Source code for openmc.mesh

from abc import ABC, abstractmethod
from collections.abc import Iterable
from math import pi
from numbers import Real, Integral
from pathlib import Path
import warnings
from xml.etree import ElementTree as ET

import numpy as np

import openmc.checkvalue as cv
import openmc
from ._xml import get_text
from .mixin import IDManagerMixin
from .surface import _BOUNDARY_TYPES


class MeshBase(IDManagerMixin, ABC):
    """A mesh that partitions geometry for tallying purposes.

    Parameters
    ----------
    mesh_id : int
        Unique identifier for the mesh
    name : str
        Name of the mesh

    Attributes
    ----------
    id : int
        Unique identifier for the mesh
    name : str
        Name of the mesh

    """

    next_id = 1
    used_ids = set()

    def __init__(self, mesh_id=None, name=''):
        # Initialize Mesh class attributes
        self.id = mesh_id
        self.name = name

    @property
    def name(self):
        return self._name

    @name.setter
    def name(self, name):
        if name is not None:
            cv.check_type(f'name for mesh ID="{self._id}"', name, str)
            self._name = name
        else:
            self._name = ''

    def __repr__(self):
        string = type(self).__name__ + '\n'
        string += '{0: <16}{1}{2}\n'.format('\tID', '=\t', self._id)
        string += '{0: <16}{1}{2}\n'.format('\tName', '=\t', self._name)
        return string

    def _volume_dim_check(self):
        if self.n_dimension != 3 or \
           any([d == 0 for d in self.dimension]):
            raise RuntimeError(f'Mesh {self.id} is not 3D. '
                               'Volumes cannot be provided.')

    @classmethod
    def from_hdf5(cls, group):
        """Create mesh from HDF5 group

        Parameters
        ----------
        group : h5py.Group
            Group in HDF5 file

        Returns
        -------
        openmc.MeshBase
            Instance of a MeshBase subclass

        """

        mesh_type = group['type'][()].decode()
        if mesh_type == 'regular':
            return RegularMesh.from_hdf5(group)
        elif mesh_type == 'rectilinear':
            return RectilinearMesh.from_hdf5(group)
        elif mesh_type == 'cylindrical':
            return CylindricalMesh.from_hdf5(group)
        elif mesh_type == 'spherical':
            return SphericalMesh.from_hdf5(group)
        elif mesh_type == 'unstructured':
            return UnstructuredMesh.from_hdf5(group)
        else:
            raise ValueError('Unrecognized mesh type: "' + mesh_type + '"')

    @classmethod
    def from_xml_element(cls, elem):
        """Generates a mesh from an XML element

        Parameters
        ----------
        elem : xml.etree.ElementTree.Element
            XML element

        Returns
        -------
        openmc.MeshBase
            an openmc mesh object

        """
        mesh_type = get_text(elem, 'type')

        if mesh_type == 'regular' or mesh_type is None:
            return RegularMesh.from_xml_element(elem)
        elif mesh_type == 'rectilinear':
            return RectilinearMesh.from_xml_element(elem)
        elif mesh_type == 'cylindrical':
            return CylindricalMesh.from_xml_element(elem)
        elif mesh_type == 'spherical':
            return SphericalMesh.from_xml_element(elem)
        elif mesh_type == 'unstructured':
            return UnstructuredMesh.from_xml_element(elem)
        else:
            raise ValueError(f'Unrecognized mesh type "{mesh_type}" found.')


class StructuredMesh(MeshBase):
    """A base class for structured mesh functionality

    Parameters
    ----------
    mesh_id : int
        Unique identifier for the mesh
    name : str
        Name of the mesh

    Attributes
    ----------
    id : int
        Unique identifier for the mesh
    name : str
        Name of the mesh

    """

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)

    @property
    @abstractmethod
    def dimension(self):
        pass

    @property
    @abstractmethod
    def n_dimension(self):
        pass

    @property
    @abstractmethod
    def _grids(self):
        pass

    @property
    def vertices(self):
        """Return coordinates of mesh vertices.

        Returns
        -------
        vertices : numpy.ndarray
            Returns a numpy.ndarray representing the coordinates of the mesh
            vertices with a shape equal to (dim1 + 1, ..., dimn + 1, ndim).

        """
        return np.stack(np.meshgrid(*self._grids, indexing='ij'), axis=-1)

    @property
    def centroids(self):
        """Return coordinates of mesh element centroids.

        Returns
        -------
        centroids : numpy.ndarray
            Returns a numpy.ndarray representing the mesh element centroid
            coordinates with a shape equal to (dim1, ..., dimn, ndim).

