energies, and
+the higher-energy photon is emitted preferentially in the direction of flight
+of the positron. It is also possible to produce a single photon if the
+interaction occurs with a bound electron, and in some cases three (or, rarely,
+even more) photons can be emitted. However, the annihilation cross section is
+largest for low-energy positrons, and as the positron energy decreases, the
+angular distribution of the emitted photons becomes isotropic.
+
+In OpenMC, we assume the most likely case in which a low-energy positron (which
+has already lost most of its energy to bremsstrahlung radiation) interacts with
+an electron which is free and at rest. Two photons with energy equal to the
+electron rest mass energy :math:`m_e c^2 = 0.511` MeV are emitted isotropically
+in opposite directions.
+
+
+.. _Kaltiaisenaho: https://aaltodoc.aalto.fi/bitstream/handle/123456789/21004/master_Kaltiaisenaho_Toni_2016.pdf
+
+.. _Salvat: https://doi.org/10.1787/32da5043-en
+
+.. _Sternheimer: https://doi.org/10.1103/PhysRevB.26.6067

docs/source/methods/cmfd.rst

@@ -266,11 +266,11 @@ and eq. :eq:`eq_cell_bound` can be written in this generic form,
 
 The parameter :math:`\widetilde{D}_{l,m,n}^{u,g}` represents the linear
 coupling term between current and flux. These current relationships can be
-sustituted into eq. :eq:`eq_neut_bal` to produce a linear system of multigroup
+substituted into eq. :eq:`eq_neut_bal` to produce a linear system of multigroup
 diffusion equations for each spatial cell and energy group. However, a solution
 to these equations is not consistent with a higher order transport solution
 unless equivalence factors are present. This is because both the diffusion
-approximation, governed by Fick's Law, and spatial trunction error will produce
+approximation, governed by Fick's Law, and spatial truncation error will produce
 differences. Therefore, a nonlinear parameter,
 :math:`\widehat{D}_{l,m,n}^{u,g}`, is added to eqs. :eq:`eq_cell_cell` and
 :eq:`eq_cell_bound`. These equations are, respectively,

docs/source/methods/cross_sections.rst

@@ -9,7 +9,7 @@ Continuous-Energy Data
 ----------------------
 
 In OpenMC, the data governing the interaction of neutrons with various nuclei
-for continous-energy problems are represented using an HDF5 format that can be
+for continuous-energy problems are represented using an HDF5 format that can be
 produced by converting files in the ACE format, which is used by MCNP_ and
 Serpent_. ACE-format data can be generated with the NJOY_ nuclear data
 processing system, which converts raw `ENDF/B data`_ into linearly-interpolable
@@ -178,6 +178,27 @@ been selected. There are three methods available:
             section data is loaded for a single temperature and is used in the
             unresolved resonance and fast energy ranges.
 
+------------------
+NCrystal materials
+------------------
+
+As an alternative of the standard thermal scattering treatment using
+:math:`S(\alpha,\beta)` tables, OpenMC allows to create materials using
+NCrystal_. In addition to the regular thermal elastic, and thermal inelastic
+processes, NCrystal allows the generation of models for materials that cannot
+currently included in ACE files such as oriented single crystals (see the
+`NCrystal paper`_), and further extend the physics `using plugins`_. Thermal
+scattering kernels are generated on the fly from dynamic and structural data, or
+loaded from :math:`S(\alpha,\beta)` tables converted from ENDF6 evaluations.
+These kernels are sampled in a direct way using a fast `rejection algorithm`_
+that does not require previous processing. A `large library`_ of materials is
+already included in the NCrystal distribution, and new materials can be easily
+defined from scratch in the `NCMAT format`_ or `combining existing files`_.
+
+The compositions of the materials defined in NCrystal are passed on to OpenMC
+all other reactions except for thermal neutron scattering are handled by
+continuous energy ACE libraries.
+
 ----------------
 Multi-Group Data
 ----------------
@@ -187,9 +208,10 @@ are represented using a multi-group library format specific to the OpenMC code.
 The format is described in the :ref:`mgxs_lib_spec`. The data itself can be
 prepared via traditional paths or directly from a continuous-energy OpenMC
 calculation by use of the Python API as is shown in an `example notebook
-<../examples/mg-mode-part-i.ipynb>`_. This multi-group library consists of
-meta-data (such as the energy group structure) and multiple `xsdata` objects
-which contains the required microscopic or macroscopic multi-group data.
+<https://nbviewer.jupyter.org/github/openmc-dev/openmc-notebooks/blob/main/mg-mode-part-i.ipynb>`_.
+This multi-group library consists of meta-data (such as the energy group
+structure) and multiple `xsdata` objects which contains the required microscopic
+or macroscopic multi-group data.
 
 At a minimum, the library must contain the absorption cross section
 (:math:`\sigma_{a,g}`) and a scattering matrix. If the problem is an eigenvalue
@@ -268,13 +290,20 @@ scattering information in the water while the fuel can be simulated with linear
 or even isotropic scattering.
 
 .. _logarithmic mapping technique:
-   https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-14-24530.pdf
+   https://mcnp.lanl.gov/pdf_files/TechReport_2014_LANL_LA-UR-14-24530_Brown.pdf
 .. _Hwang: https://doi.org/10.13182/NSE87-A16381
 .. _Josey: https://doi.org/10.1016/j.jcp.2015.08.013
 .. _WMP Library: https://github.com/mit-crpg/WMP_Library
 .. _MCNP: https://mcnp.lanl.gov
-.. _Serpent: http://montecarlo.vtt.fi
-.. _NJOY: https://www.njoy21.io/NJOY21/
-.. _ENDF/B data: https://www.nndc.bnl.gov/endf/b8.0/
+.. _Serpent: https://serpent.vtt.fi
+.. _NJOY: https://www.njoy21.io/
+.. _ENDF/B data: https://www.nndc.bnl.gov/endf-b8.0/
 .. _Leppanen: https://doi.org/10.1016/j.anucene.2009.03.019
-.. _algorithms: http://ab-initio.mit.edu/wiki/index.php/Faddeeva_Package
+.. _algorithms: http://ab-initio.mit.edu/faddeeva/
+.. _NCrystal: https://github.com/mctools/ncrystal
+.. _NCrystal paper: https://doi.org/10.1016/j.cpc.2019.07.015
+.. _using plugins: https://doi.org/10.1016/j.cpc.2021.108082
+.. _rejection algorithm: https://doi.org/10.1016/j.jcp.2018.11.043
+.. _large library: https://github.com/mctools/ncrystal/wiki/Data-library
+.. _NCMAT format: https://github.com/mctools/ncrystal/wiki/NCMAT-format
+.. _combining existing files: https://github.com/mctools/ncrystal/wiki/Announcement-Release3.0.0#2-multiphase-materials

docs/source/methods/depletion.rst

@@ -103,17 +103,18 @@ integrate over the entire timestep.
 Our aim here is not to exhaustively describe all integration methods but rather
 to give a few examples that elucidate the main considerations one must take into
 account when choosing a method. Generally, there is a tradeoff between the
-accuracy of the method and its computational expense. The expense is driven
-almost entirely by the time to compute a transport solution, i.e., to evaluate
-:math:`\mathbf{A}` for a given :math:`\mathbf{n}`. Thus, the cost of a method
-scales with the number of :math:`\mathbf{A}` evaluations that are performed per
-timestep. On the other hand, methods that require more evaluations generally
-achieve higher accuracy. The predictor method only requires one evaluation and
-its error converges as :math:`\mathcal{O}(h)`. The CE/CM method requires two
-evaluations and is thus twice as expensive as the predictor method, but achieves
-an error of :math:`\mathcal{O}(h^2)`. An exhaustive description of time
-integration methods and their merits can be found in the `thesis of Colin Josey
-<http://dspace.mit.edu/handle/1721.1/7582>`_.
+accuracy of the method and its computational expense. In the case of
+transport-coupled depletion, the expense is driven almost entirely by the time
+to compute a transport solution, i.e., to evaluate :math:`\mathbf{A}` for a
+given :math:`\mathbf{n}`. Thus, the cost of a method scales with the number of
+:math:`\mathbf{A}` evaluations that are performed per timestep. On the other
+hand, methods that require more evaluations generally achieve higher accuracy.
+The predictor method only requires one evaluation and its error converges as
+:math:`\mathcal{O}(h)`. The CE/CM method requires two evaluations and is thus
+twice as expensive as the predictor method, but achieves an error of
+:math:`\mathcal{O}(h^2)`. An exhaustive description of time integration methods
+and their merits can be found in the `thesis of Colin Josey
+<https://dspace.mit.edu/handle/1721.1/7582>`_.
 
 OpenMC does not rely on a single time integration method but rather has several
 classes that implement different algorithms. For example, the
@@ -169,12 +170,14 @@ Data Considerations
 
 In principle, solving Eq. :eq:`depletion-matrix` using CRAM is fairly simple:
 just construct the burnup matrix at various times and solve a set of sparse
-linear systems. However, constructing the burnup matrix itself involves not only
-solving the transport equation to estimate transmutation reaction rates but also
-a series of choices about what data to include. In OpenMC, the burnup matrix is
-constructed based on data inside of a *depletion chain* file, which includes
-fundamental data gathered from ENDF incident neutron, decay, and fission product
-yield sublibraries. For each nuclide, this file includes:
+linear systems. However, constructing the burnup matrix itself involves not
+only solving the transport equation to estimate transmutation reaction rates
+(in the case of transport-coupled depletion) or to obtain microscopic cross
+sections (in the case of transport-independent depletion), but also a series of
+choices about what data to include. In OpenMC, the burnup matrix is constructed
+based on data inside of a *depletion chain* file, which includes fundamental
+data gathered from ENDF incident neutron, decay, and fission product yield
+sublibraries. For each nuclide, this file includes:
 
 - What transmutation reactions are possible, their Q values, and their products;
 - If a nuclide is not stable, what decay modes are possible, their branching
@@ -185,9 +188,12 @@ yield sublibraries. For each nuclide, this file includes:
 Transmutation Reactions
 -----------------------
 
-OpenMC will setup tallies in a problem based on what transmutation reactions are
-available in a depletion chain file, so any arbitrary number of transmutation
-reactions can be tracked. The pregenerated chain files that are available on
+In transport-coupled depletion, OpenMC will setup tallies in a problem based on
+what transmutation reactions are available in a depletion chain file, so any
+arbitrary number of transmutation reactions can be tracked. In
+transport-independent depletion, OpenMC will calculate reaction rates for every
+reaction that is present in both the available cross sections and the depletion
+chain file. The pregenerated chain files that are available on
 https://openmc.org include the following transmutation reactions: fission, (n,\
 :math:`\gamma`\ ), (n,2n), (n,3n), (n,4n), (n,p), and (n,\ :math:`\alpha`\ ).
 
@@ -202,11 +208,12 @@ accurately model the branching of the capture reaction in Am241. This is
 complicated by the fact that the branching ratio may depend on the incident
 neutron energy causing capture.
 
-OpenMC does not currently allow energy-dependent capture branching ratios.
-However, the depletion chain file does allow a transmutation reaction to be
-listed multiple times with different branching ratios resulting in different
-products. Spectrum-averaged capture branching ratios have been computed in LWR
-and SFR spectra and are available at https://openmc.org/depletion-chains.
+OpenMC's transport solver does not currently allow energy-dependent capture
+branching ratios. However, the depletion chain file does allow a transmutation
+reaction to be listed multiple times with different branching ratios resulting
+in different products. Spectrum-averaged capture branching ratios have been
+computed in LWR and SFR spectra and are available at
+https://openmc.org/depletion-chains.
 
 Fission Product Yields
 ----------------------
@@ -217,26 +224,31 @@ energies. It is an open question as to what the best way to handle this energy
 dependence is. OpenMC includes three methods for treating the energy dependence
 of FPY:
 
-1. Use FPY data corresponding to a specified energy.
+1. Use FPY data corresponding to a specified energy. This is used by default in
+   both transport-coupled and transport-independent depletion.
 2. Tally fission rates above and below a specified cutoff energy. Assume that
    all fissions below the cutoff energy correspond to thermal FPY data and all
-   fission above the cutoff energy correspond to fast FPY data.
+   fission above the cutoff energy correspond to fast FPY data. Only applicable
+   to transport-coupled depletion.
 3. Compute the average energy at which fission events occur and use an effective
    FPY by linearly interpolating between FPY provided at neighboring energies.
+   Only applicable to transport-coupled depletion.
 
-The method can be selected through the ``fission_yield_mode`` argument to the
-:class:`openmc.deplete.Operator` constructor.
+The method for transport-coupled depletion can be selected through the
+``fission_yield_mode`` argument to the :class:`openmc.deplete.CoupledOperator`
+constructor.
 
 Power Normalization
 -------------------
 
-The reaction rates provided OpenMC are given in units of reactions per source
-particle. For depletion, it is necessary to compute an absolute reaction rate in
-reactions per second. To do so, the reaction rates are normalized based on a
-specified power. A complete description of how this normalization can be
-performed is described in :ref:`usersguide_tally_normalization`. Here, we simply
-note that the main depletion class, :class:`openmc.deplete.Operator`, allows the
-user to choose one of two methods for estimating the heating rate, including:
+In transport-coupled depletion, the reaction rates provided OpenMC are given in
+units of reactions per source particle. For depletion, it is necessary to
+compute an absolute reaction rate in reactions per second. To do so, the
+reaction rates are normalized based on a specified power. A complete
+description of how this normalization can be performed is described in
+:ref:`usersguide_tally_normalization`. Here, we simply note that the main
+depletion class, :class:`openmc.deplete.CoupledOperator`, allows the user to
+choose one of two methods for estimating the heating rate, including:
 
 1. Using fixed Q values from a depletion chain file (useful for comparisons to
    other codes that use fixed Q values), or
@@ -244,4 +256,86 @@ user to choose one of two methods for estimating the heating rate, including:
    energy-dependent estimate of the true heating rate.
 
 The method for normalization can be chosen through the ``normalization_mode``
-argument to the :class:`openmc.deplete.Operator` class.
+argument to the :class:`openmc.deplete.CoupledOperator` class.
+
+--------------
+Transfer Rates
+--------------
+
+OpenMC allows continuous removal or feed of nuclides by adding an
+extra transfer rate term to the depletion matrix. An application of this feature
+is the chemical processing of Molten Salt Reactors (MSRs), where one can
+model the removal of fission products or feeding fresh fuel into the system.
+
+A transfer rate as defined here is the rate at which nuclides are
+continuously removed/fed from/to a material.
+
+.. note::
+
+    A transfer rate can be positive or negative, indicating removal or feed
+    respectively.
+
+Mathematically, it can be thought of as an additional term :math:`\mathbf{T}`
+in the depletion equation that is proportional to the nuclide density, which can be written as:
+
+.. math::
+
+  \begin{aligned}\frac{dN_i(t)}{dt} = &\underbrace{\sum\limits_j f_{j\rightarrow i}
+  \int_0^\infty dE  \; \sigma_j (E,t) \phi(E,t) N_j(t)  - \int_0^\infty dE \; \sigma_i(E,t)
+  \phi(E,t) N_i(t)}_\textbf{R} \\
+  &+ \underbrace{\sum_j \left [ \lambda_{j\rightarrow i} N_j(t) - \lambda_{i\rightarrow j} N_i(t) \right ]}_\textbf{D} \\
+  &- \underbrace{t_i N_i(t)}_\textbf{T} \end{aligned}
+
+where the reaction term :math:`\mathbf{R}`, the decay term :math:`\mathbf{D}`
+and the new transfer term :math:`\mathbf{T}` have been grouped together so that
+:math:`\mathbf{A} = \mathbf{R}+\mathbf{D}-\mathbf{T}`.
+The transfer rate coefficient :math:`t_i` defines the continuous transfer of the
+nuclide :math:`i`, which behaves similar to radioactive decay.
+:math:`t_i` can also be defined as the reciprocal of a cycle time
+:math:`T_{cyc}`, intended as the time needed to process the whole inventory.
+
+Note that this formulation assumes homogeneous distribution of nuclide
+:math:`i` throughout the material.
+
+A more rigorous description of removal rate and its implementation can be found
+in the paper by `Hombourger
+<https://doi.org/10.1016/j.anucene.2020.107504>`_.
+
+The resulting burnup matrix can be solved with the same integration algorithms
+that are used in the absence of the transfer term.
+
+.. note::
+
+    If no ``destination_material`` is specified, nuclides that are removed
+    or fed will not be tracked afterwards.
+
+Coupling materials
+------------------
+
+To keep track of removed nuclides or to feed nuclides from one depletable material
+to another, the respective depletion equations have to be coupled. This can be
+achieved by defining one block matrix, with diagonal blocks corresponding to
+depletion matrices :math:`\mathbf{A_{ii}}`, where the index :math:`i` indicates
+the depletable material id, and off-diagonal blocks corresponding to inter-material
+coupling matrices :math:`\mathbf{T_{ij}}`, positioned so that that the indices :math:`i` and
+:math:`j` indicate the nuclides receiving and losing materials, respectively.
+The nuclide vectors are assembled together in one single vector and the resulting
+system is solved with the same integration algorithms seen before.
+
+As an example, consider the case of two depletable materials and one
+transfer defined from material 1 to material 2. The final system will look like:
+
+.. math::
+
+  \begin{aligned}\frac{d}{dt}\begin{pmatrix}\vec{N_1}\\ \vec{N_2}\end{pmatrix} &=
+  \begin{pmatrix}\mathbf{A_{11}} & \mathbf{0}\\ \mathbf{T_{21}} & \mathbf{A_{22 }}
+  \end{pmatrix} \begin{pmatrix}\vec{N_1}\\ \vec{N_2}\end{pmatrix} \end{aligned}
+
+where:
+
+:math:`\mathbf{A_{11}} = \mathbf{R_{11}}+\mathbf{D_{11}}-\mathbf{T_{21}}`, and
+
+:math:`\mathbf{A_{22}} = \mathbf{R_{22}}+\mathbf{D_{22}}`.
+
+Note that mass conservation is guaranteed by transferring the number
+of atoms directly.

docs/source/methods/eigenvalue.rst

@@ -55,15 +55,17 @@ in :ref:`fission-bank-algorithms`.
 Source Convergence Issues
 -------------------------
 
+.. _methods-shannon-entropy:
+
 Diagnosing Convergence with Shannon Entropy
 -------------------------------------------
 
 As discussed earlier, it is necessary to converge both :math:`k_{eff}` and the
 source distribution before any tallies can begin. Moreover, the convergence rate
-of the source distribution is in general slower than that of
-:math:`k_{eff}`. One should thus examine not only the convergence of
-:math:`k_{eff}` but also the convergence of the source distribution in order to
-make decisions on when to start active batches.
+of the source distribution is in general slower than that of :math:`k_{eff}`.
+One should thus examine not only the convergence of :math:`k_{eff}` but also the
+convergence of the source distribution in order to make decisions on when to
+start active batches.
 
