diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 60a331e89b..8b9a7d7a04 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,6 +29,7 @@ jobs: mpi: [n, y] omp: [n, y] dagmc: [n] + ncrystal: [n] libmesh: [n] event: [n] vectfit: [n] @@ -47,6 +48,10 @@ jobs: python-version: '3.10' mpi: y omp: y + - ncrystal: y + python-version: '3.10' + mpi: n + omp: n - libmesh: y python-version: '3.10' mpi: y @@ -64,7 +69,7 @@ jobs: omp: n mpi: y name: "Python ${{ matrix.python-version }} (omp=${{ matrix.omp }}, - mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, + mpi=${{ matrix.mpi }}, dagmc=${{ matrix.dagmc }}, ncrystal=${{ matrix.ncrystal }}, libmesh=${{ matrix.libmesh }}, event=${{ matrix.event }} vectfit=${{ matrix.vectfit }})" @@ -73,6 +78,7 @@ jobs: PHDF5: ${{ matrix.mpi }} OMP: ${{ matrix.omp }} DAGMC: ${{ matrix.dagmc }} + NCRYSTAL: ${{ matrix.ncrystal }} EVENT: ${{ matrix.event }} VECTFIT: ${{ matrix.vectfit }} LIBMESH: ${{ matrix.libmesh }} diff --git a/CMakeLists.txt b/CMakeLists.txt index ad43f179e7..655ff4a6f2 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -36,6 +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_NCRYSTAL "Enable support for NCrystal scattering" OFF) # Warnings for deprecated options foreach(OLD_OPT IN ITEMS "openmp" "profile" "coverage" "dagmc" "libmesh") @@ -98,6 +100,15 @@ macro(find_package_write_status pkg) endif() endmacro() +#=============================================================================== +# NCrystal Scattering Support +#=============================================================================== + +if(OPENMC_USE_NCRYSTAL) + find_package(NCrystal REQUIRED) + message(STATUS "Found NCrystal: ${NCrystal_DIR} (version ${NCrystal_VERSION})") +endif() + #=============================================================================== # DAGMC Geometry Support - need DAGMC/MOAB #=============================================================================== @@ -158,6 +169,15 @@ if(${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) + 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 #=============================================================================== @@ -331,10 +351,12 @@ list(APPEND libopenmc_SOURCES 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/nuclide.cpp src/output.cpp src/particle.cpp @@ -494,6 +516,16 @@ endif() include(CTest) add_subdirectory(tests/cpp_unit_tests) +if (OPENMC_USE_MCPL) + target_compile_definitions(libopenmc PUBLIC OPENMC_MCPL) + target_link_libraries(libopenmc MCPL::mcpl) +endif() + +if(OPENMC_USE_NCRYSTAL) + target_compile_definitions(libopenmc PRIVATE NCRYSTAL) + target_link_libraries(libopenmc NCrystal::NCrystal) +endif() + #=============================================================================== # Log build info that this executable can report later #=============================================================================== diff --git a/cmake/OpenMCConfig.cmake.in b/cmake/OpenMCConfig.cmake.in index d0e2beb827..756fe26dc0 100644 --- a/cmake/OpenMCConfig.cmake.in +++ b/cmake/OpenMCConfig.cmake.in @@ -9,6 +9,11 @@ if(@OPENMC_USE_DAGMC@) find_package(DAGMC REQUIRED HINTS @DAGMC_DIR@) endif() +if(@OPENMC_USE_NCRYSTAL@) + find_package(NCrystal REQUIRED) + message(STATUS "Found NCrystal: ${NCrystal_DIR} (version ${NCrystal_VERSION})") +endif() + if(@OPENMC_USE_LIBMESH@) include(FindPkgConfig) list(APPEND CMAKE_PREFIX_PATH @LIBMESH_PREFIX@) @@ -25,3 +30,7 @@ endif() if(@OPENMC_USE_MPI@) find_package(MPI REQUIRED) endif() + +if(@OPENMC_USE_MCPL@) + find_package(MCPL REQUIRED) +endif() diff --git a/docs/source/conf.py b/docs/source/conf.py index f083332799..ae329dd7ed 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -247,7 +247,7 @@ 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) } diff --git a/docs/source/io_formats/settings.rst b/docs/source/io_formats/settings.rst index 1a29e00ee7..6dff768381 100644 --- a/docs/source/io_formats/settings.rst +++ b/docs/source/io_formats/settings.rst @@ -32,6 +32,17 @@ standard deviation. *Default*: false +------------------------------------- +```` Element +------------------------------------- + +The ```` 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 + ------------------------------------- ```` Element ------------------------------------- @@ -732,6 +743,14 @@ attributes/sub-elements: *Default*: false + :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 ```` element + is set to true. + + *Default*: false + ------------------------------ ```` Element ------------------------------ @@ -767,6 +786,16 @@ certain surfaces and write out the source bank in a separate file called *Default*: None + :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 + ------------------------------ ```` Element ------------------------------ diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst index 3396d7f251..2cafa86916 100644 --- a/docs/source/methods/cross_sections.rst +++ b/docs/source/methods/cross_sections.rst @@ -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 ---------------- @@ -279,3 +300,10 @@ or even isotropic scattering. .. _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 +.. _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 diff --git a/docs/source/pythonapi/data.rst b/docs/source/pythonapi/data.rst index 960abec2fe..1eaf90c972 100644 --- a/docs/source/pythonapi/data.rst +++ b/docs/source/pythonapi/data.rst @@ -66,7 +66,7 @@ Core Functions decay_energy decay_photon_energy dose_coefficients - gnd_name + gnds_name half_life isotopes kalbach_slope diff --git a/docs/source/usersguide/install.rst b/docs/source/usersguide/install.rst index 74be9ba0bc..537dda8248 100644 --- a/docs/source/usersguide/install.rst +++ b/docs/source/usersguide/install.rst @@ -271,6 +271,17 @@ Prerequisites cmake -DOPENMC_USE_DAGMC=on -DCMAKE_PREFIX_PATH=/path/to/dagmc/installation .. + * NCrystal_ library for defining materials with enhanced thermal neutron transport + + Adding this option allows the creation of materials from NCrystal, which + replaces the scattering kernel treatment of ACE files with a modular, + on-the-fly approach. To use it `install + `_ and `initialize + `_ + NCrystal and turn on the option in the CMake configuration step: + + cmake -DOPENMC_USE_NCRYSTAL=on .. + * libMesh_ mesh library framework for numerical simulations of partial differential equations This optional dependency enables support for unstructured mesh tally @@ -294,6 +305,7 @@ Prerequisites .. _MOAB: https://bitbucket.org/fathomteam/moab .. _libMesh: https://libmesh.github.io/ .. _libpng: http://www.libpng.org/pub/png/libpng.html +.. _NCrystal: https://github.com/mctools/ncrystal Obtaining the Source -------------------- @@ -362,6 +374,12 @@ OPENMC_USE_DAGMC should also be defined as `DAGMC_ROOT` in the CMake configuration command. (Default: off) +OPENMC_USE_NCRYSTAL + Turns on support for NCrystal materials. NCrystal must be + `installed `_ and + `initialized `_. + (Default: off) + OPENMC_USE_LIBMESH Enables the use of unstructured mesh tallies with libMesh_. (Default: off) diff --git a/docs/source/usersguide/materials.rst b/docs/source/usersguide/materials.rst index 8b43f1a2ac..83af558057 100644 --- a/docs/source/usersguide/materials.rst +++ b/docs/source/usersguide/materials.rst @@ -101,6 +101,42 @@ you would need to add hydrogen and oxygen to a material and then assign the .. _usersguide_naming: +------------------------- +Adding NCrystal materials +------------------------- + +Additional support for thermal scattering can be added by using NCrystal_. The +:meth:`Material.from_ncrystal` class method generates a :class:`openmc.Material` +object from an `NCrystal configuration string +`_. +Temperature, material composition, and density are passed from the configuration +string and the `NCMAT file +`_ that define the +material, e.g.:: + + mat = openmc.Material.from_ncrystal('Al_sg225.ncmat;temp=300K') + +defines a material containing polycrystalline alumnium, + +:: + + mat = openmc.Material.from_ncrystal("""Ge_sg227.ncmat;dcutoff=0.5;mos=40arcsec; + dir1=@crys_hkl:5,1,1@lab:0,0,1; + dir2=@crys_hkl:0,-1,1@lab:0,1,0""") + +defines an oriented germanium single crystal with 40 arcsec mosaicity. + +NCrystal only handles low energy neutron interactions. Other interactions are +provided by standard ACE files. NCrystal_ comes with a `predefined library +`_ but more materials can +be added by creating NCMAT files or on-the-fly in the configuration string. + +.. warning:: Currently, NCrystal_ materials cannot be modified after they are created. + Density, temperature and composition should be defined in the + configuration string or the NCMAT file. + +.. _NCrystal: https://github.com/mctools/ncrystal + ------------------ Naming Conventions ------------------ @@ -222,3 +258,4 @@ been generated, you can tell OpenMC to use this file either by setting materials.cross_sections = '/path/to/cross_sections.xml' .. _MCNP: https://mcnp.lanl.gov/ + diff --git a/docs/source/usersguide/scripts.rst b/docs/source/usersguide/scripts.rst index c433ffe2c3..78ee6f7758 100644 --- a/docs/source/usersguide/scripts.rst +++ b/docs/source/usersguide/scripts.rst @@ -157,9 +157,9 @@ geometry.xml added. Any 'surfaces' attributes/elements on a cell will be renamed 'region'. materials.xml - Nuclide names will be changed from ACE aliases (e.g., Am-242m) to HDF5/GND + Nuclide names will be changed from ACE aliases (e.g., Am-242m) to HDF5/GNDS names (e.g., Am242_m1). Thermal scattering table names will be changed from - ACE aliases (e.g., HH2O) to HDF5/GND names (e.g., c_H_in_H2O). + ACE aliases (e.g., HH2O) to HDF5/GNDS names (e.g., c_H_in_H2O). ---------------------- ``openmc-update-mgxs`` diff --git a/docs/source/usersguide/settings.rst b/docs/source/usersguide/settings.rst index 336982ac6e..760a08e90c 100644 --- a/docs/source/usersguide/settings.rst +++ b/docs/source/usersguide/settings.rst @@ -474,7 +474,6 @@ selected:: Some features related to photon transport are not currently implemented, including: - * Tallying photon energy deposition. * Generating a photon source from a neutron calculation that can be used for a later fixed source photon calculation. * Photoneutron reactions. diff --git a/include/openmc/cross_sections.h b/include/openmc/cross_sections.h index 2b0473becd..06140a6a8c 100644 --- a/include/openmc/cross_sections.h +++ b/include/openmc/cross_sections.h @@ -62,6 +62,11 @@ extern vector libraries; //! libraries void read_cross_sections_xml(); +//! Read cross sections file (either XML or multigroup H5) and populate data +//! libraries +//! \param[in] root node of the cross_sections.xml +void read_cross_sections_xml(pugi::xml_node root); + //! Load nuclide and thermal scattering data from HDF5 files // //! \param[in] nuc_temps Temperatures for each nuclide in [K] diff --git a/include/openmc/file_utils.h b/include/openmc/file_utils.h index f9c23468df..9612896be7 100644 --- a/include/openmc/file_utils.h +++ b/include/openmc/file_utils.h @@ -3,14 +3,32 @@ #include // for ifstream #include +#include namespace openmc { +// TODO: replace with std::filesystem when switch to C++17 is made +//! Determine if a path is a directory +//! \param[in] path Path to check +//! \return Whether the path is a directory +inline bool dir_exists(const std::string& path) +{ + struct stat s; + if (stat(path.c_str(), &s) != 0) + return false; + + return s.st_mode & S_IFDIR; +} + //! Determine if a file exists //! \param[in] filename Path to file //! \return Whether file exists inline bool file_exists(const std::string& filename) { + // rule out file being a path to a directory + if (dir_exists(filename)) + return false; + std::ifstream s {filename}; return s.good(); } diff --git a/include/openmc/geometry_aux.h b/include/openmc/geometry_aux.h index b248d491ac..cf62debc04 100644 --- a/include/openmc/geometry_aux.h +++ b/include/openmc/geometry_aux.h @@ -10,6 +10,7 @@ #include #include "openmc/vector.h" +#include "openmc/xml_interface.h" namespace openmc { @@ -19,8 +20,13 @@ extern std::unordered_map> extern std::unordered_map universe_level_counts; } // namespace model +//! Read geometry from XML file void read_geometry_xml(); +//! Read geometry from XML node +//! \param[in] root node of geometry XML element +void read_geometry_xml(pugi::xml_node root); + //============================================================================== //! Replace Universe, Lattice, and Material IDs with indices. //============================================================================== diff --git a/include/openmc/initialize.h b/include/openmc/initialize.h index 869be44414..a9b8b336f9 100644 --- a/include/openmc/initialize.h +++ b/include/openmc/initialize.h @@ -1,6 +1,8 @@ #ifndef OPENMC_INITIALIZE_H #define OPENMC_INITIALIZE_H +#include + #ifdef OPENMC_MPI #include "mpi.h" #endif @@ -11,7 +13,13 @@ int parse_command_line(int argc, char* argv[]); #ifdef OPENMC_MPI void initialize_mpi(MPI_Comm intracomm); #endif -void read_input_xml(); + +//! Read material, geometry, settings, and tallies from a single XML file +bool read_model_xml(); +//! Read inputs from separate XML files +void read_separate_xml_files(); +//! Write some output that occurs right after initialization +void initial_output(); } // namespace openmc diff --git a/include/openmc/material.h b/include/openmc/material.h index b251a3ca85..8db9bb6283 100644 --- a/include/openmc/material.h +++ b/include/openmc/material.h @@ -12,6 +12,7 @@ #include "openmc/bremsstrahlung.h" #include "openmc/constants.h" #include "openmc/memory.h" // for unique_ptr +#include "openmc/ncrystal_interface.h" #include "openmc/particle.h" #include "openmc/vector.h" @@ -151,12 +152,17 @@ public: //! \return Temperature in [K] double temperature() const; + //! Get pointer to NCrystal material object + //! \return Pointer to NCrystal material object + const NCrystalMat& ncrystal_mat() const { return ncrystal_mat_; }; + //---------------------------------------------------------------------------- // Data int32_t id_ {C_NONE}; //!< Unique ID std::string name_; //!< Name of material vector nuclide_; //!< Indices in nuclides vector vector element_; //!< Indices in elements vector + NCrystalMat ncrystal_mat_; //!< NCrystal material object xt::xtensor atom_density_; //!< Nuclide atom density in [atom/b-cm] double density_; //!< Total atom density in [atom/b-cm] double density_gpcc_; //!< Total atom density in [g/cm^3] @@ -221,6 +227,10 @@ double density_effect(const vector& f, const vector& e_b_sq, //! Read material data from materials.xml void read_materials_xml(); +//! Read material data XML node +//! \param[in] root node of materials XML element +void read_materials_xml(pugi::xml_node root); + void free_memory_material(); } // namespace openmc diff --git a/include/openmc/mcpl_interface.h b/include/openmc/mcpl_interface.h new file mode 100644 index 0000000000..64f15c13ab --- /dev/null +++ b/include/openmc/mcpl_interface.h @@ -0,0 +1,36 @@ +#ifndef OPENMC_MCPL_INTERFACE_H +#define OPENMC_MCPL_INTERFACE_H + +#include "openmc/particle_data.h" +#include "openmc/vector.h" + +#include + +namespace openmc { + +//============================================================================== +// Constants +//============================================================================== + +extern "C" const bool MCPL_ENABLED; + +//============================================================================== +// Functions +//============================================================================== + +//! Get a vector of source sites from an MCPL file +// +//! \param[in] path Path to MCPL file +//! \return Vector of source sites +vector mcpl_source_sites(std::string path); + +//! Write an MCPL source file +// +//! \param[in] filename Path to MCPL file +//! \param[in] surf_source_bank Whether to use the surface source bank +void write_mcpl_source_point( + const char* filename, bool surf_source_bank = false); + +} // namespace openmc + +#endif // OPENMC_MCPL_INTERFACE_H diff --git a/include/openmc/ncrystal_interface.h b/include/openmc/ncrystal_interface.h new file mode 100644 index 0000000000..5a3882df9c --- /dev/null +++ b/include/openmc/ncrystal_interface.h @@ -0,0 +1,94 @@ +#ifndef OPENMC_NCRYSTAL_INTERFACE_H +#define OPENMC_NCRYSTAL_INTERFACE_H + +#ifdef NCRYSTAL +#include "NCrystal/NCRNG.hh" +#include "NCrystal/NCrystal.hh" +#endif + +#include "openmc/particle.h" + +#include // for uint64_t +#include // for numeric_limits +#include + +namespace openmc { + +//============================================================================== +// Constants +//============================================================================== + +extern "C" const bool NCRYSTAL_ENABLED; + +//! Energy in [eV] to switch between NCrystal and ENDF +constexpr double NCRYSTAL_MAX_ENERGY {5.0}; + +//============================================================================== +// Wrapper class an NCrystal material +//============================================================================== + +class NCrystalMat { +public: + //---------------------------------------------------------------------------- + // Constructors + NCrystalMat() = default; + explicit NCrystalMat(const std::string& cfg); + + //---------------------------------------------------------------------------- + // Methods + +#ifdef NCRYSTAL + //! Return configuration string + std::string cfg() const; + + //! Get cross section from NCrystal material + // + //! \param[in] p Particle object + //! \return Cross section in [b] + double xs(const Particle& p) const; + + // Process scattering event + // + //! \param[in] p Particle object + void scatter(Particle& p) const; + + //! Whether the object holds a valid NCrystal material + operator bool() const; +#else + + //---------------------------------------------------------------------------- + // Trivial methods when compiling without NCRYSTAL + std::string cfg() const + { + return ""; + } + double xs(const Particle& p) const + { + return -1.0; + } + void scatter(Particle& p) const {} + operator bool() const + { + return false; + } +#endif + +private: + //---------------------------------------------------------------------------- + // Data members (only present when compiling with NCrystal support) +#ifdef NCRYSTAL + std::string cfg_; //!< NCrystal configuration string + std::shared_ptr + ptr_; //!< Pointer to NCrystal material object +#endif +}; + +//============================================================================== +// Functions +//============================================================================== + +void ncrystal_update_micro(double xs, NuclideMicroXS& micro); + +} // namespace openmc + +#endif // OPENMC_NCRYSTAL_INTERFACE_H diff --git a/include/openmc/physics.h b/include/openmc/physics.h index 262b3a8841..6e7327d381 100644 --- a/include/openmc/physics.h +++ b/include/openmc/physics.h @@ -96,8 +96,9 @@ void inelastic_scatter(const Nuclide& nuc, const Reaction& rx, Particle& p); void sample_secondary_photons(Particle& p, int i_nuclide); -//！Split or Roulette particles based their weight and the lower weight window -// bound. +//! Split or Roulette particles based their weight and the lower weight window +//! bound. +// //! \param[in] p, particle to be split or rouletted with the weight window. void split_particle(Particle& p); diff --git a/include/openmc/plot.h b/include/openmc/plot.h index 650b7e16a1..a415b17473 100644 --- a/include/openmc/plot.h +++ b/include/openmc/plot.h @@ -279,6 +279,10 @@ void voxel_finalize(hid_t dspace, hid_t dset, hid_t memspace); //! Read plot specifications from a plots.xml file void read_plots_xml(); +//! Read plot specifications from an XML Node +//! \param[in] XML node containing plot info +void read_plots_xml(pugi::xml_node root); + //! Clear memory void free_memory_plot(); diff --git a/include/openmc/settings.h b/include/openmc/settings.h index 1e061b235b..806288efe5 100644 --- a/include/openmc/settings.h +++ b/include/openmc/settings.h @@ -28,6 +28,7 @@ extern bool check_overlaps; //!< check overlaps in geometry? extern bool confidence_intervals; //!< use confidence intervals for results? extern bool create_fission_neutrons; //!< create fission neutrons (fixed source)? +extern bool create_delayed_neutrons; //!< create delayed fission neutrons? extern "C" bool cmfd_run; //!< is a CMFD run? extern bool delayed_photon_scaling; //!< Scale fission photon yield to include delayed @@ -47,7 +48,9 @@ extern "C" bool run_CE; //!