12472509828

Committed 23 Dec 2024 08:22PM UTC coverage: 84.847% (+0.02%) from 84.827%

Build # 12472509828

Build Type

Pull #3056

github

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web-flow

Commit Message

Merge 1f28a9e8e into 775c41512

Pull Request Pull Request #3056: Differentiate materials in DAGMC universes

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92.58

/openmc/model/model.py

from __future__ import annotations
from collections.abc import Iterable
from functools import lru_cache
import os
from pathlib import Path
from numbers import Integral
from tempfile import NamedTemporaryFile
import warnings

import h5py
import lxml.etree as ET
import numpy as np

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, PathLike
from openmc.exceptions import InvalidIDError
import openmc.lib
from openmc.utility_funcs import change_directory


class Model:
    """Model container.

    This class can be used to store instances of :class:`openmc.Geometry`,
    :class:`openmc.Materials`, :class:`openmc.Settings`,
    :class:`openmc.Tallies`, and :class:`openmc.Plots`, thus making a complete
    model. The :meth:`Model.export_to_xml` method will export XML files for all
    attributes that have been set. If the :attr:`Model.materials` attribute is
    not set, it will attempt to create a ``materials.xml`` file based on all
    materials appearing in the geometry.

    .. versionchanged:: 0.13.0
        The model information can now be loaded in to OpenMC directly via
        openmc.lib

    Parameters
    ----------
    geometry : openmc.Geometry, optional
        Geometry information
    materials : openmc.Materials, optional
        Materials information
    settings : openmc.Settings, optional
        Settings information
    tallies : openmc.Tallies, optional
        Tallies information
    plots : openmc.Plots, optional
        Plot information

    Attributes
    ----------
    geometry : openmc.Geometry
        Geometry information
    materials : openmc.Materials
        Materials information
    settings : openmc.Settings
        Settings information
    tallies : openmc.Tallies
        Tallies information
    plots : openmc.Plots
        Plot information

    """

    def __init__(self, geometry=None, materials=None, settings=None,
                 tallies=None, plots=None):
        self.geometry = openmc.Geometry()
        self.materials = openmc.Materials()
        self.settings = openmc.Settings()
        self.tallies = openmc.Tallies()
        self.plots = openmc.Plots()

        if geometry is not None:
            self.geometry = geometry
        if materials is not None:
            self.materials = materials
        if settings is not None:
            self.settings = settings
        if tallies is not None:
            self.tallies = tallies
        if plots is not None:
            self.plots = plots

    @property
    def geometry(self) -> openmc.Geometry | None:
        return self._geometry

    @geometry.setter
    def geometry(self, geometry):
        check_type('geometry', geometry, openmc.Geometry)
        self._geometry = geometry

    @property
    def materials(self) -> openmc.Materials | None:
        return self._materials

    @materials.setter
    def materials(self, materials):
        check_type('materials', materials, Iterable, openmc.Material)
        if isinstance(materials, openmc.Materials):
            self._materials = materials
        else:
            del self._materials[:]
            for mat in materials:
                self._materials.append(mat)

    @property
    def settings(self) -> openmc.Settings | None:
        return self._settings

    @settings.setter
    def settings(self, settings):
        check_type('settings', settings, openmc.Settings)
        self._settings = settings

    @property
    def tallies(self) -> openmc.Tallies | None:
        return self._tallies

    @tallies.setter
    def tallies(self, tallies):
        check_type('tallies', tallies, Iterable, openmc.Tally)
        if isinstance(tallies, openmc.Tallies):
            self._tallies = tallies
        else:
            del self._tallies[:]
            for tally in tallies:
                self._tallies.append(tally)

    @property
    def plots(self) -> openmc.Plots | None:
        return self._plots

    @plots.setter
    def plots(self, plots):
        check_type('plots', plots, Iterable, openmc.Plot)
        if isinstance(plots, openmc.Plots):
            self._plots = plots
        else:
            del self._plots[:]
            for plot in plots:
                self._plots.append(plot)

    @property
    def is_initialized(self) -> bool:
        try:
            import openmc.lib
            return openmc.lib.is_initialized
        except ImportError:
            return False

    @property
    @lru_cache(maxsize=None)
    def _materials_by_id(self) -> dict:
        """Dictionary mapping material ID --> material"""
        if self.materials:
            mats = self.materials
        else:
            mats = self.geometry.get_all_materials().values()
        return {mat.id: mat for mat in mats}

    @property
    @lru_cache(maxsize=None)
    def _cells_by_id(self) -> dict:
        """Dictionary mapping cell ID --> cell"""
        cells = self.geometry.get_all_cells()
        return {cell.id: cell for cell in cells.values()}