 However, the representation of the source distribution makes it a bit more
 difficult to analyze its convergence. Since :math:`k_{eff}` is a scalar
@@ -108,6 +110,13 @@ at plots of :math:`k_{eff}` and the Shannon entropy. A number of methods have
 been proposed (see e.g. [Romano]_, [Ueki]_), but each of these is not without
 problems.
 
+Shannon entropy is calculated differently for the random ray solver, as
+described :ref:`in the random ray theory section
+<methods-shannon-entropy-random-ray>`. Additionally, as the Shannon entropy only
+serves as a diagnostic tool for convergence of the fission source distribution,
+there is currently no diagnostic to determine if the scattering source
+distribution in random ray is converged.
+
 ---------------------------
 Uniform Fission Site Method
 ---------------------------
@@ -142,7 +151,7 @@ than unity. By ensuring that the expected number of fission sites in each mesh
 cell is constant, the collision density across all cells, and hence the variance
 of tallies, is more uniform than it would be otherwise.
 
-.. _Shannon entropy: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-06-3737.pdf
+.. _Shannon entropy: https://mcnp.lanl.gov/pdf_files/TechReport_2006_LANL_LA-UR-06-3737_Brown.pdf
 
 .. [Lieberoth] J. Lieberoth, "A Monte Carlo Technique to Solve the Static
    Eigenvalue Problem of the Boltzmann Transport Equation," *Nukleonik*, **11**,

docs/source/methods/energy_deposition.rst

@@ -7,7 +7,7 @@ Heating and Energy Deposition
 As particles traverse a problem, some portion of their energy is deposited at
 collision sites. This energy is deposited when charged particles, including
 electrons and recoil nuclei, undergo electromagnetic interactions with
-surrounding electons and ions. The information describing how much energy
+surrounding electrons and ions. The information describing how much energy
 is deposited for a specific reaction is referred to as
 "heating numbers" and can be computed using a program like NJOY with the
 ``heatr`` module.
@@ -25,19 +25,38 @@ KERMA (Kinetic Energy Release in Materials) [Mack97]_ coefficients for reaction
 :math:`\times` cross-section (e.g., eV-barn) and can be used much like a reaction
 cross section for the purpose of tallying energy deposition.
 
-KERMA coefficients can be computed using the energy-balance method with
-a nuclear data processing code like NJOY, which performs the following
-iteration over all reactions :math:`r` for all isotopes :math:`i`
-requested
+KERMA coefficients can be computed using the energy-balance method with a
+nuclear data processing code like NJOY, which estimates the KERMA coefficients
+using the following equation:
 
 .. math::
 
-    k_{i, r}(E) = \left(E + Q_{i, r} - \bar{E}_{i, r, n}
+    k_{i, r}(E) = \left(E + Q_{i, r} - \sum\limits_x \bar{E}_{i, r, x}
+    \right)\sigma_{i, r}(E),
+
+where the summation is over each secondary particle type :math:`x`. This
+equation states that the energy deposited is equal to the energy of the incident
+particle plus the reaction :math:`Q` value less the energy of secondary
+particles that are transported away from the reaction site. For neutron
+interactions, the energy-balance KERMA coefficient is
+
+.. math::
+
+    k_{i, r}(E) = \left(E + Q_{i, r} - \sum\limits_x \bar{E}_{i, r, n}
     - \bar{E}_{i, r, \gamma}\right)\sigma_{i, r}(E),
 
-removing the energy of neutral particles (neutrons and photons) that are
-transported away from the reaction site :math:`\bar{E}`, and the reaction
-:math:`Q` value.
+where :math:`\bar{E}_{i, r, n}` is the average energy of secondary neutrons and
+:math:`\bar{E}_{i, r, \gamma}` is the average energy of secondary photons. For
+photon and charged particle interactions the KERMA coefficient is
+
+.. math::
+    :label: energy-balance-photon
+
+    k_{i, r}(E) = \left(E + Q_{i, r} - \sum\limits_x \bar{E}_{i, r, x}
+    \right)\sigma_{i, r}(E).
+
+where the :math:`Q` value is zero for all interactions except for pair
+production and positron annihilation.
 
 -------
 Fission
@@ -120,7 +139,7 @@ run with :math:`N918` reflecting fission heating computed from NJOY.
 This modified heating data is stored as the MT=901 reaction and will be scored
 if ``heating-local`` is included in :attr:`openmc.Tally.scores`.
 
-Coupled neutron-photon transport
+Coupled Neutron-Photon Transport
 --------------------------------
 
 Here, OpenMC instructs ``heatr`` to assume that energy from photons is not
@@ -138,6 +157,50 @@ Let :math:`N301` represent the total heating number returned from this
 This modified heating data is stored as the MT=301 reaction and will be scored
 if ``heating`` is included in :attr:`openmc.Tally.scores`.
 
+Photons and Charged Particles
+-----------------------------
+
+In OpenMC, energy deposition from photons or charged particles is scored using
+the energy balance method based on Equation :eq:`energy-balance-photon`. Special
+consideration is given to electrons and positrons as described below.
+
++++++++++++++++++
+Charged Particles
++++++++++++++++++
+
+OpenMC tracks photons interaction by interaction so the energy deposited in each
+collision is easily attributed back to the nuclide and reaction for which the
+photon interacted with. Charged particles (electrons and photons) aren't tracked
+in the same way. For charged particles, OpenMC assumes that all their energy
+(less the energy of bremsstrahlung radiation) is deposited in the material in
+which they were born. In this way it is harder to trace how much energy should
+be attributed in each nuclide.
+
+According to the CSDA approximation (see :ref:`ttb`) the energy deposited by a
+charged particle with kinetic energy :math:`T` in the :math:`i`-th element can
+be calculated as:
+
+.. math::
+
+    E_{i} = \int_{0}^{R(T)} w_{i}S_{\text{col,i}} dx
+
+where :math:`R(T)` is the CSDA range of the charged particle,
+:math:`S_{\text{col},i}` is the collision stopping power of the charged particle
+in the :math:`i`-th element and :math:`w_i` is the mass fraction of the
+:math:`i`-th element. According to the Bethe formula the collision stopping
+power of the :math:`i`-th element is proportional to :math:`Z_i/A_i`, so the
+fractional collision stopping power from the :math:`i`-th element is:
+
+.. math::
+
+    \frac{w_{i}S_{\text{col},i}(T)}{S_{\text{col}}(T)} =
+    \frac{\frac{w_{i}Z_{i}}{A_{i}}}{\sum_{i}\frac{w_{i}Z_{i}}{A_{i}}} =
+    \frac{\gamma_i Z_{i}}{\sum_{i}\gamma_i Z_{i}}.
+
+where :math:`\gamma_i` is the atomic fraction of the :math:`i`-th element.
+Therefore, the energy deposited by charged particles should be attributed to
+a given element according to its fractional charge density.
+
 ----------
 References
 ----------

docs/source/methods/geometry.rst

@@ -1066,5 +1066,5 @@ surface is known as in :ref:`reflection`.
 .. _constructive solid geometry: https://en.wikipedia.org/wiki/Constructive_solid_geometry
 .. _surfaces: https://en.wikipedia.org/wiki/Surface
 .. _MCNP: https://mcnp.lanl.gov
-.. _Serpent: http://montecarlo.vtt.fi
+.. _Serpent: https://serpent.vtt.fi
 .. _Monte Carlo Performance benchmark: https://github.com/mit-crpg/benchmarks/tree/master/mc-performance/openmc

docs/source/methods/index.rst

@@ -14,9 +14,12 @@ Theory and Methodology
     random_numbers
     neutron_physics
     photon_physics
+    charged_particles_physics
     tallies
     eigenvalue
     depletion
     energy_deposition
     parallelization
     cmfd
+    variance_reduction
+    random_ray

docs/source/methods/introduction.rst

@@ -45,7 +45,7 @@ following steps:
 
   - Initialize the pseudorandom number generator.
 
-  - Read the contiuous-energy or multi-group cross section data specified in
+  - Read the continuous-energy or multi-group cross section data specified in
     the problem.
 
   - If using a special energy grid treatment such as a union energy grid or

docs/source/methods/neutron_physics.rst

@@ -91,7 +91,7 @@ inelastic scattering reactions. The specific multi-group scattering
 implementation is discussed in the :ref:`multi-group-scatter` section.
 
 Elastic scattering refers to the process by which a neutron scatters off a
-nucleus and does not leave it in an excited. It is referred to as "elastic"
+nucleus and does not leave it in an excited state. It is referred to as "elastic"
 because in the center-of-mass system, the neutron does not actually lose
 energy. However, in lab coordinates, the neutron does indeed lose
 energy. Elastic scattering can be treated exactly in a Monte Carlo code thanks
@@ -182,7 +182,7 @@ Inelastic Scattering
 --------------------
 
 Note that the multi-group mode makes no distinction between elastic or
-inelastic scattering reactions. The spceific multi-group scattering
+inelastic scattering reactions. The specific multi-group scattering
 implementation is discussed in the :ref:`multi-group-scatter` section.
 
 The major algorithms for inelastic scattering were described in previous
@@ -290,7 +290,10 @@ create and store fission sites for the following generation. First, the average
 number of prompt and delayed neutrons must be determined to decide whether the
 secondary neutrons will be prompt or delayed. This is important because delayed
 neutrons have a markedly different spectrum from prompt neutrons, one that has a
-lower average energy of emission. The total number of neutrons emitted
+lower average energy of emission. Furthermore, in simulations where tracking
+time of neutrons is important, we need to consider the emission time delay of
+the secondary neutrons, which is dependent on the decay constant of the
+delayed neutron precursor. The total number of neutrons emitted
 :math:`\nu_t` is given as a function of incident energy in the ENDF format. Two
 representations exist for :math:`\nu_t`. The first is a polynomial of order
 :math:`N` with coefficients :math:`c_0,c_1,\dots,c_N`. If :math:`\nu_t` has this
@@ -306,8 +309,8 @@ interpolation law. The number of prompt neutrons released per fission event
 :math:`\nu_p` is also given as a function of incident energy and can be
 specified in a polynomial or tabular format. The number of delayed neutrons
 released per fission event :math:`\nu_d` can only be specified in a tabular
-format. In practice, we only need to determine :math:`nu_t` and
-:math:`nu_d`. Once these have been determined, we can calculated the delayed
+format. In practice, we only need to determine :math:`\nu_t` and
+:math:`\nu_d`. Once these have been determined, we can calculate the delayed
 neutron fraction
 
 .. math::
@@ -335,8 +338,14 @@ neutrons. Otherwise, we produce :math:`\lfloor \nu \rfloor + 1` neutrons. Then,
 for each fission site produced, we sample the outgoing angle and energy
 according to the algorithms given in :ref:`sample-angle` and
 :ref:`sample-energy` respectively. If the neutron is to be born delayed, then
-there is an extra step of sampling a delayed neutron precursor group since they
-each have an associated secondary energy distribution.
+there is an extra step of sampling a delayed neutron precursor group to get the
+associated secondary energy distribution and the decay constant
+:math:`\lambda`, which is needed to sample the emission delay time :math:`t_d`:
+
+.. math::
+    :label: sample-delay-time
+
+    t_d = -\frac{\ln \xi}{\lambda}.
 
 The sampled outgoing angle and energy of fission neutrons along with the
 position of the collision site are stored in an array called the fission
@@ -359,7 +368,7 @@ secondary energy and angle sampling.
 For a reaction with secondary products, it is necessary to determine the
 outgoing angle and energy of the products. For any reaction other than elastic
 and level inelastic scattering, the outgoing energy must be determined based on
-tabulated or parameterized data. The `ENDF-6 Format <endf102>`_ specifies a
+tabulated or parameterized data. The `ENDF-6 Format`_ specifies a
 variety of ways that the secondary energy distribution can be represented. ENDF
 File 5 contains uncorrelated energy distribution whereas ENDF File 6 contains
 correlated energy-angle distributions. The ACE format specifies its own
@@ -1403,7 +1412,7 @@ given analytically by
 .. math::
     :label: coherent-elastic-angle
 
-    \mu = 1 - \frac{E_i}{E}
+    \mu = 1 - \frac{2E_i}{E}
 
 where :math:`E_i` is the energy of the Bragg edge that scattered the neutron.
 
@@ -1416,8 +1425,7 @@ For incoherent elastic scattering, OpenMC has two methods for calculating the
 cosine of the angle of scattering. The first method uses the Debye-Waller
 integral, :math:`W'`, and the characteristic bound cross section as given
 directly in an ENDF-6 formatted file. In this case, the cosine of the angle of
-scattering can be sampled by inverting equation 7.4 from the `ENDF-6 Format
-Manual <endf102>`_:
+scattering can be sampled by inverting equation 7.4 from the `ENDF-6 Format`_:
 
 .. math::
     :label: incoherent-elastic-mu-exact
@@ -1744,19 +1752,19 @@ types.
 
 .. _Watt fission spectrum: https://doi.org/10.1103/PhysRev.87.1037
 
-.. _Foderaro: http://hdl.handle.net/1721.1/1716
+.. _Foderaro: https://dspace.mit.edu/handle/1721.1/1716
 
 .. _OECD: https://www.oecd-nea.org/tools/abstract/detail/NEA-1792
 
 .. _NJOY: https://www.njoy21.io/NJOY2016/
 
-.. _PREPRO: https://www-nds.iaea.org/ndspub/endf/prepro/
+.. _PREPRO: https://www-nds.iaea.org/public/endf/prepro/
 
-.. _endf102: https://www.oecd-nea.org/dbdata/data/manual-endf/endf102.pdf
+.. _ENDF-6 Format: https://www.oecd-nea.org/dbdata/data/manual-endf/endf102.pdf
 
-.. _Monte Carlo Sampler: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-09721-MS
+.. _Monte Carlo Sampler: https://mcnp.lanl.gov/pdf_files/TechReport_1983_LANL_LA-9721-MS_EverettCashwell.pdf
 
-.. _LA-UR-14-27694: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-14-27694
+.. _LA-UR-14-27694: https://www.osti.gov/biblio/1159204
 
 .. _MC21: https://www.osti.gov/biblio/903083
 
@@ -1764,6 +1772,4 @@ types.
 
 .. _Sutton and Brown: https://www.osti.gov/biblio/307911
 
-.. _lectures: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-05-4983.pdf
-
-.. _MCNP Manual: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-03-1987.pdf
+.. _lectures: https://mcnp.lanl.gov/pdf_files/TechReport_2005_LANL_LA-UR-05-4983_Brown.pdf

docs/source/methods/parallelization.rst

@@ -293,7 +293,7 @@ Cost of Nearest Neighbor Algorithm
 ----------------------------------
 
 With the communication cost of the traditional fission bank algorithm
-quantified, we now proceed to discuss the communicatin cost of the proposed
+quantified, we now proceed to discuss the communication cost of the proposed
 algorithm. Comparing the cost of communication of this algorithm with the
 traditional algorithm is not trivial due to fact that the cost will be a
 function of how many fission sites are sampled on each node. If each node
@@ -398,7 +398,7 @@ equation :eq:`k-to-source`, we can relate the stochastic eigenvalue to the
 integral of the noise component of the source distribution as
 
 .. math::
-    :label: noise-integeral
+    :label: noise-integral
 
     N\hat{k} = Nk + \sqrt{N} \int \hat{\epsilon}(\mathbf{r}) \: d\mathbf{r}.
 
