Merge branch 'transient' of https://github.com/ilhamv/openmc into tra…

…nsient

.github/workflows/ci.yml

@@ -96,7 +96,6 @@ jobs:
 
       - 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
 
@@ -131,6 +130,11 @@ jobs:
           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:

CMakeLists.txt

@@ -416,6 +416,7 @@ list(APPEND libopenmc_SOURCES
   src/tallies/filter_meshborn.cpp
   src/tallies/filter_meshsurface.cpp
   src/tallies/filter_mu.cpp
+  src/tallies/filter_musurface.cpp
   src/tallies/filter_particle.cpp
   src/tallies/filter_polar.cpp
   src/tallies/filter_sph_harm.cpp
@@ -509,6 +510,14 @@ endif()
 if(OPENMC_USE_DAGMC)
   target_compile_definitions(libopenmc PRIVATE DAGMC)
   target_link_libraries(libopenmc dagmc-shared)
+
+  if(OPENMC_USE_UWUW)
+    target_compile_definitions(libopenmc PRIVATE OPENMC_UWUW)
+    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)
@@ -545,11 +554,6 @@ if(OPENMC_USE_NCRYSTAL)
   target_link_libraries(libopenmc NCrystal::NCrystal)
 endif()
 
-if (OPENMC_USE_UWUW)
-  target_compile_definitions(libopenmc PRIVATE UWUW)
-  target_link_libraries(libopenmc uwuw-shared)
-endif()
-
 #===============================================================================
 # Log build info that this executable can report later
 #===============================================================================

cmake/Modules/FindLIBMESH.cmake

@@ -15,7 +15,7 @@ if(DEFINED ENV{METHOD})
 endif()
 
 find_package(PkgConfig REQUIRED)
-set(ENV{PKG_CONFIG_PATH} "$ENV{PKG_CONFIG_PATH}:${LIBMESH_PC}")
-set(PKG_CONFIG_USE_CMAKE_PREFIX_PATH True)
+
+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/OpenMCConfig.cmake.in

@@ -39,6 +39,6 @@ if(@OPENMC_USE_MCPL@)
   find_package(MCPL REQUIRED)
 endif()
 
-if(@OPENMC_USE_UWUW@)
-  find_package(UWUW 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/source/io_formats/settings.rst

@@ -923,6 +923,15 @@ 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

docs/source/methods/random_numbers.rst

@@ -7,14 +7,19 @@ 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
 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
 ---------------------
@@ -50,23 +55,35 @@ 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::
     :label: lcg-skipahead
 
     \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.
+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
+--------------------------------
+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.
 
-.. _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
 .. _linear congruential generator: https://en.wikipedia.org/wiki/Linear_congruential_generator
+
+.. _permuted congruential generator: https://en.wikipedia.org/wiki/Permuted_congruential_generator

docs/source/pythonapi/base.rst

@@ -133,6 +133,7 @@ Constructing Tallies
    openmc.EnergyFilter
    openmc.EnergyoutFilter
    openmc.MuFilter
+   openmc.MuSurfaceFilter
    openmc.PolarFilter
    openmc.AzimuthalFilter
    openmc.DistribcellFilter
@@ -190,6 +191,7 @@ Post-processing
    :template: myclass.rst
 
    openmc.Particle
+   openmc.ParticleList
    openmc.ParticleTrack
    openmc.StatePoint
    openmc.Summary

docs/source/pythonapi/model.rst

@@ -22,6 +22,7 @@ Composite Surfaces
    :nosignatures:
    :template: myclass.rst
 
+   openmc.model.ConicalFrustum
    openmc.model.CruciformPrism
    openmc.model.CylinderSector
    openmc.model.HexagonalPrism

docs/source/quickinstall.rst

@@ -137,12 +137,11 @@ packages should be installed, for example in Homebrew via:
 
 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. Consequently, the C++ compiler should explicitly be set before
-proceeding:
-
-.. code-block:: sh
-
-   export CXX=/opt/homebrew/opt/llvm/bin/clang++
+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.

docs/source/usersguide/geometry.rst

@@ -474,7 +474,7 @@ applied as universes in the OpenMC geometry file. A geometry represented
 entirely by a DAGMC geometry will contain only the DAGMC universe. Using a
 :class:`openmc.DAGMCUniverse` looks like the following::
 
-   dag_univ = openmc.DAGMCUniverse(filename='dagmc.h5m')
+   dag_univ = openmc.DAGMCUniverse('dagmc.h5m')
    geometry = openmc.Geometry(dag_univ)
    geometry.export_to_xml()
 
@@ -495,13 +495,22 @@ It is important in these cases to understand the DAGMC model's position
 with respect to the CSG geometry. DAGMC geometries can be plotted with
 OpenMC to verify that the model matches one's expectations.
 