        """
        ndim = self.n_dimension
        vertices = self.vertices
        s0 = (slice(0, -1),)*ndim + (slice(None),)
        s1 = (slice(1, None),)*ndim + (slice(None),)
        return (vertices[s0] + vertices[s1]) / 2

    @property
    def num_mesh_cells(self):
        return np.prod(self.dimension)

    def write_data_to_vtk(self, points, filename, datasets, volume_normalization=True):
        """Creates a VTK object of the mesh

        Parameters
        ----------
        points : list or np.array
            List of (X,Y,Z) tuples.
        filename : str
            Name of the VTK file to write.
        datasets : dict
            Dictionary whose keys are the data labels
            and values are the data sets.
        volume_normalization : bool, optional
            Whether or not to normalize the data by
            the volume of the mesh elements.

        Raises
        ------
        RuntimeError
            When the size of a dataset doesn't match the number of cells

        Returns
        -------
        vtk.vtkStructuredGrid
            the VTK object
        """

        import vtk
        from vtk.util import numpy_support as nps

        # check that the data sets are appropriately sized
        errmsg = "The size of the dataset {} should be equal to the number of cells"
        for label, dataset in datasets.items():
            if isinstance(dataset, np.ndarray):
                if not dataset.size == self.dimension[0] * self.dimension[1]* self.dimension[2]:
                    raise RuntimeError(errmsg.format(label))
            else:
                if len(dataset) == self.dimension[0] * self.dimension[1]* self.dimension[2]:
                    raise RuntimeError(errmsg.format(label))
            cv.check_type('label', label, str)

        vtk_grid = vtk.vtkStructuredGrid()

        vtk_grid.SetDimensions(*[dim + 1 for dim in self.dimension])

        vtkPts = vtk.vtkPoints()
        vtkPts.SetData(nps.numpy_to_vtk(points, deep=True))
        vtk_grid.SetPoints(vtkPts)

        # create VTK arrays for each of
        # the data sets

        # maintain a list of the datasets as added
        # to the VTK arrays to ensure they persist
        # in memory until the file is written
        datasets_out = []
        for label, dataset in datasets.items():
            dataset = np.asarray(dataset).flatten()
            datasets_out.append(dataset)

            if volume_normalization:
                dataset /= self.volumes.flatten()

            dataset_array = vtk.vtkDoubleArray()
            dataset_array.SetName(label)
            dataset_array.SetArray(nps.numpy_to_vtk(dataset),
                           dataset.size,
                           True)
            vtk_grid.GetCellData().AddArray(dataset_array)

        # write the .vtk file
        writer = vtk.vtkStructuredGridWriter()
        writer.SetFileName(str(filename))
        writer.SetInputData(vtk_grid)
        writer.Write()