@@ -609,17 +609,17 @@ is actually independent of the number of nodes:
 
 .. _first paper: https://doi.org/10.2307/2280232
 
-.. _work of Forrest Brown: http://hdl.handle.net/2027.42/24996
+.. _work of Forrest Brown: https://deepblue.lib.umich.edu/handle/2027.42/24996
 
 .. _Brissenden and Garlick: https://doi.org/10.1016/0306-4549(86)90095-2
 
-.. _MPICH: http://www.mpich.org
+.. _MPICH: https://www.mpich.org
 
 .. _binomial tree: https://www.mcs.anl.gov/~thakur/papers/ijhpca-coll.pdf
 
 .. _Geary: https://doi.org/10.2307/2342070
 
-.. _Barnett: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.51.7772
+.. _Barnett: https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.51.7772
 
 .. _single-instruction multiple-data: https://en.wikipedia.org/wiki/SIMD
 

docs/source/methods/photon_physics.rst

@@ -667,342 +667,6 @@ and Auger electrons:
 
 5. Repeat from step 1 for vacancy left by the transition electron.
 
-Electron-Positron Annihilation
-------------------------------
-
-When a positron collides with an electron, both particles are annihilated and
-generally two photons with equal energy are created. If the kinetic energy of
-the positron is high enough, the two photons can have different energies, and
-the higher-energy photon is emitted preferentially in the direction of flight
-of the positron. It is also possible to produce a single photon if the
-interaction occurs with a bound electron, and in some cases three (or, rarely,
-even more) photons can be emitted. However, the annihilation cross section is
-largest for low-energy positrons, and as the positron energy decreases, the
-angular distribution of the emitted photons becomes isotropic.
-
-In OpenMC, we assume the most likely case in which a low-energy positron (which
-has already lost most of its energy to bremsstrahlung radiation) interacts with
-an electron which is free and at rest. Two photons with energy equal to the
-electron rest mass energy :math:`m_e c^2 = 0.511` MeV are emitted isotropically
-in opposite directions.
-
-Bremsstrahlung
---------------
-
-When a charged particle is decelerated in the field of an atom, some of its
-kinetic energy is converted into electromagnetic radiation known as
-bremsstrahlung, or 'braking radiation'. In each event, an electron or positron
-with kinetic energy :math:`T` generates a photon with an energy :math:`E`
-between :math:`0` and :math:`T`. Bremsstrahlung is described by a cross section
-that is differential in photon energy, in the direction of the emitted photon,
-and in the final direction of the charged particle. However, in Monte Carlo
-simulations it is typical to integrate over the angular variables to obtain a
-single differential cross section with respect to photon energy, which is often
-expressed in the form
-
-.. math::
-    :label: bremsstrahlung-dcs
-
-    \frac{d\sigma_{\text{br}}}{dE} = \frac{Z^2}{\beta^2} \frac{1}{E}
-    \chi(Z, T, \kappa),
-
-where :math:`\kappa = E/T` is the reduced photon energy and :math:`\chi(Z, T,
-\kappa)` is the scaled bremsstrahlung cross section, which is experimentally
-measured.
-
-Because electrons are attracted to atomic nuclei whereas positrons are
-repulsed, the cross section for positrons is smaller, though it approaches that
-of electrons in the high energy limit. To obtain the positron cross section, we
-multiply :eq:`bremsstrahlung-dcs` by the :math:`\kappa`-independent factor used
-in Salvat_,
-
-.. math::
-    :label: positron-factor
-
-    \begin{aligned}
-    F_{\text{p}}(Z,T) =
-    & 1 - \text{exp}(-1.2359\times 10^{-1}t + 6.1274\times 10^{-2}t^2 - 3.1516\times 10^{-2}t^3 \\
-    & + 7.7446\times 10^{-3}t^4 - 1.0595\times 10^{-3}t^5 + 7.0568\times 10^{-5}t^6 \\
-    & - 1.8080\times 10^{-6}t^7),
-    \end{aligned}
-
-where
-
-.. math::
-    :label: positron-factor-t
-
-    t = \ln\left(1 + \frac{10^6}{Z^2}\frac{T}{\text{m}_\text{e}c^2} \right).
-
-:math:`F_{\text{p}}(Z,T)` is the ratio of the radiative stopping powers for
-positrons and electrons. Stopping power describes the average energy loss per
-unit path length of a charged particle as it passes through matter:
-
-.. math::
-    :label: stopping-power
-
-    -\frac{dT}{ds} = n \int E \frac{d\sigma}{dE} dE \equiv S(T),
-
-where :math:`n` is the number density of the material and :math:`d\sigma/dE` is
-the cross section differential in energy loss. The total stopping power
-:math:`S(T)` can be separated into two components: the radiative stopping
-power :math:`S_{\text{rad}}(T)`, which refers to energy loss due to
-bremsstrahlung, and the collision stopping power :math:`S_{\text{col}}(T)`,
-which refers to the energy loss due to inelastic collisions with bound
-electrons in the material that result in ionization and excitation. The
-radiative stopping power for electrons is given by
-
-.. math::
-    :label: radiative-stopping-power
-
-    S_{\text{rad}}(T) = n \frac{Z^2}{\beta^2} T \int_0^1 \chi(Z,T,\kappa)
-    d\kappa.
-
-
-To obtain the radiative stopping power for positrons,
-:eq:`radiative-stopping-power`  is multiplied by :eq:`positron-factor`.
-
-While the models for photon interactions with matter described above can safely
-assume interactions occur with free atoms, sampling the target atom based on
-the macroscopic cross sections, molecular effects cannot necessarily be
-disregarded for charged particle treatment. For compounds and mixtures, the
-bremsstrahlung cross section is calculated using Bragg's additivity rule as
-
-.. math::
-    :label: material-bremsstrahlung-dcs
-
-    \frac{d\sigma_{\text{br}}}{dE} = \frac{1}{\beta^2 E} \sum_i \gamma_i Z^2_i
-    \chi(Z_i, T, \kappa),
-
-where the sum is over the constituent elements and :math:`\gamma_i` is the
-atomic fraction of the :math:`i`-th element. Similarly, the radiative stopping
-power is calculated using Bragg's additivity rule as
-
-.. math::
-    :label: material-radiative-stopping-power
-
-    S_{\text{rad}}(T) = \sum_i w_i S_{\text{rad},i}(T),
-
-where :math:`w_i` is the mass fraction of the :math:`i`-th element and
-:math:`S_{\text{rad},i}(T)` is found for element :math:`i` using
-:eq:`radiative-stopping-power`. The collision stopping power, however, is a
-function of certain quantities such as the mean excitation energy :math:`I` and
-the density effect correction :math:`\delta_F` that depend on molecular
-properties. These quantities cannot simply be summed over constituent elements
-in a compound, but should instead be calculated for the material. The Bethe
-formula can be used to find the collision stopping power of the material:
-
-.. math::
-    :label: material-collision-stopping-power
-
-    S_{\text{col}}(T) = \frac{2 \pi r_e^2 m_e c^2}{\beta^2} N_A \frac{Z}{A_M}
-    [\ln(T^2/I^2) + \ln(1 + \tau/2) + F(\tau) - \delta_F(T)],
-
-where :math:`N_A` is Avogadro's number, :math:`A_M` is the molar mass,
-:math:`\tau = T/m_e`, and :math:`F(\tau)` depends on the particle type. For
-electrons,
-
-.. math::
-    :label: F-electron
-
-    F_{-}(\tau) = (1 - \beta^2)[1 + \tau^2/8 - (2\tau + 1) \ln2],
-
-while for positrons
-
-.. math::
-    :label: F-positron
-
-    F_{+}(\tau) = 2\ln2 - (\beta^2/12)[23 + 14/(\tau + 2) + 10/(\tau + 2)^2 +
-    4/(\tau + 2)^3].
-
-The density effect correction :math:`\delta_F` takes into account the reduction
-of the collision stopping power due to the polarization of the material the
-charged particle is passing through by the electric field of the particle.
-It can be evaluated using the method described by Sternheimer_, where the
-equation for :math:`\delta_F` is
-
-.. math::
-    :label: density-effect-correction
-
-    \delta_F(\beta) = \sum_{i=1}^n f_i \ln[(l_i^2 + l^2)/l_i^2] -
-    l^2(1-\beta^2).
-
-Here, :math:`f_i` is the oscillator strength of the :math:`i`-th transition,
-given by :math:`f_i = n_i/Z`, where :math:`n_i` is the number of electrons in
-the :math:`i`-th subshell. The frequency :math:`l` is the solution of the
-equation
-
-.. math::
-    :label: density-effect-l
-
-    \frac{1}{\beta^2} - 1 = \sum_{i=1}^{n} \frac{f_i}{\bar{\nu}_i^2 + l^2},
-
-where :math:`\bar{v}_i` is defined as
-
-.. math::
-    :label: density-effect-nubar
-
-    \bar{\nu}_i = h\nu_i \rho / h\nu_p.
-
-The plasma energy :math:`h\nu_p` of the medium is given by
-
-.. math::
-    :label: plasma-frequency
-
-    h\nu_p = \sqrt{\frac{(hc)^2 r_e \rho_m N_A Z}{\pi A}},
-
-where :math:`A` is the atomic weight and :math:`\rho_m` is the density of the
-material. In :eq:`density-effect-nubar`, :math:`h\nu_i` is the oscillator
-energy, and :math:`\rho` is an adjustment factor introduced to give agreement
-between the experimental values of the oscillator energies and the mean
-excitation energy. The :math:`l_i` in :eq:`density-effect-correction` are
-defined as
-
-.. math::
-    :label: density-effect-li
-
-    \begin{aligned}
-    l_i &= (\bar{\nu}_i^2 + 2/3f_i)^{1/2} ~~~~&\text{for}~~ \bar{\nu}_i > 0 \\
-    l_n &= f_n^{1/2} ~~~~&\text{for}~~ \bar{\nu}_n = 0,
-    \end{aligned}
-
-where the second case applies to conduction electrons. For a conductor,
-:math:`f_n` is given by :math:`n_c/Z`, where :math:`n_c` is the effective
-number of conduction electrons, and :math:`v_n = 0`. The adjustment factor
-:math:`\rho` is determined using the equation for the mean excitation energy:
-
-.. math::
-    :label: mean-excitation-energy
-
-    \ln I = \sum_{i=1}^{n-1} f_i \ln[(h\nu_i\rho)^2 + 2/3f_i(h\nu_p)^2]^{1/2} +
-    f_n \ln (h\nu_pf_n^{1/2}).
-
-.. _ttb:
-
-Thick-Target Bremsstrahlung Approximation
-+++++++++++++++++++++++++++++++++++++++++
-
-Since charged particles lose their energy on a much shorter distance scale than
-neutral particles, not much error should be introduced by neglecting to
-transport electrons. However, the bremsstrahlung emitted from high energy
-electrons and positrons can travel far from the interaction site. Thus, even
-without a full electron transport mode it is necessary to model bremsstrahlung.
-We use a thick-target bremsstrahlung (TTB) approximation based on the models in
-Salvat_ and Kaltiaisenaho_ for generating bremsstrahlung photons, which assumes
-the charged particle loses all its energy in a single homogeneous material
-region.
-
-To model bremsstrahlung using the TTB approximation, we need to know the number
-of photons emitted by the charged particle and the energy distribution of the
-photons. These quantities can be calculated using the continuous slowing down
-approximation (CSDA). The CSDA assumes charged particles lose energy
-continuously along their trajectory with a rate of energy loss equal to the
-total stopping power, ignoring fluctuations in the energy loss. The
-approximation is useful for expressing average quantities that describe how
-charged particles slow down in matter. For example, the CSDA range approximates
-the average path length a charged particle travels as it slows to rest:
-
-.. math::
-    :label: csda-range
-
-    R(T) = \int^T_0 \frac{dT'}{S(T')}.
-
-Actual path lengths will fluctuate around :math:`R(T)`. The average number of
-photons emitted per unit path length is given by the inverse bremsstrahlung
-mean free path:
-
-.. math::
-    :label: inverse-bremsstrahlung-mfp
-
-    \lambda_{\text{br}}^{-1}(T,E_{\text{cut}})
-    = n\int_{E_{\text{cut}}}^T\frac{d\sigma_{\text{br}}}{dE}dE
-    = n\frac{Z^2}{\beta^2}\int_{\kappa_{\text{cut}}}^1\frac{1}{\kappa}
-    \chi(Z,T,\kappa)d\kappa.
-
-The lower limit of the integral in :eq:`inverse-bremsstrahlung-mfp` is non-zero
-because the bremsstrahlung differential cross section diverges for small photon
-energies but is finite for photon energies above some cutoff energy
-:math:`E_{\text{cut}}`. The mean free path
-:math:`\lambda_{\text{br}}^{-1}(T,E_{\text{cut}})` is used to calculate the
-photon number yield, defined as the average number of photons emitted with
-energy greater than :math:`E_{\text{cut}}` as the charged particle slows down
-from energy :math:`T` to :math:`E_{\text{cut}}`. The photon number yield is
-given by
-
-.. math::
-    :label: photon-number-yield
-
-    Y(T,E_{\text{cut}}) = \int^{R(T)}_{R(E_{\text{cut}})}
-    \lambda_{\text{br}}^{-1}(T',E_{\text{cut}})ds = \int_{E_{\text{cut}}}^T
-    \frac{\lambda_{\text{br}}^{-1}(T',E_{\text{cut}})}{S(T')}dT'.
-
-:math:`Y(T,E_{\text{cut}})` can be used to construct the energy spectrum of
-bremsstrahlung photons: the number of photons created with energy between
-:math:`E_1` and :math:`E_2` by a charged particle with initial kinetic energy
-:math:`T` as it comes to rest is given by :math:`Y(T,E_1) - Y(T,E_2)`.
-
-To simulate the emission of bremsstrahlung photons, the total stopping power
-and bremsstrahlung differential cross section for positrons and electrons must
-be calculated for a given material using :eq:`material-bremsstrahlung-dcs` and
-:eq:`material-radiative-stopping-power`. These quantities are used to build the
-tabulated bremsstrahlung energy PDF and CDF for that material for each incident
-energy :math:`T_k` on the energy grid. The following algorithm is then applied
-to sample the photon energies:
-
-1. For an incident charged particle with energy :math:`T`, sample the number of
-   emitted photons as
-
-   .. math::
-
-       N = \lfloor Y(T,E_{\text{cut}}) + \xi_1 \rfloor.
-
-2. Rather than interpolate the PDF between indices :math:`k` and :math:`k+1`
-   for which :math:`T_k < T < T_{k+1}`, which is computationally expensive, use
-   the composition method and sample from the PDF at either :math:`k` or
-   :math:`k+1`. Using linear interpolation on a logarithmic scale, the PDF can
-   be expressed as
-
-   .. math::
-
-       p_{\text{br}}(T,E) = \pi_k p_{\text{br}}(T_k,E) + \pi_{k+1}
-       p_{\text{br}}(T_{k+1},E),
-
-   where the interpolation weights are
-
-   .. math::
-
-       \pi_k = \frac{\ln T_{k+1} - \ln T}{\ln T_{k+1} - \ln T_k},~~~
-       \pi_{k+1} = \frac{\ln T - \ln T_k}{\ln T_{k+1} - \ln T_k}.
-
-   Sample either the index :math:`i = k` or :math:`i = k+1` according to the
-   point probabilities :math:`\pi_{k}` and :math:`\pi_{k+1}`.
-
-3. Determine the maximum value of the CDF :math:`P_{\text{br,max}}`.
-
-3. Sample the photon energies using the inverse transform method with the
-   tabulated CDF :math:`P_{\text{br}}(T_i, E)` i.e.,
-
-   .. math::
-
-       E = E_j \left[ (1 + a_j) \frac{\xi_2 P_{\text{br,max}} -
-       P_{\text{br}}(T_i, E_j)} {E_j p_{\text{br}}(T_i, E_j)} + 1
-       \right]^{\frac{1}{1 + a_j}}
-
-   where the interpolation factor :math:`a_j` is given by
-
-   .. math::
-
-       a_j = \frac{\ln p_{\text{br}}(T_i,E_{j+1}) - \ln p_{\text{br}}(T_i,E_j)}
-       {\ln E_{j+1} - \ln E_j}
-
-   and :math:`P_{\text{br}}(T_i, E_j) \le \xi_2 P_{\text{br,max}} \le
-   P_{\text{br}}(T_i, E_{j+1})`.
-
-We ignore the range of the electron or positron, i.e., the bremsstrahlung
-photons are produced in the same location that the charged particle was
-created. The direction of the photons is assumed to be the same as the
-direction of the incident charged particle, which is a reasonable approximation
-at higher energies when the bremsstrahlung radiation is emitted at small
-angles.
 
 .. _photon_production:
 
@@ -1059,16 +723,14 @@ emitted photon.
 