-**Note:** DAGMC geometries used in OpenMC are currently required to be clean,
-meaning that all surfaces have been `imprinted and merged
-<https://svalinn.github.io/DAGMC/usersguide/cubit_basics.html>`_ successfully
-and that the model is `watertight
-<https://svalinn.github.io/DAGMC/usersguide/tools.html#make-watertight>`_.
-Future implementations of DAGMC geometry will support small volume overlaps and
-un-merged surfaces.
+By default, when you specify a .h5m file for a :class:`~openmc.DAGMCUniverse`
+instance, it will store the absolute path to the .h5m file. If you prefer to
+store the relative path, you can set the ``'resolve_paths'`` configuration
+variable::
+
+  openmc.config['resolve_paths'] = False
+  dag_univ = openmc.DAGMCUniverse('dagmc.h5m')
+
+.. note::
+    DAGMC geometries used in OpenMC are currently required to be clean,
+    meaning that all surfaces have been `imprinted and merged
+    <https://svalinn.github.io/DAGMC/usersguide/cubit_basics.html>`_ successfully
+    and that the model is `watertight
+    <https://svalinn.github.io/DAGMC/usersguide/tools.html#make-watertight>`_.
+    Future implementations of DAGMC geometry will support small volume overlaps and
+    un-merged surfaces.
 
 Cell, Surface, and Material IDs
 -------------------------------

docs/source/usersguide/settings.rst

@@ -336,6 +336,17 @@ or particles going to a cell::
 .. note:: The ``cell``, ``cellfrom`` and ``cellto`` attributes cannot be
           used simultaneously.
 
+To generate more than one surface source files when the maximum number of stored
+particles is reached, ``max_source_files`` is available. The surface source bank
+will be cleared in simulation memory each time a surface source file is written.
+As an example, to write a maximum of three surface source files:::
+
+  settings.surf_source_write = {
+      'surfaces_ids': [1, 2, 3],
+      'max_particles': 10000,
+      'max_source_files': 3
+  }
+
 .. _compiled_source:
 
 Compiled Sources

include/openmc/lattice.h

@@ -71,7 +71,8 @@ class Lattice {
   //! Allocate offset table for distribcell.
   void allocate_offset_table(int n_maps)
   {
-    offsets_.resize(n_maps * universes_.size(), C_NONE);
+    offsets_.resize(n_maps * universes_.size());
+    std::fill(offsets_.begin(), offsets_.end(), C_NONE);
   }
 
   //! Populate the distribcell offset tables.

include/openmc/mesh.h

@@ -83,8 +83,8 @@ class Mesh {
   virtual ~Mesh() = default;
 
   // Methods
-  //! Perform any preparation needed to support use in mesh filters
-  virtual void prepare_for_tallies() {};
+  //! Perform any preparation needed to support point location within the mesh
+  virtual void prepare_for_point_location() {};
 
   //! Update a position to the local coordinates of the mesh
   virtual void local_coords(Position& r) const {};
@@ -737,7 +737,7 @@ class MOABMesh : public UnstructuredMesh {
   // Overridden Methods
 
   //! Perform any preparation needed to support use in mesh filters
-  void prepare_for_tallies() override;
+  void prepare_for_point_location() override;
 
   Position sample_element(int32_t bin, uint64_t* seed) const override;
 

include/openmc/output.h

@@ -76,10 +76,14 @@ struct formatter<std::array<T, 2>> {
   }
 
   template<typename FormatContext>
+#if FMT_VERSION >= 110000 // Version 11.0.0 and above
+  auto format(const std::array<T, 2>& arr, FormatContext& ctx) const {
+#else // For versions below 11.0.0
   auto format(const std::array<T, 2>& arr, FormatContext& ctx)
   {
+#endif
     return format_to(ctx.out(), "({}, {})", arr[0], arr[1]);
-  }
-};
+}
+}; // namespace fmt
 