        return vtk_grid

[docs]class RegularMesh(StructuredMesh): """A regular Cartesian mesh in one, two, or three dimensions Parameters ---------- mesh_id : int Unique identifier for the mesh name : str Name of the mesh Attributes ---------- id : int Unique identifier for the mesh name : str Name of the mesh dimension : Iterable of int The number of mesh cells in each direction. n_dimension : int Number of mesh dimensions. lower_left : Iterable of float The lower-left corner of the structured mesh. If only two coordinate are given, it is assumed that the mesh is an x-y mesh. upper_right : Iterable of float The upper-right corner of the structured mesh. If only two coordinate are given, it is assumed that the mesh is an x-y mesh. width : Iterable of float The width of mesh cells in each direction. indices : Iterable of tuple An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1), (2, 1, 1), ...] """ def __init__(self, mesh_id=None, name=''): super().__init__(mesh_id, name) self._dimension = None self._lower_left = None self._upper_right = None self._width = None @property def dimension(self): return self._dimension @property def n_dimension(self): if self._dimension is not None: return len(self._dimension) else: return None @property def lower_left(self): return self._lower_left @property def upper_right(self): if self._upper_right is not None: return self._upper_right elif self._width is not None: if self._lower_left is not None and self._dimension is not None: ls = self._lower_left ws = self._width dims = self._dimension return [l + w * d for l, w, d in zip(ls, ws, dims)] @property def width(self): if self._width is not None: return self._width elif self._upper_right is not None: if self._lower_left is not None and self._dimension is not None: us = self._upper_right ls = self._lower_left dims = self._dimension return [(u - l) / d for u, l, d in zip(us, ls, dims)] @property def volumes(self): """Return Volumes for every mesh cell Returns ------- volumes : numpy.ndarray Volumes """ self._volume_dim_check() return np.full(self.dimension, np.prod(self.width)) @property def total_volume(self): return np.prod(self.dimension) * np.prod(self.width) @property def indices(self): ndim = len(self._dimension) if ndim == 3: nx, ny, nz = self.dimension return ((x, y, z) for z in range(1, nz + 1) for y in range(1, ny + 1) for x in range(1, nx + 1)) elif ndim == 2: nx, ny = self.dimension return ((x, y) for y in range(1, ny + 1) for x in range(1, nx + 1)) else: nx, = self.dimension return ((x,) for x in range(1, nx + 1)) @property def _grids(self): ndim = len(self._dimension) if ndim == 3: x0, y0, z0 = self.lower_left x1, y1, z1 = self.upper_right nx, ny, nz = self.dimension xarr = np.linspace(x0, x1, nx + 1) yarr = np.linspace(y0, y1, ny + 1) zarr = np.linspace(z0, z1, nz + 1) return (xarr, yarr, zarr) elif ndim == 2: x0, y0 = self.lower_left x1, y1 = self.upper_right nx, ny = self.dimension xarr = np.linspace(x0, x1, nx + 1) yarr = np.linspace(y0, y1, ny + 1) return (xarr, yarr) else: nx, = self.dimension x0, = self.lower_left x1, = self.upper_right return (np.linspace(x0, x1, nx + 1),) @dimension.setter def dimension(self, dimension): cv.check_type('mesh dimension', dimension, Iterable, Integral) cv.check_length('mesh dimension', dimension, 1, 3) self._dimension = dimension @lower_left.setter def lower_left(self, lower_left): cv.check_type('mesh lower_left', lower_left, Iterable, Real) cv.check_length('mesh lower_left', lower_left, 1, 3) self._lower_left = lower_left @upper_right.setter def upper_right(self, upper_right): cv.check_type('mesh upper_right', upper_right, Iterable, Real) cv.check_length('mesh upper_right', upper_right, 1, 3) self._upper_right = upper_right if self._width is not None: self._width = None warnings.warn("Unsetting width attribute.") @width.setter def width(self, width): cv.check_type('mesh width', width, Iterable, Real) cv.check_length('mesh width', width, 1, 3) self._width = width if self._upper_right is not None: self._upper_right = None warnings.warn("Unsetting upper_right attribute.") def __repr__(self): string = super().__repr__() string += '{0: <16}{1}{2}\n'.format('\tDimensions', '=\t', self.n_dimension) string += '{0: <16}{1}{2}\n'.format('\tVoxels', '=\t', self._dimension) string += '{0: <16}{1}{2}\n'.format('\tLower left', '=\t', self._lower_left) string += '{0: <16}{1}{2}\n'.format('\tUpper Right', '=\t', self._upper_right) string += '{0: <16}{1}{2}\n'.format('\tWidth', '=\t', self._width) return string