    @property
    @lru_cache(maxsize=None)
    def _cells_by_name(self) -> dict[int, openmc.Cell]:
        # Get the names maps, but since names are not unique, store a set for
        # each name key. In this way when the user requests a change by a name,
        # the change will be applied to all of the same name.
        result = {}
        for cell in self.geometry.get_all_cells().values():
            if cell.name not in result:
                result[cell.name] = set()
            result[cell.name].add(cell)
        return result

    @property
    @lru_cache(maxsize=None)
    def _materials_by_name(self) -> dict[int, openmc.Material]:
        if self.materials is None:
            mats = self.geometry.get_all_materials().values()
        else:
            mats = self.materials
        result = {}
        for mat in mats:
            if mat.name not in result:
                result[mat.name] = set()
            result[mat.name].add(mat)
        return result

    @classmethod
    def from_xml(cls, geometry='geometry.xml', materials='materials.xml',
                 settings='settings.xml', tallies='tallies.xml',
                 plots='plots.xml') -> Model:
        """Create model from existing XML files

        Parameters
        ----------
        geometry : str
            Path to geometry.xml file
        materials : str
            Path to materials.xml file
        settings : str
            Path to settings.xml file
        tallies : str
            Path to tallies.xml file

            .. versionadded:: 0.13.0
        plots : str
            Path to plots.xml file

            .. versionadded:: 0.13.0

        Returns
        -------
        openmc.model.Model
            Model created from XML files

        """
        materials = openmc.Materials.from_xml(materials)
        geometry = openmc.Geometry.from_xml(geometry, materials)
        settings = openmc.Settings.from_xml(settings)
        tallies = openmc.Tallies.from_xml(tallies) if Path(tallies).exists() else None
        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

        .. versionadded:: 0.13.3

        Parameters
        ----------
        path : str or PathLike
            Path to model.xml file
        """
        parser = ET.XMLParser(huge_tree=True)
        tree = ET.parse(path, parser=parser)
        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') is not None:
            model.tallies = openmc.Tallies.from_xml_element(root.find('tallies'), meshes)

        if root.find('plots') is not None:
            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

        .. versionadded:: 0.13.0

        Parameters
        ----------
        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 :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.
        output : bool
            Capture OpenMC output from standard out
        event_based : None or bool, optional
            Turns on event-based parallelism if True. If None, the value in
            the Settings will be used.
        intracomm : mpi4py.MPI.Intracomm or None, optional
            MPI intracommunicator
        """

        import openmc.lib

        # TODO: right now the only way to set most of the above parameters via
        # the C API are at initialization time despite use-cases existing to
        # set them for individual runs. For now this functionality is exposed
        # where it exists (here in init), but in the future the functionality
        # should be exposed so that it can be accessed via model.run(...)

        args = _process_CLI_arguments(
            volume=False, geometry_debug=geometry_debug,
            restart_file=restart_file, threads=threads, tracks=tracks,
            event_based=event_based)
        # Args adds the openmc_exec command in the first entry; remove it
        args = args[1:]

        self.finalize_lib()

        # The Model object needs to be aware of the communicator so it can
        # use it in certain cases, therefore lets store the communicator
        if intracomm is not None:
            self._intracomm = intracomm
        else:
            self._intracomm = DummyCommunicator()

        if self._intracomm.rank == 0:
            self.export_to_xml()
        self._intracomm.barrier()

        # We cannot pass DummyCommunicator to openmc.lib.init so pass instead
        # the user-provided intracomm which will either be None or an mpi4py
        # communicator
        openmc.lib.init(args=args, intracomm=intracomm, output=output)

    def sync_dagmc_universes(self):
        """
        Synchronize all DAGMC universes in the current geometry.
        This method iterates over all DAGMC universes in the geometry and
        synchronizes their cells with the current material assignments. Requires
        that the model has been initialized via :meth:`Model.init_lib`.

        .. versionadded:: 0.15.1-dev

        """
        if self.is_initialized:
            if self.materials:
                materials = self.materials
            else:
                materials = list(self.geometry.get_all_materials().values())
            for univ in self.geometry.get_all_universes().values():
                if isinstance(univ, openmc.DAGMCUniverse):
                    univ.sync_dagmc_cells(materials)
        else:
            raise ValueError("The model must be initialized before calling "
                             "this method")

    def finalize_lib(self):
        """Finalize simulation and free memory allocated for the C API

        .. versionadded:: 0.13.0

        """

        import openmc.lib

        openmc.lib.finalize()

    def deplete(self, timesteps, method='cecm', final_step=True,
                operator_kwargs=None, directory='.', output=True,
                **integrator_kwargs):
        """Deplete model using specified timesteps/power

        .. versionchanged:: 0.13.0
            The *final_step*, *operator_kwargs*, *directory*, and *output*
            arguments were added.