< run with continuous-energy data? extern bool source_latest; //!< write latest source at each batch? extern bool source_separate; //!< write source to separate file? extern bool source_write; //!< write source in HDF5 files? +extern bool source_mcpl_write; //!< write source in mcpl files? extern bool surf_source_write; //!< write surface source file? +extern bool surf_mcpl_write; //!< write surface mcpl file? extern bool surf_source_read; //!< read surface source file? extern bool survival_biasing; //!< use survival biasing? extern bool temperature_multipole; //!< use multipole data? @@ -127,9 +130,12 @@ extern double weight_survive; //!< Survival weight after Russian roulette //============================================================================== //! Read settings from XML file -//! \param[in] root XML node for void read_settings_xml(); +//! Read settings from XML node +//! \param[in] root XML node for +void read_settings_xml(pugi::xml_node root); + void free_memory_settings(); } // namespace openmc diff --git a/include/openmc/source.h b/include/openmc/source.h index 04b9ff8563..96d659dcb3 100644 --- a/include/openmc/source.h +++ b/include/openmc/source.h @@ -102,6 +102,7 @@ class FileSource : public Source { public: // Constructors explicit FileSource(std::string path); + explicit FileSource(const vector& sites) : sites_ {sites} {} // Methods SourceSite sample(uint64_t* seed) const override; diff --git a/include/openmc/tallies/tally.h b/include/openmc/tallies/tally.h index 3cead91dc7..56a51370a8 100644 --- a/include/openmc/tallies/tally.h +++ b/include/openmc/tallies/tally.h @@ -48,10 +48,10 @@ public: void set_nuclides(const vector& nuclides); //! returns vector of indices corresponding to the tally this is called on - const vector& filters() const { return filters_; } + const vector& filters() const { return filters_; } //! \brief Returns the tally filter at index i - int32_t filters(int i) const { return filters_[i]; } + int32_t filters(int i) const { return filters_[i]; } void set_filters(gsl::span filters); @@ -178,6 +178,10 @@ extern double global_tally_leakage; //! Read tally specification from tallies.xml void read_tallies_xml(); +//! Read tally specification from an XML node +//! \param[in] root node of tallies XML element +void read_tallies_xml(pugi::xml_node root); + //! \brief Accumulate the sum of the contributions from each history within the //! batch to a new random variable void accumulate_tallies(); diff --git a/openmc/_xml.py b/openmc/_xml.py index 32679fd89e..6799a4e2d8 100644 --- a/openmc/_xml.py +++ b/openmc/_xml.py @@ -1,22 +1,40 @@ -def clean_indentation(element, level=0, spaces_per_level=2): - """ - copy and paste from https://effbot.org/zone/element-lib.htm#prettyprint - it basically walks your tree and adds spaces and newlines so the tree is - printed in a nice way +def clean_indentation(element, level=0, spaces_per_level=2, trailing_indent=True): + """Set indentation of XML element and its sub-elements. + Copied and pasted from https://effbot.org/zone/element-lib.htm#prettyprint. + It walks your tree and adds spaces and newlines so the tree is + printed in a nice way. + + Parameters + ---------- + level : int + Indentation level for the element passed in (default 0) + spaces_per_level : int + Number of spaces per indentation level (default 2) + trailing_indent : bool + Whether or not to add indentation after closing the element + """ i = "\n" + level*spaces_per_level*" " + # ensure there's always some tail for the element passed in + if not element.tail: + element.tail = "" + if len(element): if not element.text or not element.text.strip(): element.text = i + spaces_per_level*" " - if not element.tail or not element.tail.strip(): + if trailing_indent and (not element.tail or not element.tail.strip()): element.tail = i for sub_element in element: + # `trailing_indent` is intentionally not forwarded to the recursive + # call. Any child element of the topmost element should add + # indentation at the end to ensure its parent's indentation is + # correct. clean_indentation(sub_element, level+1, spaces_per_level) if not sub_element.tail or not sub_element.tail.strip(): sub_element.tail = i else: - if level and (not element.tail or not element.tail.strip()): + if trailing_indent and level and (not element.tail or not element.tail.strip()): element.tail = i diff --git a/openmc/cell.py b/openmc/cell.py index 9a7c00962c..a8e1178f41 100644 --- a/openmc/cell.py +++ b/openmc/cell.py @@ -1,6 +1,5 @@ from collections import OrderedDict from collections.abc import Iterable -from copy import deepcopy from math import cos, sin, pi from numbers import Real from xml.etree import ElementTree as ET @@ -519,8 +518,14 @@ class Cell(IDManagerMixin): paths = self._paths self._paths = None - clone = deepcopy(self) - clone.id = None + clone = openmc.Cell(name=self.name) + clone.volume = self.volume + if self.temperature is not None: + clone.temperature = self.temperature + if self.translation is not None: + clone.translation = self.translation + if self.rotation is not None: + clone.rotation = self.rotation clone._num_instances = None # Restore paths on original instance @@ -650,7 +655,7 @@ class Cell(IDManagerMixin): surfaces : dict Dictionary mapping surface IDs to :class:`openmc.Surface` instances materials : dict - Dictionary mapping material IDs to :class:`openmc.Material` + Dictionary mapping material ID strings to :class:`openmc.Material` instances (defined in :math:`openmc.Geometry.from_xml`) get_universe : function Function returning universe (defined in diff --git a/openmc/data/ace.py b/openmc/data/ace.py index 06c581b426..91cbe41960 100644 --- a/openmc/data/ace.py +++ b/openmc/data/ace.py @@ -24,7 +24,7 @@ import numpy as np import openmc.checkvalue as cv from openmc.mixin import EqualityMixin -from .data import ATOMIC_SYMBOL, gnd_name, EV_PER_MEV, K_BOLTZMANN +from .data import ATOMIC_SYMBOL, gnds_name, EV_PER_MEV, K_BOLTZMANN from .endf import ENDF_FLOAT_RE @@ -88,7 +88,7 @@ def get_metadata(zaid, metastable_scheme='nndc'): # Determine name element = ATOMIC_SYMBOL[Z] - name = gnd_name(Z, mass_number, metastable) + name = gnds_name(Z, mass_number, metastable) return (name, element, Z, mass_number, metastable) diff --git a/openmc/data/data.py b/openmc/data/data.py index 55bfb4f096..d5521d9980 100644 --- a/openmc/data/data.py +++ b/openmc/data/data.py @@ -197,8 +197,8 @@ NEUTRON_MASS = 1.00866491595 # Used in atomic_mass function as a cache _ATOMIC_MASS = {} -# Regex for GND nuclide names (used in zam function) -_GND_NAME_RE = re.compile(r'([A-Zn][a-z]*)(\d+)((?:_[em]\d+)?)') +# Regex for GNDS nuclide names (used in zam function) +_GNDS_NAME_RE = re.compile(r'([A-Zn][a-z]*)(\d+)((?:_[em]\d+)?)') # Used in half_life function as a cache _HALF_LIFE = {} @@ -436,8 +436,11 @@ def water_density(temperature, pressure=0.1013): return coeff / pi / gamma1_pi -def gnd_name(Z, A, m=0): - """Return nuclide name using GND convention +def gnds_name(Z, A, m=0): + """Return nuclide name using GNDS convention + + .. versionchanged:: 0.14.0 + Function name changed from ``gnd_name`` to ``gnds_name`` Parameters ---------- @@ -451,7 +454,7 @@ def gnd_name(Z, A, m=0): Returns ------- str - Nuclide name in GND convention, e.g., 'Am242_m1' + Nuclide name in GNDS convention, e.g., 'Am242_m1' """ if m > 0: @@ -502,7 +505,7 @@ def zam(name): Parameters ---------- name : str - Name of nuclide using GND convention, e.g., 'Am242_m1' + Name of nuclide using GNDS convention, e.g., 'Am242_m1' Returns ------- @@ -511,10 +514,10 @@ def zam(name): """ try: - symbol, A, state = _GND_NAME_RE.match(name).groups() + symbol, A, state = _GNDS_NAME_RE.match(name).groups() except AttributeError: raise ValueError(f"'{name}' does not appear to be a nuclide name in " - "GND format") + "GNDS format") if symbol not in ATOMIC_NUMBER: raise ValueError(f"'{symbol}' is not a recognized element symbol") diff --git a/openmc/data/decay.py b/openmc/data/decay.py index 0db8422010..d002424385 100644 --- a/openmc/data/decay.py +++ b/openmc/data/decay.py @@ -144,7 +144,7 @@ class FissionProductYields(EqualityMixin): # Assign basic nuclide properties self.nuclide = { - 'name': ev.gnd_name, + 'name': ev.gnds_name, 'atomic_number': ev.target['atomic_number'], 'mass_number': ev.target['mass_number'], 'isomeric_state': ev.target['isomeric_state'] diff --git a/openmc/data/endf.py b/openmc/data/endf.py index f9b9d06941..d526bc53f5 100644 --- a/openmc/data/endf.py +++ b/openmc/data/endf.py @@ -12,7 +12,7 @@ import re import numpy as np -from .data import gnd_name +from .data import gnds_name from .function import Tabulated1D try: from ._endf import float_endf @@ -520,10 +520,10 @@ class Evaluation: self.reaction_list.append((mf, mt, nc, mod)) @property - def gnd_name(self): - return gnd_name(self.target['atomic_number'], - self.target['mass_number'], - self.target['isomeric_state']) + def gnds_name(self): + return gnds_name(self.target['atomic_number'], + self.target['mass_number'], + self.target['isomeric_state']) class Tabulated2D: @@ -531,7 +531,7 @@ class Tabulated2D: This is a dummy class that is not really used other than to store the interpolation information for a two-dimensional function. Once we refactor - to adopt GND-like data containers, this will probably be removed or + to adopt GNDS-like data containers, this will probably be removed or extended. Parameters diff --git a/openmc/data/multipole.py b/openmc/data/multipole.py index 508c76ac43..0be70cdba2 100644 --- a/openmc/data/multipole.py +++ b/openmc/data/multipole.py @@ -748,12 +748,12 @@ class WindowedMultipole(EqualityMixin): Parameters ---------- name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention Attributes ---------- name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention spacing : float The width of each window in sqrt(E)-space. For example, the frst window will end at (sqrt(E_min) + spacing)**2 and the second window at diff --git a/openmc/data/neutron.py b/openmc/data/neutron.py index e0574d76d4..2d4c139635 100644 --- a/openmc/data/neutron.py +++ b/openmc/data/neutron.py @@ -44,7 +44,7 @@ class IncidentNeutron(EqualityMixin): Parameters ---------- name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention atomic_number : int Number of protons in the target nucleus mass_number : int @@ -75,7 +75,7 @@ class IncidentNeutron(EqualityMixin): Metastable state of the target nucleus. A value of zero indicates ground state. name : str - Name of the nuclide using the GND naming convention + Name of the nuclide using the GNDS naming convention reactions : collections.OrderedDict Contains the cross sections, secondary angle and energy distributions, and other associated data for each reaction. The keys are the MT values diff --git a/openmc/data/reaction.py b/openmc/data/reaction.py index a2431cf1ce..ac9d7f14e9 100644 --- a/openmc/data/reaction.py +++ b/openmc/data/reaction.py @@ -555,7 +555,7 @@ def _get_activation_products(ev, rx): Z, A = divmod(items[2], 1000) excited_state = items[3] - # Get GND name for product + # Get GNDS name for product symbol = ATOMIC_SYMBOL[Z] if excited_state > 0: name = '{}{}_e{}'.format(symbol, A, excited_state) diff --git a/openmc/data/thermal.py b/openmc/data/thermal.py index e6213e5f0d..48f6bfc9b3 100644 --- a/openmc/data/thermal.py +++ b/openmc/data/thermal.py @@ -104,7 +104,7 @@ def get_thermal_name(name): Returns ------- str - GND-format thermal scattering name + GNDS-format thermal scattering name """ if name in _THERMAL_NAMES: @@ -396,7 +396,7 @@ class ThermalScattering(EqualityMixin): Parameters ---------- name : str - Name of the material using GND convention, e.g. c_H_in_H2O + Name of the material using GNDS convention, e.g. c_H_in_H2O atomic_weight_ratio : float Atomic mass ratio of the target nuclide. kTs : Iterable of float @@ -415,7 +415,7 @@ class ThermalScattering(EqualityMixin): Inelastic scattering cross section derived in the incoherent approximation name : str - Name of the material using GND convention, e.g. c_H_in_H2O + Name of the material using GNDS convention, e.g. c_H_in_H2O temperatures : Iterable of str List of string representations the temperatures of the target nuclide in the data set. The temperatures are strings of the temperature, @@ -491,7 +491,7 @@ class ThermalScattering(EqualityMixin): ACE table to read from. If given as a string, it is assumed to be the filename for the ACE file. name : str - GND-conforming name of the material, e.g. c_H_in_H2O. If none is + GNDS-conforming name of the material, e.g. c_H_in_H2O. If none is passed, the appropriate name is guessed based on the name of the ACE table. @@ -596,7 +596,7 @@ class ThermalScattering(EqualityMixin): ACE table to read from. If given as a string, it is assumed to be the filename for the ACE file. name : str - GND-conforming name of the material, e.g. c_H_in_H2O. If none is + GNDS-conforming name of the material, e.g. c_H_in_H2O. If none is passed, the appropriate name is guessed based on the name of the ACE table. diff --git a/openmc/deplete/chain.py b/openmc/deplete/chain.py index f439cedc34..372ed35108 100644 --- a/openmc/deplete/chain.py +++ b/openmc/deplete/chain.py @@ -15,7 +15,7 @@ from numbers import Real, Integral from warnings import warn from openmc.checkvalue import check_type, check_greater_than -from openmc.data import gnd_name, zam, DataLibrary +from openmc.data import gnds_name, zam, DataLibrary from openmc.exceptions import DataError from .nuclide import FissionYieldDistribution @@ -135,14 +135,14 @@ def replace_missing(product, decay_data): Parameters ---------- product : str - Name of product in GND format, e.g. 'Y86_m1'. + Name of product in GNDS format, e.g. 'Y86_m1'. decay_data : dict Dictionary of decay data Returns ------- product : str - Replacement for missing product in GND format. + Replacement for missing product in GNDS format. """ # Determine atomic number, mass number, and metastable state @@ -213,7 +213,7 @@ def replace_missing_fpy(actinide, fpy_data, decay_data): # Check if metastable state has data (e.g., Am242m) Z, A, m = zam(actinide) if m == 0: - metastable = gnd_name(Z, A, 1) + metastable = gnds_name(Z, A, 1) if metastable in fpy_data: return metastable @@ -222,7 +222,7 @@ def replace_missing_fpy(actinide, fpy_data, decay_data): while isotone in decay_data: Z += 1 A += 1 - isotone = gnd_name(Z, A, 0) + isotone = gnds_name(Z, A, 0) if isotone in fpy_data: return isotone @@ -231,7 +231,7 @@ def replace_missing_fpy(actinide, fpy_data, decay_data): while isotone in decay_data: Z -= 1 A -= 1 - isotone = gnd_name(Z, A, 0) + isotone = gnds_name(Z, A, 0) if isotone in fpy_data: return isotone @@ -357,7 +357,7 @@ class Chain: reactions = {} for f in neutron_files: evaluation = openmc.data.endf.Evaluation(f) - name = evaluation.gnd_name + name = evaluation.gnds_name reactions[name] = {} for mf, mt, nc, mod in evaluation.reaction_list: if mf == 3: @@ -904,7 +904,7 @@ class Chain: ground_target = grounds.get(parent_name) if ground_target is None: pz, pa, pm = zam(parent_name) - ground_target = gnd_name(pz, pa + 1, 0) + ground_target = gnds_name(pz, pa + 1, 0) new_ratios[ground_target] = ground_br parent.add_reaction(reaction, ground_target, rxn_Q, ground_br) diff --git a/openmc/deplete/nuclide.py b/openmc/deplete/nuclide.py index b84b91a7ff..2e9673d5f7 100644 --- a/openmc/deplete/nuclide.py +++ b/openmc/deplete/nuclide.py @@ -82,7 +82,7 @@ class Nuclide: Parameters ---------- name : str, optional - GND name of this nuclide, e.g. ``"He4"``, ``"Am242_m1"`` + GNDS name of this nuclide, e.g. ``"He4"``, ``"Am242_m1"`` Attributes ---------- diff --git a/openmc/executor.py b/openmc/executor.py index a73d896ffe..22862a7cf9 100644 --- a/openmc/executor.py +++ b/openmc/executor.py @@ -9,7 +9,7 @@ from .plots import _get_plot_image def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, plot=False, restart_file=None, threads=None, tracks=False, event_based=None, - openmc_exec='openmc', mpi_args=None): + openmc_exec='openmc', mpi_args=None, path_input=None): """Converts user-readable flags in to command-line arguments to be run with the OpenMC executable via subprocess. @@ -42,6 +42,9 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, mpi_args : list of str, optional MPI execute command and any additional MPI arguments to pass, e.g. ['mpiexec', '-n', '8']. + path_input : str or Pathlike + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. .. versionadded:: 0.13.0 @@ -82,6 +85,9 @@ def _process_CLI_arguments(volume=False, geometry_debug=False, particles=None, if mpi_args is not None: args = mpi_args + args + if path_input is not None: + args += [path_input] + return args @@ -118,7 +124,7 @@ def _run(args, output, cwd): raise RuntimeError(error_msg) -def plot_geometry(output=True, openmc_exec='openmc', cwd='.'): +def plot_geometry(output=True, openmc_exec='openmc', cwd='.', path_input=None): """Run OpenMC in plotting mode Parameters @@ -129,6 +135,9 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.'): Path to OpenMC executable cwd : str, optional Path to working directory to run in + path_input : str + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. Raises ------ @@ -136,10 +145,13 @@ def plot_geometry(output=True, openmc_exec='openmc', cwd='.'): If the `openmc` executable returns a non-zero status """ - _run([openmc_exec, '-p'], output, cwd) + args = [openmc_exec, '-p'] + if path_input is not None: + args += [path_input] + _run(args, output, cwd) -def plot_inline(plots, openmc_exec='openmc', cwd='.'): +def plot_inline(plots, openmc_exec='openmc', cwd='.', path_input=None): """Display plots inline in a Jupyter notebook. .. versionchanged:: 0.13.0 @@ -155,6 +167,9 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'): Path to OpenMC executable cwd : str, optional Path to working directory to run in + path_input : str + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. Raises ------ @@ -171,7 +186,7 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'): openmc.Plots(plots).export_to_xml(cwd) # Run OpenMC in geometry plotting mode - plot_geometry(False, openmc_exec, cwd) + plot_geometry(False, openmc_exec, cwd, path_input) if plots is not None: images = [_get_plot_image(p, cwd) for p in plots] @@ -179,7 +194,8 @@ def plot_inline(plots, openmc_exec='openmc', cwd='.'): def calculate_volumes(threads=None, output=True, cwd='.', - openmc_exec='openmc', mpi_args=None): + openmc_exec='openmc', mpi_args=None, + path_input=None): """Run stochastic volume calculations in OpenMC. This function runs OpenMC in stochastic volume calculation mode. To specify @@ -210,6 +226,10 @@ def calculate_volumes(threads=None, output=True, cwd='.', cwd : str, optional Path to working directory to run in. Defaults to the current working directory. + path_input : str or Pathlike + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. + Raises ------ @@ -223,14 +243,16 @@ def calculate_volumes(threads=None, output=True, cwd='.', """ args = _process_CLI_arguments(volume=True, threads=threads, - openmc_exec=openmc_exec, mpi_args=mpi_args) + openmc_exec=openmc_exec, mpi_args=mpi_args, + path_input=path_input) _run(args, output, cwd) def run(particles=None, threads=None, geometry_debug=False, restart_file=None, tracks=False, output=True, cwd='.', - openmc_exec='openmc', mpi_args=None, event_based=False): + openmc_exec='openmc', mpi_args=None, event_based=False, + path_input=None): """Run an OpenMC simulation. Parameters @@ -239,17 +261,17 @@ def run(particles=None, threads=None, geometry_debug=False, Number of particles to simulate per generation. threads : int, optional Number of OpenMP threads. If OpenMC is compiled with OpenMP threading - enabled, the default is implementation-dependent but is usually equal - to the number of hardware threads available (or a value set by the + enabled, the default is implementation-dependent but is usually equal to + the number of hardware threads available (or a value set by the :envvar:`OMP_NUM_THREADS` environment variable). geometry_debug : bool, optional Turn on geometry debugging during simulation. Defaults to False. restart_file : str, optional Path to restart file to use tracks : bool, optional - Enables the writing of particles tracks. The number of particle - tracks written to tracks.h5 is limited to 1000 unless - Settings.max_tracks is set. Defaults to False. + Enables the writing