[docs] @classmethod def from_hdf5(cls, group): mesh_id = int(group.name.split('/')[-1].lstrip('mesh ')) # Read and assign mesh properties mesh = cls(mesh_id) mesh.dimension = group['dimension'][()] mesh.lower_left = group['lower_left'][()] if 'width' in group: mesh.width = group['width'][()] elif 'upper_right' in group: mesh.upper_right = group['upper_right'][()] else: raise IOError('Invalid mesh: must have one of "upper_right" or "width"') return mesh
[docs] @classmethod def from_rect_lattice(cls, lattice, division=1, mesh_id=None, name=''): """Create mesh from an existing rectangular lattice Parameters ---------- lattice : openmc.RectLattice Rectangular lattice used as a template for this mesh division : int Number of mesh cells per lattice cell. If not specified, there will be 1 mesh cell per lattice cell. mesh_id : int Unique identifier for the mesh name : str Name of the mesh Returns ------- openmc.RegularMesh RegularMesh instance """ cv.check_type('rectangular lattice', lattice, openmc.RectLattice) shape = np.array(lattice.shape) width = lattice.pitch*shape mesh = cls(mesh_id, name) mesh.lower_left = lattice.lower_left mesh.upper_right = lattice.lower_left + width mesh.dimension = shape*division return mesh
[docs] def to_xml_element(self): """Return XML representation of the mesh Returns ------- element : xml.etree.ElementTree.Element XML element containing mesh data """ element = ET.Element("mesh") element.set("id", str(self._id)) if self._dimension is not None: subelement = ET.SubElement(element, "dimension") subelement.text = ' '.join(map(str, self._dimension)) subelement = ET.SubElement(element, "lower_left") subelement.text = ' '.join(map(str, self._lower_left)) if self._upper_right is not None: subelement = ET.SubElement(element, "upper_right") subelement.text = ' '.join(map(str, self._upper_right)) if self._width is not None: subelement = ET.SubElement(element, "width") subelement.text = ' '.join(map(str, self._width)) return element
[docs] @classmethod def from_xml_element(cls, elem): """Generate mesh from an XML element Parameters ---------- elem : xml.etree.ElementTree.Element XML element Returns ------- openmc.Mesh Mesh generated from XML element """ mesh_id = int(get_text(elem, 'id')) mesh = cls(mesh_id) mesh_type = get_text(elem, 'type') if mesh_type is not None: mesh.type = mesh_type dimension = get_text(elem, 'dimension') if dimension is not None: mesh.dimension = [int(x) for x in dimension.split()] lower_left = get_text(elem, 'lower_left') if lower_left is not None: mesh.lower_left = [float(x) for x in lower_left.split()] upper_right = get_text(elem, 'upper_right') if upper_right is not None: mesh.upper_right = [float(x) for x in upper_right.split()] width = get_text(elem, 'width') if width is not None: mesh.width = [float(x) for x in width.split()] return mesh
[docs] def build_cells(self, bc=None): """Generates a lattice of universes with the same dimensionality as the mesh object. The individual cells/universes produced will not have material definitions applied and so downstream code will have to apply that information. Parameters ---------- bc : iterable of {'reflective', 'periodic', 'transmission', 'vacuum', or 'white'} Boundary conditions for each of the four faces of a rectangle (if applying to a 2D mesh) or six faces of a parallelepiped (if applying to a 3D mesh) provided in the following order: [x min, x max, y min, y max, z min, z max]. 2-D cells do not contain the z min and z max entries. Defaults to 'reflective' for all faces. Returns ------- root_cell : openmc.Cell The cell containing the lattice representing the mesh geometry; this cell is a single parallelepiped with boundaries matching the outermost mesh boundary with the boundary conditions from bc applied. cells : iterable of openmc.Cell The list of cells within each lattice position mimicking the mesh geometry. """ if bc is None: bc = ['reflective'] * 6 if len(bc) not in (4, 6): raise ValueError('Boundary condition must be of length 4 or 6') for entry in bc: cv.check_value('bc', entry, _BOUNDARY_TYPES) n_dim = self.n_dimension # Build the cell which will contain the lattice xplanes = [openmc.XPlane(self.lower_left[0], boundary_type=bc[0]), openmc.XPlane(self.upper_right[0], boundary_type=bc[1])] if n_dim == 1: yplanes = [openmc.YPlane(-1e10, boundary_type='reflective'), openmc.YPlane(1e10, boundary_type='reflective')] else: yplanes = [openmc.YPlane(self.lower_left[1], boundary_type=bc[2]), openmc.YPlane(self.upper_right[1], boundary_type=bc[3])] if n_dim <= 2: # Would prefer to have the z ranges be the max supported float, but # these values are apparently different between python and Fortran. # Choosing a safe and sane default. # Values of +/-1e10 are used here as there seems to be an # inconsistency between what numpy uses as the max float and what # Fortran expects for a real(8), so this avoids code complication # and achieves the same goal. zplanes = [openmc.ZPlane(-1e10, boundary_type='reflective'), openmc.ZPlane(1e10, boundary_type='reflective')] else: zplanes = [openmc.ZPlane(self.lower_left[2], boundary_type=bc[4]), openmc.ZPlane(self.upper_right[2], boundary_type=bc[5])] root_cell = openmc.Cell() root_cell.region = ((+xplanes[0] & -xplanes[1]) & (+yplanes[0] & -yplanes[1]) & (+zplanes[0] & -zplanes[1])) # Build the universes which will be used for each of the (i,j,k) # locations within the mesh. # We will concurrently build cells to assign to these universes cells = [] universes = [] for _ in self.indices: cells.append(openmc.Cell()) universes.append(openmc.Universe()) universes[-1].add_cell(cells[-1]) lattice = openmc.RectLattice() lattice.lower_left = self.lower_left # Assign the universe and rotate to match the indexing expected for # the lattice if n_dim == 1: universe_array = np.array([universes]) elif n_dim == 2: universe_array = np.empty(self.dimension[::-1], dtype=openmc.Universe) i = 0 for y in range(self.dimension[1] - 1, -1, -1): for x in range(self.dimension[0]): universe_array[y][x] = universes[i] i += 1 else: universe_array = np.empty(self.dimension[::-1], dtype=openmc.Universe) i = 0 for z in range(self.dimension[2]): for y in range(self.dimension[1] - 1, -1, -1): for x in range(self.dimension[0]): universe_array[z][y][x] = universes[i] i += 1 lattice.universes = universe_array if self.width is not None: lattice.pitch = self.width else: dx = ((self.upper_right[0] - self.lower_left[0]) / self.dimension[0]) if n_dim == 1: lattice.pitch = [dx] elif n_dim == 2: dy = ((self.upper_right[1] - self.lower_left[1]) / self.dimension[1]) lattice.pitch = [dx, dy] else: dy = ((self.upper_right[1] - self.lower_left[1]) / self.dimension[1]) dz = ((self.upper_right[2] - self.lower_left[2]) / self.dimension[2]) lattice.pitch = [dx, dy, dz] # Fill Cell with the Lattice root_cell.fill = lattice return root_cell, cells
[docs] def write_data_to_vtk(self, filename, datasets, volume_normalization=True): """Creates a VTK object of the mesh Parameters ---------- filename : str or pathlib.Path Name of the VTK file to write. datasets : dict Dictionary whose keys are the data labels and values are the data sets. volume_normalization : bool, optional Whether or not to normalize the data by the volume of the mesh elements. Defaults to True. Returns ------- vtk.vtkStructuredGrid the VTK object """ ll, ur = self.lower_left, self.upper_right x_vals = np.linspace(ll[0], ur[0], num=self.dimension[0] + 1) y_vals = np.linspace(ll[1], ur[1], num=self.dimension[1] + 1) z_vals = np.linspace(ll[2], ur[2], num=self.dimension[2] + 1) # create points pts_cartesian = np.array([[x, y, z] for z in z_vals for y in y_vals for x in x_vals]) return super().write_data_to_vtk( points=pts_cartesian, filename=filename, datasets=datasets, volume_normalization=volume_normalization )
def Mesh(*args, **kwargs): warnings.warn("Mesh has been renamed RegularMesh. Future versions of " "OpenMC will not accept the name Mesh.") return RegularMesh(*args, **kwargs)
[docs]class RectilinearMesh(StructuredMesh): """A 3D rectilinear Cartesian mesh Parameters ---------- mesh_id : int Unique identifier for the mesh name : str Name of the mesh Attributes ---------- id : int Unique identifier for the mesh name : str Name of the mesh dimension : Iterable of int The number of mesh cells in each direction. n_dimension : int Number of mesh dimensions (always 3 for a RectilinearMesh). x_grid : numpy.ndarray 1-D array of mesh boundary points along the x-axis. y_grid : numpy.ndarray 1-D array of mesh boundary points along the y-axis. z_grid : numpy.ndarray 1-D array of mesh boundary points along the z-axis. indices : Iterable of tuple An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1), (2, 1, 1), ...] """ def __init__(self, mesh_id=None, name=''): super().