Merge remote-tracking branch 'upstream/develop' into develop

Author: Jilang Miao@roarcollab

.github/workflows/ci.yml

@@ -75,6 +75,7 @@ jobs:
       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.
@@ -171,11 +172,37 @@ jobs:
         uses: mxschmitt/action-tmate@v3
         timeout-minutes: 10
 
-      - name: after_success
+      - name: Generate C++ coverage (gcovr)
         shell: bash
         run: |
-          cpp-coveralls -i src -i include -e src/external --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
@@ -184,5 +211,5 @@ jobs:
       - name: Coveralls Finished
         uses: coverallsapp/github-action@v2
         with:
-          github-token: ${{ secrets.github_token }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
           parallel-finished: true

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

@@ -36,8 +36,8 @@ option(OPENMC_ENABLE_COVERAGE "Compile with coverage analysis flags"
 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_MCPL        "Enable MCPL"                                          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}")
@@ -46,8 +46,8 @@ 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_MCPL ${OPENMC_USE_MCPL}")
 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")
@@ -189,22 +189,6 @@ if(${HDF5_VERSION} VERSION_GREATER_EQUAL 1.12.0)
   list(APPEND cxxflags -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1)
 endif()
 
-#===============================================================================
-# MCPL
-#===============================================================================
-
-if (OPENMC_USE_MCPL)
-  if (NOT DEFINED MCPL_DIR)
-    execute_process(
-      COMMAND mcpl-config --show cmakedir
-      OUTPUT_VARIABLE MCPL_DIR
-      OUTPUT_STRIP_TRAILING_WHITESPACE
-    )
-  endif()
-  find_package(MCPL REQUIRED)
-  message(STATUS "Found MCPL: ${MCPL_DIR} (found version \"${MCPL_VERSION}\")")
-endif()
-
 #===============================================================================
 # Set compile/link flags based on which compiler is being used
 #===============================================================================
@@ -256,41 +240,61 @@ endif()
 # pugixml library
 #===============================================================================
 
-find_package_write_status(pugixml)
-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
 #===============================================================================
 
-find_package_write_status(fmt)
-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
 #===============================================================================
 
-find_package_write_status(xtensor)
-if (NOT xtensor_FOUND)
+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()
 
 #===============================================================================
 # Catch2 library
 #===============================================================================
 
 if(OPENMC_BUILD_TESTS)
-  find_package_write_status(Catch2)
-  if (NOT Catch2_FOUND)
+  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()
 
@@ -334,6 +338,7 @@ list(APPEND libopenmc_SOURCES
   src/cell.cpp
   src/chain.cpp
   src/cmfd_solver.cpp
+  src/collision_track.cpp
   src/cross_sections.cpp
   src/dagmc.cpp
   src/distribution.cpp
@@ -414,6 +419,7 @@ list(APPEND libopenmc_SOURCES
   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
@@ -498,11 +504,11 @@ else()
 endif()
 
 if(OPENMC_USE_DAGMC)
-  target_compile_definitions(libopenmc PRIVATE 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)
+    target_compile_definitions(libopenmc PRIVATE OPENMC_UWUW_ENABLED)
     target_link_libraries(libopenmc uwuw-shared)
   endif()
 elseif(OPENMC_USE_UWUW)
@@ -511,7 +517,7 @@ elseif(OPENMC_USE_UWUW)
 endif()
 
 if(OPENMC_USE_LIBMESH)
-  target_compile_definitions(libopenmc PRIVATE LIBMESH)
+  target_compile_definitions(libopenmc PRIVATE OPENMC_LIBMESH_ENABLED)
   target_link_libraries(libopenmc PkgConfig::LIBMESH)
 endif()
 
@@ -534,11 +540,6 @@ if (OPENMC_BUILD_TESTS)
   add_subdirectory(tests/cpp_unit_tests)
 endif()
 
-if (OPENMC_USE_MCPL)
-  target_compile_definitions(libopenmc PUBLIC OPENMC_MCPL)
-  target_link_libraries(libopenmc MCPL::mcpl)
-endif()
-
 #===============================================================================
 # Log build info that this executable can report later
 #===============================================================================