of particles tracks. The number of particle tracks + written to tracks.h5 is limited to 1000 unless Settings.max_tracks is + set. Defaults to False. output : bool Capture OpenMC output from standard out cwd : str, optional @@ -258,13 +280,17 @@ def run(particles=None, threads=None, geometry_debug=False, openmc_exec : str, optional Path to OpenMC executable. Defaults to 'openmc'. mpi_args : list of str, optional - MPI execute command and any additional MPI arguments to pass, - e.g. ['mpiexec', '-n', '8']. + MPI execute command and any additional MPI arguments to pass, e.g. + ['mpiexec', '-n', '8']. event_based : bool, optional Turns on event-based parallelism, instead of default history-based .. versionadded:: 0.12 + path_input : str or Pathlike + Path to a single XML file or a directory containing XML files for the + OpenMC executable to read. + Raises ------ RuntimeError @@ -275,6 +301,7 @@ def run(particles=None, threads=None, geometry_debug=False, args = _process_CLI_arguments( volume=False, geometry_debug=geometry_debug, particles=particles, restart_file=restart_file, threads=threads, tracks=tracks, - event_based=event_based, openmc_exec=openmc_exec, mpi_args=mpi_args) + event_based=event_based, openmc_exec=openmc_exec, mpi_args=mpi_args, + path_input=path_input) _run(args, output, cwd) diff --git a/openmc/geometry.py b/openmc/geometry.py index 3b69333625..511a3da409 100644 --- a/openmc/geometry.py +++ b/openmc/geometry.py @@ -1,3 +1,5 @@ +import os +import typing from collections import OrderedDict, defaultdict from collections.abc import Iterable from copy import deepcopy @@ -7,7 +9,7 @@ import warnings import openmc import openmc._xml as xml -from .checkvalue import check_type, check_less_than, check_greater_than +from .checkvalue import check_type, check_less_than, check_greater_than, PathLike class Geometry: @@ -103,6 +105,39 @@ class Geometry: if universe.id in volume_calc.volumes: universe.add_volume_information(volume_calc) + def to_xml_element(self, remove_surfs=False): + """Creates a 'geometry' element to be written to an XML file. + + Parameters + ---------- + remove_surfs : bool + Whether or not to remove redundant surfaces from the geometry when + exporting + + """ + # Find and remove redundant surfaces from the geometry + if remove_surfs: + warnings.warn("remove_surfs kwarg will be deprecated soon, please " + "set the Geometry.merge_surfaces attribute instead.") + self.merge_surfaces = True + + if self.merge_surfaces: + self.remove_redundant_surfaces() + + # Create XML representation + element = ET.Element("geometry") + self.root_universe.create_xml_subelement(element, memo=set()) + + # Sort the elements in the file + element[:] = sorted(element, key=lambda x: ( + x.tag, int(x.get('id')))) + + # Clean the indentation in the file to be user-readable + xml.clean_indentation(element) + xml.reorder_attributes(element) # TODO: Remove when support is Python 3.8+ + + return element + def export_to_xml(self, path='geometry.xml', remove_surfs=False): """Export geometry to an XML file. @@ -117,25 +152,7 @@ class Geometry: .. versionadded:: 0.12 """ - # Find and remove redundant surfaces from the geometry - if remove_surfs: - warnings.warn("remove_surfs kwarg will be deprecated soon, please " - "set the Geometry.merge_surfaces attribute instead.") - self.merge_surfaces = True - - if self.merge_surfaces: - self.remove_redundant_surfaces() - - # Create XML representation - root_element = ET.Element("geometry") - self.root_universe.create_xml_subelement(root_element, memo=set()) - - # Sort the elements in the file - root_element[:] = sorted(root_element, key=lambda x: ( - x.tag, int(x.get('id')))) - - # Clean the indentation in the file to be user-readable - xml.clean_indentation(root_element) + root_element = self.to_xml_element(remove_surfs) # Check if path is a directory p = Path(path) @@ -143,18 +160,17 @@ class Geometry: p /= 'geometry.xml' # Write the XML Tree to the geometry.xml file - xml.reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') @classmethod - def from_xml(cls, path='geometry.xml', materials=None): - """Generate geometry from XML file + def from_xml_element(cls, elem, materials=None): + """Generate geometry from an XML element Parameters ---------- - path : str, optional - Path to geometry XML file + elem : xml.etree.ElementTree.Element + XML element materials : openmc.Materials or None Materials used to assign to cells. If None, an attempt is made to generate it from the materials.xml file. @@ -165,6 +181,11 @@ class Geometry: Geometry object """ + mats = dict() + if materials is not None: + mats.update({str(m.id): m for m in materials}) + mats['void'] = None + # Helper function for keeping a cache of Universe instances universes = {} def get_universe(univ_id): @@ -173,13 +194,10 @@ class Geometry: universes[univ_id] = univ return universes[univ_id] - tree = ET.parse(path) - root = tree.getroot() - # Get surfaces surfaces = {} periodic = {} - for surface in root.findall('surface'): + for surface in elem.findall('surface'): s = openmc.Surface.from_xml_element(surface) surfaces[s.id] = s @@ -193,24 +211,24 @@ class Geometry: surfaces[s1].periodic_surface = surfaces[s2] # Add any DAGMC universes - for elem in root.findall('dagmc_universe'): - dag_univ = openmc.DAGMCUniverse.from_xml_element(elem) + for e in elem.findall('dagmc_universe'): + dag_univ = openmc.DAGMCUniverse.from_xml_element(e) universes[dag_univ.id] = dag_univ # Dictionary that maps each universe to a list of cells/lattices that - # contain it (needed to determine which universe is the root) + # contain it (needed to determine which universe is the elem) child_of = defaultdict(list) - for elem in root.findall('lattice'): - lat = openmc.RectLattice.from_xml_element(elem, get_universe) + for e in elem.findall('lattice'): + lat = openmc.RectLattice.from_xml_element(e, get_universe) universes[lat.id] = lat if lat.outer is not None: child_of[lat.outer].append(lat) for u in lat.universes.ravel(): child_of[u].append(lat) - for elem in root.findall('hex_lattice'): - lat = openmc.HexLattice.from_xml_element(elem, get_universe) + for e in elem.findall('hex_lattice'): + lat = openmc.HexLattice.from_xml_element(e, get_universe) universes[lat.id] = lat if lat.outer is not None: child_of[lat.outer].append(lat) @@ -224,15 +242,8 @@ class Geometry: for u in ring: child_of[u].append(lat) - # Create dictionary to easily look up materials - if materials is None: - filename = Path(path).parent / 'materials.xml' - materials = openmc.Materials.from_xml(str(filename)) - mats = {str(m.id): m for m in materials} - mats['void'] = None - - for elem in root.findall('cell'): - c = openmc.Cell.from_xml_element(elem, surfaces, mats, get_universe) + for e in elem.findall('cell'): + c = openmc.Cell.from_xml_element(e, surfaces, mats, get_universe) if c.fill_type in ('universe', 'lattice'): child_of[c.fill].append(c) @@ -244,6 +255,41 @@ class Geometry: else: raise ValueError('Error determining root universe.') + @classmethod + def from_xml( + cls, + path: PathLike = 'geometry.xml', + materials: typing.Optional[typing.Union[PathLike, 'openmc.Materials']] = 'materials.xml' + ): + """Generate geometry from XML file + + Parameters + ---------- + path : PathLike, optional + Path to geometry XML file + materials : openmc.Materials or PathLike + Materials used to assign to cells. If PathLike, an attempt is made + to generate materials from the provided xml file. + + Returns + ------- + openmc.Geometry + Geometry object + + """ + + # Using str and os.Pathlike here to avoid error when using just the imported PathLike + # TypeError: Subscripted generics cannot be used with class and instance checks + check_type('materials', materials, (str, os.PathLike, openmc.Materials)) + + if isinstance(materials, (str, os.PathLike)): + materials = openmc.Materials.from_xml(materials) + + tree = ET.parse(path) + root = tree.getroot() + + return cls.from_xml_element(root, materials) + def find(self, point): """Find cells/universes/lattices which contain a given point @@ -488,6 +534,27 @@ class Geometry: """ return self._get_domains_by_name(name, case_sensitive, matching, 'cell') + def get_surfaces_by_name(self, name, case_sensitive=False, matching=False): + """Return a list of surfaces with matching names. + + Parameters + ---------- + name : str + The name to search match + case_sensitive : bool + Whether to distinguish upper and lower case letters in each + surface's name (default is False) + matching : bool + Whether the names must match completely (default is False) + + Returns + ------- + list of openmc.Surface + Surfaces matching the queried name + + """ + return self._get_domains_by_name(name, case_sensitive, matching, 'surface') + def get_cells_by_fill_name(self, name, case_sensitive=False, matching=False): """Return a list of cells with fills with matching names. diff --git a/openmc/lib/__init__.py b/openmc/lib/__init__.py index c14b0d9c28..eef18be881 100644 --- a/openmc/lib/__init__.py +++ b/openmc/lib/__init__.py @@ -42,12 +42,18 @@ else: def _dagmc_enabled(): return c_bool.in_dll(_dll, "DAGMC_ENABLED").value +def _ncrystal_enabled(): + return c_bool.in_dll(_dll, "NCRYSTAL_ENABLED").value + def _coord_levels(): return c_int.in_dll(_dll, "n_coord_levels").value def _libmesh_enabled(): return c_bool.in_dll(_dll, "LIBMESH_ENABLED").value +def _mcpl_enabled(): + return c_bool.in_dll(_dll, "MCPL_ENABLED").value + from .error import * from .core import * from .nuclide import * diff --git a/openmc/material.py b/openmc/material.py index 420a085216..7844ec131c 100644 --- a/openmc/material.py +++ b/openmc/material.py @@ -99,6 +99,10 @@ class Material(IDManagerMixin): [decay/sec]. .. versionadded:: 0.13.2 + ncrystal_cfg : str + NCrystal configuration string + + .. versionadded:: 0.13.3 """ @@ -118,6 +122,7 @@ class Material(IDManagerMixin): self._volume = None self._atoms = {} self._isotropic = [] + self._ncrystal_cfg = None # A list of tuples (nuclide, percent, percent type) self._nuclides = [] @@ -140,6 +145,9 @@ class Material(IDManagerMixin): string += '{: <16}\n'.format('\tS(a,b) Tables') + if self._ncrystal_cfg: + string += '{: <16}=\t{}\n'.format('\tNCrystal conf', self._ncrystal_cfg) + for sab in self._sab: string += '{: <16}=\t{}\n'.format('\tS(a,b)', sab) @@ -219,6 +227,10 @@ class Material(IDManagerMixin): def volume(self): return self._volume + @property + def ncrystal_cfg(self): + return self._ncrystal_cfg + @name.setter def name(self, name: Optional[str]): if name is not None: @@ -331,6 +343,64 @@ class Material(IDManagerMixin): return material + @classmethod + def from_ncrystal(cls, cfg, **kwargs): + """Create material from NCrystal configuration string. + + Density, temperature, and material composition, and (ultimately) thermal + neutron scattering will be automatically be provided by NCrystal based + on this string. The name and material_id parameters are simply passed on + to the Material constructor. + + Parameters + ---------- + cfg : str + NCrystal configuration string + **kwargs + Keyword arguments passed to :class:`openmc.Material` + + Returns + ------- + openmc.Material + Material instance + + """ + + import NCrystal + nc_mat = NCrystal.createInfo(cfg) + + def openmc_natabund(Z): + #nc_mat.getFlattenedComposition might need natural abundancies. + #This call-back function is used so NCrystal can flatten composition + #using OpenMC's natural abundancies. In practice this function will + #only get invoked in the unlikely case where a material is specified + #by referring both to natural elements and specific isotopes of the + #same element. + elem_name = openmc.data.ATOMIC_SYMBOL[Z] + return [ + (int(iso_name[len(elem_name):]), abund) + for iso_name, abund in openmc.data.isotopes(elem_name) + ] + + flat_compos = nc_mat.getFlattenedComposition( + preferNaturalElements=True, naturalAbundProvider=openmc_natabund) + + # Create the Material + material = cls(temperature=nc_mat.getTemperature(), **kwargs) + + for Z, A_vals in flat_compos: + elemname = openmc.data.ATOMIC_SYMBOL[Z] + for A, frac in A_vals: + if A: + material.add_nuclide(f'{elemname}{A}', frac) + else: + material.add_element(elemname, frac) + + material.set_density('g/cm3', nc_mat.getDensity()) + material._ncrystal_cfg = NCrystal.normaliseCfg(cfg) + + return material + def add_volume_information(self, volume_calc): """Add volume information to a material. @@ -405,6 +475,9 @@ class Material(IDManagerMixin): 'macroscopic data-set has already been added'.format(self._id) raise ValueError(msg) + if self._ncrystal_cfg is not None: + raise ValueError("Cannot add nuclides to NCrystal material") + # If nuclide name doesn't look valid, give a warning try: Z, _, _ = openmc.data.zam(nuclide) @@ -609,6 +682,9 @@ class Material(IDManagerMixin): raise ValueError("Element name should be given by the " "element's symbol or name, e.g., 'Zr', 'zirconium'") + if self._ncrystal_cfg is not None: + raise ValueError("Cannot add elements to NCrystal material") + # Allow for element identifier to be given as a symbol or name if len(element) > 2: el = element.lower() @@ -990,7 +1066,7 @@ class Material(IDManagerMixin): activity[nuclide] = inv_seconds * 1e24 * atoms_per_bcm * multiplier return activity if by_nuclide else sum(activity.values()) - + def get_decay_heat(self, units: str = 'W', by_nuclide: bool = False): """Returns the decay heat of the material or for each nuclide in the material in units of [W], [W/g] or [W/cm3]. @@ -1024,16 +1100,16 @@ class Material(IDManagerMixin): multiplier = 1 elif units == 'W/g': multiplier = 1.0 / self.get_mass_density() - - decayheat = {} + + decayheat = {} for nuclide, atoms_per_bcm in self.get_nuclide_atom_densities().items(): decay_erg = openmc.data.decay_energy(nuclide) inv_seconds = openmc.data.decay_constant(nuclide) decay_erg *= openmc.data.JOULE_PER_EV decayheat[nuclide] = inv_seconds * decay_erg * 1e24 * atoms_per_bcm * multiplier - return decayheat if by_nuclide else sum(decayheat.values()) - + return decayheat if by_nuclide else sum(decayheat.values()) + def get_nuclide_atoms(self): """Return number of atoms of each nuclide in the material @@ -1182,6 +1258,14 @@ class Material(IDManagerMixin): if self._volume: element.set("volume", str(self._volume)) + if self._ncrystal_cfg: + if self._sab: + raise ValueError("NCrystal materials are not compatible with S(a,b).") + if self._macroscopic is not None: + raise ValueError("NCrystal materials are not compatible with macroscopic cross sections.") + + element.set("cfg", str(self._ncrystal_cfg)) + # Create temperature XML subelement if self.temperature is not None: element.set("temperature", str(self.temperature)) @@ -1449,6 +1533,57 @@ class Materials(cv.CheckedList): for material in self: material.make_isotropic_in_lab() + def _write_xml(self, file, header=True, level=0, spaces_per_level=2, trailing_indent=True): + """Writes XML content of the materials to an open file handle. + + Parameters + ---------- + file : IOTextWrapper + Open file handle to write content into. + header : bool + Whether or not to write the XML header + level : int + Indentation level of materials element + spaces_per_level : int + Number of spaces per indentation + trailing_indentation : bool + Whether or not to write a trailing indentation for the materials element + + """ + indentation = level*spaces_per_level*' ' + # Write the header and the opening tag for the root element. + if header: + file.write("\n") + file.write(indentation+'\n') + + # Write the element. + if self.cross_sections is not None: + element = ET.Element('cross_sections') + element.text = str(self.cross_sections) + clean_indentation(element, level=level+1) + element.tail = element.tail.strip(' ') + file.write((level+1)*spaces_per_level*' ') + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ + ET.ElementTree(element).write(file, encoding='unicode') + + # Write the elements. + for material in sorted(self, key=lambda x: x.id): + element = material.to_xml_element() + clean_indentation(element, level=level+1) + element.tail = element.tail.strip(' ') + file.write((level+1)*spaces_per_level*' ') + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ + ET.ElementTree(element).write(file, encoding='unicode') + + # Write the closing tag for the root element. + file.write(indentation+'\n') + + # Write a trailing indentation for the next element + # at this level if needed + if trailing_indent: + file.write(indentation) + + def export_to_xml(self, path: PathLike = 'materials.xml'): """Export material collection to an XML file. @@ -1468,32 +1603,34 @@ class Materials(cv.CheckedList): # one go. with open(str(p), 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh: + self._write_xml(fh) - # Write the header and the opening tag for the root element. - fh.write("\n") - fh.write('\n') + @classmethod + def from_xml_element(cls, elem): + """Generate materials collection from XML file - # Write the element. - if self.cross_sections is not None: - element = ET.Element('cross_sections') - element.text = str(self.cross_sections) - clean_indentation(element, level=1) - element.tail = element.tail.strip(' ') - fh.write(' ') - reorder_attributes(element) # TODO: Remove when support is Python 3.8+ - ET.ElementTree(element).write(fh, encoding='unicode') + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element - # Write the elements. - for material in sorted(self, key=lambda x: x.id): - element = material.to_xml_element() - clean_indentation(element, level=1) - element.tail = element.tail.strip(' ') - fh.write(' ') - reorder_attributes(element) # TODO: Remove when support is Python 3.8+ - ET.ElementTree(element).write(fh, encoding='unicode') + Returns + ------- + openmc.Materials + Materials collection - # Write the closing tag for the root element. - fh.write('\n') + """ + # Generate each material + materials = cls() + for material in elem.findall('material'): + materials.append(Material.from_xml_element(material)) + + # Check for cross sections settings + xs = elem.find('cross_sections') + if xs is not None: + materials.cross_sections = xs.text + + return materials @classmethod def from_xml(cls, path: PathLike = 'materials.xml'): @@ -1513,14 +1650,4 @@ class Materials(cv.CheckedList): tree = ET.parse(path) root = tree.getroot() - # Generate each material - materials = cls() - for material in root.findall('material'): - materials.append(Material.from_xml_element(material)) - - # Check for cross sections settings - xs = tree.find('cross_sections') - if xs is not None: - materials.cross_sections = xs.text - - return materials + return cls.from_xml_element(root) diff --git a/openmc/mgxs/mgxs.py b/openmc/mgxs/mgxs.py index 15a1128f89..c93b42b88b 100644 --- a/openmc/mgxs/mgxs.py +++ b/openmc/mgxs/mgxs.py @@ -925,7 +925,7 @@ class MGXS: # Tabulate the atomic number densities for all nuclides elif nuclides == 'all': nuclides = self.get_nuclides() - densities = np.zeros(self.num_nuclides, dtype=np.float) + densities = np.zeros(self.num_nuclides, dtype=float) for i, nuclide in enumerate(nuclides): densities[i] += self.get_nuclide_density(nuclide) @@ -3019,7 +3019,7 @@ class DiffusionCoefficient(TransportXS): new_filt = openmc.EnergyFilter(old_filt.values) p1_tally.filters[-2] = new_filt - p1_tally = p1_tally.get_slice(filters=[openmc.LegendreFilter], + p1_tally = p1_tally.get_slice(filters=[openmc.LegendreFilter], filter_bins=[('P1',)],squeeze=True) p1_tally._scores = ['scatter-1'] total_xs = self.tallies['total'] / self.tallies['flux (tracklength)'] diff --git a/openmc/model/model.py b/openmc/model/model.py index 98136b2d59..2f44890844 100644 --- a/openmc/model/model.py +++ b/openmc/model/model.py @@ -6,10 +6,12 @@ from pathlib import Path from numbers import Integral from tempfile import NamedTemporaryFile import warnings +from xml.etree import ElementTree as ET import h5py import openmc +import openmc._xml as xml from openmc.dummy_comm import DummyCommunicator from openmc.executor import _process_CLI_arguments from openmc.checkvalue import check_type, check_value @@ -238,6 +240,35 @@ class Model: plots = openmc.Plots.from_xml(plots) if Path(plots).exists() else None return cls(geometry, materials, settings, tallies, plots) + @classmethod + def from_model_xml(cls, path='model.xml'): + """Create model from single XML file + + .. vesionadded:: 0.13.3 + + Parameters + ---------- + path : str or Pathlike + Path to model.xml file + """ + tree = ET.parse(path) + root = tree.getroot() + + model = cls() + + meshes = {} + model.settings = openmc.Settings.from_xml_element(root.find('settings'), meshes) + model.materials = openmc.Materials.from_xml_element(root.find('materials')) + model.geometry = openmc.Geometry.from_xml_element(root.find('geometry'), model.materials) + + if root.find('tallies'): + model.tallies = openmc.Tallies.from_xml_element(root.find('tallies'), meshes) + + if root.find('plots'): + model.plots = openmc.Plots.from_xml_element(root.find('plots')) + + return model + def init_lib(self, threads=None, geometry_debug=False, restart_file=None, tracks=False, output=True, event_based=None, intracomm=None): """Initializes the model in memory via the C API @@ -399,7 +430,7 @@ class Model: depletion_operator.finalize() def export_to_xml(self, directory='.', remove_surfs=False): - """Export model to XML files. + """Export model to separate XML files. Parameters ---------- @@ -418,14 +449,7 @@ class Model: d.mkdir(parents=True) self.settings.export_to_xml(d) - if remove_surfs: - warnings.warn("remove_surfs kwarg will be deprecated soon, please " - "set the Geometry.merge_surfaces attribute instead.") - self.geometry.merge_surfaces = True - # Can be used to modify tallies in case any surfaces are redundant - redundant_surfaces = self.geometry.remove_redundant_surfaces() - - self.geometry.export_to_xml(d) + self.geometry.export_to_xml(d, remove_surfs=remove_surfs) # If a materials collection was specified, export it. Otherwise, look # for all materials in the geometry and use that to automatically build @@ -442,6 +466,78 @@ class Model: if self.plots: self.plots.export_to_xml(d) + def export_to_model_xml(self, path='model.xml', remove_surfs=False): + """Export model to a single XML file. + + .. versionadded:: 0.13.3 + + Parameters + ---------- + path : str or Pathlike + Location of the XML file to write (default is 'model.xml'). Can be a + directory or file path. + remove_surfs : bool + Whether or not to remove redundant surfaces from the geometry when + exporting. + + """ + xml_path = Path(path) + # if the provided path doesn't end with the XML extension, assume the + # input path is meant to be a directory. If the directory does not + # exist, create it and place a 'model.xml' file there. + if not str(xml_path).endswith('.xml') and not xml_path.exists(): + os.mkdir(xml_path) + xml_path /= 'model.xml' + # if this is an XML file location and the file's parent directory does + # not exist, create it before continuing + elif not xml_path.parent.exists(): + os.mkdir(xml_path.parent) + + if remove_surfs: + warnings.warn("remove_surfs kwarg will be deprecated soon, please " + "set the Geometry.merge_surfaces attribute instead.") + self.geometry.merge_surfaces = True + # Can be used to modify tallies in case any surfaces are redundant + redundant_surfaces = self.geometry.remove_redundant_surfaces() + + # provide a memo to track which meshes have been written + mesh_memo = set() + settings_element = self.settings.to_xml_element(mesh_memo) + geometry_element = self.geometry.to_xml_element() + + xml.clean_indentation(geometry_element, level=1) + xml.clean_indentation(settings_element, level=1) + + # If a materials collection was specified, export it. Otherwise, look + # for all materials in the geometry and use that to automatically build + # a collection. + if self.materials: + materials = self.materials + else: + materials = openmc.Materials(self.geometry.get_all_materials() + .values()) + + with open(xml_path, 'w', encoding='utf-8', errors='xmlcharrefreplace') as fh: + # write the XML header + fh.write("\n") + fh.write("\n") + # Write the materials collection to the open XML file first. + # This will write the XML header also + materials._write_xml(fh, False, level=1) + # Write remaining elements as a tree + ET.ElementTree(geometry_element).write(fh, encoding='unicode') + ET.ElementTree(settings_element).write(fh, encoding='unicode') + + if self.tallies: + tallies_element = self.tallies.to_xml_element(mesh_memo) + xml.clean_indentation(tallies_element, level=1, trailing_indent=self.plots) + ET.ElementTree(tallies_element).write(fh, encoding='unicode') + if self.plots: + plots_element = self.plots.to_xml_element() + xml.clean_indentation(plots_element, level=1, trailing_indent=False) + ET.ElementTree(plots_element).write(fh, encoding='unicode') + fh.write("\n") + def import_properties(self, filename): """Import physical properties diff --git a/openmc/nuclide.py b/openmc/nuclide.py index 196c8d7701..d5ae4bddbb 100644 --- a/openmc/nuclide.py +++ b/openmc/nuclide.py @@ -26,7 +26,7 @@ class Nuclide(str): if name.endswith('m'): name = name[:-1] + '_m1' - msg = ('OpenMC nuclides follow the GND naming convention. ' + msg = ('OpenMC nuclides follow the GNDS naming convention. ' f'Nuclide "{orig_name}" is being renamed as "{name}".') warnings.warn(msg) diff --git a/openmc/plots.py b/openmc/plots.py index 2708683b1a..0a04516259 100644 --- a/openmc/plots.py +++ b/openmc/plots.py @@ -909,13 +909,13 @@ class Plots(cv.CheckedList): self._plots_file.append(xml_element) - def export_to_xml(self, path='plots.xml'): - """Export plot specifications to an XML file. + def to_xml_element(self): + """Create a 'plots' element to be written to an XML file. - Parameters - ---------- - path : str - Path to file to write. Defaults to 'plots.xml'. + Returns + ------- + element : xml.etree.ElementTree.Element + XML element containing all plot elements """ # Reset xml element tree @@ -925,17 +925,50 @@ class Plots(cv.CheckedList): # Clean the indentation in the file to be user-readable clean_indentation(self._plots_file) + reorder_attributes(self._plots_file) # TODO: Remove when support is Python 3.8+ + return self._plots_file + + def export_to_xml(self, path='plots.xml'): + """Export plot specifications to an XML file. + + Parameters + ---------- + path : str + Path to file to write. Defaults to 'plots.xml'. + + """ # Check if path is a directory p = Path(path) if p.is_dir(): p /= 'plots.xml' + self.to_xml_element() # Write the XML Tree to the plots.xml file - reorder_attributes(self._plots_file) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(self._plots_file) tree.write(str(p), xml_declaration=True, encoding='utf-8') + @classmethod + def from_xml_element(cls, elem): + """Generate plots collection from XML file + + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element + + Returns + ------- + openmc.Plots + Plots collection + + """ + # Generate each plot + plots = cls() + for e in elem.findall('plot'): + plots.append(Plot.from_xml_element(e)) + return plots + @classmethod def from_xml(cls, path='plots.xml'): """Generate plots collection from XML file @@ -953,9 +986,6 @@ class Plots(cv.CheckedList): """ tree = ET.parse(path) root = tree.getroot() + return cls.from_xml_element(root) + - # Generate each plot - plots = cls() - for elem in root.findall('plot'): - plots.append(Plot.from_xml_element(elem)) - return plots diff --git a/openmc/plotter.py b/openmc/plotter.py index 16760868e3..e2d18d0857 100644 --- a/openmc/plotter.py +++ b/openmc/plotter.py @@ -563,7 +563,7 @@ def _calculate_cexs_elem_mat(this, types, temperature=294., for nuclide in nuclides.items(): sabs[nuclide[0]] = None if isinstance(this, openmc.Material): - for sab_name in this._sab: + for sab_name, _ in this._sab: sab = openmc.data.ThermalScattering.from_hdf5( library.get_by_material(sab_name, data_type='thermal')['path']) for nuc in sab.nuclides: diff --git a/openmc/settings.py b/openmc/settings.py index 7d327ce7cf..22a83509f3 100644 --- a/openmc/settings.py +++ b/openmc/settings.py @@ -157,6 +157,7 @@ class Settings: :separate: bool indicating whether the source should be written as a separate file :write: bool indicating whether or not to write the source + :mcpl: bool indicating whether to write the source as an MCPL file statepoint : dict Options for writing state points. Acceptable keys are: @@ -172,6 +173,7 @@ class Settings: banked (int) :max_particles: Maximum number of particles to be banked on surfaces per process (int) + :mcpl: Output in the form of an MCPL-file (bool) survival_biasing : bool Indicate whether survival biasing is to be used tabular_legendre : dict @@ -223,6 +225,10 @@ class Settings: Weight windows to use for variance reduction .. versionadded:: 0.13 + create_delayed_neutrons : bool + Whether delayed neutrons are created in fission. + + .. versionadded:: 0.13.3 weight_windows_on : bool Whether weight windows are enabled @@ -294,6 +300,7 @@ class Settings: VolumeCalculation, 'volume calculations') self._create_fission_neutrons = None + self._create_delayed_neutrons = None self._delayed_photon_scaling = None self._material_cell_offsets = None self._log_grid_bins = None @@ -457,6 +464,10 @@ class Settings: def create_fission_neutrons(self) -> bool: return self._create_fission_neutrons + @property + def create_delayed_neutrons(self) -> bool: + return self._create_delayed_neutrons + @property def delayed_photon_scaling(self) -> bool: return self._delayed_photon_scaling @@ -622,6 +633,8 @@ class Settings: cv.check_type('sourcepoint write', value, bool) elif key == 'overwrite': cv.check_type('sourcepoint overwrite', value, bool) + elif key == 'mcpl': + cv.check_type('sourcepoint mcpl', value, bool) else: raise ValueError(f"Unknown key '{key}' encountered when " "setting sourcepoint options.") @@ -655,7 +668,7 @@ class Settings: cv.check_type('surface source writing options', surf_source_write, Mapping) for key, value in surf_source_write.items(): cv.check_value('surface source writing key', key, - ('surface_ids', 'max_particles')) + ('surface_ids', 'max_particles', 'mcpl')) if key == 'surface_ids': cv.check_type('surface ids for source banking', value, Iterable, Integral) @@ -667,6 +680,9 @@ class Settings: value, Integral) cv.check_greater_than('maximum particle banks on surfaces per process', value, 0) + elif key == 'mcpl': + cv.check_type('write to an MCPL-format file', value, bool) + self._surf_source_write = surf_source_write @confidence_intervals.setter @@ -859,6 +875,12 @@ class Settings: create_fission_neutrons, bool) self._create_fission_neutrons = create_fission_neutrons + @create_delayed_neutrons.setter + def create_delayed_neutrons(self, create_delayed_neutrons: bool): + cv.check_type('Whether create only prompt neutrons', + create_delayed_neutrons, bool) + self._create_delayed_neutrons = create_delayed_neutrons + @delayed_photon_scaling.setter def delayed_photon_scaling(self, value: bool): cv.check_type('delayed photon scaling', value, bool) @@ -1018,6 +1040,10 @@ class Settings: subelement = ET.SubElement(element, "overwrite_latest") subelement.text = str(self._sourcepoint['overwrite']).lower() + if 'mcpl' in self._sourcepoint: + subelement = ET.SubElement(element, "mcpl") + subelement.text = str(self._sourcepoint['mcpl']).lower() + def _create_surf_source_read_subelement(self, root): if self._surf_source_read: element = ET.SubElement(root, "surf_source_read") @@ -1035,6 +1061,9 @@ class Settings: if 'max_particles' in self._surf_source_write: subelement = ET.SubElement(element, "max_particles") subelement.text = str(self._surf_source_write['max_particles']) + if 'mcpl' in self._surf_source_write: + subelement = ET.SubElement(element, "mcpl") + subelement.text = str(self._surf_source_write['mcpl']).lower() def _create_confidence_intervals(self, root): if self._confidence_intervals is not None: @@ -1073,25 +1102,35 @@ class Settings: subelement = ET.SubElement(element, key) subelement.text = str(value) - def _create_entropy_mesh_subelement(self, root): - if self.entropy_mesh is not None: - # use default heuristic for entropy mesh if not set by user - if self.entropy_mesh.dimension is None: - if self.particles is None: - raise RuntimeError("Number of particles must be set in order to " \ - "use entropy mesh dimension heuristic") - else: - n = ceil((self.particles / 20.0)**(1.0 / 3.0)) - d = len(self.entropy_mesh.lower_left) - self.entropy_mesh.dimension = (n,)*d + def _create_entropy_mesh_subelement(self, root, mesh_memo=None): + if self.entropy_mesh is None: + return - # See if a element already exists -- if not, add it - path = f"./mesh[@id='{self.entropy_mesh.id}']" - if root.find(path) is None: - root.append(self.entropy_mesh.to_xml_element()) + # use default heuristic for entropy mesh if not set by user + if self.entropy_mesh.dimension is None: + if self.particles is None: + raise RuntimeError("Number of particles must be set in order to " \ + "use entropy mesh dimension heuristic") + else: + n = ceil((self.particles / 20.0)**(1.0 / 3.0)) + d = len(self.entropy_mesh.lower_left) + self.entropy_mesh.dimension = (n,)*d - subelement = ET.SubElement(root, "entropy_mesh") - subelement.text = str(self.entropy_mesh.id) + # add mesh ID to this element + subelement = ET.SubElement(root, "entropy_mesh") + subelement.text = str(self.entropy_mesh.id) + + # If this mesh has already been written outside the + # settings element, skip writing it again + if mesh_memo and self.entropy_mesh.id in mesh_memo: + return + + # See if a element already exists -- if not, add it + path = f"./mesh[@id='{self.entropy_mesh.id}']" + if root.find(path) is None: + root.append(self.entropy_mesh.to_xml_element()) + if mesh_memo is not None: + mesh_memo.add(self.entropy_mesh.id) def _create_trigger_subelement(self, root): if self._trigger_active is not None: @@ -1142,15 +1181,21 @@ class Settings: element = ET.SubElement(root, "track") element.text = ' '.join(map(str, itertools.chain(*self._track))) - def _create_ufs_mesh_subelement(self, root): - if self.ufs_mesh is not None: - # See if a element already exists -- if not, add it - path = f"./mesh[@id='{self.ufs_mesh.id}']" - if root.find(path) is None: - root.append(self.ufs_mesh.to_xml_element()) + def _create_ufs_mesh_subelement(self, root, mesh_memo=None): + if self.ufs_mesh is None: + return - subelement = ET.SubElement(root, "ufs_mesh") - subelement.text = str(self.ufs_mesh.id) + subelement = ET.SubElement(root, "ufs_mesh") + subelement.text = str(self.ufs_mesh.id) + + if mesh_memo and self.ufs_mesh.id in mesh_memo: + return + + # See if a element already exists -- if not, add it + path = f"./mesh[@id='{self.ufs_mesh.id}']" + if root.find(path) is None: + root.append(self.ufs_mesh.to_xml_element()) + if mesh_memo is not None: mesh_memo.add(self.ufs_mesh.id) def _create_resonance_scattering_subelement(self, root): res = self.resonance_scattering @@ -1177,6 +1222,11 @@ class Settings: elem = ET.SubElement(root, "create_fission_neutrons") elem.text = str(self._create_fission_neutrons).lower() + def _create_create_delayed_neutrons_subelement(self, root): + if self._create_delayed_neutrons is not None: + elem = ET.SubElement(root, "create_delayed_neutrons") + elem.text = str(self._create_delayed_neutrons).lower() + def _create_delayed_photon_scaling_subelement(self, root): if self._delayed_photon_scaling is not None: elem = ET.SubElement(root, "delayed_photon_scaling") @@ -1207,15 +1257,21 @@ class Settings: elem = ET.SubElement(root, "write_initial_source") elem.text = str(self._write_initial_source).lower() - def _create_weight_windows_subelement(self, root): + def _create_weight_windows_subelement(self, root, mesh_memo=None): for ww in self._weight_windows: # Add weight window information root.append(ww.to_xml_element()) + # if this mesh has already been written, + # skip writing the mesh element + if mesh_memo and ww.mesh.id in mesh_memo: + continue + # See if a element already exists -- if not, add it path = f"./mesh[@id='{ww.mesh.id}']" if root.find(path) is None: root.append(ww.mesh.to_xml_element()) + if mesh_memo is not None: mesh_memo.add(ww.mesh.id) if self._weight_windows_on is not None: elem = ET.SubElement(root, "weight_windows_on") @@ -1315,10 +1371,10 @@ class Settings: def _sourcepoint_from_xml_element(self, root): elem = root.find('source_point') if elem is not None: - for key in ('separate', 'write', 'overwrite_latest', 'batches'): + for key in ('separate', 'write', 'overwrite_latest', 'batches', 'mcpl'): value = get_text(elem, key) if value is not None: - if key in ('separate', 'write'): + if key in ('separate', 'write', 'mcpl'): value = value in ('true', '1') elif key == 'overwrite_latest': value = value in ('true', '1') @@ -1337,13 +1393,15 @@ class Settings: def _surf_source_write_from_xml_element(self, root): elem = root.find('surf_source_write') if elem is not None: - for key in ('surface_ids', 'max_particles'): + for key in ('surface_ids', 'max_particles','mcpl'): value = get_text(elem, key) if value is not None: if key == 'surface_ids': value = [int(x) for x in value.split()] elif key in ('max_particles'): value = int(value) + elif key == 'mcpl': + value = value in ('true', '1') self.surf_source_write[key] = value def _confidence_intervals_from_xml_element(self, root): @@ -1396,13 +1454,15 @@ class Settings: if value is not None: self.cutoff[key] = float(value) - def _entropy_mesh_from_xml_element(self, root): + def _entropy_mesh_from_xml_element(self, root, meshes=None): text = get_text(root, 'entropy_mesh') if text is not None: path = f"./mesh[@id='{int(text)}']" elem = root.find(path) if elem is not None: self.entropy_mesh = RegularMesh.from_xml_element(elem) + if meshes is not None and self.entropy_mesh is not None: + meshes[self.entropy_mesh.id] = self.entropy_mesh def _trigger_from_xml_element(self, root): elem = root.find('trigger') @@ -1462,13 +1522,15 @@ class Settings: values = [int(x) for x in text.split()] self.track = list(zip(values[::3], values[1::3], values[2::3])) - def _ufs_mesh_from_xml_element(self, root): + def _ufs_mesh_from_xml_element(self, root, meshes=None): text = get_text(root, 'ufs_mesh') if text is not None: path = f"./mesh[@id='{int(text)}']" elem = root.find(path) if elem is not None: self.ufs_mesh = RegularMesh.from_xml_element(elem) + if meshes is not None and self.ufs_mesh is not None: + meshes[self.ufs_mesh.id] = self.ufs_mesh def _resonance_scattering_from_xml_element(self, root): elem = root.find('resonance_scattering') @@ -1490,6 +1552,11 @@ class Settings: if text is not None: self.create_fission_neutrons = text in ('true', '1') + def _create_delayed_neutrons_from_xml_element(self, root): + text = get_text(root, 'create_delayed_neutrons') + if text is not None: + self.create_delayed_neutrons = text in ('true', '1') + def _delayed_photon_scaling_from_xml_element(self, root): text = get_text(root, 'delayed_photon_scaling') if text is not None: @@ -1520,7 +1587,7 @@ class Settings: if text is not None: self.write_initial_source = text in ('true', '1') - def _weight_windows_from_xml_element(self, root): + def _weight_windows_from_xml_element(self, root, meshes=None): for elem in root.findall('weight_windows'): ww = WeightWindows.from_xml_element(elem, root) self.weight_windows.append(ww) @@ -1529,6 +1596,9 @@ class Settings: if text is not None: self.weight_windows_on = text in ('true', '1') + if meshes is not None and self.weight_windows: + meshes.update({ww.mesh.id: ww.mesh for ww in self.weight_windows}) + def _max_splits_from_xml_element(self, root): text = get_text(root, 'max_splits') if text is not None: @@ -1539,6 +1609,69 @@ class Settings: if text is not None: self.max_tracks = int(text) + def to_xml_element(self, mesh_memo=None): + """Create a 'settings' element to be written to an XML file. + + Parameters + ---------- + mesh_memo : set of ints + A set of mesh IDs to keep track of whether a mesh has already been written. + """ + # Reset xml element tree + element = ET.Element("settings") + + self._create_run_mode_subelement(element) + self._create_particles_subelement(element) + self._create_batches_subelement(element) + self._create_inactive_subelement(element) + self._create_max_lost_particles_subelement(element) + self._create_rel_max_lost_particles_subelement(element) + self._create_generations_per_batch_subelement(element) + self._create_keff_trigger_subelement(element) + self._create_source_subelement(element) + self._create_output_subelement(element) + self._create_statepoint_subelement(element) + self._create_sourcepoint_subelement(element) + self._create_surf_source_read_subelement(element) + self._create_surf_source_write_subelement(element) + self._create_confidence_intervals(element) + self._create_electron_treatment_subelement(element) + self._create_energy_mode_subelement(element) + self._create_max_order_subelement(element) + self._create_photon_transport_subelement(element) + self._create_ptables_subelement(element) + self._create_seed_subelement(element) + self._create_survival_biasing_subelement(element) + self._create_cutoff_subelement(element) + self._create_entropy_mesh_subelement(element, mesh_memo) + self._create_trigger_subelement(element) + self._create_no_reduce_subelement(element) + self._create_verbosity_subelement(element) + self._create_tabular_legendre_subelements(element) + self._create_temperature_subelements(element) + self._create_trace_subelement(element) + self._create_track_subelement(element) + self._create_ufs_mesh_subelement(element, mesh_memo) + self._create_resonance_scattering_subelement(element) + self._create_volume_calcs_subelement(element) + self._create_create_fission_neutrons_subelement(element) + self._create_create_delayed_neutrons_subelement(element) + self._create_delayed_photon_scaling_subelement(element) + self._create_event_based_subelement(element) + self._create_max_particles_in_flight_subelement(element) + self._create_material_cell_offsets_subelement(element) + self._create_log_grid_bins_subelement(element) + self._create_write_initial_source_subelement(element) + self._create_weight_windows_subelement(element, mesh_memo) + self._create_max_splits_subelement(element) + self._create_max_tracks_subelement(element) + + # Clean the indentation in the file to be user-readable + clean_indentation(element) + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ + + return element + def export_to_xml(self, path: PathLike = 'settings.xml'): """Export simulation settings to an XML file. @@ -1548,57 +1681,7 @@ class Settings: Path to file to write. Defaults to 'settings.xml'. """ - - # Reset xml element tree - root_element = ET.Element("settings") - - self._create_run_mode_subelement(root_element) - self._create_particles_subelement(root_element) - self._create_batches_subelement(root_element) - self._create_inactive_subelement(root_element) - self._create_max_lost_particles_subelement(root_element) - self._create_rel_max_lost_particles_subelement(root_element) - self._create_generations_per_batch_subelement(root_element) - self._create_keff_trigger_subelement(root_element) - self._create_source_subelement(root_element) - self._create_output_subelement(root_element) - self._create_statepoint_subelement(root_element) - self._create_sourcepoint_subelement(root_element) - self._create_surf_source_read_subelement(root_element) - self._create_surf_source_write_subelement(root_element) - self._create_confidence_intervals(root_element) - self._create_electron_treatment_subelement(root_element) - self._create_energy_mode_subelement(root_element) - self._create_max_order_subelement(root_element) - self._create_photon_transport_subelement(root_element) - self._create_ptables_subelement(root_element) - self._create_seed_subelement(root_element) - self._create_survival_biasing_subelement(root_element) - self._create_cutoff_subelement(root_element) - self._create_entropy_mesh_subelement(root_element) - self._create_trigger_subelement(root_element) - self._create_no_reduce_subelement(root_element) - self._create_verbosity_subelement(root_element) - self._create_tabular_legendre_subelements(root_element) - self._create_temperature_subelements(root_element) - self._create_trace_subelement(root_element) - self._create_track_subelement(root_element) - self._create_ufs_mesh_subelement(root_element) - self._create_resonance_scattering_subelement(root_element) - self._create_volume_calcs_subelement(root_element) - self._create_create_fission_neutrons_subelement(root_element) - self._create_delayed_photon_scaling_subelement(root_element) - self._create_event_based_subelement(root_element) - self._create_max_particles_in_flight_subelement(root_element) - self._create_material_cell_offsets_subelement(root_element) - self._create_log_grid_bins_subelement(root_element) - self._create_write_initial_source_subelement(root_element) - self._create_weight_windows_subelement(root_element) - self._create_max_splits_subelement(root_element) - self._create_max_tracks_subelement(root_element) - - # Clean the indentation in the file to be user-readable - clean_indentation(root_element) + root_element = self.to_xml_element() # Check if path is a directory p = Path(path) @@ -1606,10 +1689,79 @@ class Settings: p /= 'settings.xml' # Write the XML Tree to the settings.xml file - reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') + @classmethod + def from_xml_element(cls, elem, meshes=None): + """Generate settings from XML element + + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element + meshes : dict or None + A dictionary with mesh IDs as keys and mesh instances as values that + have already been read from XML. Pre-existing meshes are used + and new meshes are added to when creating tally objects. + + Returns + ------- + openmc.Settings + Settings object + + """ + settings = cls() + settings._eigenvalue_from_xml_element(elem) + settings._run_mode_from_xml_element(elem) + settings._particles_from_xml_element(elem) + settings._batches_from_xml_element(elem) + settings._inactive_from_xml_element(elem) + settings._max_lost_particles_from_xml_element(elem) + settings._rel_max_lost_particles_from_xml_element(elem) + settings._generations_per_batch_from_xml_element(elem) + settings._keff_trigger_from_xml_element(elem) + settings._source_from_xml_element(elem) + settings._volume_calcs_from_xml_element(elem) + settings._output_from_xml_element(elem) + settings._statepoint_from_xml_element(elem) + settings._sourcepoint_from_xml_element(elem) + settings._surf_source_read_from_xml_element(elem) + settings._surf_source_write_from_xml_element(elem) + settings._confidence_intervals_from_xml_element(elem) + settings._electron_treatment_from_xml_element(elem) + settings._energy_mode_from_xml_element(elem) + settings._max_order_from_xml_element(elem) + settings._photon_transport_from_xml_element(elem) + settings._ptables_from_xml_element(elem) + settings._seed_from_xml_element(elem) + settings._survival_biasing_from_xml_element(elem) + settings._cutoff_from_xml_element(elem) + settings._entropy_mesh_from_xml_element(elem, meshes) + settings._trigger_from_xml_element(elem) + settings._no_reduce_from_xml_element(elem) + settings._verbosity_from_xml_element(elem) + settings._tabular_legendre_from_xml_element(elem) + settings._temperature_from_xml_element(elem) + settings._trace_from_xml_element(elem) + settings._track_from_xml_element(elem) + settings._ufs_mesh_from_xml_element(elem, meshes) + settings._resonance_scattering_from_xml_element(elem) + settings._create_fission_neutrons_from_xml_element(elem) + settings._create_delayed_neutrons_from_xml_element(elem) + settings._delayed_photon_scaling_from_xml_element(elem) + settings._event_based_from_xml_element(elem) + settings._max_particles_in_flight_from_xml_element(elem) + settings._material_cell_offsets_from_xml_element(elem) + settings._log_grid_bins_from_xml_element(elem) + settings._write_initial_source_from_xml_element(elem) + settings._weight_windows_from_xml_element(elem, meshes) + settings._max_splits_from_xml_element(elem) + settings._max_tracks_from_xml_element(elem) + + # TODO: Get volume calculations + return settings + @classmethod def from_xml(cls, path: PathLike = 'settings.xml'): """Generate settings from XML file @@ -1629,54 +1781,4 @@ class Settings: """ tree = ET.parse(path) root = tree.getroot() - - settings = cls() - settings._eigenvalue_from_xml_element(root) - settings._run_mode_from_xml_element(root) - settings._particles_from_xml_element(root) - settings._batches_from_xml_element(root) - settings._inactive_from_xml_element(root) - settings._max_lost_particles_from_xml_element(root) - settings._rel_max_lost_particles_from_xml_element(root) - settings._generations_per_batch_from_xml_element(root) - settings._keff_trigger_from_xml_element(root) - settings._source_from_xml_element(root) - settings._volume_calcs_from_xml_element(root) - settings._output_from_xml_element(root) - settings._statepoint_from_xml_element(root) - settings._sourcepoint_from_xml_element(root) - settings._surf_source_read_from_xml_element(root) - settings._surf_source_write_from_xml_element(root) - settings._confidence_intervals_from_xml_element(root) - settings._electron_treatment_from_xml_element(root) - settings._energy_mode_from_xml_element(root) - settings._max_order_from_xml_element(root) - settings._photon_transport_from_xml_element(root) - settings._ptables_from_xml_element(root) - settings._seed_from_xml_element(root) - settings._survival_biasing_from_xml_element(root) - settings._cutoff_from_xml_element(root) - settings._entropy_mesh_from_xml_element(root) - settings._trigger_from_xml_element(root) - settings._no_reduce_from_xml_element(root) - settings._verbosity_from_xml_element(root) - settings._tabular_legendre_from_xml_element(root) - settings._temperature_from_xml_element(root) - settings._trace_from_xml_element(root) - settings._track_from_xml_element(root) - settings._ufs_mesh_from_xml_element(root) - settings._resonance_scattering_from_xml_element(root) - settings._create_fission_neutrons_from_xml_element(root) - settings._delayed_photon_scaling_from_xml_element(root) - settings._event_based_from_xml_element(root) - settings._max_particles_in_flight_from_xml_element(root) - settings._material_cell_offsets_from_xml_element(root) - settings._log_grid_bins_from_xml_element(root) - settings._write_initial_source_from_xml_element(root) - settings._weight_windows_from_xml_element(root) - settings._max_splits_from_xml_element(root) - settings._max_tracks_from_xml_element(root) - - # TODO: Get volume calculations - - return settings + return cls.from_xml_element(root) diff --git a/openmc/tallies.py b/openmc/tallies.py index d0355f14ee..b22cc4cf0a 100644 --- a/openmc/tallies.py +++ b/openmc/tallies.py @@ -3119,17 +3119,17 @@ class Tallies(cv.CheckedList): for tally in self: root_element.append(tally.to_xml_element()) - def _create_mesh_subelements(self, root_element): - already_written = set() + def _create_mesh_subelements(self, root_element, memo=None): + already_written = memo if memo else set() for tally in self: for f in tally.filters: if isinstance(f, openmc.MeshFilter): - if f.mesh.id not in already_written: - if len(f.mesh.name) > 0: - root_element.append(ET.Comment(f.mesh.name)) - - root_element.append(f.mesh.to_xml_element()) - already_written.add(f.mesh.id) + if f.mesh.id in already_written: + continue + if len(f.mesh.name) > 0: + root_element.append(ET.Comment(f.mesh.name)) + root_element.append(f.mesh.to_xml_element()) + already_written.add(f.mesh.id) def _create_filter_subelements(self, root_element): already_written = dict() @@ -3155,6 +3155,22 @@ class Tallies(cv.CheckedList): for d in derivs: root_element.append(d.to_xml_element()) + def to_xml_element(self, memo=None): + """Creates a 'tallies' element to be written to an XML file. + """ + element = ET.Element("tallies") + self._create_mesh_subelements(element, memo) + self._create_filter_subelements(element) + self._create_tally_subelements(element) + self._create_derivative_subelements(element) + + # Clean the indentation in the file to be user-readable + clean_indentation(element) + reorder_attributes(element) # TODO: Remove when support is Python 3.8+ + + return element + + def export_to_xml(self, path='tallies.xml'): """Create a tallies.xml file that can be used for a simulation. @@ -3164,15 +3180,7 @@ class Tallies(cv.CheckedList): Path to file to write. Defaults to 'tallies.xml'. """ - - root_element = ET.Element("tallies") - self._create_mesh_subelements(root_element) - self._create_filter_subelements(root_element) - self._create_tally_subelements(root_element) - self._create_derivative_subelements(root_element) - - # Clean the indentation in the file to be user-readable - clean_indentation(root_element) + root_element = self.to_xml_element() # Check if path is a directory p = Path(path) @@ -3180,10 +3188,56 @@ class Tallies(cv.CheckedList): p /= 'tallies.xml' # Write the XML Tree to the tallies.xml file - reorder_attributes(root_element) # TODO: Remove when support is Python 3.8+ tree = ET.ElementTree(root_element) tree.write(str(p), xml_declaration=True, encoding='utf-8') + @classmethod + def from_xml_element(cls, elem, meshes=None): + """Generate tallies from an XML element + + Parameters + ---------- + elem : xml.etree.ElementTree.Element + XML element + meshes : dict or None + A dictionary with mesh IDs as keys and mesh instances as values that + have already been read from XML. Pre-existing meshes are used + and new meshes are added to when creating tally objects. + + Returns + ------- + openmc.Tallies + Tallies object + + """ + # Read mesh elements + meshes = {} if meshes is None else meshes + for e in elem.findall('mesh'): + mesh = MeshBase.from_xml_element(e) + meshes[mesh.id] = mesh + + # Read filter elements + filters = {} + for e in elem.findall('filter'): + filter = openmc.Filter.from_xml_element(e, meshes=meshes) + filters[filter.id] = filter + + # Read derivative elements + derivatives = {} + for e in elem.findall('derivative'): + deriv = openmc.TallyDerivative.from_xml_element(e) + derivatives[deriv.id] = deriv + + # Read tally elements + tallies = [] + for e in elem.findall('tally'): + tally = openmc.Tally.from_xml_element( + e, filters=filters, derivatives=derivatives + ) + tallies.append(tally) + + return cls(tallies) + @classmethod def from_xml(cls, path='tallies.xml'): """Generate tallies from XML file @@ -3201,31 +3255,4 @@ class Tallies(cv.CheckedList): """ tree = ET.parse(path) root = tree.getroot() - - # Read mesh elements - meshes = {} - for elem in root.findall('mesh'): - mesh = MeshBase.from_xml_element(elem) - meshes[mesh.id] = mesh - - # Read filter elements - filters = {} - for elem in root.findall('filter'): - filter = openmc.Filter.from_xml_element(elem, meshes=meshes) - filters[filter.id] = filter - - # Read derivative elements - derivatives = {} - for elem in root.findall('derivative'): - deriv = openmc.TallyDerivative.from_xml_element(elem) - derivatives[deriv.id] = deriv - - # Read tally elements - tallies = [] - for elem in root.findall('tally'): - tally = openmc.Tally.from_xml_element( - elem, filters=filters, derivatives=derivatives - ) - tallies.append(tally) - - return cls(tallies) + return cls.from_xml_element(root) diff --git a/scripts/openmc-update-inputs b/scripts/openmc-update-inputs index c47f888c83..2d49c0626e 100755 --- a/scripts/openmc-update-inputs +++ b/scripts/openmc-update-inputs @@ -4,7 +4,6 @@ """ import argparse -from difflib import get_close_matches from itertools import chain from random import randint from shutil import move @@ -27,8 +26,8 @@ geometry.xml: Lattices containing 'outside' attributes/tags will be replaced will be renamed 'region'. materials.xml: Nuclide names will be changed from ACE aliases (e.g., Am-242m) to - HDF5/GND names (e.g., Am242_m1). Thermal scattering table names will be - changed from ACE aliases (e.g., HH2O) to HDF5/GND names (e.g., c_H_in_H2O). + HDF5/GNDS names (e.g., Am242_m1). Thermal scattering table names will be + changed from ACE aliases (e.g., HH2O) to HDF5/GNDS names (e.g., c_H_in_H2O). """ diff --git a/src/cross_sections.cpp b/src/cross_sections.cpp index afb0a1f36c..a7bd86095b 100644 --- a/src/cross_sections.cpp +++ b/src/cross_sections.cpp @@ -104,6 +104,11 @@ void read_cross_sections_xml() auto root = doc.document_element(); + read_cross_sections_xml(root); +} + +void read_cross_sections_xml(pugi::xml_node root) +{ // Find cross_sections.xml file -- the first place to look is the // materials.xml file. If no file is found there, then we check the // OPENMC_CROSS_SECTIONS environment variable diff --git a/src/finalize.cpp b/src/finalize.cpp index 0c2c62310e..59294b28c9 100644 --- a/src/finalize.cpp +++ b/src/finalize.cpp @@ -74,6 +74,7 @@ int openmc_finalize() settings::check_overlaps = false; settings::confidence_intervals = false; settings::create_fission_neutrons = true; + settings::create_delayed_neutrons = true; settings::electron_treatment = ElectronTreatment::LED; settings::delayed_photon_scaling = true; settings::energy_cutoff = {0.0, 1000.0, 0.0, 0.0}; diff --git a/src/geometry_aux.cpp b/src/geometry_aux.cpp index 2614719840..eabdc9f70d 100644 --- a/src/geometry_aux.cpp +++ b/src/geometry_aux.cpp @@ -61,6 +61,11 @@ void read_geometry_xml() // Get root element pugi::xml_node root = doc.document_element(); + read_geometry_xml(root); +} + +void read_geometry_xml(pugi::xml_node root) +{ // Read surfaces, cells, lattice read_surfaces(root); read_cells(root); diff --git a/src/initialize.cpp b/src/initialize.cpp index aa353aa9cb..1f9e40548a 100644 --- a/src/initialize.cpp +++ b/src/initialize.cpp @@ -14,6 +14,7 @@ #include "openmc/constants.h" #include "openmc/cross_sections.h" #include "openmc/error.h" +#include "openmc/file_utils.h" #include "openmc/geometry_aux.h" #include "openmc/hdf5_interface.h" #include "openmc/material.h" @@ -105,7 +106,11 @@ int openmc_init(int argc, char* argv[], const void* intracomm) openmc::openmc_set_seed(DEFAULT_SEED); // Read XML input files - read_input_xml(); + if (!read_model_xml()) + read_separate_xml_files(); + + // Write some initial output under the header if needed + initial_output(); // Check for particle restart run if (settings::particle_restart_run) @@ -177,10 +182,8 @@ int parse_command_line(int argc, char* argv[]) } else if (arg == "-e" || arg == "--event") { settings::event_based = true; - } else if (arg == "-r" || arg == "--restart") { i += 1; - // Check what type of file this is hid_t file_id = file_open(argv[i], 'r', true); std::string filetype; @@ -280,7 +283,15 @@ int parse_command_line(int argc, char* argv[]) if (argc > 1 && last_flag < argc - 1) { settings::path_input = std::string(argv[last_flag + 1]); - // Add slash at end of directory if it isn't there + // check that the path is either a valid directory or file + if (!dir_exists(settings::path_input) && + !file_exists(settings::path_input)) { + fatal_error(fmt::format( + "The path specified to the OpenMC executable '{}' does not exist.", + settings::path_input)); + } + + // Add slash at end of directory if it isn't the if (!ends_with(settings::path_input, "/")) { settings::path_input += "/"; } @@ -289,7 +300,105 @@ int parse_command_line(int argc, char* argv[]) return 0; } -void read_input_xml() +bool read_model_xml() +{ + std::string model_filename = + settings::path_input.empty() ? "." : settings::path_input; + + // some string cleanup + // a trailing "/" is applied to path_input if it's specified, + // remove it for the first attempt at reading the input file + if (ends_with(model_filename, "/")) + model_filename.pop_back(); + + // if the current filename is a directory, append the default model filename + if (dir_exists(model_filename)) + model_filename += "/model.xml"; + + // if this file doesn't exist, stop here + if (!file_exists(model_filename)) + return false; + + // try to process the path input as an XML file + pugi::xml_document doc; + if (!doc.load_file(model_filename.c_str())) { + fatal_error(fmt::format( + "Error reading from single XML input file '{}'", model_filename)); + } + + pugi::xml_node root = doc.document_element(); + + // Read settings + if (!check_for_node(root, "settings")) { + fatal_error("No node present in the model.xml file."); + } + auto settings_root = root.child("settings"); + + // Verbosity + if (check_for_node(settings_root, "verbosity")) { + settings::verbosity = std::stoi(get_node_value(settings_root, "verbosity")); + } + + // To this point, we haven't displayed any output since we didn't know what + // the verbosity is. Now that we checked for it, show the title if necessary + if (mpi::master) { + if (settings::verbosity >= 2) + title(); + } + + write_message( + fmt::format("Reading model XML file '{}' ...", model_filename), 5); + + read_settings_xml(settings_root); + + // If other XML files are present, display warning + // that they will be ignored + auto other_inputs = {"materials.xml", "geometry.xml", "settings.xml", + "tallies.xml", "plots.xml"}; + for (const auto& input : other_inputs) { + if (file_exists(settings::path_input + input)) { + warning((fmt::format("Other XML file input(s) are present. These files " + "will be ignored in