__init__(mesh_id, name) self._x_grid = None self._y_grid = None self._z_grid = None @property def dimension(self): return (len(self.x_grid) - 1, len(self.y_grid) - 1, len(self.z_grid) - 1) @property def n_dimension(self): return 3 @property def x_grid(self): return self._x_grid @property def y_grid(self): return self._y_grid @property def z_grid(self): return self._z_grid @property def _grids(self): return (self.x_grid, self.y_grid, self.z_grid) @property def volumes(self): """Return Volumes for every mesh cell Returns ------- volumes : numpy.ndarray Volumes """ self._volume_dim_check() V_x = np.diff(self.x_grid) V_y = np.diff(self.y_grid) V_z = np.diff(self.z_grid) return np.multiply.outer(np.outer(V_x, V_y), V_z) @property def total_volume(self): return np.sum(self.volumes) @property def indices(self): nx = len(self.x_grid) - 1 ny = len(self.y_grid) - 1 nz = len(self.z_grid) - 1 return ((x, y, z) for z in range(1, nz + 1) for y in range(1, ny + 1) for x in range(1, nx + 1)) @x_grid.setter def x_grid(self, grid): cv.check_type('mesh x_grid', grid, Iterable, Real) self._x_grid = np.asarray(grid) @y_grid.setter def y_grid(self, grid): cv.check_type('mesh y_grid', grid, Iterable, Real) self._y_grid = np.asarray(grid) @z_grid.setter def z_grid(self, grid): cv.check_type('mesh z_grid', grid, Iterable, Real) self._z_grid = np.asarray(grid) def __repr__(self): fmt = '{0: <16}{1}{2}\n' string = super().__repr__() string += fmt.format('\tDimensions', '=\t', self.n_dimension) x_grid_str = str(self._x_grid) if self._x_grid is None else len(self._x_grid) string += fmt.format('\tN X pnts:', '=\t', x_grid_str) if self._x_grid is not None: string += fmt.format('\tX Min:', '=\t', self._x_grid[0]) string += fmt.format('\tX Max:', '=\t', self._x_grid[-1]) y_grid_str = str(self._y_grid) if self._y_grid is None else len(self._y_grid) string += fmt.format('\tN Y pnts:', '=\t', y_grid_str) if self._y_grid is not None: string += fmt.format('\tY Min:', '=\t', self._y_grid[0]) string += fmt.format('\tY Max:', '=\t', self._y_grid[-1]) z_grid_str = str(self._z_grid) if self._z_grid is None else len(self._z_grid) string += fmt.format('\tN Z pnts:', '=\t', z_grid_str) if self._z_grid is not None: string += fmt.format('\tZ Min:', '=\t', self._z_grid[0]) string += fmt.format('\tZ Max:', '=\t', self._z_grid[-1]) return string
[docs] @classmethod def from_hdf5(cls, group): mesh_id = int(group.name.split('/')[-1].lstrip('mesh ')) # Read and assign mesh properties mesh = cls(mesh_id) mesh.x_grid = group['x_grid'][()] mesh.y_grid = group['y_grid'][()] mesh.z_grid = group['z_grid'][()] return mesh
[docs] @classmethod def from_xml_element(cls, elem): """Generate a rectilinear mesh from an XML element Parameters ---------- elem : xml.etree.ElementTree.Element XML element Returns ------- openmc.RectilinearMesh Rectilinear mesh object """ id = int(get_text(elem, 'id')) mesh = cls(id) mesh.x_grid = [float(x) for x in get_text(elem, 'x_grid').split()] mesh.y_grid = [float(y) for y in get_text(elem, 'y_grid').split()] mesh.z_grid = [float(z) for z in get_text(elem, 'z_grid').split()] return mesh
[docs] def to_xml_element(self): """Return XML representation of the mesh Returns ------- element : xml.etree.ElementTree.Element XML element containing mesh data """ element = ET.Element("mesh") element.set("id", str(self._id)) element.set("type", "rectilinear") subelement = ET.SubElement(element, "x_grid") subelement.text = ' '.join(map(str, self.x_grid)) subelement = ET.SubElement(element, "y_grid") subelement.text = ' '.join(map(str, self.y_grid)) subelement = ET.SubElement(element, "z_grid") subelement.text = ' '.join(map(str, self.z_grid)) return element
[docs] def write_data_to_vtk(self, filename, datasets, volume_normalization=True): """Creates a VTK object of the mesh Parameters ---------- filename : str or pathlib.Path Name of the VTK file to write. datasets : dict Dictionary whose keys are the data labels and values are the data sets. volume_normalization : bool, optional Whether or not to normalize the data by the volume of the mesh elements. Defaults to True. Returns ------- vtk.vtkStructuredGrid the VTK object """ # create points pts_cartesian = np.array([[x, y, z] for z in self.z_grid for y in self.y_grid for x in self.x_grid]) return super().write_data_to_vtk( points=pts_cartesian, filename=filename, datasets=datasets, volume_normalization=volume_normalization )