 .. _anomalous scattering: http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm
 
-.. _Kahn's rejection method: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/aecu-3259_kahn.pdf
+.. _Kahn's rejection method: https://doi.org/10.2172/4353680
 
 .. _Klein-Nishina: https://en.wikipedia.org/wiki/Klein%E2%80%93Nishina_formula
 
-.. _LA-UR-04-0487: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-04-0487.pdf
+.. _LA-UR-04-0487: https://mcnp.lanl.gov/pdf_files/TechReport_2004_LANL_LA-UR-04-0487_Sood.pdf
 
-.. _LA-UR-04-0488: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-04-0488.pdf
+.. _LA-UR-04-0488: https://mcnp.lanl.gov/pdf_files/TechReport_2004_LANL_LA-UR-04-0488_SoodWhite.pdf
 
 .. _Kaltiaisenaho: https://aaltodoc.aalto.fi/bitstream/handle/123456789/21004/master_Kaltiaisenaho_Toni_2016.pdf
 
-.. _Salvat: https://www.oecd-nea.org/globalsearch/download.php?doc=77434
-
-.. _Sternheimer: https://doi.org/10.1103/PhysRevB.26.6067
+.. _Salvat: https://doi.org/10.1787/32da5043-en

docs/source/methods/random_numbers.rst

@@ -7,7 +7,7 @@ Random Number Generation
 In order to sample probability distributions, one must be able to produce random
 numbers. The standard technique to do this is to generate numbers on the
 interval :math:`[0,1)` from a deterministic sequence that has properties that
-make it appear to be random, e.g. being uniformly distributed and not exhibiting
+make it appear to be random, e.g., being uniformly distributed and not exhibiting
 correlation between successive terms. Since the numbers produced this way are
 not truly "random" in a strict sense, they are typically referred to as
 pseudorandom numbers, and the techniques used to generate them are pseudorandom
@@ -15,6 +15,11 @@ number generators (PRNGs). Numbers sampled on the unit interval can then be
 transformed for the purpose of sampling other continuous or discrete probability
 distributions.
 
+There are many different algorithms for pseudorandom number generation. OpenMC
+currently uses `permuted congruential generator`_ (PCG), which builds on top of
+the simpler linear congruential generator (LCG). Both algorithms are described
+below.
+
 ------------------------------
 Linear Congruential Generators
 ------------------------------
@@ -37,8 +42,8 @@ be generated with a method chosen at random. Some theory should be used."
 Typically, :math:`M` is chosen to be a power of two as this enables :math:`x
 \mod M` to be performed using the bitwise AND operator with a bit mask. The
 constants for the linear congruential generator used by default in OpenMC are
-:math:`g = 2806196910506780709`, :math:`c = 1`, and :math:`M = 2^{63}` (see
-`L'Ecuyer`_).
+:math:`g = 2806196910506780709`, :math:`c = 1`, and :math:`M = 2^{63}` (from
+`L'Ecuyer <https://doi.org/10.1090/S0025-5718-99-00996-5>`_).
 
 Skip-ahead Capability
 ---------------------
@@ -50,7 +55,8 @@ want to skip ahead :math:`N` random numbers and :math:`N` is large, the cost of
 sampling :math:`N` random numbers to get to that position may be prohibitively
 expensive. Fortunately, algorithms have been developed that allow us to skip
 ahead in :math:`O(\log_2 N)` operations instead of :math:`O(N)`. One algorithm
-to do so is described in a paper by Brown_. This algorithm relies on the following
+to do so is described in a `paper by Brown
+<https://www.osti.gov/biblio/976209>`_. This algorithm relies on the following
 relationship:
 
 .. math::
@@ -58,15 +64,26 @@ relationship:
 
     \xi_{i+k} = g^k \xi_i + c \frac{g^k - 1}{g - 1} \mod M
 
-Note that equation :eq:`lcg-skipahead` has the same general form as equation :eq:`lcg`, so
-the idea is to determine the new multiplicative and additive constants in
-:math:`O(\log_2 N)` operations.
-
-.. only:: html
-
-   .. rubric:: References
+Note that equation :eq:`lcg-skipahead` has the same general form as equation
+:eq:`lcg`, so the idea is to determine the new multiplicative and additive
+constants in :math:`O(\log_2 N)` operations.
 
 
-.. _L'Ecuyer: https://doi.org/10.1090/S0025-5718-99-00996-5
-.. _Brown: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/anl-rn-arb-stride.pdf
+--------------------------------
+Permuted Congruential Generators
+--------------------------------
+
+The `permuted congruential generator`_ (PCG) algorithm aims to improve upon the
+LCG algorithm by permuting the output. The algorithm works on the basic
+principle of first advancing the generator state using the LCG algorithm and
+then applying a permutation function on the LCG state to obtain the output. This
+results in increased statistical quality as measured by common statistical tests
+while exhibiting a very small performance overhead relative to the LCG algorithm
+and an equivalent memory footprint. For further details, see the original
+technical report by `O'Neill
+<https://www.pcg-random.org/pdf/hmc-cs-2014-0905.pdf>`_.  OpenMC uses the
+PCG-RXS-M-XS variant with a 64-bit state and 64-bit output.
+
 .. _linear congruential generator: https://en.wikipedia.org/wiki/Linear_congruential_generator
+
+.. _permuted congruential generator: https://en.wikipedia.org/wiki/Permuted_congruential_generator

docs/source/methods/tallies.rst

@@ -4,9 +4,9 @@
 Tallies
 =======
 
-Note that the methods discussed in this section are written specifically for
-continuous-energy mode but equivalent apply to the multi-group mode if the
-particle's energy is replaced with the particle's group
+The methods discussed in this section are written specifically for continuous-
+energy mode. However, they can also apply to the multi-group mode if the
+particle's energy is instead interpreted as the particle's group.
 
 ------------------
 Filters and Scores
@@ -179,12 +179,12 @@ n(\mathbf{r}, \mathbf{\hat{\Omega}}, E, t)` and :math:`d\ell = v \, dt` where
 
 Equation :eq:`track-length-integral` indicates that we can use the length of a
 particle's trajectory as an estimate for the flux, i.e. the track-length
-estimator of the flux would be
+estimator of the volume-integrated flux would be
 
 .. math::
     :label: track-length-flux
 
-    \phi = \frac{1}{W} \sum_{i \in T} w_i \ell_i
+    V \phi = \frac{1}{W} \sum_{i \in T} w_i \ell_i
 
 where :math:`T` is the set of all the particle's trajectories within the desired
 volume and :math:`\ell_i` is the length of the :math:`i`-th trajectory. In the
@@ -207,6 +207,8 @@ the change-in-angle), we must use an analog estimator.
 
 .. TODO: Add description of surface current tallies
 
+.. _tallies_statistics:
+
 ----------
 Statistics
 ----------
@@ -268,6 +270,14 @@ normal, log-normal, Weibull, etc. The central limit theorem states that as
 Estimating Statistics of a Random Variable
 ------------------------------------------
 
+After running OpenMC, each tallied quantity has a reported mean and standard
+deviation. The below sections explain how these quantities are computed. Note
+that OpenMC uses **batch statistics**, meaning that each observation for a tally
+random variable corresponds to the aggregation of tally contributions from
+multiple source particles that are grouped together into a single batch. See
+:ref:`usersguide_particles` for more information on how the number of source
+particles and statistical batches are specified.
+
 Mean
 ++++
 
@@ -377,6 +387,33 @@ of this is that the longer you run a simulation, the better you know your
 results. Therefore, by running a simulation long enough, it is possible to
 reduce the stochastic uncertainty to arbitrarily low levels.
 
+Figure of Merit
++++++++++++++++
+
+The figure of merit (FOM) is an indicator that accounts for both the statistical
+uncertainty and the execution time and represents how much information is
+obtained per unit time in the simulation. The FOM is defined as
+
+.. math::
+    :label: figure_of_merit
+
+    FOM = \frac{1}{r^2 t},
+
+where :math:`t` is the total execution time and :math:`r` is the relative error
+defined as
+
+.. math::
+    :label: relative_error
+
+    r = \frac{s_\bar{X}}{\bar{x}}.
+
+Based on this definition, one can see that a higher FOM is desirable. The FOM is
+useful as a comparative tool. For example, if a variance reduction technique is
+being applied to a simulation, the FOM with variance reduction can be compared
+to the FOM without variance reduction to ascertain whether the reduction in
+variance outweighs the potential increase in execution time (e.g., due to
+particle splitting).
+
 Confidence Intervals
 ++++++++++++++++++++
 
@@ -510,6 +547,6 @@ improve the estimate of the percentile.
 
 .. _Cauchy distribution: https://en.wikipedia.org/wiki/Cauchy_distribution
 
-.. _unpublished rational approximation: https://web.archive.org/web/20150926021742/http://home.online.no/~pjacklam/notes/invnorm/
+.. _unpublished rational approximation: https://stackedboxes.org/2017/05/01/acklams-normal-quantile-function/
 
-.. _MC21: http://www.osti.gov/bridge/servlets/purl/903083-HT5p1o/903083.pdf
+.. _MC21: https://www.osti.gov/servlets/purl/903083

docs/source/methods/variance_reduction.rst

@@ -0,0 +1,134 @@
+.. _methods_variance_reduction:
+
+==================
+Variance Reduction
+==================
+
+.. _methods_variance_reduction_intro:
+
+------------
+Introduction
+------------
+
+Transport problems can sometimes involve a significant degree of attenuation
+between the source and a detector (tally) region, which can result in a flux
+differential of ten orders of magnitude (or more) throughout the simulation
+domain. As Monte Carlo uncertainties tend to be inversely proportional to the
+physical flux density, it can be extremely difficult to accurately resolve
+tallies in locations that are optically far from the source. This issue is
+particularly common in fixed source simulations, where some tally locations may
+not experience a single scoring event, even after billions of analog histories.
+
+Variance reduction techniques aim to either flatten the global uncertainty
+distribution, such that all regions of phase space have a fairly similar
+uncertainty, or to reduce the uncertainty in specific locations (such as a
+detector). There are two strategies available in OpenMC for variance reduction:
+the Monte Carlo MAGIC method and the FW-CADIS method. Both strategies work by
+developing a weight window mesh that can be utilized by subsequent Monte Carlo
+solves to split particles heading towards areas of lower flux densities while
+terminating particles in higher flux regions---all while maintaining a fair
+game.
+
+------------
+MAGIC Method
+------------
+
+The Method of Automatic Generation of Importances by Calculation, or `MAGIC
+method <https://doi.org/10.1016/j.fusengdes.2011.01.059>`_, is an iterative
+technique that uses spatial flux information :math:`\phi(r)` obtained from a
+normal Monte Carlo solve to produce weight windows :math:`w(r)` that can be
+utilized by a subsequent iteration of Monte Carlo. While the first generation of
+weight windows produced may only help to reduce variance slightly, use of these
+weights to generate another set of weight windows results in a progressively
+improving iterative scheme.
+
+Equation :eq:`magic` defines how the lower bound of weight windows
+:math:`w_{\ell}(r)` are generated with MAGIC using forward flux information.
+Here, we can see that the flux at location :math:`r` is normalized by the
+maximum flux in any group at that location. We can also see that the weights are
+divided by a factor of two, which accounts for the typical :math:`5\times`
+factor separating the lower and upper weight window bounds in OpenMC.
+
+.. math::
+    :label: magic
+
+    w_{\ell}(r) = \frac{\phi(r)}{2\,\text{max}(\phi(r))}
+
+A major advantage of this technique is that it does not require any special
+transport machinery; it simply uses multiple Monte Carlo simulations to
+iteratively improve a set of weight windows (which are typically defined on a
+mesh covering the simulation domain). The downside to this method is that as the
+flux differential increases between areas near and far from the source, it
+requires more outer Monte Carlo iterations, each of which can be expensive in
+itself. Additionally, computation of weight windows based on regular (forward)
+neutron flux tally information does not produce the most numerically effective
+set of weight windows. Nonetheless, MAGIC remains a simple and effective
+technique for generating weight windows.
+
+--------
+FW-CADIS
+--------
+
+As discussed in the previous section, computation of weight windows based on
+regular (forward) neutron flux tally information does not produce the most
+numerically efficient set of weight windows. It is highly preferable to generate
+weight windows based on spatial adjoint flux :math:`\phi^{\dag}(r)`
+information. The adjoint flux is essentially the "reverse" simulation problem,
+where we sample a random point and assume this is where a particle was absorbed,
+and then trace it backwards (upscattering in energy), until we sample the point
+where it was born from.
+
+The Forward-Weighted Consistent Adjoint Driven Importance Sampling method, or
+`FW-CADIS method <https://doi.org/10.13182/NSE12-33>`_, produces weight windows
+for global variance reduction given adjoint flux information throughout the
+entire domain. The weight window lower bound is defined in Equation
+:eq:`fw_cadis`, and also involves a normalization step not shown here.
+
+.. math::
+    :label: fw_cadis
+
+    w_{\ell}(r) = \frac{1}{2\phi^{\dag}(r)}
+
+While the algorithm itself is quite simple, it requires estimates of the global
+adjoint flux distribution, which is difficult to generate directly with Monte
+Carlo transport. Thus, FW-CADIS typically uses an alternative solver (often
+deterministic) that can be more readily adapted for generating adjoint flux
+information, and which is often much cheaper than Monte Carlo given that a rough
+solution is often sufficient for weight window generation.
+
+The FW-CADIS implementation in OpenMC utilizes its own internal random ray
+multigroup transport solver to generate the adjoint source distribution. No
+coupling to any external transport is solver is necessary. The random ray solver
+operates on the same geometry as the Monte Carlo solver, so no redefinition of
+the simulation geometry is required. More details on how the adjoint flux is
+computed are given in the :ref:`adjoint methods section <adjoint>`.
+
+More information on the workflow is available in the :ref:`user guide
+<variance_reduction>`, but generally production of weight windows with FW-CADIS
+involves several stages (some of which are highly automated). These tasks
+include generation of approximate multigroup cross section data for use by the
+random ray solver, running of the random ray solver in normal (forward flux)
+mode to generate a source for the adjoint solver, running of the random ray
+solver in adjoint mode to generate adjoint flux tallies, and finally the
+production of weight windows via the FW-CADIS method. As is discussed in the
+user guide, most of these steps are automated together, making the additional
+burden on the user fairly small.
+
+The major advantage of this technique is that it typically produces much more
+numerically efficient weight windows as compared to those generated with MAGIC,
+sometimes with an order-of-magnitude improvement in the figure of merit
+(Equation :eq:`variance_fom`), which accounts for both the variance and the
+execution time. Another major advantage is that the cost of the random ray
+solver is typically negligible compared to the cost of the subsequent Monte
+Carlo solve itself, making it a very cheap method to deploy. The downside to
+this method is that it introduces a second transport method into the mix (random
+ray), such that there are more free input parameters for the user to know about
+and adjust, potentially making the method more complex to use. However, as many
+of the parameters have natural choices, much of this parameterization can be
+handled automatically behind the scenes without the need for the user to be
+aware of this.
+
+.. math::
+    :label: variance_fom
+
+    \text{FOM} = \frac{1}{\text{Time} \times \sigma^2}

docs/source/publications.rst

@@ -138,8 +138,8 @@ Geometry and Visualization
   *Trans. Am. Nucl. Soc.*, **114**, 391-394 (2016).
 
 - Derek M. Lax, "`Memory efficient indexing algorithm for physical properties in
-  OpenMC <http://hdl.handle.net/1721.1/97862>`_," S. M. Thesis, Massachusetts
-  Institute of Technology (2015).
+  OpenMC <https://dspace.mit.edu/handle/1721.1/97862>`_," S. M. Thesis,
+  Massachusetts Institute of Technology (2015).
 
 - Derek Lax, William Boyd, Nicholas Horelik, Benoit Forget, and Kord Smith, "A
   memory efficient algorithm for classifying unique regions in constructive
@@ -399,7 +399,8 @@ Doppler Broadening
 - Jonathan A. Walsh, Benoit Forget, Kord S. Smith, Brian C. Kiedrowski, and
   Forrest B. Brown, "`Direct, on-the-fly calculation of unresolved resonance
   region cross sections in Monte Carlo simulations
-  <http://hdl.handle.net/1721.1/108644>`_," *Proc. Joint Int. Conf. M&C+SNA+MC*,
+  <https://dspace.mit.edu/handle/1721.1/108644>`_," *Proc. Joint Int. Conf.
+  M&C+SNA+MC*,
   Nashville, Tennessee, Apr. 19--23 (2015).
 
 - Colin Josey, Benoit Forget, and Kord Smith, "`Windowed multipole sensitivity
@@ -596,7 +597,8 @@ Depletion
 
 - Matthew S. Ellis, Colin Josey, Benoit Forget, and Kord Smith, "`Spatially
   Continuous Depletion Algorithm for Monte Carlo Simulations
-  <http://hdl.handle.net/1721.1/107880>`_," *Trans. Am. Nucl. Soc.*, **115**,
+  <https://dspace.mit.edu/handle/1721.1/107880>`_," *Trans. Am. Nucl. Soc.*,
+  **115**,
   1221-1224 (2016).
 