        Parameters
        ----------
        timesteps : iterable of float
            Array of timesteps in units of [s]. Note that values are not
            cumulative.
        method : str, optional
             Integration method used for depletion (e.g., 'cecm', 'predictor').
             Defaults to 'cecm'.
        final_step : bool, optional
            Indicate whether or not a transport solve should be run at the end
            of the last timestep. Defaults to running this transport solve.
        operator_kwargs : dict
            Keyword arguments passed to the depletion operator initializer
            (e.g., :func:`openmc.deplete.Operator`)
        directory : str, optional
            Directory to write XML files to. If it doesn't exist already, it
            will be created. Defaults to the current working directory
        output : bool
            Capture OpenMC output from standard out
        integrator_kwargs : dict
            Remaining keyword arguments passed to the depletion Integrator
            initializer (e.g., :func:`openmc.deplete.integrator.cecm`).

        """

        if operator_kwargs is None:
            op_kwargs = {}
        elif isinstance(operator_kwargs, dict):
            op_kwargs = operator_kwargs
        else:
            raise ValueError("operator_kwargs must be a dict or None")

        # Import openmc.deplete here so the Model can be used even if the
        # shared library is unavailable.
        import openmc.deplete as dep

        # Store whether or not the library was initialized when we started
        started_initialized = self.is_initialized

        with change_directory(directory):
            with openmc.lib.quiet_dll(output):
                # TODO: Support use of IndependentOperator too
                depletion_operator = dep.CoupledOperator(self, **op_kwargs)

            # Tell depletion_operator.finalize NOT to clear C API memory when
            # it is done
            depletion_operator.cleanup_when_done = False

            # Set up the integrator
            check_value('method', method,
                        dep.integrators.integrator_by_name.keys())
            integrator_class = dep.integrators.integrator_by_name[method]
            integrator = integrator_class(depletion_operator, timesteps,
                                          **integrator_kwargs)

            # Now perform the depletion
            with openmc.lib.quiet_dll(output):
                integrator.integrate(final_step)

            # Now make the python Materials match the C API material data
            for mat_id, mat in self._materials_by_id.items():
                if mat.depletable:
                    # Get the C data
                    c_mat = openmc.lib.materials[mat_id]
                    nuclides, densities = c_mat._get_densities()
                    # And now we can remove isotopes and add these ones in
                    mat.nuclides.clear()
                    for nuc, density in zip(nuclides, densities):
                        mat.add_nuclide(nuc, density)
                    mat.set_density('atom/b-cm', sum(densities))

            # If we didnt start intialized, we should cleanup after ourselves
            if not started_initialized:
                depletion_operator.cleanup_when_done = True
                depletion_operator.finalize()

    def export_to_xml(self, directory='.', remove_surfs=False):
        """Export model to separate XML files.

        Parameters
        ----------
        directory : str
            Directory to write XML files to. If it doesn't exist already, it
            will be created.
        remove_surfs : bool
            Whether or not to remove redundant surfaces from the geometry when
            exporting.

            .. versionadded:: 0.13.1
        """
        # Create directory if required
        d = Path(directory)
        if not d.is_dir():
            d.mkdir(parents=True, exist_ok=True)

        self.settings.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
        # a collection.
        if self.materials:
            self.materials.export_to_xml(d)
        else:
            materials = openmc.Materials(self.geometry.get_all_materials()
                                         .values())
            materials.export_to_xml(d)

        if self.tallies:
            self.tallies.export_to_xml(d)
        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'):
            if not xml_path.exists():
                xml_path.mkdir(parents=True, exist_ok=True)
            elif not xml_path.is_dir():
                raise FileExistsError(f"File exists and is not a directory: '{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():
            xml_path.parent.mkdir(parents=True, exist_ok=True)

        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

        # 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("<?xml version='1.0' encoding='utf-8'?>\n")
            fh.write("<model>\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
            fh.write(ET.tostring(geometry_element, encoding="unicode"))
            fh.write(ET.tostring(settings_element, 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)
                fh.write(ET.tostring(tallies_element, encoding="unicode"))
            if self.plots:
                plots_element = self.plots.to_xml_element()
                xml.clean_indentation(plots_element, level=1, trailing_indent=False)
                fh.write(ET.tostring(plots_element, encoding="unicode"))
            fh.write("</model>\n")

    def import_properties(self, filename):
        """Import physical properties

        .. versionchanged:: 0.13.0
            This method now updates values as loaded in memory with the C API

        Parameters
        ----------
        filename : str
            Path to properties HDF5 file

        See Also
        --------
        openmc.lib.export_properties

        """
        import openmc.lib

        cells = self.geometry.get_all_cells()
        materials = self.geometry.get_all_materials()

        with h5py.File(filename, 'r') as fh:
            cells_group = fh['geometry/cells']

            # Make sure number of cells matches
            n_cells = fh['geometry'].attrs['n_cells']
            if n_cells != len(cells):
                raise ValueError("Number of cells in properties file doesn't "
                                 "match current model.")