Dockerfile

@@ -24,7 +24,7 @@ ARG compile_cores=1
 ARG build_dagmc=off
 ARG build_libmesh=off
 
-FROM debian:bookworm-slim AS dependencies
+FROM ubuntu:24.04 AS dependencies
 
 ARG compile_cores
 ARG build_dagmc
@@ -96,6 +96,7 @@ 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 \
+        && 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} \

cmake/OpenMCConfig.cmake.in

@@ -1,9 +1,12 @@
 get_filename_component(OpenMC_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" DIRECTORY)
 
-find_package(fmt REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../fmt)
-find_package(pugixml REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../pugixml)
-find_package(xtl REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtl)
-find_package(xtensor REQUIRED HINTS ${OpenMC_CMAKE_DIR}/../xtensor)
+# Compute the install prefix from this file's location
+get_filename_component(_OPENMC_PREFIX "${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()
@@ -29,10 +32,6 @@ if(@OPENMC_USE_OPENMP@)
   find_package(OpenMP REQUIRED)
 endif()
 
-if(@OPENMC_USE_MCPL@)
-  find_package(MCPL REQUIRED HINTS @MCPL_DIR@)
-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/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

docs/source/conf.py

@@ -121,9 +121,7 @@
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages
-import sphinx_rtd_theme
 html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 html_baseurl = "https://docs.openmc.org/en/stable/"
 
 html_logo = '_images/openmc_logo.png'

docs/source/io_formats/collision_track.rst

@@ -0,0 +1,46 @@
+.. _io_collision_track:
+
+===========================
+Collision Track File Format
+===========================
+
+When collision tracking is enabled with ``mcpl=false`` (the default), OpenMC
+writes binary data to an HDF5 file named ``collision_track.h5``. The same data
+may also be written after each batch when multiple files are requested
+(``collision_track.N.h5``) or when the run is performed in parallel. The file
+contains the information needed to reconstruct each recorded collision.
+
+The current revision of the collision track file format is 1.0.
+
+**/**
+
+:Attributes:
+            - **filetype** (*char[]*) -- String indicating the type of file.
+              For collision-track files the value is ``"collision_track"``.
+
+:Datasets:
+
+          - **collision_track_bank** (Compound type) -- Collision information
+            for each stored event. Each entry in the dataset corresponds to one
+            collision and contains the following fields:
+
+              - ``r`` (*double[3]*) -- Position of the collision in [cm].
+              - ``u`` (*double[3]*) -- Direction unit vector immediately after the collision.
+              - ``E`` (*double*) -- Incident particle energy before the collision in [eV].
+              - ``dE`` (*double*) -- Energy loss over the collision (:math:`E_\text{before} - E_\text{after}`) in [eV].
+              - ``time`` (*double*) -- Time of the collision in [s].
+              - ``wgt`` (*double*) -- Particle weight at the collision.
+              - ``event_mt`` (*int*) -- ENDF MT number identifying the reaction.
+              - ``delayed_group`` (*int*) -- Delayed neutron group index (non-zero for delayed events).
+              - ``cell_id`` (*int*) -- ID of the cell in which the collision occurred.
+              - ``nuclide_id`` (*int*) -- ZA identifier of the nuclide (ZZZAAAM format).
+              - ``material_id`` (*int*) -- ID of the material containing the collision site.
+              - ``universe_id`` (*int*) -- ID of the universe containing the collision site.
+              - ``n_collision`` (*int*) -- Collision counter for the particle history.
+              - ``particle`` (*int*) -- Particle type (0=neutron, 1=photon, 2=electron, 3=positron).
+              - ``parent_id`` (*int64*) -- Unique ID of the parent particle.
+              - ``progeny_id`` (*int64*) -- Progeny ID of the particle.
+
+In an MPI run, OpenMC writes the combined dataset by gathering collision-track
+entries from all ranks before flushing them to disk, so the final file appears
+as though it were produced serially.