 - Anas Gul, K. S. Chaudri, R. Khan, and M. Azeen, "`Development and verification

docs/source/pythonapi/base.rst

@@ -21,19 +21,21 @@ Simulation Settings
    :nosignatures:
    :template: myclass.rst
 
-   openmc.Source
+   openmc.SourceBase
+   openmc.IndependentSource
+   openmc.FileSource
+   openmc.CompiledSource
+   openmc.MeshSource
    openmc.SourceParticle
    openmc.VolumeCalculation
-   openmc.WeightWindows
    openmc.Settings
 
-The following function can be used for generating a source file:
-
 .. autosummary::
    :toctree: generated
    :nosignatures:
    :template: myfunction.rst
 
+   openmc.read_source_file
    openmc.write_source_file
 
 Material Specification
@@ -44,9 +46,6 @@ Material Specification
    :nosignatures:
    :template: myclass.rst
 
-   openmc.Nuclide
-   openmc.Element
-   openmc.Macroscopic
    openmc.Material
    openmc.Materials
 
@@ -88,6 +87,7 @@ Building geometry
    openmc.Intersection
    openmc.Union
    openmc.Complement
+   openmc.BoundingBox
    openmc.Cell
    openmc.Universe
    openmc.DAGMCUniverse
@@ -119,17 +119,21 @@ Constructing Tallies
    openmc.Filter
    openmc.UniverseFilter
    openmc.MaterialFilter
+   openmc.MaterialFromFilter
    openmc.CellFilter
    openmc.CellFromFilter
-   openmc.CellbornFilter
+   openmc.CellBornFilter
    openmc.CellInstanceFilter
    openmc.CollisionFilter
    openmc.SurfaceFilter
    openmc.MeshFilter
+   openmc.MeshBornFilter
+   openmc.MeshMaterialFilter
    openmc.MeshSurfaceFilter
    openmc.EnergyFilter
    openmc.EnergyoutFilter
    openmc.MuFilter
+   openmc.MuSurfaceFilter
    openmc.PolarFilter
    openmc.AzimuthalFilter
    openmc.DistribcellFilter
@@ -139,18 +143,30 @@ Constructing Tallies
    openmc.SpatialLegendreFilter
    openmc.SphericalHarmonicsFilter
    openmc.TimeFilter
+   openmc.WeightFilter
    openmc.ZernikeFilter
    openmc.ZernikeRadialFilter
+   openmc.ParentNuclideFilter
    openmc.ParticleFilter
+   openmc.MeshMaterialVolumes
+   openmc.Trigger
+   openmc.TallyDerivative
+   openmc.Tally
+   openmc.Tallies
+
+Meshes
+------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclassinherit.rst
+
    openmc.RegularMesh
    openmc.RectilinearMesh
    openmc.CylindricalMesh
    openmc.SphericalMesh
    openmc.UnstructuredMesh
-   openmc.Trigger
-   openmc.TallyDerivative
-   openmc.Tally
-   openmc.Tallies
 
 Geometry Plotting
 -----------------
@@ -161,6 +177,8 @@ Geometry Plotting
    :template: myclass.rst
 
    openmc.Plot
+   openmc.WireframeRayTracePlot
+   openmc.SolidRayTracePlot
    openmc.Plots
 
 Running OpenMC
@@ -186,8 +204,19 @@ Post-processing
    :template: myclass.rst
 
    openmc.Particle
+   openmc.ParticleList
+   openmc.ParticleTrack
    openmc.StatePoint
    openmc.Summary
+   openmc.Track
+   openmc.Tracks
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   openmc.voxel_to_vtk
 
 The following classes and functions are used for functional expansion reconstruction.
 
@@ -220,6 +249,27 @@ Various classes may be created when performing tally slicing and/or arithmetic:
    openmc.arithmetic.AggregateNuclide
    openmc.arithmetic.AggregateFilter
 
+Variance Reduction
+------------------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass
+
+   openmc.WeightWindows
+   openmc.WeightWindowsList
+   openmc.WeightWindowGenerator
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   openmc.hdf5_to_wws
+   openmc.wwinp_to_wws
+
+
 Coarse Mesh Finite Difference Acceleration
 ------------------------------------------
 

docs/source/pythonapi/capi.rst

@@ -13,25 +13,38 @@ Functions
    :template: myfunction.rst
 
    calculate_volumes
+   current_batch
    export_properties
+   export_weight_windows
    finalize
    find_cell
    find_material
+   dagmc_universe_cell_ids
+   global_bounding_box
+   global_tallies
    hard_reset
+   id_map
    import_properties
+   import_weight_windows
    init
+   is_statepoint_batch
    iter_batches
    keff
    load_nuclide
+   master
    next_batch
    num_realizations
    plot_geometry
+   property_map
    reset
+   reset_timers
    run
    run_in_memory
-   simulation_init
+   sample_external_source
    simulation_finalize
+   simulation_init
    source_bank
+   statepoint_load
    statepoint_write
 
 Classes
@@ -42,12 +55,89 @@ Classes
    :nosignatures:
    :template: myclass.rst
 
+   AzimuthalFilter
    Cell
+   CellFilter
+   CellInstanceFilter
+   CellbornFilter
+   CellfromFilter
+   CollisionFilter
+   CylindricalMesh
+   DelayedGroupFilter
+   DistribcellFilter
    EnergyFilter
-   MaterialFilter
+   EnergyFunctionFilter
+   EnergyoutFilter
+   Filter
+   LegendreFilter
    Material
+   MaterialFilter
+   MaterialFromFilter
+   Mesh
    MeshFilter
+   MeshBornFilter
    MeshSurfaceFilter
+   MuFilter
    Nuclide
+   ParentNuclideFilter
+   ParticleFilter
+   PolarFilter
+   RectilinearMesh
    RegularMesh
+   SpatialLegendreFilter
+   SphericalHarmonicsFilter
+   SphericalMesh
+   SurfaceFilter
    Tally
+   TemporarySession
+   UniverseFilter
+   UnstructuredMesh
+   WeightFilter
+   WeightWindows
+   ZernikeFilter
+   ZernikeRadialFilter
+
+Data
+----
+
+.. data:: cells
+
+   Mapping of cell ID to :class:`openmc.lib.Cell` instances.
+
+   :type: dict
+
+.. data:: filters
+
+   Mapping of filter ID to :class:`openmc.lib.Filter` instances.
+
+   :type: dict
+
+.. data:: materials
+
+   Mapping of material ID to :class:`openmc.lib.Material` instances.
+
+   :type: dict
+
+.. data:: meshes
+
+   Mapping of mesh ID to :class:`openmc.lib.Mesh` instances.
+
+   :type: dict
+
+.. data:: nuclides
+
+   Mapping of nuclide name to :class:`openmc.lib.Nuclide` instances.
+
+   :type: dict
+
+.. data:: tallies
+
+   Mapping of tally ID to :class:`openmc.lib.Tally` instances.
+
+   :type: dict
+
+.. data:: weight_windows
+
+   Mapping of weight window ID to :class:`openmc.lib.WeightWindows` instances.
+
+   :type: dict

docs/source/pythonapi/data.rst

@@ -61,9 +61,15 @@ Core Functions
 
     atomic_mass
     atomic_weight
+    combine_distributions
+    decay_constant
+    decay_energy
+    decay_photon_energy
     dose_coefficients
-    gnd_name
+    gnds_name
+    half_life
     isotopes
+    kalbach_slope
     linearize
     thin
     water_density
@@ -114,6 +120,7 @@ Angle-Energy Distributions
     IncoherentElasticAE
     IncoherentElasticAEDiscrete
     IncoherentInelasticAEDiscrete
+    MixedElasticAE
 
 Resonance Data
 --------------

docs/source/pythonapi/deplete.rst

@@ -15,16 +15,18 @@ are:
     1) A transport operator
     2) A time-integration scheme
 
-The former is responsible for executing a transport code, like OpenMC,
-and retaining important information required for depletion. The most common examples
-are reaction rates and power normalization data. The latter is responsible for
-projecting reaction rates and compositions forward in calendar time across
-some step size :math:`\Delta t`, and obtaining new compositions given a power
-or power density. The :class:`Operator` is provided to handle communicating with
-OpenMC. Several classes are provided that implement different time-integration
-algorithms for depletion calculations, which are described in detail in Colin
-Josey's thesis, `Development and analysis of high order neutron
-transport-depletion coupling algorithms <http://hdl.handle.net/1721.1/113721>`_.
+The former is responsible for calculating and retaining important information
+required for depletion. The most common examples are reaction rates and power
+normalization data. The latter is responsible for projecting reaction rates and
+compositions forward in calendar time across some step size :math:`\Delta t`,
+and obtaining new compositions given a power or power density. The
+:class:`CoupledOperator` class is provided to obtain reaction rates via tallies
+through OpenMC's transport solver, and the :class:`IndependentOperator` class is
+provided to obtain reaction rates from cross-section data. Several classes are
+provided that implement different time-integration algorithms for depletion
+calculations, which are described in detail in Colin Josey's thesis,
+`Development and analysis of high order neutron transport-depletion coupling
+algorithms <https://dspace.mit.edu/handle/1721.1/113721>`_.
 
 .. autosummary::
     :toctree: generated
@@ -40,18 +42,30 @@ transport-depletion coupling algorithms <http://hdl.handle.net/1721.1/113721>`_.
     SICELIIntegrator
     SILEQIIntegrator
 
-Each of these classes expects a "transport operator" to be passed. An operator
-specific to OpenMC is available using the following class:
+Each of these classes expects a "transport operator" to be passed. OpenMC
+provides the following transport operator classes:
 
 .. autosummary::
    :toctree: generated
    :nosignatures:
    :template: mycallable.rst
 
-   Operator
+   CoupledOperator
+   IndependentOperator
 
-The :class:`Operator` must also have some knowledge of how nuclides transmute
-and decay. This is handled by the :class:`Chain`.
+The :class:`CoupledOperator` and :class:`IndependentOperator` classes must also
+have some knowledge of how nuclides transmute and decay. This is handled by the
+:class:`Chain` class.
+
+The :class:`IndependentOperator` class requires a set of fluxes and microscopic
+cross sections. The following function can be used to generate this information:
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   get_microxs_and_flux
 
 Minimal Example
 ---------------
@@ -64,19 +78,18 @@ A minimal example for performing depletion would be:
     >>> import openmc.deplete
     >>> geometry = openmc.Geometry.from_xml()
     >>> settings = openmc.Settings.from_xml()
+    >>> model = openmc.Model(geometry, settings)
 
     # Representation of a depletion chain
     >>> chain_file = "chain_casl.xml"
-    >>> operator = openmc.deplete.Operator(
-    ...     geometry, settings, chain_file)
+    >>> operator = openmc.deplete.CoupledOperator(model, chain_file)
 
     # Set up 5 time steps of one day each
     >>> dt = [24 * 60 * 60] * 5
     >>> power = 1e6  # constant power of 1 MW
 
     # Deplete using mid-point predictor-corrector
-    >>> cecm = openmc.deplete.CECMIntegrator(
-    ...     operator, dt, power)
+    >>> cecm = openmc.deplete.CECMIntegrator(operator, dt, power)
     >>> cecm.integrate()
 
 Internal Classes and Functions
@@ -131,10 +144,11 @@ data, such as number densities and reaction rates for each material.
    :template: myclass.rst
 
    AtomNumber
+   MicroXS
    OperatorResult
    ReactionRates
    Results
-   ResultsList
+   StepResult
 
 The following class and functions are used to solve the depletion equations,
 with :func:`cram.CRAM48` being the default.
@@ -166,7 +180,13 @@ with :func:`cram.CRAM48` being the default.
 
    :type: bool
 
-The following classes are used to help the :class:`openmc.deplete.Operator`
+.. data:: pool.NUM_PROCESSES
+
+   Number of worker processes used for depletion calculations, which rely on the
+   :class:`multiprocessing.pool.Pool` class. If set to ``None`` (default), the
+   number returned by :func:`os.cpu_count` is used.
+
+The following classes are used to help the :class:`openmc.deplete.CoupledOperator`
 compute quantities like effective fission yields, reaction rates, and
 total system energy.
 
@@ -183,14 +203,56 @@ total system energy.
    helpers.FissionYieldCutoffHelper
    helpers.FluxCollapseHelper
 
+The :class:`openmc.deplete.IndependentOperator` uses inner classes subclassed
+from those listed above to perform similar calculations.
+
+The following classes are used to define external source rates or transfer rates
+to model continuous removal or feed of nuclides during depletion.
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass.rst
+
+   transfer_rates.ExternalSourceRates
+   transfer_rates.TransferRates
+
+Intermediate Classes
+--------------------
+
+Specific implementations of abstract base classes may utilize some of
+the same methods and data structures. These methods and data are stored
+in intermediate classes.
+
+Methods common to tally-based implementation of :class:`FissionYieldHelper`
+are stored in :class:`helpers.TalliedFissionYieldHelper`
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myclass.rst
+
+   helpers.TalliedFissionYieldHelper
+
+Methods common to OpenMC-specific implementations of :class:`TransportOperator`
+are stored in :class:`openmc_operator.OpenMCOperator`
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: mycallable.rst
+
+   openmc_operator.OpenMCOperator
+
+
 Abstract Base Classes
 ---------------------
 
 A good starting point for extending capabilities in :mod:`openmc.deplete` is
 to examine the following abstract base classes. Custom classes can
 inherit from :class:`abc.TransportOperator` to implement alternative
-schemes for collecting reaction rates and other data from a transport code
-prior to depleting materials
+schemes for collecting reaction rates and other data prior to depleting
+materials
 
 .. autosummary::
    :toctree: generated
@@ -200,7 +262,9 @@ prior to depleting materials
    abc.TransportOperator
 
 The following classes are abstract classes used to pass information from
-OpenMC simulations back on to the :class:`abc.TransportOperator`
+transport simulations (in the case of transport-coupled depletion) or to
+simply calculate these quantities directly (in the case of
+transport-independent depletion) back on to the :class:`abc.TransportOperator`
 
 .. autosummary::
    :toctree: generated
@@ -210,7 +274,6 @@ OpenMC simulations back on to the :class:`abc.TransportOperator`
    abc.NormalizationHelper
    abc.FissionYieldHelper
    abc.ReactionRateHelper
-   abc.TalliedFissionYieldHelper
 
 Custom integrators or depletion solvers can be developed by subclassing from
 the following abstract base classes:
@@ -223,3 +286,15 @@ the following abstract base classes:
    abc.Integrator
    abc.SIIntegrator
    abc.DepSystemSolver
+
+D1S Functions
+-------------
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   d1s.prepare_tallies
+   d1s.time_correction_factors
+   d1s.apply_time_correction

docs/source/pythonapi/mgxs.rst

@@ -41,6 +41,7 @@ Multi-group Cross Sections
     openmc.mgxs.KappaFissionXS
     openmc.mgxs.MultiplicityMatrixXS
     openmc.mgxs.NuFissionMatrixXS
+    openmc.mgxs.ReducedAbsorptionXS
     openmc.mgxs.ScatterXS
     openmc.mgxs.ScatterMatrixXS
     openmc.mgxs.ScatterProbabilityMatrix

docs/source/pythonapi/model.rst

@@ -11,9 +11,6 @@ Convenience Functions
    :template: myfunction.rst
 
    openmc.model.borated_water
-   openmc.model.cylinder_from_points
-   openmc.model.hexagonal_prism
-   openmc.model.rectangular_prism
    openmc.model.subdivide
    openmc.model.pin
 
@@ -25,8 +22,17 @@ Composite Surfaces
    :nosignatures:
    :template: myclass.rst
 
+   openmc.model.ConicalFrustum
+   openmc.model.CruciformPrism
+   openmc.model.CylinderSector
+   openmc.model.HexagonalPrism
+   openmc.model.IsogonalOctagon
+   openmc.model.OrthogonalBox
+   openmc.model.Polygon
    openmc.model.RectangularParallelepiped
+   openmc.model.RectangularPrism
    openmc.model.RightCircularCylinder
+   openmc.model.Vessel
    openmc.model.XConeOneSided
    openmc.model.YConeOneSided
    openmc.model.ZConeOneSided

docs/source/pythonapi/stats.rst

@@ -22,7 +22,14 @@ Univariate Probability Distributions
    openmc.stats.Legendre
    openmc.stats.Mixture
    openmc.stats.Normal
-   openmc.stats.Muir
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   openmc.stats.delta_function
+   openmc.stats.muir
 
 Angular Distributions
 ---------------------
@@ -51,3 +58,12 @@ Spatial Distributions
    openmc.stats.SphericalIndependent
    openmc.stats.Box
    openmc.stats.Point
+   openmc.stats.MeshSpatial
+   openmc.stats.PointCloud
+
+.. autosummary::
+   :toctree: generated
+   :nosignatures:
+   :template: myfunction.rst
+
+   openmc.stats.spherical_uniform

docs/source/quickinstall.rst

@@ -8,40 +8,43 @@ This quick install guide outlines the basic steps needed to install OpenMC on
 your computer. For more detailed instructions on configuring and installing
 OpenMC, see :ref:`usersguide_install` in the User's Manual.
 