favor of the {} file.", + model_filename))); + break; + } + } + + // Read materials and cross sections + if (!check_for_node(root, "materials")) { + fatal_error(fmt::format( + "No node present in the {} file.", model_filename)); + } + + read_cross_sections_xml(root.child("materials")); + read_materials_xml(root.child("materials")); + + // Read geometry + if (!check_for_node(root, "geometry")) { + fatal_error(fmt::format( + "No node present in the {} file.", model_filename)); + } + read_geometry_xml(root.child("geometry")); + + // Final geometry setup and assign temperatures + finalize_geometry(); + + // Finalize cross sections having assigned temperatures + finalize_cross_sections(); + + if (check_for_node(root, "tallies")) + read_tallies_xml(root.child("tallies")); + + // Initialize distribcell_filters + prepare_distribcell(); + + if (check_for_node(root, "plots")) + read_plots_xml(root.child("plots")); + + return true; +} + +void read_separate_xml_files() { read_settings_xml(); read_cross_sections_xml(); @@ -310,6 +419,11 @@ void read_input_xml() // Read the plots.xml regardless of plot mode in case plots are requested // via the API read_plots_xml(); +} + +void initial_output() +{ + // write initial output if (settings::run_mode == RunMode::PLOTTING) { // Read plots.xml if it exists if (mpi::master && settings::verbosity >= 5) diff --git a/src/material.cpp b/src/material.cpp index 30dfa5ed50..74a8d7e350 100644 --- a/src/material.cpp +++ b/src/material.cpp @@ -60,6 +60,13 @@ Material::Material(pugi::xml_node node) name_ = get_node_value(node, "name"); } + if (check_for_node(node, "cfg")) { + auto cfg = get_node_value(node, "cfg"); + write_message( + 5, "NCrystal config string for material #{}: '{}'", this->id(), cfg); + ncrystal_mat_ = NCrystalMat(cfg); + } + if (check_for_node(node, "depletable")) { depletable_ = get_node_value_bool(node, "depletable"); } @@ -367,8 +374,8 @@ void Material::finalize() this->init_thermal(); } -// Normalize density -this->normalize_density(); + // Normalize density + this->normalize_density(); } void Material::normalize_density() @@ -792,6 +799,12 @@ void Material::calculate_neutron_xs(Particle& p) const // Initialize position in i_sab_nuclides int j = 0; + // Calculate NCrystal cross section + double ncrystal_xs = -1.0; + if (ncrystal_mat_ && p.E() < NCRYSTAL_MAX_ENERGY) { + ncrystal_xs = ncrystal_mat_.xs(p); + } + // Add contribution from each nuclide in material for (int i = 0; i < nuclide_.size(); ++i) { // ====================================================================== @@ -830,10 +843,16 @@ void Material::calculate_neutron_xs(Particle& p) const int i_nuclide = nuclide_[i]; // Calculate microscopic cross section for this nuclide - const auto& micro {p.neutron_xs(i_nuclide)}; + auto& micro {p.neutron_xs(i_nuclide)}; if (p.E() != micro.last_E || p.sqrtkT() != micro.last_sqrtkT || i_sab != micro.index_sab || sab_frac != micro.sab_frac) { data::nuclides[i_nuclide]->calculate_xs(i_sab, i_grid, sab_frac, p); + + // If NCrystal is being used, update micro cross section cache + if (ncrystal_xs >= 0.0) { + data::nuclides[i_nuclide]->calculate_elastic_xs(p); + ncrystal_update_micro(ncrystal_xs, micro); + } } // ====================================================================== @@ -1281,6 +1300,12 @@ void read_materials_xml() // Loop over XML material elements and populate the array. pugi::xml_node root = doc.document_element(); + + read_materials_xml(root); +} + +void read_materials_xml(pugi::xml_node root) +{ for (pugi::xml_node material_node : root.children("material")) { model::materials.push_back(make_unique(material_node)); } diff --git a/src/mcpl_interface.cpp b/src/mcpl_interface.cpp new file mode 100644 index 0000000000..a388914782 --- /dev/null +++ b/src/mcpl_interface.cpp @@ -0,0 +1,247 @@ +#include "openmc/mcpl_interface.h" + +#include "openmc/bank.h" +#include "openmc/error.h" +#include "openmc/message_passing.h" +#include "openmc/settings.h" +#include "openmc/simulation.h" +#include "openmc/state_point.h" +#include "openmc/vector.h" + +#include + +#ifdef OPENMC_MCPL +#include +#endif + +namespace openmc { + +//============================================================================== +// Constants +//============================================================================== + +#ifdef OPENMC_MCPL +const bool MCPL_ENABLED = true; +#else +const bool MCPL_ENABLED = false; +#endif + +//============================================================================== +// Functions +//============================================================================== + +#ifdef OPENMC_MCPL +SourceSite mcpl_particle_to_site(const mcpl_particle_t* particle) +{ + SourceSite site; + + switch (particle->pdgcode) { + case 2112: + site.particle = ParticleType::neutron; + break; + case 22: + site.particle = ParticleType::photon; + break; + case 11: + site.particle = ParticleType::electron; + break; + case -11: + site.particle = ParticleType::positron; + break; + } + + // Copy position and direction + site.r.x = particle->position[0]; + site.r.y = particle->position[1]; + site.r.z = particle->position[2]; + site.u.x = particle->direction[0]; + site.u.y = particle->direction[1]; + site.u.z = particle->direction[2]; + + // MCPL stores kinetic energy in [MeV], time in [ms] + site.E = particle->ekin * 1e6; + site.time = particle->time * 1e-3; + site.wgt = particle->weight; + + return site; +} +#endif + +//============================================================================== + +vector mcpl_source_sites(std::string path) +{ + vector sites; + +#ifdef OPENMC_MCPL + // Open MCPL file and determine number of particles + auto mcpl_file = mcpl_open_file(path.c_str()); + size_t n_sites = mcpl_hdr_nparticles(mcpl_file); + + for (int i = 0; i < n_sites; i++) { + // Extract particle from mcpl-file, checking if it is a neutron, photon, + // electron, or positron. Otherwise skip. + const mcpl_particle_t* particle; + int pdg = 0; + while (pdg != 2112 && pdg != 22 && pdg != 11 && pdg != -11) { + particle = mcpl_read(mcpl_file); + pdg = particle->pdgcode; + } + + // Convert to source site and add to vector + sites.push_back(mcpl_particle_to_site(particle)); + } + + // Check that some sites were read + if (sites.empty()) { + fatal_error("MCPL file contained no neutron, photon, electron, or positron " + "source particles."); + } + + mcpl_close_file(mcpl_file); +#else + fatal_error( + "Your build of OpenMC does not support reading MCPL source files."); +#endif + + return sites; +} + +//============================================================================== + +#ifdef OPENMC_MCPL +void write_mcpl_source_bank(mcpl_outfile_t file_id, bool surf_source_bank) +{ + int64_t dims_size = settings::n_particles; + int64_t count_size = simulation::work_per_rank; + + // Set vectors for source bank and starting bank index of each process + vector* bank_index = &simulation::work_index; + vector* source_bank = &simulation::source_bank; + vector surf_source_index_vector; + vector surf_source_bank_vector; + + if (surf_source_bank) { + surf_source_index_vector = calculate_surf_source_size(); + dims_size = surf_source_index_vector[mpi::n_procs]; + count_size = simulation::surf_source_bank.size(); + + bank_index = &surf_source_index_vector; + + // Copy data in a SharedArray into a vector. + surf_source_bank_vector.resize(count_size); + surf_source_bank_vector.assign(simulation::surf_source_bank.data(), + simulation::surf_source_bank.data() + count_size); + source_bank = &surf_source_bank_vector; + } + + if (mpi::master) { + // Particles are writeen to disk from the master node only + + // Save source bank sites since the array is overwritten below +#ifdef OPENMC_MPI + vector temp_source {source_bank->begin(), source_bank->end()}; +#endif + + // loop over the other nodes and receive data - then write those. + for (int i = 0; i < mpi::n_procs; ++i) { + // number of particles for node node i + size_t count[] { + static_cast((*bank_index)[i + 1] - (*bank_index)[i])}; + +#ifdef OPENMC_MPI + if (i > 0) + MPI_Recv(source_bank->data(), count[0], mpi::source_site, i, i, + mpi::intracomm, MPI_STATUS_IGNORE); +#endif + // now write the source_bank data again. + for (const auto& site : *source_bank) { + // particle is now at the iterator + // write it to the mcpl-file + mcpl_particle_t p; + p.position[0] = site.r.x; + p.position[1] = site.r.y; + p.position[2] = site.r.z; + + // mcpl requires that the direction vector is unit length + // which is also the case in openmc + p.direction[0] = site.u.x; + p.direction[1] = site.u.y; + p.direction[2] = site.u.z; + + // MCPL stores kinetic energy in [MeV], time in [ms] + p.ekin = site.E * 1e-6; + p.time = site.time * 1e3; + p.weight = site.wgt; + + switch (site.particle) { + case ParticleType::neutron: + p.pdgcode = 2112; + break; + case ParticleType::photon: + p.pdgcode = 22; + break; + case ParticleType::electron: + p.pdgcode = 11; + break; + case ParticleType::positron: + p.pdgcode = -11; + break; + } + + mcpl_add_particle(file_id, &p); + } + } +#ifdef OPENMC_MPI + // Restore state of source bank + std::copy(temp_source.begin(), temp_source.end(), source_bank->begin()); +#endif + } else { +#ifdef OPENMC_MPI + MPI_Send(source_bank->data(), count_size, mpi::source_site, 0, mpi::rank, + mpi::intracomm); +#endif + } +} +#endif + +//============================================================================== + +void write_mcpl_source_point(const char* filename, bool surf_source_bank) +{ + std::string filename_; + if (filename) { + filename_ = filename; + } else { + // Determine width for zero padding + int w = std::to_string(settings::n_max_batches).size(); + + filename_ = fmt::format("{0}source.{1:0{2}}.mcpl", settings::path_output, + simulation::current_batch, w); + } + +#ifdef OPENMC_MCPL + mcpl_outfile_t file_id; + + std::string line; + if (mpi::master) { + file_id = mcpl_create_outfile(filename_.c_str()); + if (VERSION_DEV) { + line = fmt::format("OpenMC {0}.{1}.{2}-development", VERSION_MAJOR, + VERSION_MINOR, VERSION_RELEASE); + } else { + line = fmt::format( + "OpenMC {0}.{1}.{2}", VERSION_MAJOR, VERSION_MINOR, VERSION_RELEASE); + } + mcpl_hdr_set_srcname(file_id, line.c_str()); + } + + write_mcpl_source_bank(file_id, surf_source_bank); + + if (mpi::master) { + mcpl_close_outfile(file_id); + } +#endif +} + +} // namespace openmc diff --git a/src/ncrystal_interface.cpp b/src/ncrystal_interface.cpp new file mode 100644 index 0000000000..b39f62d902 --- /dev/null +++ b/src/ncrystal_interface.cpp @@ -0,0 +1,108 @@ +#include "openmc/ncrystal_interface.h" + +#include "openmc/error.h" +#include "openmc/material.h" +#include "openmc/random_lcg.h" + +namespace openmc { + +//============================================================================== +// Constants +//============================================================================== + +#ifdef NCRYSTAL +const bool NCRYSTAL_ENABLED = true; +#else +const bool NCRYSTAL_ENABLED = false; +#endif + +//============================================================================== +// NCrystal wrapper class for the OpenMC random number generator +//============================================================================== + +#ifdef NCRYSTAL +class NCrystalRNGWrapper : public NCrystal::RNGStream { +public: + constexpr NCrystalRNGWrapper(uint64_t* seed) noexcept : openmc_seed_(seed) {} + +protected: + double actualGenerate() override + { + return std::max( + std::numeric_limits::min(), prn(openmc_seed_)); + } + +private: + uint64_t* openmc_seed_; +}; +#endif + +//============================================================================== +// NCrystal implementation +//============================================================================== + +NCrystalMat::NCrystalMat(const std::string& cfg) +{ +#ifdef NCRYSTAL + cfg_ = cfg; + ptr_ = NCrystal::FactImpl::createScatter(cfg); +#else + fatal_error("Your build of OpenMC does not support NCrystal materials."); +#endif +} + +#ifdef NCRYSTAL +std::string NCrystalMat::cfg() const +{ + return cfg_; +} + +double NCrystalMat::xs(const Particle& p) const +{ + // Calculate scattering XS per atom with NCrystal, only once per material + NCrystal::CachePtr dummy_cache; + auto nc_energy = NCrystal::NeutronEnergy {p.E()}; + return ptr_->crossSection(dummy_cache, nc_energy, {p.u().x, p.u().y, p.u().z}) + .get(); +} + +void NCrystalMat::scatter(Particle& p) const +{ + NCrystalRNGWrapper rng(p.current_seed()); // Initialize RNG + // create a cache pointer for multi thread physics + NCrystal::CachePtr dummy_cache; + auto nc_energy = NCrystal::NeutronEnergy {p.E()}; + auto outcome = ptr_->sampleScatter( + dummy_cache, rng, nc_energy, {p.u().x, p.u().y, p.u().z}); + + // Modify attributes of particle + p.E() = outcome.ekin.get(); + Direction u_old {p.u()}; + p.u() = + Direction(outcome.direction[0], outcome.direction[1], outcome.direction[2]); + p.mu() = u_old.dot(p.u()); + p.event_mt() = ELASTIC; +} + +NCrystalMat::operator bool() const +{ + return ptr_.get(); +} +#endif + +//============================================================================== +// Functions +//============================================================================== + +void ncrystal_update_micro(double xs, NuclideMicroXS& micro) +{ + if (micro.thermal > 0 || micro.thermal_elastic > 0) { + fatal_error("S(a,b) treatment and NCrystal are not compatible."); + } + // remove free atom cross section + // and replace it by scattering cross section per atom from NCrystal + micro.total = micro.total - micro.elastic + xs; + micro.elastic = xs; +} + +} // namespace openmc diff --git a/src/nuclide.cpp b/src/nuclide.cpp index 134e2d6b9a..99ed44b112 100644 --- a/src/nuclide.cpp +++ b/src/nuclide.cpp @@ -519,7 +519,7 @@ double Nuclide::nu(double E, EmissionMode mode, int group) const case EmissionMode::prompt: return (*fission_rx_[0]->products_[0].yield_)(E); case EmissionMode::delayed: - if (n_precursor_ > 0) { + if (n_precursor_ > 0 && settings::create_delayed_neutrons) { auto rx = fission_rx_[0]; if (group >= 1 && group < rx->products_.size()) { // If delayed group specified, determine yield immediately @@ -544,7 +544,7 @@ double Nuclide::nu(double E, EmissionMode mode, int group) const return 0.0; } case EmissionMode::total: - if (total_nu_) { + if (total_nu_ && settings::create_delayed_neutrons) { return (*total_nu_)(E); } else { return (*fission_rx_[0]->products_[0].yield_)(E); diff --git a/src/physics.cpp b/src/physics.cpp index 7d391fdf62..7cb8040f63 100644 --- a/src/physics.cpp +++ b/src/physics.cpp @@ -10,6 +10,7 @@ #include "openmc/material.h" #include "openmc/math_functions.h" #include "openmc/message_passing.h" +#include "openmc/ncrystal_interface.h" #include "openmc/nuclide.h" #include "openmc/photon.h" #include "openmc/physics_common.h" @@ -140,7 +141,12 @@ void sample_neutron_reaction(Particle& p) // Sample a scattering reaction and determine the secondary energy of the // exiting neutron - scatter(p, i_nuclide); + const auto& ncrystal_mat = model::materials[p.material()]->ncrystal_mat(); + if (ncrystal_mat && p.E() < NCRYSTAL_MAX_ENERGY) { + ncrystal_mat.scatter(p); + } else { + scatter(p, i_nuclide); + } // Advance URR seed stream 'N' times after energy changes if (p.E() != p.E_last()) { diff --git a/src/plot.cpp b/src/plot.cpp index b012ed1311..fac13a1f4a 100644 --- a/src/plot.cpp +++ b/src/plot.cpp @@ -141,6 +141,12 @@ void read_plots_xml() doc.load_file(filename.c_str()); pugi::xml_node root = doc.document_element(); + + read_plots_xml(root); +} + +void read_plots_xml(pugi::xml_node root) +{ for (auto node : root.children("plot")) { model::plots.emplace_back(node); model::plot_map[model::plots.back().id_] = model::plots.size() - 1; diff --git a/src/settings.cpp b/src/settings.cpp index eb0d4936c7..feff4fbd32 100644 --- a/src/settings.cpp +++ b/src/settings.cpp @@ -18,6 +18,7 @@ #include "openmc/eigenvalue.h" #include "openmc/error.h" #include "openmc/file_utils.h" +#include "openmc/mcpl_interface.h" #include "openmc/mesh.h" #include "openmc/message_passing.h" #include "openmc/output.h" @@ -43,6 +44,7 @@ bool assume_separate {false}; bool check_overlaps {false}; bool cmfd_run {false}; bool confidence_intervals {false}; +bool create_delayed_neutrons {true}; bool create_fission_neutrons {true}; bool delayed_photon_scaling {true}; bool entropy_on {false}; @@ -60,7 +62,9 @@ bool run_CE {true}; bool source_latest {false}; bool source_separate {false}; bool source_write {true}; +bool source_mcpl_write {false}; bool surf_source_write {false}; +bool surf_mcpl_write {false}; bool surf_source_read {false}; bool survival_biasing {false}; bool temperature_multipole {false}; @@ -215,16 +219,16 @@ void read_settings_xml() { using namespace settings; using namespace pugi; - // Check if settings.xml exists - std::string filename = path_input + "settings.xml"; + std::string filename = settings::path_input + "settings.xml"; if (!file_exists(filename)) { if (run_mode != RunMode::PLOTTING) { fatal_error( fmt::format("Settings XML file '{}' does not exist! In order " "to run OpenMC, you first need a set of input files; at a " "minimum, this " - "includes settings.xml, geometry.xml, and materials.xml. " + "includes settings.xml, geometry.xml, and materials.xml " + "or a single XML file containing all of these files. " "Please consult " "the user's guide at https://docs.openmc.org for further " "information.", @@ -256,8 +260,17 @@ void read_settings_xml() if (verbosity >= 2) title(); } + write_message("Reading settings XML file...", 5); + read_settings_xml(root); +} + +void read_settings_xml(pugi::xml_node root) +{ + using namespace settings; + using namespace pugi; + // Find if a multi-group or continuous-energy simulation is desired if (check_for_node(root, "energy_mode")) { std::string temp_str = get_node_value(root, "energy_mode", true, true); @@ -429,7 +442,12 @@ void read_settings_xml() for (pugi::xml_node node : root.children("source")) { if (check_for_node(node, "file")) { auto path = get_node_value(node, "file", false, true); - model::external_sources.push_back(make_unique(path)); + if (ends_with(path, ".mcpl") || ends_with(path, ".mcpl.gz")) { + auto sites = mcpl_source_sites(path); + model::external_sources.push_back(make_unique(sites)); + } else { + model::external_sources.push_back(make_unique(path)); + } } else if (check_for_node(node, "library")) { // Get shared library path and parameters auto path = get_node_value(node, "library", false, true); @@ -647,6 +665,15 @@ void read_settings_xml() if (check_for_node(node_sp, "write")) { source_write = get_node_value_bool(node_sp, "write"); } + if (check_for_node(node_sp, "mcpl")) { + source_mcpl_write = get_node_value_bool(node_sp, "mcpl"); + + // Make sure MCPL support is enabled + if (source_mcpl_write && !MCPL_ENABLED) { + fatal_error( + "Your build of OpenMC does not support writing MCPL source files."); + } + } if (check_for_node(node_sp, "overwrite_latest")) { source_latest = get_node_value_bool(node_sp, "overwrite_latest"); source_separate = source_latest; @@ -677,9 +704,18 @@ void read_settings_xml() max_surface_particles = std::stoll(get_node_value(node_ssw, "max_particles")); } + if (check_for_node(node_ssw, "mcpl")) { + surf_mcpl_write = get_node_value_bool(node_ssw, "mcpl"); + + // Make sure MCPL support is enabled + if (surf_mcpl_write && !MCPL_ENABLED) { + fatal_error("Your build of OpenMC does not support writing MCPL " + "surface source files."); + } + } } - // If source is not seperate and is to be written out in the statepoint file, + // If source is not separate and is to be written out in the statepoint file, // make sure that the sourcepoint batch numbers are contained in the // statepoint list if (!source_separate) { @@ -838,6 +874,12 @@ void read_settings_xml() } } + // Check whether create delayed neutrons in fission + if (check_for_node(root, "create_delayed_neutrons")) { + create_delayed_neutrons = + get_node_value_bool(root, "create_delayed_neutrons"); + } + // Check whether create fission sites if (run_mode == RunMode::FIXED_SOURCE) { if (check_for_node(root, "create_fission_neutrons")) { diff --git a/src/simulation.cpp b/src/simulation.cpp index d7292cb9d9..2f07f8124f 100644 --- a/src/simulation.cpp +++ b/src/simulation.cpp @@ -8,6 +8,7 @@ #include "openmc/event.h" #include "openmc/geometry_aux.h" #include "openmc/material.h" +#include "openmc/mcpl_interface.h" #include "openmc/message_passing.h" #include "openmc/nuclide.h" #include "openmc/output.h" @@ -391,21 +392,35 @@ void finalize_batch() // Write out a separate source point if it's been specified for this batch if (contains(settings::sourcepoint_batch, simulation::current_batch) && settings::source_write && settings::source_separate) { - write_source_point(nullptr); + if (settings::source_mcpl_write) { + write_mcpl_source_point(nullptr); + } else { + write_source_point(nullptr); + } } // Write a continously-overwritten source point if requested. if (settings::source_latest) { - auto filename = settings::path_output + "source.h5"; - write_source_point(filename.c_str()); + if (settings::source_mcpl_write) { + auto filename = settings::path_output + "source.mcpl"; + write_mcpl_source_point(filename.c_str()); + } else { + auto filename = settings::path_output + "source.h5"; + write_source_point(filename.c_str()); + } } } // Write out surface source if requested. if (settings::surf_source_write && simulation::current_batch == settings::n_batches) { - auto filename = settings::path_output + "surface_source.h5"; - write_source_point(filename.c_str(), true); + if (settings::surf_mcpl_write) { + auto filename = settings::path_output + "surface_source.mcpl"; + write_mcpl_source_point(filename.c_str(), true); + } else { + auto filename = settings::path_output + "surface_source.h5"; + write_source_point(filename.c_str(), true); + } } } diff --git a/src/tallies/tally.cpp b/src/tallies/tally.cpp index 51194684ae..94bfc6cd49 100644 --- a/src/tallies/tally.cpp +++ b/src/tallies/tally.cpp @@ -719,6 +719,11 @@ void read_tallies_xml() doc.load_file(filename.c_str()); pugi::xml_node root = doc.document_element(); + read_tallies_xml(root); +} + +void read_tallies_xml(pugi::xml_node root) +{ // Check for setting if (check_for_node(root, "assume_separate")) { settings::assume_separate = get_node_value_bool(root, "assume_separate"); diff --git a/src/tallies/trigger.cpp b/src/tallies/trigger.cpp index 2c155980e7..79af658793 100644 --- a/src/tallies/trigger.cpp +++ b/src/tallies/trigger.cpp @@ -37,6 +37,10 @@ std::pair get_tally_uncertainty( int n = tally->n_realizations_; auto mean = sum / n; + + // if the result has no contributions, return an invalid pair + if (mean == 0) return {-1 , -1}; + double std_dev = std::sqrt((sum_sq / n - mean * mean) / (n - 1)); double rel_err = (mean != 0.) ? std_dev / std::abs(mean) : 0.; @@ -68,42 +72,49 @@ void check_tally_triggers(double& ratio, int& tally_id, int& score) const auto& results = t.results_; for (auto filter_index = 0; filter_index < results.shape()[0]; ++filter_index) { - for (auto score_index = 0; score_index < results.shape()[1]; - ++score_index) { - // Compute the tally uncertainty metrics. - auto uncert_pair = - get_tally_uncertainty(i_tally, score_index, filter_index); - double std_dev = uncert_pair.first; - double rel_err = uncert_pair.second; + // Compute the tally uncertainty metrics. + auto uncert_pair = + get_tally_uncertainty(i_tally, trigger.score_index, filter_index); - // Pick out the relevant uncertainty metric for this trigger. - double uncertainty; - switch (trigger.metric) { - case TriggerMetric::variance: - uncertainty = std_dev * std_dev; - break; - case TriggerMetric::standard_deviation: - uncertainty = std_dev; - break; - case TriggerMetric::relative_error: - uncertainty = rel_err; - break; - case TriggerMetric::not_active: - UNREACHABLE(); - } + // if there is a score without contributions, set ratio to inf and + // exit early + if (uncert_pair.first == -1) { + ratio = INFINITY; + score = t.scores_[trigger.score_index]; + tally_id = t.id_; + return; + } - // Compute the uncertainty / threshold ratio. - double this_ratio = uncertainty / trigger.threshold; - if (trigger.metric == TriggerMetric::variance) { - this_ratio = std::sqrt(ratio); - } + double std_dev = uncert_pair.first; + double rel_err = uncert_pair.second; - // If this is the most uncertain value, set the output variables. - if (this_ratio > ratio) { - ratio = this_ratio; - score = t.scores_[trigger.score_index]; - tally_id = t.id_; - } + // Pick out the relevant uncertainty metric for this trigger. + double uncertainty; + switch (trigger.metric) { + case TriggerMetric::variance: + uncertainty = std_dev * std_dev; + break; + case TriggerMetric::standard_deviation: + uncertainty = std_dev; + break; + case TriggerMetric::relative_error: + uncertainty = rel_err; + break; + case TriggerMetric::not_active: + UNREACHABLE(); + } + + // Compute the uncertainty / threshold ratio. + double this_ratio = uncertainty / trigger.threshold; + if (trigger.metric == TriggerMetric::variance) { + this_ratio = std::sqrt(ratio); + } + + // If this is the most uncertain value, set the output variables. + if (this_ratio > ratio) { + ratio = this_ratio; + score = t.scores_[trigger.score_index]; + tally_id = t.id_; } } } @@ -181,9 +192,13 @@ void check_triggers() "eigenvalue", keff_ratio); } else { - msg = fmt::format( - "Triggers unsatisfied, max unc./thresh. is {} for {} in tally {}", - tally_ratio, reaction_name(score), tally_id); + if (tally_ratio == INFINITY) { + msg = fmt::format("Triggers unsatisfied, no result tallied for score {} in tally {}", reaction_name(score), tally_id); + } else{ + msg = fmt::format( + "Triggers unsatisfied, max unc./thresh. is {} for {} in tally {}", + tally_ratio, reaction_name(score), tally_id); + } } write_message(msg, 7); diff --git a/src/thermal.cpp b/src/thermal.cpp index 982bf226a9..741f89ed10 100644 --- a/src/thermal.cpp +++ b/src/thermal.cpp @@ -119,22 +119,24 @@ ThermalScattering::ThermalScattering( if (!found) { // If no pairs found, check if the desired temperature falls within // bounds' tolerance - if (std::abs(T - temps_available[0]) <= settings::temperature_tolerance){ - if (std::find(temps_to_read.begin(), temps_to_read.end(), std::round(temps_available[0])) == - temps_to_read.end()) { - temps_to_read.push_back(std::round(temps_available[0])); - }} - else if (std::abs(T - temps_available[n - 1]) <= settings::temperature_tolerance){ - if (std::find(temps_to_read.begin(), temps_to_read.end(), std::round(temps_available[n - 1])) == - temps_to_read.end()){ - temps_to_read.push_back(std::round(temps_available[n - 1])); - }} - else { + if (std::abs(T - temps_available[0]) <= + settings::temperature_tolerance) { + if (std::find(temps_to_read.begin(), temps_to_read.end(), + std::round(temps_available[0])) == temps_to_read.end()) { + temps_to_read.push_back(std::round(temps_available[0])); + } + } else if (std::abs(T - temps_available[n - 1]) <= + settings::temperature_tolerance) { + if (std::find(temps_to_read.begin(), temps_to_read.end(), + std::round(temps_available[n - 1])) == temps_to_read.end()) { + temps_to_read.push_back(std::round(temps_available[n - 1])); + } + } else { fatal_error( - fmt::format("Nuclear data library does not contain cross " - "sections for {} at temperatures that bound {} K.", - name_, std::round(T))); - } + fmt::format("Nuclear data library does not contain cross " + "sections for {} at temperatures that bound {} K.", + name_, std::round(T))); + } } } } diff --git a/tests/regression_tests/diff_tally/test.py b/tests/regression_tests/diff_tally/test.py index b688e6d233..18c5013722 100644 --- a/tests/regression_tests/diff_tally/test.py +++ b/tests/regression_tests/diff_tally/test.py @@ -103,9 +103,8 @@ class DiffTallyTestHarness(PyAPITestHarness): sp = openmc.StatePoint(statepoint) # Extract the tally data as a Pandas DataFrame. - df = pd.DataFrame() - for t in sp.tallies.values(): - df = df.append(t.get_pandas_dataframe(), ignore_index=True) + tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()] + df = pd.concat(tally_dfs, ignore_index=True) # Extract the relevant data as a CSV string. cols = ('d_material', 'd_nuclide', 'd_variable', 'score', 'mean', diff --git a/tests/regression_tests/model_xml/__init__.py b/tests/regression_tests/model_xml/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat b/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat new file mode 100644 index 0000000000..1c4516f42d --- /dev/null +++ b/tests/regression_tests/model_xml/adj_cell_rotation_inputs_true.dat @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + eigenvalue + 10000 + 10 + 5 + + + -4.0 -4.0 -4.0 4.0 4.0 4.0 + + + + diff --git a/tests/regression_tests/model_xml/energy_laws_inputs_true.dat b/tests/regression_tests/model_xml/energy_laws_inputs_true.dat new file mode 100644 index 0000000000..c89ccc97ee --- /dev/null +++ b/tests/regression_tests/model_xml/energy_laws_inputs_true.dat @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + eigenvalue + 1000 + 10 + 5 + + diff --git a/tests/regression_tests/model_xml/inputs_true.dat b/tests/regression_tests/model_xml/inputs_true.dat new file mode 100644 index 0000000000..c408026316 --- /dev/null +++ b/tests/regression_tests/model_xml/inputs_true.dat @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + fixed source + 10000 + 1 + + + 0 0 0 + + + + 14000000.0 1.0 + + + ttb + true + + 1000.0 + + + + + 16 + + + neutron photon electron positron + + + 1 2 + current + + + 2 + Al27 total + total (n,gamma) + tracklength + + + 2 + Al27 total + total heating (n,gamma) + collision + + + 2 + Al27 total + total heating (n,gamma) + analog + + + diff --git a/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat b/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat new file mode 100644 index 0000000000..0eed3c2015 --- /dev/null +++ b/tests/regression_tests/model_xml/lattice_multiple_inputs_true.dat @@ -0,0 +1,53 @@ + + + + + + + + + + + + + + + + + + + + + + + + 1.2 1.2 + 1 + 2 2 + -1.2 -1.2 + +2 1 +1 1 + + + 2.4 2.4 + 2 2 + -2.4 -2.4 + +4 4 +4 4 + + + + + + + + + + eigenvalue + 1000 + 10 + 5 + + diff --git a/tests/regression_tests/model_xml/photon_production_inputs_true.dat b/tests/regression_tests/model_xml/photon_production_inputs_true.dat new file mode 100644 index 0000000000..0b2b434681 --- /dev/null +++ b/tests/regression_tests/model_xml/photon_production_inputs_true.dat @@ -0,0 +1,67 @@ + + + + + + + + + + + + + + + + + + + fixed source + 10000 + 1 + + + 0 0 0 + + + + 14000000.0 1.0 + + + ttb + true + + 1000.0 + + + + + 1 + + + neutron photon electron positron + + + 1 2 + current + + + 2 + Al27 total + total (n,gamma) + tracklength + + + 2 + Al27 total + total heating (n,gamma) + collision + + + 2 + Al27 total + total heating (n,gamma) + analog + + + diff --git a/tests/regression_tests/model_xml/test.py b/tests/regression_tests/model_xml/test.py new file mode 100644 index 0000000000..c67a72ed37 --- /dev/null +++ b/tests/regression_tests/model_xml/test.py @@ -0,0 +1,100 @@ +from difflib import unified_diff +import glob +import filecmp +import os +from pathlib import Path + +import openmc +import pytest + +from tests.testing_harness import PyAPITestHarness, colorize + +# use a few models from other tests to make sure the same results are +# produced when using a single model.xml file as input +from ..adj_cell_rotation.test import model as adj_cell_rotation_model +from ..lattice_multiple.test import model as lattice_multiple_model +from ..energy_laws.test import model as energy_laws_model +from ..photon_production.test import model as photon_production_model + + +class ModelXMLTestHarness(PyAPITestHarness): + """Accept a results file to check against and assume inputs_true is the contents of a model.xml file. + """ + def __init__(self, model=None, inputs_true=None, results_true=None): + statepoint_name = f'statepoint.{model.settings.batches}.h5' + super().__init__(statepoint_name, model, inputs_true) + + self.results_true = 'results_true.dat' if results_true is None else results_true + + def _build_inputs(self): + self._model.export_to_model_xml() + + def _get_inputs(self): + return open('model.xml').read() + + def _compare_results(self): + """Make sure the current results agree with the reference.""" + compare = filecmp.cmp('results_test.dat', self.results_true) + if not compare: + expected = open(self.results_true).readlines() + actual = open('results_test.dat').readlines() + diff = unified_diff(expected, actual, self.results_true, + 'results_test.dat') + print('Result differences:') + print(''.join(colorize(diff))) + os.rename('results_test.dat', 'results_error.dat') + assert compare, 'Results do not agree' + + def _cleanup(self): + super()._cleanup() + if os.path.exists('model.xml'): + os.remove('model.xml') + + +test_names = [ + 'adj_cell_rotation', + 'lattice_multiple', + 'energy_laws', + 'photon_production' +] + + +@pytest.mark.parametrize("test_name", test_names, ids=lambda test: test) +def test_model_xml(test_name, request): + openmc.reset_auto_ids() + + test_path = '../' + test_name + results = test_path + "/results_true.dat" + inputs = test_name + "_inputs_true.dat" + model_name = test_name + "_model" + harness = ModelXMLTestHarness(request.getfixturevalue(model_name), inputs, results) + harness.main() + +def test_input_arg(run_in_tmpdir): + + pincell = openmc.examples.pwr_pin_cell() + + pincell.settings.particles = 100 + + # export to separate XML files and run + pincell.export_to_xml() + openmc.run() + + # make sure the executable isn't falling back on the separate XMLs + for f in glob.glob('*.xml'): + os.remove(f) + # now export to a single XML file with a custom name + pincell.export_to_model_xml('pincell.xml') + assert Path('pincell.xml').exists() + + # run by specifying that single file + openmc.run(path_input='pincell.xml') + + # check that this works for plotting too + openmc.plot_geometry(path_input='pincell.xml') + + # now ensure we get an error for an incorrect filename, + # even in the presence of other, valid XML files + pincell.export_to_model_xml() + with pytest.raises(RuntimeError, match='ex-em-ell.xml'): + openmc.run(path_input='ex-em-ell.xml') \ No newline at end of file diff --git a/tests/regression_tests/ncrystal/__init__.py b/tests/regression_tests/ncrystal/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/regression_tests/ncrystal/inputs_true.dat b/tests/regression_tests/ncrystal/inputs_true.dat new file mode 100644 index 0000000000..7a3f20eb3f --- /dev/null +++ b/tests/regression_tests/ncrystal/inputs_true.dat @@ -0,0 +1,45 @@ + + + + + + + + + + + + + + + + + fixed source + 100000 + 10 + + + 0 0 -20 + + + + 0.012 1.0 + + + + + + + 1 + + + 0.0 0.017453292519943295 0.03490658503988659 0.05235987755982989 0.06981317007977318 0.08726646259971647 0.10471975511965978 0.12217304763960307 0.13962634015954636 0.15707963267948966 0.17453292519943295 0.19198621771937624 0.20943951023931956 0.22689280275926285 0.24434609527920614 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current 1.30e-05 2.13e-06 +146 1 2.55e+00 2.57e+00 1 total current 1.10e-05 2.33e-06 +147 1 2.57e+00 2.58e+00 1 total current 1.50e-05 3.07e-06 +148 1 2.58e+00 2.60e+00 1 total current 1.20e-05 2.49e-06 +149 1 2.60e+00 2.62e+00 1 total current 1.80e-05 5.54e-06 +150 1 2.62e+00 2.64e+00 1 total current 1.30e-05 3.67e-06 +151 1 2.64e+00 2.65e+00 1 total current 1.60e-05 3.40e-06 +152 1 2.65e+00 2.67e+00 1 total current 7.00e-06 3.35e-06 +153 1 2.67e+00 2.69e+00 1 total current 1.00e-05 2.98e-06 +154 1 2.69e+00 2.71e+00 1 total current 7.00e-06 3.35e-06 +155 1 2.71e+00 2.72e+00 1 total current 1.20e-05 2.91e-06 +156 1 2.72e+00 2.74e+00 1 total current 9.00e-06 2.33e-06 +157 1 2.74e+00 2.76e+00 1 total current 1.00e-05 3.33e-06 +158 1 2.76e+00 2.78e+00 1 total current 1.10e-05 3.14e-06 +159 1 2.78e+00 2.79e+00 1 total current 1.00e-05 3.33e-06 +160 1 2.79e+00 2.81e+00 1 total current 1.40e-05 4.76e-06 +161 1 2.81e+00 2.83e+00 1 total current 8.00e-06 2.91e-06 +162 1 2.83e+00 2.84e+00 1 total current 5.00e-06 2.69e-06 +163 1 2.84e+00 2.86e+00 1 total current 6.00e-06 2.21e-06 +164 1 2.86e+00 2.88e+00 1 total current 5.00e-06 1.67e-06 +165 1 2.88e+00 2.90e+00 1 total current 4.00e-06 2.21e-06 +166 1 2.90e+00 2.91e+00 1 total current 7.00e-06 2.13e-06 +167 1 2.91e+00 2.93e+00 1 total current 6.00e-06 2.67e-06 +168 1 2.93e+00 2.95e+00 1 total current 7.00e-06 2.13e-06 +169 1 2.95e+00 2.97e+00 1 total current 5.00e-06 1.67e-06 +170 1 2.97e+00 2.98e+00 1 total current 3.00e-06 1.53e-06 +171 1 2.98e+00 3.00e+00 1 total current 6.00e-06 2.21e-06 +172 1 3.00e+00 3.02e+00 1 total current 3.00e-06 1.53e-06 +173 1 3.02e+00 3.04e+00 1 total current 1.00e-05 2.98e-06 +174 1 3.04e+00 3.05e+00 1 total current 2.00e-06 1.33e-06 +175 1 3.05e+00 3.07e+00 1 total current 1.00e-06 1.00e-06 +176 1 3.07e+00 3.09e+00 1 total current 2.00e-06 1.33e-06 +177 1 3.09e+00 3.11e+00 1 total current 0.00e+00 0.00e+00 +178 1 3.11e+00 3.12e+00 1 total current 1.00e-06 1.00e-06 +179 1 3.12e+00 3.14e+00 1 total current 0.00e+00 0.00e+00 \ No newline at end of file diff --git a/tests/regression_tests/ncrystal/test.py b/tests/regression_tests/ncrystal/test.py new file mode 100644 index 0000000000..cb6421b034 --- /dev/null +++ b/tests/regression_tests/ncrystal/test.py @@ -0,0 +1,80 @@ +from math import pi + +import numpy as np +import openmc +import openmc.lib +import pytest + +from tests.testing_harness import PyAPITestHarness + +pytestmark = pytest.mark.skipif( + not openmc.lib._ncrystal_enabled(), + reason="NCrystal materials are not enabled.") + + +def pencil_beam_model(cfg, E0, N): + """Return an openmc.Model() object for a monoenergetic pencil + beam hitting a 1 mm sphere filled with the material defined by + the cfg string, and compute the angular distribution""" + + # Material definition + + m1 = openmc.Material.from_ncrystal(cfg) + materials = openmc.Materials([m1]) + + # Geometry definition + + sample_sphere = openmc.Sphere(r=0.1) + outer_sphere = openmc.Sphere(r=100, boundary_type="vacuum") + cell1 = openmc.Cell(region=-sample_sphere, fill=m1) + cell2_region = +sample_sphere & -outer_sphere + cell2 = openmc.Cell(region=cell2_region, fill=None) + geometry = openmc.Geometry([cell1, cell2]) + + # Source definition + + source = openmc.Source() + source.space = openmc.stats.Point((0, 0, -20)) + source.angle = openmc.stats.Monodirectional(reference_uvw=(0, 0, 1)) + source.energy = openmc.stats.Discrete([E0], [1.0]) + + # Execution settings + + settings = openmc.Settings() + settings.source = source + settings.run_mode = "fixed source" + settings.batches = 10 + settings.particles = N + + # Tally definition + + tally1 = openmc.Tally(name="angular distribution") + tally1.scores = ["current"] + filter1 = openmc.SurfaceFilter(sample_sphere) + filter2 = openmc.PolarFilter(np.linspace(0, pi, 180+1)) + filter3 = openmc.CellFromFilter(cell1) + tally1.filters = [filter1, filter2, filter3] + tallies = openmc.Tallies([tally1]) + + return openmc.Model(geometry, materials, settings, tallies) + + +class NCrystalTest(PyAPITestHarness): + def _get_results(self): + """Digest info in the statepoint and return as a string.""" + + # Read the statepoint file. + with openmc.StatePoint(self._sp_name) as sp: + tal = sp.get_tally(name='angular distribution') + df = tal.get_pandas_dataframe() + return df.to_string() + + +def test_ncrystal(): + n_particles = 100000 + T = 293.6 # K + E0 = 0.012 # eV + cfg = 'Al_sg225.ncmat' + test = pencil_beam_model(cfg, E0, n_particles) + harness = NCrystalTest('statepoint.10.h5', model=test) + harness.main() diff --git a/tests/regression_tests/source_mcpl_file/__init__.py b/tests/regression_tests/source_mcpl_file/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/tests/regression_tests/source_mcpl_file/geometry.xml b/tests/regression_tests/source_mcpl_file/geometry.xml new file mode 100644 index 0000000000..bc56030e18 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/geometry.xml @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/tests/regression_tests/source_mcpl_file/materials.xml b/tests/regression_tests/source_mcpl_file/materials.xml new file mode 100644 index 0000000000..2472a74717 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/materials.xml @@ -0,0 +1,9 @@ + + + + + + + + + diff --git a/tests/regression_tests/source_mcpl_file/results_true.dat b/tests/regression_tests/source_mcpl_file/results_true.dat new file mode 100644 index 0000000000..0a98e9d8cc --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/results_true.dat @@ -0,0 +1,2 @@ +k-combined: +3.009416E-01 3.229999E-03 diff --git a/tests/regression_tests/source_mcpl_file/settings.xml b/tests/regression_tests/source_mcpl_file/settings.xml new file mode 100644 index 0000000000..47b010bffe --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/settings.xml @@ -0,0 +1,15 @@ + + + + + + 10 + 5 + 1000 + + + + -4 -4 -4 4 4 4 + + + diff --git a/tests/regression_tests/source_mcpl_file/test.py b/tests/regression_tests/source_mcpl_file/test.py new file mode 100644 index 0000000000..84ec005ae1 --- /dev/null +++ b/tests/regression_tests/source_mcpl_file/test.