            # Update temperatures for cells filled with materials
            for name, group in cells_group.items():
                cell_id = int(name.split()[1])
                cell = cells[cell_id]
                if cell.fill_type in ('material', 'distribmat'):
                    temperature = group['temperature'][()]
                    cell.temperature = temperature
                    if self.is_initialized:
                        lib_cell = openmc.lib.cells[cell_id]
                        if temperature.size > 1:
                            for i, T in enumerate(temperature):
                                lib_cell.set_temperature(T, i)
                        else:
                            lib_cell.set_temperature(temperature[0])

            # Make sure number of materials matches
            mats_group = fh['materials']
            n_cells = mats_group.attrs['n_materials']
            if n_cells != len(materials):
                raise ValueError("Number of materials in properties file "
                                 "doesn't match current model.")

            # Update material densities
            for name, group in mats_group.items():
                mat_id = int(name.split()[1])
                atom_density = group.attrs['atom_density']
                materials[mat_id].set_density('atom/b-cm', atom_density)
                if self.is_initialized:
                    C_mat = openmc.lib.materials[mat_id]
                    C_mat.set_density(atom_density, 'atom/b-cm')

    def run(self, particles=None, threads=None, geometry_debug=False,
            restart_file=None, tracks=False, output=True, cwd='.',
            openmc_exec='openmc', mpi_args=None, event_based=None,
            export_model_xml=True, **export_kwargs):
        """Run OpenMC

        If the C API has been initialized, then the C API is used, otherwise,
        this method creates the XML files and runs OpenMC via a system call. In
        both cases this method returns the path to the last statepoint file
        generated.

        .. versionchanged:: 0.12
            Instead of returning the final k-effective value, this function now
            returns the path to the final statepoint written.

        .. versionchanged:: 0.13.0
            This method can utilize the C API for execution

        Parameters
        ----------
        particles : int, optional
            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 :envvar:`OMP_NUM_THREADS` environment variable).
        geometry_debug : bool, optional
            Turn on geometry debugging during simulation. Defaults to False.
        restart_file : str or PathLike
            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.
        output : bool, optional
            Capture OpenMC output from standard out
        cwd : PathLike, optional
            Path to working directory to run in. Defaults to the current working
            directory.
        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'].
        event_based : None or bool, optional
            Turns on event-based parallelism if True. If None, the value in the
            Settings will be used.
        export_model_xml : bool, optional
            Exports a single model.xml file rather than separate files. Defaults
            to True.

            .. versionadded:: 0.13.3
        **export_kwargs
            Keyword arguments passed to either :meth:`Model.export_to_model_xml`
            or :meth:`Model.export_to_xml`.

        Returns
        -------
        Path
            Path to the last statepoint written by this run (None if no
            statepoint was written)

        """

        # Setting tstart here ensures we don't pick up any pre-existing
        # statepoint files in the output directory -- just in case there are
        # differences between the system clock and the filesystem, we get the
        # time of a just-created temporary file
        with NamedTemporaryFile() as fp:
            tstart = Path(fp.name).stat().st_mtime
        last_statepoint = None

        # Operate in the provided working directory
        with change_directory(cwd):
            if self.is_initialized:
                # Handle the run options as applicable
                # First dont allow ones that must be set via init
                for arg_name, arg, default in zip(
                    ['threads', 'geometry_debug', 'restart_file', 'tracks'],
                    [threads, geometry_debug, restart_file, tracks],
                    [None, False, None, False]
                ):
                    if arg != default:
                        msg = f"{arg_name} must be set via Model.is_initialized(...)"
                        raise ValueError(msg)

                init_particles = openmc.lib.settings.particles
                if particles is not None:
                    if isinstance(particles, Integral) and particles > 0:
                        openmc.lib.settings.particles = particles

                init_event_based = openmc.lib.settings.event_based
                if event_based is not None:
                    openmc.lib.settings.event_based = event_based