-----------------------------------------
-Installing on Linux/Mac with conda-forge
-----------------------------------------
+----------------------------------
+Installing on Linux/Mac with Conda
+----------------------------------
 
-`Conda <https://conda.io/en/latest/>`_ is an open source package management
-system and environment management system for installing multiple versions of
-software packages and their dependencies and switching easily between them. If
-you have `conda` installed on your system, OpenMC can be installed via the
-`conda-forge` channel. First, add the `conda-forge` channel with:
+`Conda <https://docs.conda.io/en/latest/>`_ is an open source package management
+system and environments management system for installing multiple versions of
+software packages and their dependencies and switching easily between them.
+OpenMC can be installed in a `conda` environment. First, `conda` should be
+`installed <https://www.anaconda.com/docs/getting-started/getting-started>`_
+with either Anaconda Distribution or Miniconda. Once you have `conda` installed
+on your system, OpenMC can be installed via the `conda-forge` channel.
+
+First, add the `conda-forge` channel with:
 
 .. code-block:: sh
 
     conda config --add channels conda-forge
+    conda config --set channel_priority strict
 
-To list the versions of OpenMC that are available on the `conda-forge` channel,
-in your terminal window or an Anaconda Prompt run:
-
-.. code-block:: sh
-
-    conda search openmc
-
-OpenMC can then be installed with:
-
-.. code-block:: sh
-
-    conda create -n openmc-env openmc
-
-This will install OpenMC in a conda environment called `openmc-env`. To activate
-the environment, run:
+Then create and activate a new conda enviroment called `openmc-env` (or whatever
+you wish) with OpenMC installed.
 
 .. code-block:: sh
 
+    conda create --name openmc-env openmc
     conda activate openmc-env
 
+If you are installing on macOS with an Apple silicon ARM-based processor, you
+will also need to specify the `--platform` option:
+
+.. code-block:: sh
+
+    conda create --name openmc-env --platform osx-64 openmc
+
+You are now in a conda environment called `openmc-env` that has OpenMC
+installed.
+
 -------------------------------------------
 Installing on Linux/Mac/Windows with Docker
 -------------------------------------------
@@ -90,31 +93,53 @@ can be used to access the installed packages.
 .. _Spack: https://spack.readthedocs.io/en/latest/
 .. _setup guide: https://spack.readthedocs.io/en/latest/getting_started.html
 
---------------------------------
-Installing from Source on Ubuntu
---------------------------------
+-------------------------------
+Manually Installing from Source
+-------------------------------
 
-To build OpenMC from source, several :ref:`prerequisites <prerequisites>` are
-needed. If you are using Ubuntu or higher, all prerequisites can be installed
-directly from the package manager:
+Obtaining prerequisites on Ubuntu
+---------------------------------
+
+When building OpenMC from source, all :ref:`prerequisites <prerequisites>` can
+be installed using the package manager:
 
 .. code-block:: sh
 
     sudo apt install g++ cmake libhdf5-dev libpng-dev
 
-After the packages have been installed, follow the instructions below for
-building and installing OpenMC from source.
+After the packages have been installed, follow the instructions to build from
+source below.
 
--------------------------------------------
-Installing from Source on Linux or Mac OS X
--------------------------------------------
+Obtaining prerequisites on macOS
+--------------------------------
+
+For an OpenMC build with multithreading enabled, a package manager like
+`Homebrew <https://brew.sh>`_ should first be installed. Then, the following
+packages should be installed, for example in Homebrew via:
+
+.. code-block:: sh
+
+   brew install llvm cmake xtensor hdf5 python libomp libpng
+
+The compiler provided by the above LLVM package should be used in place of the
+one provisioned by XCode, which does not support the multithreading library used
+by OpenMC. To ensure CMake picks up the correct compiler, make sure that either
+the :envvar:`CXX` environment variable is set to the brew-installed ``clang++``
+or that the directory containing it is on your :envvar:`PATH` environment
+variable. Common locations for the brew-installed compiler are
+``/opt/homebrew/opt/llvm/bin`` and ``/usr/local/opt/llvm/bin``.
+
+After the packages have been installed, follow the instructions to build from
+source below.
+
+Building Source on Linux or macOS
+---------------------------------
 
 All OpenMC source code is hosted on `GitHub
 <https://github.com/openmc-dev/openmc>`_. If you have `git
-<https://git-scm.com>`_, the `gcc <https://gcc.gnu.org/>`_ compiler suite,
-`CMake <https://cmake.org>`_, and `HDF5
-<https://www.hdfgroup.org/solutions/hdf5/>`_ installed, you can download and
-install OpenMC be entering the following commands in a terminal:
+<https://git-scm.com>`_, a modern C++ compiler, `CMake <https://cmake.org>`_,
+and `HDF5 <https://www.hdfgroup.org/solutions/hdf5/>`_ installed, you can
+download and install OpenMC by entering the following commands in a terminal:
 
 .. code-block:: sh
 
@@ -134,14 +159,14 @@ should specify an installation directory where you have write access, e.g.
     cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local ..
 
 The :mod:`openmc` Python package must be installed separately. The easiest way
-to install it is using `pip <https://pip.pypa.io/en/stable/>`_, which is
-included by default in Python 3.4+. From the root directory of the OpenMC
-distribution/repository, run:
+to install it is using `pip <https://pip.pypa.io/en/stable/>`_.
+From the root directory of the OpenMC 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
+By default, OpenMC will be built with multithreading support. To build
+distributed-memory parallel versions of OpenMC using MPI or to configure other
+options, directions can be found in the :ref:`detailed installation instructions
 <usersguide_build>`.

docs/source/releasenotes/0.13.1.rst

@@ -0,0 +1,182 @@
+====================
+What's New in 0.13.1
+====================
+
+.. currentmodule:: openmc
+
+-------
+Summary
+-------
+
+This release of OpenMC includes many bug fixes as well as improvements in
+geometry modeling, mesh functionality, source specification, depletion
+capabilities, and other general enhancements. The depletion module features a
+new transport operator, :class:`openmc.deplete.IndependentOperator`, that allows
+a depletion calculation to be performed using arbitrary one-group cross sections
+(e.g., generated by an external solver) along with a
+:class:`openmc.deplete.MicroXS` class for managing one-group cross sections. The
+track file generation capability has been significantly overhauled and a new
+:class:`openmc.Tracks` class was introduced to allow access to information in
+track files from the Python API. Support has been added for new ENDF thermal
+scattering evaluations that use mixed coherent/incoherent elastic scattering.
+
+------------------------------------
+Compatibility Notes and Deprecations
+------------------------------------
+
+- The ``openmc.deplete.Operator`` class has been renamed
+  :class:`openmc.deplete.CoupledOperator`.
+- The ``openmc.deplete.ResultsList`` class has been renamed to
+  :class:`openmc.deplete.Results` and no longer requires you to call the
+  ``from_hdf5()`` method in order to create it; instead, you can directly
+  instantiate it.
+- A few methods that represent k-effective have been renamed for the sake of
+  consistency:
+
+  - ``openmc.StatePoint.k_combined`` is now :attr:`openmc.StatePoint.keff`
+  - ``openmc.deplete.ResultsList.get_eigenvalue`` is now
+    :meth:`openmc.deplete.Results.get_keff`
+
+- The :class:`openmc.stats.SphericalIndependent` class, which used to
+  accept a distribution for ``theta`` now accepts a distribution for ``cos_theta``
+  instead in order to more easily handle the common case of specifying a uniform
+  spatial distribution over a sphere (also see the new
+  :func:`openmc.stats.spherical_uniform` function).
+
+- If you are building OpenMC from source, note that several of our CMake options
+  have been changed:
+
+  ==========  ======================
+  Old option  New option
+  ==========  ======================
+  debug       ---
+  optimize    ---
+  profile     OPENMC_ENABLE_PROFILE
+  coverage    OPENMC_ENABLE_COVERAGE
+  openmp      OPENMC_USE_OPENMP
+  ---         OPENMC_USE_MPI
+  dagmc       OPENMC_USE_DAGMC
+  libmesh     OPENMC_USE_LIBMESH
+  ==========  ======================
+
+  The ``debug`` and ``optimize`` options have been removed; instead, use the
+  standard `CMAKE_BUILD_TYPE
+  <https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html>`_
+  variable.
+
+------------
+New Features
+------------
+
+- Two new composite surfaces: :class:`openmc.model.IsogonalOctagon` and
+  :class:`openmc.model.CylinderSector`.
+- The :class:`~openmc.DAGMCUniverse` class now has a
+  :attr:`~openmc.DAGMCUniverse.bounding_box` attribute and a
+  :meth:`~openmc.DAGMCUniverse.bounding_region` method.
+- When translating a :class:`~openmc.Region` using the
+  :meth:`~openmc.Region.translate` method, there is now an ``inplace`` argument.
+- The :class:`~openmc.Material` class has several new methods and attributes:
+
+  - The :meth:`~openmc.Material.add_components` methods allows you to add
+    multiple nuclides/elements to a material with a single call by passing a
+    dictionary.
+  - The :meth:`~openmc.Material.get_activity` method returns the activity of a
+    material in Bq, Bq/g, or Bq/cm³.
+  - The :meth:`~openmc.Material.remove_element` method removes an element from a
+    material
+  - The :meth:`~openmc.Material.get_nuclide_atoms` method gives the number of
+    atoms of each nuclide in a material
+
+- All mesh classes now have a ``volumes`` property that provides the volume of
+  each mesh element as well as ``write_data_to_vtk`` methods.
+- Support for externally managed MOAB meshes or libMesh meshes.
+- Multiple discrete distributions can be merged with the new
+  :meth:`~openmc.stats.Discrete.merge` method.
+- The :func:`openmc.stats.spherical_uniform` function creates a uniform
+  distribution over a sphere using the
+  :class:`~openmc.stats.SphericalIndependent` class.
+- Univariate distributions in the :mod:`openmc.stats` module now have
+  ``sample()`` methods.
+- An ``openmc_sample_external_source`` function has been added to the C API with
+  a corresponding Python binding :func:`openmc.lib.sample_external_source`.
+- The track file generation capability has been completely overhauled. Track
+  files now include much more information, and a new :class:`~openmc.Tracks`
+  class allows access to track file information from the Python API and has a
+  :meth:`~openmc.Tracks.write_to_vtk` method for writing a VTK file. Multiple
+  tracks are now written to a single file (one per MPI rank).
+- A new :func:`openmc.wwinp_to_wws` function that converts weight windows from a
+  ``wwinp`` file to a list of :class:`~openmc.WeightWindows` objects.
+- The new :meth:`openmc.EnergyFilter.from_group_structure` method provides a
+  way of creating an energy filter with a group structure identified by name.
+- The :class:`openmc.data.Decay` class now has a
+  :attr:`~openmc.data.Decay.sources` property that provides radioactive decay
+  source distributions.
+- A :class:`openmc.mgxs.ReducedAbsorptionXS` class produces a multigroup cross
+  section representing "reduced" absorption (absorption less neutron production
+  from (n,xn) reactions).
+- Added support in the Python API and HDF5 nuclear data format for new ENDF
+  thermal neutron scattering evaluations with mixed coherent elastic and
+  incoherent elastic.
+- CMake now relies on ``find_package(MPI)`` for a more standard means of
+  identifying an MPI compiler configuration.
+
+---------
+Bug Fixes
+---------
+
+- `Fix bug when a rotation matrix is passed to Halfspace.rotate <https://github.com/openmc-dev/openmc/pull/1974>`_
+- `Fix bug for spherical mesh string repr <https://github.com/openmc-dev/openmc/pull/1983>`_
+- `Fix package_data specification to include pyx files <https://github.com/openmc-dev/openmc/pull/1989>`_
+- `Allow meshes with same ID to appear in multiple files <https://github.com/openmc-dev/openmc/pull/1990>`_
+- `Fix overwritten variable in get_libraries_from_xsdata <https://github.com/openmc-dev/openmc/pull/1994>`_
+- `Write output files to correct directory <https://github.com/openmc-dev/openmc/pull/1998>`_
+- `Allow CMake to properly find third-party packages <https://github.com/openmc-dev/openmc/pull/2006>`_
+- `Fix Region.from_expression when ")(" appears in specification <https://github.com/openmc-dev/openmc/pull/2012>`_
+- `Move lost particle reset from finalize() to reset() <https://github.com/openmc-dev/openmc/pull/2015>`_
+- `Minor typo fixes in test_lattice.py <https://github.com/openmc-dev/openmc/pull/2024>`_
+- `Fix color assignment in Universe.plot <https://github.com/openmc-dev/openmc/pull/2034>`_
+- `Several depletion-related fixes <https://github.com/openmc-dev/openmc/pull/2037>`_
+- `Allow control of C++ standard used by compiler <https://github.com/openmc-dev/openmc/pull/2040/files>`_
+- `Fix IO format documentation for surface source read/write <https://github.com/openmc-dev/openmc/pull/2048>`_
+- `Make sure basis gets set in Plot.from_geometry <https://github.com/openmc-dev/openmc/pull/2050>`_
+- `Improve robustness of torus distance calculation <https://github.com/openmc-dev/openmc/pull/2053>`_
+- `Allow use of redundant fission when adjusting KERMA in from_njoy <https://github.com/openmc-dev/openmc/pull/2055>`_
+- `Disable GNU extensions for CMake target <https://github.com/openmc-dev/openmc/pull/2072>`_
+- `Two from_xml fixes <https://github.com/openmc-dev/openmc/pull/2074>`_
+- `Fix for rare infinite loop when finding cell <https://github.com/openmc-dev/openmc/pull/2075>`_
+- `Allow photon heating to be tallied by nuclide <https://github.com/openmc-dev/openmc/pull/2076>`_
+- `Use UTF-8 encoding when reading dose coefficients <https://github.com/openmc-dev/openmc/pull/2078>`_
+- `Fix a corner case in Region.from_expression <https://github.com/openmc-dev/openmc/pull/2081>`_
+- `Fix bug in spherical and cylindrical meshes <https://github.com/openmc-dev/openmc/pull/2108>`_
+- `Ensure weight window bounds are flattened when writing to XML <https://github.com/openmc-dev/openmc/pull/2113>`_
+- `Fix for std::cout sync bug in output.cpp <https://github.com/openmc-dev/openmc/pull/2122>`_
+- `Allow compiling against fmt v9 <https://github.com/openmc-dev/openmc/pull/2136>`_
+- `Fix TimeFilter for small time intervals <https://github.com/openmc-dev/openmc/pull/2168>`_
+
+------------
+Contributors
+------------
+
+- `David Andrs <https://github.com/andrsd>`_
+- `Hunter Belanger <https://github.com/HunterBelanger>`_
+- `Helen Brooks <https://github.com/helen-brooks>`_
+- `Rémi Delaporte-Mathurin <https://github.com/RemDelaporteMathurin>`_
+- `Joffrey Dorville <https://github.com/JoffreyDorville>`_
+- `Christopher Fichtlscherer <https://github.com/cfichtlscherer>`_
+- `Lewis Gross <https://github.com/lewisgross1296>`_
+- `Andrew Johnson <https://github.com/drewejohnson>`_
+- `Kalin Kiesling <https://github.com/kkiesling>`_
+- `Amanda Lund <https://github.com/amandalund>`_
+- `Richard Morrison <https://github.com/richmorrison>`_
+- `Patrick Myers <https://github.com/myerspat>`_
+- `Adam Nelson <https://github.com/nelsonag>`_
+- `April Novak <https://github.com/aprilnovak>`_
+- `Ethan Peterson <https://github.com/eepeterson>`_
+- `Gavin Ridley <https://github.com/gridley>`_
+- `Paul Romano <https://github.com/paulromano>`_
+- `Jonathan Shimwell <https://github.com/Shimwell>`_
+- `Patrick Shriwise <https://github.com/pshriwise>`_
+- `Amelia Trainer <https://github.com/ameliojo>`_
+- `John Tramm <https://github.com/jtramm>`_
+- `Bob Urberger <https://github.com/burberger>`_
+- `Olek Yardas <https://github.com/yardasol>`_