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python +import openmc.lib +import pytest +import glob +import os + +from tests.testing_harness import * +pytestmark = pytest.mark.skipif( + not openmc.lib._mcpl_enabled(), + reason="MCPL is not enabled.") + +settings1=""" + + + + + 10 + 5 + 1000 + + + + -4 -4 -4 4 4 4 + + + +""" + +settings2 = """ + + + 10 + 5 + 1000 + + + source.10.{} + + +""" + + +class SourceFileTestHarness(TestHarness): + def execute_test(self): + """Run OpenMC with the appropriate arguments and check the outputs.""" + try: + self._run_openmc() + self._test_output_created() + self._run_openmc_restart() + results = self._get_results() + self._write_results(results) + self._compare_results() + finally: + self._cleanup() + + def update_results(self): + """Update the results_true using the current version of OpenMC.""" + try: + self._run_openmc() + self._test_output_created() + self._run_openmc_restart() + results = self._get_results() + self._write_results(results) + self._overwrite_results() + finally: + self._cleanup() + + def _test_output_created(self): + """Make sure statepoint and source files have been created.""" + statepoint = glob.glob(os.path.join(os.getcwd(), self._sp_name)) + assert len(statepoint) == 1, 'Either multiple or no statepoint files ' \ + 'exist.' + assert statepoint[0].endswith('h5'), \ + 'Statepoint file is not a HDF5 file.' + + source = glob.glob(os.path.join(os.getcwd(), 'source.10.mcpl*')) + assert len(source) == 1, 'Either multiple or no source files exist.' + assert source[0].endswith('mcpl') or source[0].endswith('mcpl.gz'), \ + 'Source file is not a MCPL file.' + + def _run_openmc_restart(self): + # Get the name of the source file. + source = glob.glob(os.path.join(os.getcwd(), 'source.10.*')) + + # Write the new settings.xml file. + with open('settings.xml','w') as fh: + fh.write(settings2.format(source[0].split('.')[-1])) + + # Run OpenMC. + self._run_openmc() + + def _cleanup(self): + TestHarness._cleanup(self) + output = glob.glob(os.path.join(os.getcwd(), 'source.*')) + with open('settings.xml','w') as fh: + fh.write(settings1) + + +def test_source_file(): + harness = SourceFileTestHarness('statepoint.10.h5') + harness.main() diff --git a/tests/regression_tests/surface_tally/test.py b/tests/regression_tests/surface_tally/test.py index 96199ec2a4..d21f361e64 100644 --- a/tests/regression_tests/surface_tally/test.py +++ b/tests/regression_tests/surface_tally/test.py @@ -164,9 +164,8 @@ class SurfaceTallyTestHarness(PyAPITestHarness): sp = openmc.StatePoint(self._sp_name) # Extract the tally data as a Pandas DataFrame. - df = pd.DataFrame() - for t in sp.tallies.values(): - df = df.append(t.get_pandas_dataframe(), ignore_index=True) + tally_dfs = [t.get_pandas_dataframe() for t in sp.tallies.values()] + df = pd.concat(tally_dfs, ignore_index=True) # Extract the relevant data as a CSV string. cols = ('mean', 'std. dev.') diff --git a/tests/unit_tests/test_cell.py b/tests/unit_tests/test_cell.py index 1c2e1b70e4..cef77f1608 100644 --- a/tests/unit_tests/test_cell.py +++ b/tests/unit_tests/test_cell.py @@ -57,25 +57,51 @@ def test_clone(): m = openmc.Material() cyl = openmc.ZCylinder() c = openmc.Cell(fill=m, region=-cyl) - c.temperature = 650. + # Check cloning with all optional params as the defaults c2 = c.clone() assert c2.id != c.id assert c2.fill != c.fill assert c2.region != c.region - assert c2.temperature == c.temperature c3 = c.clone(clone_materials=False) assert c3.id != c.id assert c3.fill == c.fill assert c3.region != c.region - assert c3.temperature == c.temperature c4 = c.clone(clone_regions=False) assert c4.id != c.id assert c4.fill != c.fill assert c4.region == c.region - assert c4.temperature == c.temperature + + # Add optional properties to the original cell to ensure they're cloned successfully + c.temperature = 650. + c.translation = (1., 2., 3.) + c.rotation = (4., 5., 6.) + c.volume = 100 + + c5 = c.clone(clone_materials=False, clone_regions=False) + assert c5.id != c.id + assert c5.fill == c.fill + assert c5.region == c.region + assert c5.temperature == c.temperature + assert c5.volume == c.volume + assert all(c5.translation == c.translation) + assert all(c5.rotation == c.rotation) + + # Mutate the original to ensure the changes are not seen in the clones + c.fill = openmc.Material() + c.region = +openmc.ZCylinder() + c.translation = (-1., -2., -3.) + c.rotation = (-4., -5., -6.) + c.temperature = 1 + c.volume = 1 + assert c5.fill != c.fill + assert c5.region != c.region + assert c5.temperature != c.temperature + assert c5.volume != c.volume + assert all(c5.translation != c.translation) + assert all(c5.rotation != c.rotation) def test_temperature(cell_with_lattice): diff --git a/tests/unit_tests/test_data_misc.py b/tests/unit_tests/test_data_misc.py index 37e024fe23..f88be2602d 100644 --- a/tests/unit_tests/test_data_misc.py +++ b/tests/unit_tests/test_data_misc.py @@ -101,12 +101,12 @@ def test_water_density(): assert dens(500.0, 3.0) == pytest.approx(1e-3/0.120241800e-2, 1e-6) -def test_gnd_name(): - assert openmc.data.gnd_name(1, 1) == 'H1' - assert openmc.data.gnd_name(40, 90) == ('Zr90') - assert openmc.data.gnd_name(95, 242, 0) == ('Am242') - assert openmc.data.gnd_name(95, 242, 1) == ('Am242_m1') - assert openmc.data.gnd_name(95, 242, 10) == ('Am242_m10') +def test_gnds_name(): + assert openmc.data.gnds_name(1, 1) == 'H1' + assert openmc.data.gnds_name(40, 90) == ('Zr90') + assert openmc.data.gnds_name(95, 242, 0) == ('Am242') + assert openmc.data.gnds_name(95, 242, 1) == ('Am242_m1') + assert openmc.data.gnds_name(95, 242, 10) == ('Am242_m10') def test_isotopes(): diff --git a/tests/unit_tests/test_geometry.py b/tests/unit_tests/test_geometry.py index 9db112fd29..f99232ff25 100644 --- a/tests/unit_tests/test_geometry.py +++ b/tests/unit_tests/test_geometry.py @@ -1,4 +1,5 @@ import xml.etree.ElementTree as ET +from pathlib import Path import numpy as np import openmc @@ -159,12 +160,13 @@ def test_get_by_name(): m2 = openmc.Material(name='Zirconium') m2.add_element('Zr', 1.0) - c1 = openmc.Cell(fill=m1, name='cell1') + s1 = openmc.Sphere(name='surface1') + c1 = openmc.Cell(fill=m1, region=-s1, name='cell1') u1 = openmc.Universe(name='Zircaloy universe', cells=[c1]) - cyl = openmc.ZCylinder() - c2 = openmc.Cell(fill=u1, region=-cyl, name='cell2') - c3 = openmc.Cell(fill=m2, region=+cyl, name='Cell3') + s2 = openmc.ZCylinder(name='surface2') + c2 = openmc.Cell(fill=u1, region=-s2, name='cell2') + c3 = openmc.Cell(fill=m2, region=+s2, name='Cell3') root = openmc.Universe(name='root Universe', cells=[c2, c3]) geom = openmc.Geometry(root) @@ -177,6 +179,13 @@ def test_get_by_name(): mats = geom.get_materials_by_name('zirconium', True, True) assert not mats + surfaces = set(geom.get_surfaces_by_name('surface')) + assert not surfaces ^ {s1, s2} + surfaces = set(geom.get_surfaces_by_name('Surface2', False, True)) + assert not surfaces ^ {s2} + surfaces = geom.get_surfaces_by_name('Surface2', True, True) + assert not surfaces + cells = set(geom.get_cells_by_name('cell')) assert not cells ^ {c1, c2, c3} cells = set(geom.get_cells_by_name('cell', True)) @@ -274,7 +283,22 @@ def test_from_xml(run_in_tmpdir, mixed_lattice_model): # Export model mixed_lattice_model.export_to_xml() - # Import geometry + mats_from_xml = openmc.Materials.from_xml('materials.xml') + # checking string a Path are both acceptable + for path in ['geometry.xml', Path('geometry.xml')]: + for materials in [mats_from_xml, 'materials.xml']: + # Import geometry from file + geom = openmc.Geometry.from_xml(path=path, materials=materials) + assert isinstance(geom, openmc.Geometry) + ll, ur = geom.bounding_box + assert ll == pytest.approx((-6.0, -6.0, -np.inf)) + assert ur == pytest.approx((6.0, 6.0, np.inf)) + + with pytest.raises(TypeError) as excinfo: + geom = openmc.Geometry.from_xml(path='geometry.xml', materials=None) + assert 'Unable to set "materials" to "None"' in str(excinfo.value) + + # checking that the default args also work geom = openmc.Geometry.from_xml() assert isinstance(geom, openmc.Geometry) ll, ur = geom.bounding_box diff --git a/tests/unit_tests/test_mesh_to_vtk.py b/tests/unit_tests/test_mesh_to_vtk.py index d7d5907a22..bc3633c8c0 100644 --- a/tests/unit_tests/test_mesh_to_vtk.py +++ b/tests/unit_tests/test_mesh_to_vtk.py @@ -77,8 +77,8 @@ def test_write_data_to_vtk_size_mismatch(mesh): # by regex. These are needed to make the test string match the error message # string when using the match argument as that uses regular expression expected_error_msg = ( - f"The size of the dataset 'label' \({len(data)}\) should be equal to " - f"the number of mesh cells \({mesh.num_mesh_cells}\)" + fr"The size of the dataset 'label' \({len(data)}\) should be equal to " + fr"the number of mesh cells \({mesh.num_mesh_cells}\)" ) with pytest.raises(ValueError, match=expected_error_msg): mesh.write_data_to_vtk(filename="out.vtk", datasets={"label": data}) diff --git a/tests/unit_tests/test_model.py b/tests/unit_tests/test_model.py index 9b05ed2a5c..6c483aeb94 100644 --- a/tests/unit_tests/test_model.py +++ b/tests/unit_tests/test_model.py @@ -1,5 +1,6 @@ from math import pi from pathlib import Path +import os import numpy as np import pytest @@ -529,3 +530,40 @@ def test_calc_volumes(run_in_tmpdir, pin_model_attributes, mpi_intracomm): assert openmc.lib.materials[3].volume == mats[2].volume test_model.finalize_lib() + +def test_model_xml(run_in_tmpdir): + + # load a model from examples + pwr_model = openmc.examples.pwr_core() + + # export to separate XMLs manually + pwr_model.settings.export_to_xml('settings_ref.xml') + pwr_model.materials.export_to_xml('materials_ref.xml') + pwr_model.geometry.export_to_xml('geometry_ref.xml') + + # now write and read a model.xml file + pwr_model.export_to_model_xml() + new_model = openmc.Model.from_model_xml() + + # make sure we can also export this again to separate + # XML files + new_model.export_to_xml() + +def test_single_xml_exec(run_in_tmpdir): + + pincell_model = openmc.examples.pwr_pin_cell() + + pincell_model.export_to_model_xml('pwr_pincell.xml') + + openmc.run(path_input='pwr_pincell.xml') + + with pytest.raises(RuntimeError, match='ex-em-ell.xml'): + openmc.run(path_input='ex-em-ell.xml') + + # test that a file in a different directory can be used + os.mkdir('inputs') + pincell_model.export_to_model_xml('./inputs/pincell.xml') + openmc.run(path_input='./inputs/pincell.xml') + + with pytest.raises(RuntimeError, match='input_dir'): + openmc.run(path_input='input_dir/pincell.xml') \ No newline at end of file diff --git a/tests/unit_tests/test_plotter.py b/tests/unit_tests/test_plotter.py new file mode 100644 index 0000000000..a3f1ff6662 --- /dev/null +++ b/tests/unit_tests/test_plotter.py @@ -0,0 +1,27 @@ +import openmc +import numpy as np + + +def test_calculate_cexs_elem_mat_sab(): + """Checks that sab cross sections are included in the + _calculate_cexs_elem_mat method and have the correct shape""" + + mat_1 = openmc.Material() + mat_1.add_element("H", 4.0, "ao") + mat_1.add_element("O", 4.0, "ao") + mat_1.add_element("C", 4.0, "ao") + + mat_1.add_s_alpha_beta("c_C6H6") + mat_1.set_density("g/cm3", 0.865) + + energy_grid, data = openmc.plotter._calculate_cexs_elem_mat( + mat_1, + ["inelastic"], + sab_name="c_C6H6", + ) + + assert isinstance(energy_grid, np.ndarray) + assert isinstance(data, np.ndarray) + assert len(energy_grid) > 1 + assert len(data) == 1 + assert len(data[0]) == len(energy_grid) diff --git a/tests/unit_tests/test_settings.py b/tests/unit_tests/test_settings.py index 3603b57c18..15e86ca619 100644 --- a/tests/unit_tests/test_settings.py +++ b/tests/unit_tests/test_settings.py @@ -17,7 +17,7 @@ def test_export_to_xml(run_in_tmpdir): s.output = {'summary': True, 'tallies': False, 'path': 'here'} s.verbosity = 7 s.sourcepoint = {'batches': [50, 150, 500, 1000], 'separate': True, - 'write': True, 'overwrite': True} + 'write': True, 'overwrite': True, 'mcpl': True} s.statepoint = {'batches': [50, 150, 500, 1000]} s.surf_source_read = {'path': 'surface_source_1.h5'} s.surf_source_write = {'surface_ids': [2], 'max_particles': 200} @@ -49,6 +49,7 @@ def test_export_to_xml(run_in_tmpdir): domains=[openmc.Cell()], samples=1000, lower_left=(-10., -10., -10.), upper_right = (10., 10., 10.)) s.create_fission_neutrons = True + s.create_delayed_neutrons = False s.log_grid_bins = 2000 s.photon_transport = False s.electron_treatment = 'led' @@ -75,7 +76,7 @@ def test_export_to_xml(run_in_tmpdir): assert s.output == {'summary': True, 'tallies': False, 'path': 'here'} assert s.verbosity == 7 assert s.sourcepoint == {'batches': [50, 150, 500, 1000], 'separate': True, - 'write': True, 'overwrite': True} + 'write': True, 'overwrite': True, 'mcpl': True} assert s.statepoint == {'batches': [50, 150, 500, 1000]} assert s.surf_source_read == {'path': 'surface_source_1.h5'} assert s.surf_source_write == {'surface_ids': [2], 'max_particles': 200} @@ -107,6 +108,7 @@ def test_export_to_xml(run_in_tmpdir): 'energy_min': 1.0, 'energy_max': 1000.0, 'nuclides': ['U235', 'U238', 'Pu239']} assert s.create_fission_neutrons + assert not s.create_delayed_neutrons assert s.log_grid_bins == 2000 assert not s.photon_transport assert s.electron_treatment == 'led' diff --git a/tests/unit_tests/test_triggers.py b/tests/unit_tests/test_triggers.py new file mode 100644 index 0000000000..4fe6e044ab --- /dev/null +++ b/tests/unit_tests/test_triggers.py @@ -0,0 +1,75 @@ + +import openmc + +def test_tally_trigger(run_in_tmpdir): + pincell = openmc.examples.pwr_pin_cell() + + # create a tally filter on the materials + mat_filter = openmc.MaterialFilter(pincell.materials) + + # create a tally with triggers applied + tally = openmc.Tally() + tally.filters = [mat_filter] + tally.scores = ['scatter'] + + trigger = openmc.Trigger('rel_err', 0.05) + trigger.scores = ['scatter'] + + tally.triggers = [trigger] + + pincell.tallies = [tally] + + pincell.settings.trigger_active = True + pincell.settings.trigger_max_batches = 100 + pincell.settings.trigger_batch_interval = 5 + + sp_file = pincell.run() + with openmc.StatePoint(sp_file) as sp: + expected_realizations = sp.n_realizations + + # adding other scores to the tally should not change the + # number of batches required to satisfy the trigger + tally.scores = ['total', 'absorption', 'scatter'] + + sp_file = pincell.run() + + with openmc.StatePoint(sp_file) as sp: + realizations = sp.n_realizations + + assert realizations == expected_realizations + + +def test_tally_trigger_null_score(run_in_tmpdir): + pincell = openmc.examples.pwr_pin_cell() + + # create a tally filter on the materials + mat_filter = openmc.MaterialFilter(pincell.materials) + + # apply a tally with a score that be tallied in this model + tally = openmc.Tally() + tally.filters = [mat_filter] + tally.scores = ['pair-production'] + + trigger = openmc.Trigger('rel_err', 0.05) + trigger.scores = ['pair-production'] + + tally.triggers = [trigger] + + pincell.tallies = [tally] + + pincell.settings.trigger_active = True + pincell.settings.trigger_max_batches = 50 + pincell.settings.trigger_batch_interval = 5 + + sp_file = pincell.run() + + with openmc.StatePoint(sp_file) as sp: + # verify that the tally mean is zero + tally_out = sp.get_tally(id=tally.id) + assert all(tally_out.mean == 0.0) + + # we expect that this simulation will run + # up to the max allowed batches + total_batches = sp.n_realizations + sp.n_inactive + assert total_batches == pincell.settings.trigger_max_batches + diff --git a/tools/ci/gha-install-mcpl.sh b/tools/ci/gha-install-mcpl.sh new file mode 100755 index 0000000000..9b8609398a --- /dev/null +++ b/tools/ci/gha-install-mcpl.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -ex +cd $HOME +git clone https://github.com/mctools/mcpl +cd mcpl +mkdir build && cd build +cmake .. && make 2>/dev/null && sudo make install diff --git a/tools/ci/gha-install-ncrystal.sh b/tools/ci/gha-install-ncrystal.sh new file mode 100755 index 0000000000..16f77e13e2 --- /dev/null +++ b/tools/ci/gha-install-ncrystal.sh @@ -0,0 +1,46 @@ +#!/bin/bash +set -ex +cd $HOME + +#Use the NCrystal develop branch (in the near future we can move this to master): +git clone https://github.com/mctools/ncrystal --branch develop --single-branch --depth 1 ncrystal_src + +SRC_DIR="$PWD/ncrystal_src" +BLD_DIR="$PWD/ncrystal_bld" +INST_DIR="$PWD/ncrystal_inst" +PYTHON=$(which python3) + +CPU_COUNT=1 + +mkdir "$BLD_DIR" +cd ncrystal_bld + +cmake \ + "${SRC_DIR}" \ + -DBUILD_SHARED_LIBS=ON \ + -DNCRYSTAL_NOTOUCH_CMAKE_BUILD_TYPE=ON \ + -DNCRYSTAL_MODIFY_RPATH=OFF \ + -DCMAKE_BUILD_TYPE=Release \ + -DNCRYSTAL_ENABLE_EXAMPLES=OFF \ + -DNCRYSTAL_ENABLE_SETUPSH=OFF \ + -DNCRYSTAL_ENABLE_DATA=EMBED \ + -DCMAKE_INSTALL_PREFIX="${INST_DIR}" \ + -DPython3_EXECUTABLE="$PYTHON" + +make -j${CPU_COUNT:-1} +make install + +#Note: There is no "make test" or "make ctest" functionality for NCrystal +# yet. If it appears in the future, we should add it here. + +# Output the configuration to the log + +"${INST_DIR}/bin/ncrystal-config" --setup + +# Change environmental variables + +eval $( "${INST_DIR}/bin/ncrystal-config" --setup ) + +# Check installation worked + +nctool --test diff --git a/tools/ci/gha-install.py b/tools/ci/gha-install.py index 4c69ba70b0..f4b2fbb318 100644 --- a/tools/ci/gha-install.py +++ b/tools/ci/gha-install.py @@ -19,14 +19,14 @@ def which(program): return None -def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False): +def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False, ncrystal=False): # Create build directory and change to it shutil.rmtree('build', ignore_errors=True) os.mkdir('build') os.chdir('build') - # Build in debug mode by default - cmake_cmd = ['cmake', '-DCMAKE_BUILD_TYPE=Debug'] + # Build in debug mode by default with support for MCPL + cmake_cmd = ['cmake', '-DCMAKE_BUILD_TYPE=Debug', '-DOPENMC_USE_MCPL=on'] # Turn off OpenMP if specified if not omp: @@ -54,6 +54,11 @@ def install(omp=False, mpi=False, phdf5=False, dagmc=False, libmesh=False): libmesh_path = os.environ.get('HOME') + '/LIBMESH' cmake_cmd.append('-DCMAKE_PREFIX_PATH=' + libmesh_path) + if ncrystal: + cmake_cmd.append('-DOPENMC_USE_NCRYSTAL=ON') + ncrystal_cmake_path = os.environ.get('HOME') + '/ncrystal_inst/lib/cmake' + cmake_cmd.append(f'-DCMAKE_PREFIX_PATH={ncrystal_cmake_path}') + # Build in coverage mode for coverage testing cmake_cmd.append('-DOPENMC_ENABLE_COVERAGE=on') @@ -70,10 +75,11 @@ def main(): mpi = (os.environ.get('MPI') == 'y') phdf5 = (os.environ.get('PHDF5') == 'y') dagmc = (os.environ.get('DAGMC') == 'y') + ncrystal = (os.environ.get('NCRYSTAL') == 'y') libmesh = (os.environ.get('LIBMESH') == 'y') # Build and install - install(omp, mpi, phdf5, dagmc, libmesh) + install(omp, mpi, phdf5, dagmc, libmesh, ncrystal) if __name__ == '__main__': main() diff --git a/tools/ci/gha-install.sh b/tools/ci/gha-install.sh index aa40eb90b1..4042977c95 100755 --- a/tools/ci/gha-install.sh +++ b/tools/ci/gha-install.sh @@ -17,6 +17,11 @@ if [[ $DAGMC = 'y' ]]; then ./tools/ci/gha-install-dagmc.sh fi +# Install NCrystal if needed +if [[ $NCRYSTAL = 'y' ]]; then + ./tools/ci/gha-install-ncrystal.sh +fi + # Install vectfit for WMP generation if needed if [[ $VECTFIT = 'y' ]]; then ./tools/ci/gha-install-vectfit.sh @@ -27,6 +32,9 @@ if [[ $LIBMESH = 'y' ]]; then ./tools/ci/gha-install-libmesh.sh fi +# Install MCPL +./tools/ci/gha-install-mcpl.sh + # For MPI configurations, make sure mpi4py and h5py are built against the # correct version of MPI if [[ $MPI == 'y' ]]; then diff --git a/tools/ci/gha-script.sh b/tools/ci/gha-script.sh index c791167e99..1f1c3a1ebe 100755 --- a/tools/ci/gha-script.sh +++ b/tools/ci/gha-script.sh @@ -14,5 +14,12 @@ if [[ $EVENT == 'y' ]]; then args="${args} --event " fi +# Check NCrystal installation +if [[ $NCRYSTAL = 'y' ]]; then + # Change environmental variables + eval $( "${HOME}/ncrystal_inst/bin/ncrystal-config" --setup ) + nctool --test +fi + # Run regression and unit tests pytest --cov=openmc -v $args tests