[docs]class CylindricalMesh(StructuredMesh): """A 3D cylindrical mesh Parameters ---------- mesh_id : int Unique identifier for the mesh name : str Name of the mesh Attributes ---------- id : int Unique identifier for the mesh name : str Name of the mesh dimension : Iterable of int The number of mesh cells in each direction. n_dimension : int Number of mesh dimensions (always 3 for a CylindricalMesh). r_grid : numpy.ndarray 1-D array of mesh boundary points along the r-axis. Requirement is r >= 0. phi_grid : numpy.ndarray 1-D array of mesh boundary points along the phi-axis in radians. The default value is [0, 2π], i.e. the full phi range. z_grid : numpy.ndarray 1-D array of mesh boundary points along the z-axis. indices : Iterable of tuple An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1), (2, 1, 1), ...] """ def __init__(self, mesh_id=None, name=''): super().__init__(mesh_id, name) self._r_grid = None self._phi_grid = [0.0, 2*pi] self._z_grid = None @property def dimension(self): return (len(self.r_grid) - 1, len(self.phi_grid) - 1, len(self.z_grid) - 1) @property def n_dimension(self): return 3 @property def r_grid(self): return self._r_grid @property def phi_grid(self): return self._phi_grid @property def z_grid(self): return self._z_grid @property def _grids(self): return (self.r_grid, self.phi_grid, self.z_grid) @property def indices(self): nr, np, nz = self.dimension np = len(self.phi_grid) - 1 nz = len(self.z_grid) - 1 return ((r, p, z) for z in range(1, nz + 1) for p in range(1, np + 1) for r in range(1, nr + 1)) @r_grid.setter def r_grid(self, grid): cv.check_type('mesh r_grid', grid, Iterable, Real) self._r_grid = np.asarray(grid) @phi_grid.setter def phi_grid(self, grid): cv.check_type('mesh phi_grid', grid, Iterable, Real) self._phi_grid = np.asarray(grid) @z_grid.setter def z_grid(self, grid): cv.check_type('mesh z_grid', grid, Iterable, Real) self._z_grid = np.asarray(grid) def __repr__(self): fmt = '{0: <16}{1}{2}\n' string = super().__repr__() string += fmt.format('\tDimensions', '=\t', self.n_dimension) r_grid_str = str(self._r_grid) if self._r_grid is None else len(self._r_grid) string += fmt.format('\tN R pnts:', '=\t', r_grid_str) if self._r_grid is not None: string += fmt.format('\tR Min:', '=\t', self._r_grid[0]) string += fmt.format('\tR Max:', '=\t', self._r_grid[-1]) phi_grid_str = str(self._phi_grid) if self._phi_grid is None else len(self._phi_grid) string += fmt.format('\tN Phi pnts:', '=\t', phi_grid_str) if self._phi_grid is not None: string += fmt.format('\tPhi Min:', '=\t', self._phi_grid[0]) string += fmt.format('\tPhi Max:', '=\t', self._phi_grid[-1]) z_grid_str = str(self._z_grid) if self._z_grid is None else len(self._z_grid) string += fmt.format('\tN Z pnts:', '=\t', z_grid_str) if self._z_grid is not None: string += fmt.format('\tZ Min:', '=\t', self._z_grid[0]) string += fmt.format('\tZ Max:', '=\t', self._z_grid[-1]) return string
[docs] @classmethod def from_hdf5(cls, group): mesh_id = int(group.name.split('/')[-1].lstrip('mesh ')) # Read and assign mesh properties mesh = cls(mesh_id) mesh.r_grid = group['r_grid'][()] mesh.phi_grid = group['phi_grid'][()] mesh.z_grid = group['z_grid'][()] return mesh
[docs] def to_xml_element(self): """Return XML representation of the mesh Returns ------- element : xml.etree.ElementTree.Element XML element containing mesh data """ element = ET.Element("mesh") element.set("id", str(self._id)) element.set("type", "cylindrical") subelement = ET.SubElement(element, "r_grid") subelement.text = ' '.join(map(str, self.r_grid)) subelement = ET.SubElement(element, "phi_grid") subelement.text = ' '.join(map(str, self.phi_grid)) subelement = ET.SubElement(element, "z_grid") subelement.text = ' '.join(map(str, self.z_grid)) return element
[docs] @classmethod def from_xml_element(cls, elem): """Generate a cylindrical mesh from an XML element Parameters ---------- elem : xml.etree.ElementTree.Element XML element Returns ------- openmc.CylindricalMesh Cylindrical mesh object """ mesh_id = int(get_text(elem, 'id')) mesh = cls(mesh_id) mesh.r_grid = [float(x) for x in get_text(elem, "r_grid").split()] mesh.phi_grid = [float(x) for x in get_text(elem, "phi_grid").split()] mesh.z_grid = [float(x) for x in get_text(elem, "z_grid").split()] return mesh
@property def volumes(self): """Return Volumes for every mesh cell Returns ------- volumes : Iterable of float Volumes """ self._volume_dim_check() V_r = np.diff(np.asarray(self.r_grid)**2 / 2) V_p = np.diff(self.phi_grid) V_z = np.diff(self.z_grid) return np.multiply.outer(np.outer(V_r, V_p), V_z)