                # Then run using the C API
                openmc.lib.run(output)

                # Reset changes for the openmc.run kwargs handling
                openmc.lib.settings.particles = init_particles
                openmc.lib.settings.event_based = init_event_based

            else:
                # Then run via the command line
                if export_model_xml:
                    self.export_to_model_xml(**export_kwargs)
                else:
                    self.export_to_xml(**export_kwargs)
                path_input = export_kwargs.get("path", None)
                openmc.run(particles, threads, geometry_debug, restart_file,
                           tracks, output, Path('.'), openmc_exec, mpi_args,
                           event_based, path_input)

            # Get output directory and return the last statepoint written
            if self.settings.output and 'path' in self.settings.output:
                output_dir = Path(self.settings.output['path'])
            else:
                output_dir = Path.cwd()
            for sp in output_dir.glob('statepoint.*.h5'):
                mtime = sp.stat().st_mtime
                if mtime >= tstart:  # >= allows for poor clock resolution
                    tstart = mtime
                    last_statepoint = sp
        return last_statepoint

    def calculate_volumes(self, threads=None, output=True, cwd='.',
                          openmc_exec='openmc', mpi_args=None,
                          apply_volumes=True, export_model_xml=True,
                          **export_kwargs):
        """Runs an OpenMC stochastic volume calculation and, if requested,
        applies volumes to the model

        .. versionadded:: 0.13.0

        Parameters
        ----------
        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 :envvar:`OMP_NUM_THREADS` environment variable).
            This currenty only applies to the case when not using the C API.
        output : bool, optional
            Capture OpenMC output from standard out
        openmc_exec : str, optional
            Path to OpenMC executable. Defaults to 'openmc'.
            This only applies to the case when not using the C API.
        mpi_args : list of str, optional
            MPI execute command and any additional MPI arguments to pass,
            e.g. ['mpiexec', '-n', '8'].
            This only applies to the case when not using the C API.
        cwd : str, optional
            Path to working directory to run in. Defaults to the current
            working directory.
        apply_volumes : bool, optional
            Whether apply the volume calculation results from this calculation
            to the model. Defaults to applying the volumes.
        export_model_xml : bool, optional
            Exports a single model.xml file rather than separate files. Defaults
            to True.
        **export_kwargs
            Keyword arguments passed to either :meth:`Model.export_to_model_xml`
            or :meth:`Model.export_to_xml`.

        """

        if len(self.settings.volume_calculations) == 0:
            # Then there is no volume calculation specified
            raise ValueError("The Settings.volume_calculations attribute must"
                             " be specified before executing this method!")

        with change_directory(cwd):
            if self.is_initialized:
                if threads is not None:
                    msg = "Threads must be set via Model.is_initialized(...)"
                    raise ValueError(msg)
                if mpi_args is not None:
                    msg = "The MPI environment must be set otherwise such as" \
                        "with the call to mpi4py"
                    raise ValueError(msg)

                # Compute the volumes
                openmc.lib.calculate_volumes(output)

            else:
                if export_model_xml:
                    self.export_to_model_xml(**export_kwargs)
                else:
                    self.export_to_xml(**export_kwargs)
                path_input = export_kwargs.get("path", None)
                openmc.calculate_volumes(
                    threads=threads, output=output, openmc_exec=openmc_exec,
                    mpi_args=mpi_args, path_input=path_input
                )

            # Now we apply the volumes
            if apply_volumes:
                # Load the results and add them to the model
                for i, vol_calc in enumerate(self.settings.volume_calculations):
                    vol_calc.load_results(f"volume_{i + 1}.h5")
                    # First add them to the Python side
                    if vol_calc.domain_type == "material" and self.materials:
                        for material in self.materials:
                            if material.id in vol_calc.volumes:
                                material.add_volume_information(vol_calc)
                    else:
                        self.geometry.add_volume_information(vol_calc)

                    # And now repeat for the C API
                    if self.is_initialized and vol_calc.domain_type == 'material':
                        # Then we can do this in the C API
                        for domain_id in vol_calc.ids:
                            openmc.lib.materials[domain_id].volume = \
                                vol_calc.volumes[domain_id].n

    def plot(
        self,
        n_samples: int | None = None,
        plane_tolerance: float = 1.,
        source_kwargs: dict | None = None,
        **kwargs,
    ):
        """Display a slice plot of the geometry.