 } // namespace fmt

include/openmc/position.h

@@ -221,12 +221,16 @@ namespace fmt {
 template<>
 struct formatter<openmc::Position> : formatter<std::string> {
   template<typename FormatContext>
+#if FMT_VERSION >= 110000 // Version 11.0.0 and above
+  auto format(const openmc::Position& pos, FormatContext& ctx) const {
+#else // For versions below 11.0.0
   auto format(const openmc::Position& pos, FormatContext& ctx)
   {
+#endif
     return formatter<std::string>::format(
       fmt::format("({}, {}, {})", pos.x, pos.y, pos.z), ctx);
-  }
-};
+}
+}; // namespace fmt
 
 } // namespace fmt
 

include/openmc/settings.h

@@ -129,15 +129,18 @@ extern std::unordered_set<int>
   statepoint_batch; //!< Batches when state should be written
 extern std::unordered_set<int>
   source_write_surf_id; //!< Surface ids where sources will be written
+
 extern int
   max_history_splits; //!< maximum number of particle splits for weight windows
-extern int64_t max_surface_particles; //!< maximum number of particles to be
-                                      //!< banked on surfaces per process
 extern int max_secondaries; //!< maximum number of secondaries in the bank
-extern int64_t ssw_cell_id;           //!< Cell id for the surface source
-                                      //!< write setting
-extern SSWCellType ssw_cell_type;     //!< Type of option for the cell
-                                      //!< argument of surface source write
+extern int64_t ssw_max_particles; //!< maximum number of particles to be
+                                  //!< banked on surfaces per process
+extern int64_t ssw_max_files;     //!< maximum number of surface source files
+                                  //!<  to be created
+extern int64_t ssw_cell_id;       //!< Cell id for the surface source
+                                  //!< write setting
+extern SSWCellType ssw_cell_type; //!< Type of option for the cell
+                                  //!< argument of surface source write
 extern TemperatureMethod
   temperature_method; //!< method for choosing temperatures
 extern double

include/openmc/simulation.h

@@ -37,6 +37,7 @@ extern "C" int n_lost_particles;   //!< cumulative number of lost particles
 extern "C" bool need_depletion_rx; //!< need to calculate depletion rx?
 extern "C" int restart_batch;      //!< batch at which a restart job resumed
 extern "C" bool satisfy_triggers;  //!< have tally triggers been satisfied?
+extern int ssw_current_file;       //!< current surface source file
 extern "C" int total_gen;          //!< total number of generations simulated
 extern double total_weight;        //!< Total source weight in a batch
 extern int64_t work_per_rank;      //!< number of particles per MPI rank

include/openmc/state_point.h

@@ -2,6 +2,7 @@
 #define OPENMC_STATE_POINT_H
 
 #include <cstdint>
+#include <string>
 
 #include <gsl/gsl-lite.hpp>
 
@@ -33,8 +34,11 @@ void load_state_point();
 // values on each rank, used to create global indexing. This vector
 // can be created by calling calculate_parallel_index_vector on
 // source_bank.size() if such a vector is not already available.
-void write_source_point(const char* filename, gsl::span<SourceSite> source_bank,
-  const vector<int64_t>& bank_index);
+void write_h5_source_point(const char* filename,
+  gsl::span<SourceSite> source_bank, const vector<int64_t>& bank_index);
+
+void write_source_point(std::string, gsl::span<SourceSite> source_bank,
+  const vector<int64_t>& bank_index, bool use_mcpl);
 
 // This appends a source bank specification to an HDF5 file
 // that's already open. It is used internally by write_source_point.

include/openmc/tallies/filter.h

@@ -36,6 +36,7 @@ enum class FilterType {
   MESHBORN,
   MESH_SURFACE,
   MU,
+  MUSURFACE,
   PARTICLE,
   POLAR,
   SPHERICAL_HARMONICS,