docs/source/releasenotes/0.13.2.rst

@@ -0,0 +1,99 @@
+====================
+What's New in 0.13.2
+====================
+
+.. currentmodule:: openmc
+
+-------
+Summary
+-------
+
+This release of OpenMC includes several bug fixes, performance improvements for
+complex geometries and depletion simulations, and other general enhancements.
+Notably, a capability has been added to compute the photon spectra from decay of
+unstable nuclides. Alongside that, a new :data:`openmc.config` configuration
+variable has been introduced that allows easier configuration of data sources.
+Additionally, users can now perform cell or material rejection when sampling
+external source distributions.
+
+------------------------------------
+Compatibility Notes and Deprecations
+------------------------------------
+
+- If you are building against libMesh for unstructured mesh tally support,
+  version 1.6 or higher is now required.
+- The ``openmc.stats.Muir`` class has been replaced by a
+  :func:`openmc.stats.muir` function that returns an instance of
+  :class:`openmc.stats.Normal`.
+
+------------
+New Features
+------------
+
+- The :meth:`openmc.Material.get_nuclide_atom_densities` method now takes an
+  optional ``nuclide`` argument.
+- Functions/methods in the :mod:`openmc.deplete` module now accept times in
+  Julian years (``'a'``).
+- The :meth:`openmc.Universe.plot` method now allows a pre-existing axes object
+  to be passed in.
+- Performance optimization for geometries with many complex regions.
+- Performance optimization for depletion by avoiding deepcopies and caching
+  reaction rates.
+- The :class:`openmc.RegularMesh` class now has a
+  :meth:`~openmc.RegularMesh.from_domain` classmethod.
+- The :class:`openmc.CylindricalMesh` class now has a
+  :meth:`~openmc.CylindricalMesh.from_domain` classmethod.
+- Improved method to condense diffusion coefficients from the :mod:`openmc.mgxs`
+  module.
+- A new :data:`openmc.config` configuration variable has been introduced that
+  allows data sources to be specified at runtime or via environment variables.
+- The :class:`openmc.EnergyFunctionFilter` class now supports multiple
+  interpolation schemes, not just linear-linear interpolation.
+- The :class:`openmc.DAGMCUniverse` class now has ``material_names``,
+  ``n_cells``, and ``n_surfaces`` attributes.
+- A new :func:`openmc.data.decay_photon_energy` function has been added that
+  returns the energy spectrum of photons emitted from the decay of an unstable
+  nuclide.
+- The :class:`openmc.Material` class also has a new
+  :attr:`~openmc.Material.decay_photon_energy` attribute that gives the decay
+  photon energy spectrum from the material based on its constituent nuclides.
+- The :class:`openmc.deplete.StepResult` now has a
+  :meth:`~openmc.deplete.StepResult.get_material` method.
+- The :class:`openmc.Source` class now takes a ``domains`` argument that
+  specifies a list of cells, materials, or universes that is used to reject
+  source sites (i.e., if the sampled sites are not within the specified domain,
+  they are rejected).
+
+---------
+Bug Fixes
+---------
+
+- `Delay call to Tally::set_strides <https://github.com/openmc-dev/openmc/pull/2183>`_
+- `Fix reading reference direction from XML for angular distributions <https://github.com/openmc-dev/openmc/pull/2204>`_
+- `Fix erroneous behavior in Material.add_components <https://github.com/openmc-dev/openmc/pull/2205>`_
+- `Fix reading thermal elastic data from ACE <https://github.com/openmc-dev/openmc/pull/2226>`_
+- `Fix reading source file with time attribute <https://github.com/openmc-dev/openmc/pull/2228>`_
+- `Fix conversion of multiple thermal scattering data files from ACE <https://github.com/openmc-dev/openmc/pull/2232>`_
+- `Fix reading values from wwinp file <https://github.com/openmc-dev/openmc/pull/2242>`_
+- `Handle possibility of .ppm file in Universe.plot <https://github.com/openmc-dev/openmc/pull/2251>`_
+- `Update volume calc types to mitigate overflow issues <https://github.com/openmc-dev/openmc/pull/2270>`_
+
+------------
+Contributors
+------------
+
+- `Lewis Gross <https://github.com/lewisgross1296>`_
+- `Andrew Johnson <https://github.com/drewejohnson>`_
+- `Miriam Kreher <https://github.com/mkreher13>`_
+- `James Logan <https://github.com/jlogan03>`_
+- `Jose Ignacio Marquez Damien <https://github.com/marquezj>`_
+- `Josh May <https://github.com/joshmay1>`_
+- `Patrick Myers <https://github.com/myerspat>`_
+- `Adam Nelson <https://github.com/nelsonag>`_
+- `April Novak <https://github.com/aprilnovak>`_
+- `Ethan Peterson <https://github.com/eepeterson>`_
+- `Gavin Ridley <https://github.com/gridley>`_
+- `Paul Romano <https://github.com/paulromano>`_
+- `Patrick Shriwise <https://github.com/pshriwise>`_
+- `Jonathan Shimwell <https://github.com/Shimwell>`_
+- `Olek Yardas <https://github.com/yardasol>`_

docs/source/releasenotes/0.13.3.rst

@@ -0,0 +1,134 @@
+====================
+What's New in 0.13.3
+====================
+
+.. currentmodule:: openmc
+
+-------
+Summary
+-------
+
+This release of OpenMC includes many bug fixes, performance improvements, and
+several notable new features. Some of the highlights include support for MCPL
+source files, NCrystal thermal scattering materials, and a new
+:class:`openmc.stats.MeshSpatial` class that allows a source distribution to be
+specified over a mesh. Additionally, OpenMC now allows you to export your model
+as a single XML file rather than separate XML files for geometry, materials,
+settings, and tallies.
+
+------------------------------------
+Compatibility Notes and Deprecations
+------------------------------------
+
+- Atomic mass data used in :func:`openmc.data.atomic_mass` has been updated to
+  AME 2020, which results in slightly different masses.
+
+------------
+New Features
+------------
+
+- Support was added for `MCPL <https://mctools.github.io/mcpl/>`_ files to be
+  used as external sources. Additionally, source points and surfaces sources can
+  be written as MCPL files instead of HDF5 files. (`#2116
+  <https://github.com/openmc-dev/openmc/pull/2116>`_)
+- Support was added for `NCrystal <https://github.com/mctools/ncrystal>`_
+  thermal scattering materials. (`#2222
+  <https://github.com/openmc-dev/openmc/pull/2222>`_)
+- The :class:`~openmc.CylindricalMesh` and :class:`~openmc.SphericalMesh`
+  classes now have an ``origin`` attribute that changes the center of the mesh.
+  (`#2256 <https://github.com/openmc-dev/openmc/pull/2256>`_)
+- A new :class:`openmc.model.Polygon` class allows defining generalized 2D
+  polygons. (`#2266 <https://github.com/openmc-dev/openmc/pull/2266>`_)
+- A new :func:`openmc.data.decay_energy` function and
+  :meth:`openmc.Material.get_decay_heat` method enable determination of decay
+  heat from a single nuclide or material. (`#2287
+  <https://github.com/openmc-dev/openmc/pull/2287>`_)
+- Full models can now be written as a single XML file rather than separate
+  geometry, materials, settings, and tallies XML files. (`#2291
+  <https://github.com/openmc-dev/openmc/pull/2291>`_)
+- Discrete distributions are now sampled using alias sampling, which is O(1) in
+  time. (`#2329 <https://github.com/openmc-dev/openmc/pull/2329>`_)
+- The new :class:`openmc.stats.MeshSpatial` allows a spatial source distribution
+  to be specified with source strengths for each mesh element. (`#2334
+  <https://github.com/openmc-dev/openmc/pull/2334>`_)
+- The new :meth:`openmc.Geometry.get_surfaces_by_name` method returns a list of
+  matching surfaces in a geometry. (`#2347
+  <https://github.com/openmc-dev/openmc/pull/2347>`_)
+- A new :attr:`openmc.Settings.create_delayed_neutrons` attribute controls
+  whether delayed neutrons are created during a simulation. (`#2348
+  <https://github.com/openmc-dev/openmc/pull/2348>`_)
+- The :meth:`openmc.deplete.Results.export_to_materials` method now takes a
+  ``path`` argument. (`#2364 <https://github.com/openmc-dev/openmc/pull/2364>`_)
+- A new :meth:`openmc.EnergyFilter.get_tabular` method allows one to create a
+  tabular distribution based on tally results using an energy filter. (`#2371
+  <https://github.com/openmc-dev/openmc/pull/2371>`_)
+- Several methods in the :class:`openmc.Material` class that require a volume to
+  be set (e.g., :meth:`~openmc.Material.get_mass`) now accept a ``volume``
+  argument. (`#2412 <https://github.com/openmc-dev/openmc/pull/2412>`_)
+
+---------
+Bug Fixes
+---------
+
+- Fix for finding redundant surfaces (`#2263 <https://github.com/openmc-dev/openmc/pull/2263>`_)
+- Adds tolerance for temperatures slightly out of bounds (`#2265 <https://github.com/openmc-dev/openmc/pull/2265>`_)
+- Fix getter/setter for weight window bounds (`#2275 <https://github.com/openmc-dev/openmc/pull/2275>`_)
+- Make sure Chain.reduce preserves decay source (`#2283 <https://github.com/openmc-dev/openmc/pull/2283>`_)
+- Fix array shape for weight window bounds (`#2284 <https://github.com/openmc-dev/openmc/pull/2284>`_)
+- Fix for non-zero CDF start points in TSL data (`#2290 <https://github.com/openmc-dev/openmc/pull/2290>`_)
+- Fix a case where inelastic scattering yield is zero (`#2295 <https://github.com/openmc-dev/openmc/pull/2295>`_)
+- Prevent Compton profile out-of-bounds memory access (`#2297 <https://github.com/openmc-dev/openmc/pull/2297>`_)
+- Produce light particles from decay (`#2301 <https://github.com/openmc-dev/openmc/pull/2301>`_)
+- Fix zero runtime attributes in depletion statepoints (`#2302 <https://github.com/openmc-dev/openmc/pull/2302>`_)
+- Fix bug in openmc.Universe.get_nuclide_densities (`#2310 <https://github.com/openmc-dev/openmc/pull/2310>`_)
+- Only show print output from depletion on rank 0 (`#2311 <https://github.com/openmc-dev/openmc/pull/2311>`_)
+- Fix photon transport with no atomic relaxation data (`#2312 <https://github.com/openmc-dev/openmc/pull/2312>`_)
+- Fix for precedence in region expressions (`#2318 <https://github.com/openmc-dev/openmc/pull/2318>`_)
+- Allow source particles with energy below cutoff (`#2319 <https://github.com/openmc-dev/openmc/pull/2319>`_)
+- Fix IncidentNeutron.from_njoy for high temperatures (`#2320 <https://github.com/openmc-dev/openmc/pull/2320>`_)
+- Add capability to unset cell temperatures (`#2323 <https://github.com/openmc-dev/openmc/pull/2323>`_)
+- Fix in plot_xs when S(a,b) tables are present (`#2335 <https://github.com/openmc-dev/openmc/pull/2335>`_)
+- Various fixes for tally triggers (`#2344 <https://github.com/openmc-dev/openmc/pull/2344>`_)
+- Raise error when mesh is flat (`#2363 <https://github.com/openmc-dev/openmc/pull/2363>`_)
+- Don't call normalize inside Tabular.mean (`#2375 <https://github.com/openmc-dev/openmc/pull/2375>`_)
+- Avoid out-of-bounds access in inelastic scatter sampling (`#2378 <https://github.com/openmc-dev/openmc/pull/2378>`_)
+- Use correct direction for anisotropic fission (`#2381 <https://github.com/openmc-dev/openmc/pull/2381>`_)
+- Fix several thermal scattering nuclide assignments (`#2382 <https://github.com/openmc-dev/openmc/pull/2382>`_)
+- Fix _materials_by_id attribute in Model (`#2385 <https://github.com/openmc-dev/openmc/pull/2385>`_)
+- Updates to batch checks for simulation restarts (`#2390 <https://github.com/openmc-dev/openmc/pull/2390>`_)
+- write_data_to_vtk volume normalization correction (`#2397 <https://github.com/openmc-dev/openmc/pull/2397>`_)
+- Enable generation of JEFF 3.3 depletion chain (`#2410 <https://github.com/openmc-dev/openmc/pull/2410>`_)
+- Fix spherical to Cartesian coordinate conversion (`#2417 <https://github.com/openmc-dev/openmc/pull/2417>`_)
+- Handle zero photon cross sections in IncidentPhoton.from_ace (`#2433 <https://github.com/openmc-dev/openmc/pull/2433>`_)
+- Fix hybrid depletion when nuclides are not present (`#2436 <https://github.com/openmc-dev/openmc/pull/2436>`_)
+- Fix bug in cylindrical and spherical meshes (`#2439 <https://github.com/openmc-dev/openmc/pull/2439>`_)
+- Improvements to mesh radial boundary coincidence (`#2443 <https://github.com/openmc-dev/openmc/pull/2443>`_)
+
+------------
+Contributors
+------------
+
+- `Hunter Belanger <https://github.com/HunterBelanger>`_
+- `Rémi Delaporte-Mathurin <https://github.com/RemDelaporteMathurin>`_
+- `Christopher Fichtlscherer <https://github.com/cfichtlscherer>`_
+- `Valerio Giusti <https://github.com/valeriogiusti>`_
+- `Chris Keckler <https://github.com/keckler>`_
+- `Kalin Kiesling <https://github.com/kkiesling>`_
+- `Thomas Kittelmann <https://github.com/tkittel>`_
+- `Erik Knudsen <https://github.com/ebknudsen>`_
+- `Colin Larmier <https://github.com/colinelarmier>`_
+- `Amanda Lund <https://github.com/amandalund>`_
+- `Jose Ignacio Marquez Damien <https://github.com/marquezj>`_
+- `Josh May <https://github.com/joshmay1>`_
+- `Patrick Myers <https://github.com/myerspat>`_
+- `Baptiste Mouginot <https://github.com/bam241>`_
+- `April Novak <https://github.com/aprilnovak>`_
+- `Matthew Nyberg <https://github.com/NybergWISC>`_
+- `Ethan Peterson <https://github.com/eepeterson>`_
+- `Gavin Ridley <https://github.com/gridley>`_
+- `Paul Romano <https://github.com/paulromano>`_
+- `Patrick Shriwise <https://github.com/pshriwise>`_
+- `Jonathan Shimwell <https://github.com/Shimwell>`_
+- `Paul Wilson <https://github.com/gonuke>`_
+- `Olek Yardas <https://github.com/yardasol>`_
+- `Jiankai Yu <https://github.com/rockfool>`_