        .. versionadded:: 0.15.1

        Parameters
        ----------
        n_samples : int, optional
            The number of source particles to sample and add to plot. Defaults
            to None which doesn't plot any particles on the plot.
        plane_tolerance: float
            When plotting a plane the source locations within the plane +/-
            the plane_tolerance will be included and those outside of the
            plane_tolerance will not be shown
        source_kwargs : dict, optional
            Keyword arguments passed to :func:`matplotlib.pyplot.scatter`.
        **kwargs
            Keyword arguments passed to :func:`openmc.Universe.plot`

        Returns
        -------
        matplotlib.axes.Axes
            Axes containing resulting image
        """

        check_type('n_samples', n_samples, int | None)
        check_type('plane_tolerance', plane_tolerance, float)
        if source_kwargs is None:
            source_kwargs = {}
        source_kwargs.setdefault('marker', 'x')

        ax = self.geometry.plot(**kwargs)
        if n_samples:
            # Sample external source particles
            particles = self.sample_external_source(n_samples)

            # Determine plotting parameters and bounding box of geometry
            bbox = self.geometry.bounding_box
            origin = kwargs.get('origin', None)
            basis = kwargs.get('basis', 'xy')
            indices = {'xy': (0, 1, 2), 'xz': (0, 2, 1), 'yz': (1, 2, 0)}[basis]

            # Infer origin if not provided
            if np.isinf(bbox.extent[basis]).any():
                if origin is None:
                    origin = (0, 0, 0)
            else:
                if origin is None:
                    # if nan values in the bbox.center they get replaced with 0.0
                    # this happens when the bounding_box contains inf values
                    with warnings.catch_warnings():
                        warnings.simplefilter("ignore", RuntimeWarning)
                        origin = np.nan_to_num(bbox.center)

            slice_index = indices[2]
            slice_value = origin[slice_index]

            xs = []
            ys = []
            tol = plane_tolerance
            for particle in particles:
                if (slice_value - tol < particle.r[slice_index] < slice_value + tol):
                    xs.append(particle.r[indices[0]])
                    ys.append(particle.r[indices[1]])
            ax.scatter(xs, ys, **source_kwargs)
        return ax

    def sample_external_source(
            self,
            n_samples: int = 1000,
            prn_seed: int | None = None,
            **init_kwargs
    ) -> openmc.ParticleList:
        """Sample external source and return source particles.

        .. versionadded:: 0.15.1

        Parameters
        ----------
        n_samples : int
            Number of samples
        prn_seed : int
            Pseudorandom number generator (PRNG) seed; if None, one will be
            generated randomly.
        **init_kwargs
            Keyword arguments passed to :func:`openmc.lib.init`

        Returns
        -------
        openmc.ParticleList
            List of samples source particles
        """
        import openmc.lib

        # Silence output by default. Also set arguments to start in volume
        # calculation mode to avoid loading cross sections
        init_kwargs.setdefault('output', False)
        init_kwargs.setdefault('args', ['-c'])

        with change_directory(tmpdir=True):
            # Export model within temporary directory
            self.export_to_model_xml()

            # Sample external source sites
            with openmc.lib.run_in_memory(**init_kwargs):
                return openmc.lib.sample_external_source(
                    n_samples=n_samples, prn_seed=prn_seed
                )

    def plot_geometry(self, output=True, cwd='.', openmc_exec='openmc',
                      export_model_xml=True, **export_kwargs):
        """Creates plot images as specified by the Model.plots attribute

        .. versionadded:: 0.13.0

        Parameters
        ----------
        output : bool, optional
            Capture OpenMC output from standard out
        cwd : str, optional
            Path to working directory to run in. Defaults to the current
            working directory.
        openmc_exec : str, optional
            Path to OpenMC executable. Defaults to 'openmc'.
            This only applies to the case when not using the C API.
        export_model_xml : bool, optional
            Exports a single model.xml file rather than separate files. Defaults
            to True.
        **export_kwargs
            Keyword arguments passed to either :meth:`Model.export_to_model_xml`
            or :meth:`Model.export_to_xml`.

        """

        if len(self.plots) == 0:
            # Then there is no volume calculation specified
            raise ValueError("The Model.plots attribute must be specified "
                             "before executing this method!")

        with change_directory(cwd):
            if self.is_initialized:
                # Compute the volumes
                openmc.lib.plot_geometry(output)
            else:
                if export_model_xml:
                    self.export_to_model_xml(**export_kwargs)
                else:
                    self.export_to_xml(**export_kwargs)
                path_input = export_kwargs.get("path", None)
                openmc.plot_geometry(output=output, openmc_exec=openmc_exec,
                                     path_input=path_input)

    def _change_py_lib_attribs(self, names_or_ids, value, obj_type,
                               attrib_name, density_units='atom/b-cm'):
        # Method to do the same work whether it is a cell or material and
        # a temperature or volume
        check_type('names_or_ids', names_or_ids, Iterable, (Integral, str))
        check_type('obj_type', obj_type, str)
        obj_type = obj_type.lower()
        check_value('obj_type', obj_type, ('material', 'cell'))
        check_value('attrib_name', attrib_name,
                    ('temperature', 'volume', 'density', 'rotation',
                     'translation'))
        # The C API only allows setting density units of atom/b-cm and g/cm3
        check_value('density_units', density_units, ('atom/b-cm', 'g/cm3'))
        # The C API has no way to set cell volume or material temperature
        # so lets raise exceptions as needed
        if obj_type == 'cell' and attrib_name == 'volume':
            raise NotImplementedError(
                'Setting a Cell volume is not supported!')
        if obj_type == 'material' and attrib_name == 'temperature':
            raise NotImplementedError(
                'Setting a material temperature is not supported!')

        # And some items just dont make sense
        if obj_type == 'cell' and attrib_name == 'density':
            raise ValueError('Cannot set a Cell density!')
        if obj_type == 'material' and attrib_name in ('rotation',
                                                      'translation'):
            raise ValueError('Cannot set a material rotation/translation!')

        # Set the
        if obj_type == 'cell':
            by_name = self._cells_by_name
            by_id = self._cells_by_id
            if self.is_initialized:
                obj_by_id = openmc.lib.cells
        else:
            by_name = self._materials_by_name
            by_id = self._materials_by_id
            if self.is_initialized:
                obj_by_id = openmc.lib.materials
        # Get the list of ids to use if converting from names and accepting
        # only values that have actual ids
        ids = []
        for name_or_id in names_or_ids:
            if isinstance(name_or_id, Integral):
                if name_or_id in by_id:
                    ids.append(int(name_or_id))
                else:
                    cap_obj = obj_type.capitalize()
                    msg = f'{cap_obj} ID {name_or_id} " \
                        "is not present in the model!'
                    raise InvalidIDError(msg)
            elif isinstance(name_or_id, str):
                if name_or_id in by_name:
                    # Then by_name[name_or_id] is a list so we need to add all
                    # entries
                    ids.extend([obj.id for obj in by_name[name_or_id]])
                else:
                    cap_obj = obj_type.capitalize()
                    msg = f'{cap_obj} {name_or_id} " \
                        "is not present in the model!'
                    raise InvalidIDError(msg)

        # Now perform the change to both python and C API
        for id_ in ids:
            obj = by_id[id_]
            if attrib_name == 'density':
                obj.set_density(density_units, value)
            else:
                setattr(obj, attrib_name, value)
            # Next lets keep what is in C API memory up to date as well
            if self.is_initialized:
                lib_obj = obj_by_id[id_]
                if attrib_name == 'density':
                    lib_obj.set_density(value, density_units)
                elif attrib_name == 'temperature':
                    lib_obj.set_temperature(value)
                else:
                    setattr(lib_obj, attrib_name, value)

    def rotate_cells(self, names_or_ids, vector):
        """Rotate the identified cell(s) by the specified rotation vector.
        The rotation is only applied to cells filled with a universe.

        .. note:: If applying this change to a name that is not unique, then
                  the change will be applied to all objects of that name.

        .. versionadded:: 0.13.0

        Parameters
        ----------
        names_or_ids : Iterable of str or int
            The cell names (if str) or id (if int) that are to be translated
            or rotated. This parameter can include a mix of names and ids.
        vector : Iterable of float
            The rotation vector of length 3 to apply. This array specifies the
            angles in degrees about the x, y, and z axes, respectively.

        """

        self._change_py_lib_attribs(names_or_ids, vector, 'cell', 'rotation')

    def translate_cells(self, names_or_ids, vector):
        """Translate the identified cell(s) by the specified translation vector.
        The translation is only applied to cells filled with a universe.

        .. note:: If applying this change to a name that is not unique, then
                  the change will be applied to all objects of that name.

        .. versionadded:: 0.13.0

        Parameters
        ----------
        names_or_ids : Iterable of str or int
            The cell names (if str) or id (if int) that are to be translated
            or rotated. This parameter can include a mix of names and ids.
        vector : Iterable of float
            The translation vector of length 3 to apply. This array specifies
            the x, y, and z dimensions of the translation.

        """

        self._change_py_lib_attribs(names_or_ids, vector, 'cell',
                                    'translation')

    def update_densities(self, names_or_ids, density, density_units='atom/b-cm'):
        """Update the density of a given set of materials to a new value

        .. note:: If applying this change to a name that is not unique, then
                  the change will be applied to all objects of that name.