docs/source/releasenotes/0.14.0.rst

@@ -0,0 +1,284 @@
+====================
+What's New in 0.14.0
+====================
+
+.. currentmodule:: openmc
+
+-------
+Summary
+-------
+
+This release of OpenMC includes many bug fixes, performance improvements, and
+several notable new features. Some of the highlights include projection plots,
+pulse height tallies for photons, weight window generation, and an ability to
+specify continuous removal or feed of nuclides/elements during depletion.
+Additionally, one of the longstanding annoyances of depletion calculations,
+namely the need to include initial "dilute" nuclides, has been eliminated. There
+are also a wide array of general improvements in the Python API.
+
+------------------------------------
+Compatibility Notes and Deprecations
+------------------------------------
+
+- The :class:`openmc.deplete.MicroXS` has been completely redesigned and
+  improved. See further comments below under "New Features". (`#2572
+  <https://github.com/openmc-dev/openmc/pull/2572>`_, `#2579
+  <https://github.com/openmc-dev/openmc/pull/2579>`_, `#2595
+  <https://github.com/openmc-dev/openmc/pull/2595>`_, `#2700
+  <https://github.com/openmc-dev/openmc/pull/2700>`_)
+- The ``rectangular_prism`` function has been replaced by the
+  :class:`openmc.model.RectangularPrism` class and the ``hexagonal_prism``
+  function has been replaced by the :class:`openmc.model.HexagonalPrism` class.
+  Note that whereas the ``rectangular_prism`` and ``hexagonal_prism`` functions
+  returned a region representing the interior of the prism, the new
+  :class:`~openmc.model.RectangularPrism` and
+  :class:`~openmc.model.HexagonalPrism` classes return composite surfaces, so
+  you need to use the unary ``-`` or ``+`` operators to obtain a region that can
+  be assigned to a cell. (`#2739
+  <https://github.com/openmc-dev/openmc/pull/2739>`_)
+- The ``Source`` class has been refactored and split up into three separate
+  classes: :class:`~openmc.IndependentSource`, :class:`~openmc.FileSource`, and
+  :class:`~openmc.CompiledSource`. (`#2524
+  <https://github.com/openmc-dev/openmc/pull/2524>`_)
+- The ``vertices`` and ``centroids`` attributes on mesh classes now always
+  return Cartesian coordinates and the shape of the returned arrays has changed
+  to allow `ijk` indexing using a tuple (i.e., `xyz = vertices[i, j, k]`).
+  (`#2711 <https://github.com/openmc-dev/openmc/pull/2711>`_)
+- The :attr:`openmc.Material.decay_photon_energy` attribute has been replaced by
+  the :meth:`openmc.Material.get_decay_photon_energy` method. (`#2715
+  <https://github.com/openmc-dev/openmc/pull/2715>`_)
+
+------------
+New Features
+------------
+
+- A new :class:`openmc.WireframeRayTracePlot` class enables the generation of orthographic or
+  perspective projection plots. (`#1926
+  <https://github.com/openmc-dev/openmc/pull/1926>`_)
+- The :class:`openmc.model.RightCircularCylinder` class now supports optional
+  filleted edges. (`#2309 <https://github.com/openmc-dev/openmc/pull/2309>`_)
+- Continuous removal or feed of nuclides/elements between materials can now be
+  modeled during depletion via the
+  :meth:`openmc.deplete.abc.Integrator.add_transfer_rate` method. (`#2358
+  <https://github.com/openmc-dev/openmc/pull/2358>`_, `#2564
+  <https://github.com/openmc-dev/openmc/pull/2564>`_, `#2626
+  <https://github.com/openmc-dev/openmc/pull/2626>`_)
+- The MAGIC method for global weight window generation has been implemented as
+  part of the C++ API. (`#2359
+  <https://github.com/openmc-dev/openmc/pull/2359>`_)
+- A new capability for pulse height tallies (currently limited to photons) has
+  been added and can be used via the "pulse-height" tally score. (`#2452
+  <https://github.com/openmc-dev/openmc/pull/2452>`_)
+- A :class:`openmc.model.CruciformPrism` class has been added that provides a
+  generalized cruciform prism composite surface. (`#2457
+  <https://github.com/openmc-dev/openmc/pull/2457>`_)
+- Type hints have been added in various places throughout the Python API.
+  (`#2462 <https://github.com/openmc-dev/openmc/pull/2462>`_, `#2467
+  <https://github.com/openmc-dev/openmc/pull/2467>`_, `#2468
+  <https://github.com/openmc-dev/openmc/pull/2468>`_, `#2470
+  <https://github.com/openmc-dev/openmc/pull/2470>`_, `#2471
+  <https://github.com/openmc-dev/openmc/pull/2471>`_, `#2601
+  <https://github.com/openmc-dev/openmc/pull/2601>`_)
+- Voxel plots can now be generated through the :meth:`openmc.Plot.to_vtk`
+  method. (`#2464 <https://github.com/openmc-dev/openmc/pull/2464>`_)
+- The :class:`openmc.mgxs.EnergyGroups` class now allows you to alternatively
+  pass a string of the group structure name (e.g., "CCFE-709") instead of the
+  energy group boundaries. (`#2466
+  <https://github.com/openmc-dev/openmc/pull/2466>`_)
+- Several enhancements have been made to the :meth:`openmc.Universe.plot` method
+  (addition of axis labels with units, ability to show legend and/or outlines, automatic
+  determination of origin/width, ability to pass total number of pixels).
+  (`#2472 <https://github.com/openmc-dev/openmc/pull/2472>`_, `#2482
+  <https://github.com/openmc-dev/openmc/pull/2482>`_, `#2483
+  <https://github.com/openmc-dev/openmc/pull/2483>`_, `#2492
+  <https://github.com/openmc-dev/openmc/pull/2492>`_, `#2513
+  <https://github.com/openmc-dev/openmc/pull/2513>`_, `#2575
+  <https://github.com/openmc-dev/openmc/pull/2575>`_)
+- Functionality in the Python dealing with bounding boxes now relies on a new
+  :class:`openmc.BoundingBox` class. (`#2475
+  <https://github.com/openmc-dev/openmc/pull/2475>`_)
+- Users now have more flexibility in specifying nuclides and reactions in the
+  :func:`openmc.plot_xs` function. (`#2478
+  <https://github.com/openmc-dev/openmc/pull/2478>`_)
+- The import time of the :mod:`openmc` Python module has been improved by
+  deferring the import of matplotlib. (`#2488
+  <https://github.com/openmc-dev/openmc/pull/2488>`_)
+- Mesh clases in the Python API now support a ``bounding_box`` property. (`#2507
+  <https://github.com/openmc-dev/openmc/pull/2507>`_, `#2620
+  <https://github.com/openmc-dev/openmc/pull/2620>`_, `#2621
+  <https://github.com/openmc-dev/openmc/pull/2621>`_)
+- The ``Source`` class has been refactored and split up into three separate
+  classes: :class:`~openmc.IndependentSource`, :class:`~openmc.FileSource`, and
+  :class:`~openmc.CompiledSource`. (`#2524
+  <https://github.com/openmc-dev/openmc/pull/2524>`_)
+- Support was added for curvilinear elements when exporting cylindrical and
+  spherical meshes to VTK. (`#2533
+  <https://github.com/openmc-dev/openmc/pull/2533>`_)
+- The :class:`openmc.Tally` class now has a
+  :attr:`~openmc.Tally.multiply_density` attribute that indicates whether
+  reaction rate tallies should include the number density of the nuclide of
+  interest. (`#2539 <https://github.com/openmc-dev/openmc/pull/2539>`_)
+- The :func:`~openmc.wwinp_to_wws` function now supports ``wwinp`` files with
+  cylindrical or spherical meshes. (`#2556
+  <https://github.com/openmc-dev/openmc/pull/2556>`_)
+- Depletion no longer relies on adding initial "dilute" nuclides to each
+  depletable material in order to compute reaction rates. (`#2559
+  <https://github.com/openmc-dev/openmc/pull/2559>`_, `#2568
+  <https://github.com/openmc-dev/openmc/pull/2568>`_)
+- The :class:`openmc.deplete.Results` class now has
+  :meth:`~openmc.deplete.Results.get_mass` (`#2565
+  <https://github.com/openmc-dev/openmc/pull/2565>`_),
+  :meth:`~openmc.deplete.Results.get_activity` (`#2617
+  <https://github.com/openmc-dev/openmc/pull/2617>`_), and
+  :meth:`~openmc.deplete.Results.get_decay_heat` (`#2625
+  <https://github.com/openmc-dev/openmc/pull/2625>`_) methods.
+- The :meth:`openmc.deplete.StepResult.save` method now supports a ``path``
+  argument. (`#2567 <https://github.com/openmc-dev/openmc/pull/2567>`_)
+- The :class:`openmc.deplete.MicroXS` has been completely redesigned and
+  improved. First, it no longer relies on the :mod:`openmc.mgxs` module, no
+  longer subclasses :class:`pandas.DataFrame`, and doesn't require adding
+  initial "dilute" nuclides into material compositions. It now enables users to
+  specify an energy group structure to collect multigroup cross sections,
+  specify nuclides/reactions, and works with mesh domains in addition to the
+  existing domains. A new :func:`openmc.deplete.get_microxs_and_flux` function
+  was added that improves the workflow for calculating microscopic cross
+  sections along with fluxes. Altogether, these changes make it straightforward
+  to switch between coupled and independent operators for depletion/activation
+  calculations. (`#2572 <https://github.com/openmc-dev/openmc/pull/2572>`_,
+  `#2579 <https://github.com/openmc-dev/openmc/pull/2579>`_, `#2595
+  <https://github.com/openmc-dev/openmc/pull/2595>`_, `#2700
+  <https://github.com/openmc-dev/openmc/pull/2700>`_)
+- The :class:`openmc.Geometry` class now has ``merge_surfaces`` and
+  ``surface_precision`` arguments. (`#2602
+  <https://github.com/openmc-dev/openmc/pull/2602>`_)
+- Several predefined energy group structures have been added ("MPACT-51",
+  "MPACT-60", "MPACT-69", "SCALE-252"). (`#2614
+  <https://github.com/openmc-dev/openmc/pull/2614>`_)
+- When running a depletion calculation, you are now allowed to include nuclides
+  in the initial material compositions that do not have neutron cross sections
+  (decay-only nuclides). (`#2616
+  <https://github.com/openmc-dev/openmc/pull/2616>`_)
+- The :class:`~openmc.CylindricalMesh` and :class:`~openmc.SphericalMesh`
+  classes can now be fully formed using the constructor. (`#2619
+  <https://github.com/openmc-dev/openmc/pull/2619>`_)
+- A time cutoff can now be specified in the :attr:`openmc.Settings.cutoff`
+  attribute. (`#2631 <https://github.com/openmc-dev/openmc/pull/2631>`_)
+- The :meth:`openmc.Material.add_element` method now supports a
+  ``cross_sections`` argument that allows a cross section data source to be
+  specified. (`#2633 <https://github.com/openmc-dev/openmc/pull/2633>`_)
+- The :class:`~openmc.Cell` class now has a :meth:`~openmc.Cell.plot` method.
+  (`#2648 <https://github.com/openmc-dev/openmc/pull/2648>`_)
+- The :class:`~openmc.Geometry` class now has a :meth:`~openmc.Geometry.plot`
+  method. (`#2661 <https://github.com/openmc-dev/openmc/pull/2661>`_)
+- When weight window checks are performed can now be explicitly specified with
+  the :attr:`openmc.Settings.weight_window_checkpoints` attribute. (`#2670
+  <https://github.com/openmc-dev/openmc/pull/2670>`_)
+- The :class:`~openmc.Settings` class now has a
+  :attr:`~openmc.Settings.max_write_lost_particles` attribute that can limit the
+  number of lost particle files written. (`#2688
+  <https://github.com/openmc-dev/openmc/pull/2688>`_)
+- The :class:`~openmc.deplete.CoupledOperator` class now has a
+  ``diff_volume_method`` argument that specifies how the volume of new materials
+  should be determined. (`#2691
+  <https://github.com/openmc-dev/openmc/pull/2691>`_)
+- The :meth:`openmc.DAGMCUniverse.bounding_region` method now has a
+  ``padding_distance`` argument. (`#2701
+  <https://github.com/openmc-dev/openmc/pull/2701>`_)
+- A new :meth:`openmc.Material.get_decay_photon_energy` method replaces the
+  :attr:`decay_photon_energy` attribute and includes an ability to eliminate
+  low-importance points. This is facilitated by a new
+  :meth:`openmc.stats.Discrete.clip` method. (`#2715
+  <https://github.com/openmc-dev/openmc/pull/2715>`_)
+- The :meth:`openmc.model.Model.differentiate_depletable_mats` method allows
+  depletable materials to be differentiated independent of the depletion
+  calculation itself. (`#2718
+  <https://github.com/openmc-dev/openmc/pull/2718>`_)
+- Albedos can now be specified on surface boundary conditions. (`#2724
+  <https://github.com/openmc-dev/openmc/pull/2724>`_)
+
+---------
+Bug Fixes
+---------
+
+- Enable use of NCrystal materials in plot_xs (`#2435 <https://github.com/openmc-dev/openmc/pull/2435>`_)
+- Avoid segfault from extern "C" std::string (`#2455 <https://github.com/openmc-dev/openmc/pull/2455>`_)
+- Fix several issues with the Model class (`#2465 <https://github.com/openmc-dev/openmc/pull/2465>`_)
+- Provide alternative batch estimation message (`#2479 <https://github.com/openmc-dev/openmc/pull/2479>`_)
+- Correct index check for remove_tally (`#2494 <https://github.com/openmc-dev/openmc/pull/2494>`_)
+- Support for NCrystal material in from_xml_element (`#2496 <https://github.com/openmc-dev/openmc/pull/2496>`_)
+- Fix compilation with gcc 5 (`#2498 <https://github.com/openmc-dev/openmc/pull/2498>`_)
+- Fixed in the Tally::add_filter method (`#2501 <https://github.com/openmc-dev/openmc/pull/2501>`_)
+- Fix meaning of "masking" for plots (`#2510 <https://github.com/openmc-dev/openmc/pull/2510>`_)
+- Fix description of statepoint.batches in Settings class (`#2514 <https://github.com/openmc-dev/openmc/pull/2514>`_)
+- Reorder list initialization of Plot constructor (`#2519 <https://github.com/openmc-dev/openmc/pull/2519>`_)
+- Added mkdir to cwd argument in Model.run (`#2523 <https://github.com/openmc-dev/openmc/pull/2523>`_)
+- Fix export of spherical coordinates in SphericalMesh (`#2538 <https://github.com/openmc-dev/openmc/pull/2538>`_)
+- Add virtual destructor on PlottableInterface (`#2541 <https://github.com/openmc-dev/openmc/pull/2541>`_)
+- Ensure parent directory is created during depletion (`#2543 <https://github.com/openmc-dev/openmc/pull/2543>`_)
+- Fix potential out-of-bounds access in TimeFilter (`#2532 <https://github.com/openmc-dev/openmc/pull/2532>`_)
+- Remove use of sscanf for reading surface coefficients (`#2574 <https://github.com/openmc-dev/openmc/pull/2574>`_)
+- Fix torus intersection bug (`#2589 <https://github.com/openmc-dev/openmc/pull/2589>`_)
+- Multigroup per-thread cache fixes (`#2591 <https://github.com/openmc-dev/openmc/pull/2591>`_)
+- Bank surface source particles in all active cycles (`#2592 <https://github.com/openmc-dev/openmc/pull/2592>`_)
+- Fix for muir standard deviation (`#2598 <https://github.com/openmc-dev/openmc/pull/2598>`_)
+- Check for zero fission cross section (`#2600 <https://github.com/openmc-dev/openmc/pull/2600>`_)
+- XML read fixes in Plot classes (`#2623 <https://github.com/openmc-dev/openmc/pull/2623>`_)
+- Added infinity check in VolumeCalculation (`#2634 <https://github.com/openmc-dev/openmc/pull/2634>`_)
+- Fix sampling issue in Mixture distributions (`#2658 <https://github.com/openmc-dev/openmc/pull/2658>`_)
+- Prevent segfault in distance to boundary calculation (`#2659 <https://github.com/openmc-dev/openmc/pull/2659>`_)
+- Several CylindricalMesh fixes (`#2676
+  <https://github.com/openmc-dev/openmc/pull/2676>`_, `#2680
+  <https://github.com/openmc-dev/openmc/pull/2680>`_, `#2684
+  <https://github.com/openmc-dev/openmc/pull/2684>`_, `#2710
+  <https://github.com/openmc-dev/openmc/pull/2710>`_)
+- Add type checks on Intersection, Union, Complement (`#2685 <https://github.com/openmc-dev/openmc/pull/2685>`_)
+- Fixed typo in CF4Integrator docstring (`#2704 <https://github.com/openmc-dev/openmc/pull/2704>`_)
+- Ensure property setters are used in CylindricalMesh and SphericalMesh (`#2709 <https://github.com/openmc-dev/openmc/pull/2709>`_)
+- Fix sample_external_source bug (`#2713 <https://github.com/openmc-dev/openmc/pull/2713>`_)
+- Fix localization issue affecting openmc-plotter (`#2723 <https://github.com/openmc-dev/openmc/pull/2723>`_)
+- Correct openmc.lib wrapper for evaluate_legendre (`#2729 <https://github.com/openmc-dev/openmc/pull/2729>`_)
+- Bug fix in Region.from_expression during tokenization (`#2733 <https://github.com/openmc-dev/openmc/pull/2733>`_)
+- Fix bug in temperature interpolation (`#2734 <https://github.com/openmc-dev/openmc/pull/2734>`_)
+- Check for invalid domain IDs in volume calculations (`#2742 <https://github.com/openmc-dev/openmc/pull/2742>`_)
+- Skip boundary condition check for volume calculations (`#2743 <https://github.com/openmc-dev/openmc/pull/2743>`_)
+- Fix loop over coordinates for source domain rejection (`#2751 <https://github.com/openmc-dev/openmc/pull/2751>`_)
+
+------------
+Contributors
+------------
+
+- `April Novak <https://github.com/aprilnovak>`_
+- `Baptiste Mouginot <https://github.com/bam241>`_
+- `Ben Collins <https://github.com/bscollin>`_
+- `Chritopher Billingham <https://github.com/cadarache2014>`_
+- `Christopher Fichtlscherer <https://github.com/cfichtlscherer>`_
+- `Christina Cai <https://github.com/christinacai123>`_
+- `Lorenzo Chierici <https://github.com/church89>`_
+- `Huw Rhys Jones <https://github.com/dubway420>`_
+- `Emilio Castro <https://github.com/ecasglez>`_
+- `Erik Knudsen <https://github.com/ebknudsen>`_
+- `Ethan Peterson <https://github.com/eepeterson>`_
+- `Egor Afanasenko <https://github.com/egor1abs>`_
+- `Paul Wilson <https://github.com/gonuke>`_
+- `Gavin Ridley <https://github.com/gridley>`_
+- `Hunter Belanger <https://github.com/HunterBelanger>`_
+- `Jack Fletcher <https://github.com/j-fletcher>`_
+- `John Vincent Cauilan <https://github.com/johvincau>`_
+- `Josh May <https://github.com/joshmay1>`_
+- `John Tramm <https://github.com/jtramm>`_
+- `Kevin McLaughlin <https://github.com/kevinm387>`_
+- `Yue Jin <https://github.com/kingyue737>`_
+- `Lewis Gross <https://github.com/lewisgross1296>`_
+- `Luke Labrie-Cleary <https://github.com/LukeLabie>`_
+- `Patrick Myers <https://github.com/myerspat>`_
+- `Nicola Rizzi <https://github.com/nicriz>`_
+- `Yuvraj Jain <https://github.com/nutcasev15>`_
+- `Paul Romano <https://github.com/paulromano>`_
+- `Patrick Shriwise <https://github.com/pshriwise>`_
+- `Rosie Barker <https://github.com/rlbarker>`_
+- `Jonathan Shimwell <https://github.com/Shimwell>`_
+- `John Tchakerian <https://github.com/stchaker>`_
+- `Travis Labossiere-Hickman <https://github.com/tjlaboss>`_
+- `Xinyan Wang <https://github.com/XinyanBradley>`_
+- `Olek Yardas <https://github.com/yardasol>`_
+- `Zoe Prieto <https://github.com/zoeprieto>`_