        .. versionadded:: 0.13.0

        Parameters
        ----------
        names_or_ids : Iterable of str or int
            The material names (if str) or id (if int) that are to be updated.
            This parameter can include a mix of names and ids.
        density : float
            The density to apply in the units specified by `density_units`
        density_units : {'atom/b-cm', 'g/cm3'}, optional
            Units for `density`. Defaults to 'atom/b-cm'

        """

        self._change_py_lib_attribs(names_or_ids, density, 'material',
                                    'density', density_units)

    def update_cell_temperatures(self, names_or_ids, temperature):
        """Update the temperature of a set of cells to the given value

        .. note:: If applying this change to a name that is not unique, then
                  the change will be applied to all objects of that name.

        .. versionadded:: 0.13.0

        Parameters
        ----------
        names_or_ids : Iterable of str or int
            The cell names (if str) or id (if int) that are to be updated.
            This parameter can include a mix of names and ids.
        temperature : float
            The temperature to apply in units of Kelvin

        """

        self._change_py_lib_attribs(names_or_ids, temperature, 'cell',
                                    'temperature')

    def update_material_volumes(self, names_or_ids, volume):
        """Update the volume of a set of materials to the given value

        .. note:: If applying this change to a name that is not unique, then
                  the change will be applied to all objects of that name.

        .. versionadded:: 0.13.0

        Parameters
        ----------
        names_or_ids : Iterable of str or int
            The material names (if str) or id (if int) that are to be updated.
            This parameter can include a mix of names and ids.
        volume : float
            The volume to apply in units of cm^3

        """

        self._change_py_lib_attribs(names_or_ids, volume, 'material', 'volume')

    def differentiate_depletable_mats(self, diff_volume_method : str = None):
        """Assign distribmats for each depletable material

        .. versionadded:: 0.14.0

        .. version added:: 0.15.1-dev
            diff_volume_method default is None, do not apply volume to the new
            materials. Is now a convenience method for
            differentiate_mats(diff_volume_method, depletable_only=True)

        Parameters
        ----------
        diff_volume_method : str
            Specifies how the volumes of the new materials should be found.
            Default is 'None', do not apply volume to the new materials,
            'divide equally' which divides the original material
            volume equally between the new materials,
            'match cell' sets the volume of the material to volume of the cell
            they fill.
        """
        self.differentiate_mats(diff_volume_method, depletable_only=True)

    def differentiate_mats(self, diff_volume_method: str = None, depletable_only: bool = True):
        """Assign distribmats for each material

        .. versionadded:: 0.15.1-dev

        Parameters
        ----------
        diff_volume_method : str
            Specifies how the volumes of the new materials should be found.
            - None: Do not assign volumes to the new materials (Default)
            - 'divide_equally': Divide the original material volume equally between the new materials
            - 'match cell': Set the volume of the material to the volume of the cell they fill
        depletable_only : bool
            Default is True, only depletable materials will be differentiated. If False, all materials will be
            differentiated.
        """
        check_value('volume differentiation method', diff_volume_method, ("divide equally", "match cell", None))

        # Count the number of instances for each cell and material
        self.geometry.determine_paths(instances_only=True)

        # Find all or depletable_only materials which have multiple instance
        distribmats = set()
        for mat in self.materials:
            # Differentiate all materials with multiple instances
            diff_mat = mat.num_instances > 1
            # If depletable_only is True, differentiate only depletable materials
            if depletable_only:
                diff_mat = diff_mat and mat.depletable
            if diff_mat:
                # Assign volumes to the materials according to requirements
                if diff_volume_method == "divide equally":
                    if mat.volume is None:
                        raise RuntimeError(
                            "Volume not specified for "
                            f"material with ID={mat.id}.")
                    else:
                        mat.volume /= mat.num_instances
                elif diff_volume_method == "match cell":
                    for cell in self.geometry.get_all_material_cells().values():
                        if cell.fill == mat:
                            if not cell.volume:
                                raise ValueError(
                                    f"Volume of cell ID={cell.id} not specified. "
                                    "Set volumes of cells prior to using "
                                    "diff_volume_method='match cell'.")
                distribmats.add(mat)

        if not distribmats:
            return

        # Assign distribmats to cells
        for cell in self.geometry.get_all_material_cells().values():
            if cell.fill in distribmats:
                mat = cell.fill
                if diff_volume_method != 'match cell':
                    cell.fill = [mat.clone() for _ in range(cell.num_instances)]
                elif diff_volume_method == 'match cell':
                    cell.fill = mat.clone()
                    cell.fill.volume = cell.volume

        if self.materials is not None:
            self.materials = openmc.Materials(
                self.geometry.get_all_materials().values()
            )

openmc-dev / openmc / 12472509828

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