[docs] def write_data_to_vtk(self, filename, datasets, volume_normalization=True): """Creates a VTK object of the mesh Parameters ---------- filename : str or pathlib.Path Name of the VTK file to write. datasets : dict Dictionary whose keys are the data labels and values are the data sets. volume_normalization : bool, optional Whether or not to normalize the data by the volume of the mesh elements. Defaults to True. Returns ------- vtk.vtkStructuredGrid the VTK object """ # create points pts_cylindrical = np.array( [ [r, phi, z] for z in self.z_grid for phi in self.phi_grid for r in self.r_grid ] ) pts_cartesian = np.copy(pts_cylindrical) r, phi = pts_cylindrical[:, 0], pts_cylindrical[:, 1] pts_cartesian[:, 0] = r * np.cos(phi) pts_cartesian[:, 1] = r * np.sin(phi) return super().write_data_to_vtk( points=pts_cartesian, filename=filename, datasets=datasets, volume_normalization=volume_normalization )
[docs]class SphericalMesh(StructuredMesh): """A 3D spherical mesh Parameters ---------- mesh_id : int Unique identifier for the mesh name : str Name of the mesh Attributes ---------- id : int Unique identifier for the mesh name : str Name of the mesh dimension : Iterable of int The number of mesh cells in each direction. n_dimension : int Number of mesh dimensions (always 3 for a SphericalMesh). r_grid : numpy.ndarray 1-D array of mesh boundary points along the r-axis. Requirement is r >= 0. theta_grid : numpy.ndarray 1-D array of mesh boundary points along the theta-axis in radians. The default value is [0, π], i.e. the full theta range. phi_grid : numpy.ndarray 1-D array of mesh boundary points along the phi-axis in radians. The default value is [0, 2π], i.e. the full phi range. indices : Iterable of tuple An iterable of mesh indices for each mesh element, e.g. [(1, 1, 1), (2, 1, 1), ...] """ def __init__(self, mesh_id=None, name=''): super().__init__(mesh_id, name) self._r_grid = None self._theta_grid = [0, pi] self._phi_grid = [0, 2*pi] @property def dimension(self): return (len(self.r_grid) - 1, len(self.theta_grid) - 1, len(self.phi_grid) - 1) @property def n_dimension(self): return 3 @property def r_grid(self): return self._r_grid @property def theta_grid(self): return self._theta_grid @property def phi_grid(self): return self._phi_grid @property def _grids(self): return (self.r_grid, self.theta_grid, self.phi_grid) @property def indices(self): nr, nt, np = self.dimension nt = len(self.theta_grid) - 1 np = len(self.phi_grid) - 1 return ((r, t, p) for p in range(1, np + 1) for t in range(1, nt + 1) for r in range(1, nr + 1)) @r_grid.setter def r_grid(self, grid): cv.check_type('mesh r_grid', grid, Iterable, Real) self._r_grid = np.asarray(grid) @theta_grid.setter def theta_grid(self, grid): cv.check_type('mesh theta_grid', grid, Iterable, Real) self._theta_grid = np.asarray(grid) @phi_grid.setter def phi_grid(self, grid): cv.check_type('mesh phi_grid', grid, Iterable, Real) self._phi_grid = np.asarray(grid) def __repr__(self): fmt = '{0: <16}{1}{2}\n' string = super().__repr__() string += fmt.format('\tDimensions', '=\t', self.n_dimension) r_grid_str = str(self._r_grid) if self._r_grid is None else len(self._r_grid) string += fmt.format('\tN R pnts:', '=\t', r_grid_str) if self._r_grid is not None: string += fmt.format('\tR Min:', '=\t', self._r_grid[0]) string += fmt.format('\tR Max:', '=\t', self._r_grid[-1]) theta_grid_str = str(self._theta_grid) if self._theta_grid is None else len(self._theta_grid) string += fmt.format('\tN Theta pnts:', '=\t', theta_grid_str) if self._theta_grid is not None: string += fmt.format('\tTheta Min:', '=\t', self._theta_grid[0]) string += fmt.format('\tTheta Max:', '=\t', self._theta_grid[-1]) phi_grid_str = str(self._phi_grid) if self._phi_grid is None else len(self._phi_grid) string += fmt.format('\tN Phi pnts:', '=\t', phi_grid_str) if self._phi_grid is not None: string += fmt.format('\tPhi Min:', '=\t', self._phi_grid[0]) string += fmt.format('\tPhi Max:', '=\t', self._phi_grid[-1]) return string
[docs] @classmethod def from_hdf5(cls, group): mesh_id = int(group.name.split('/')[-1].lstrip('mesh ')) # Read and assign mesh properties mesh = cls(mesh_id) mesh.r_grid = group['r_grid'][()] mesh.theta_grid = group['theta_grid'][()] mesh.phi_grid = group['phi_grid'][()] return mesh
[docs] def to_xml_element(self): """Return XML representation of the mesh Returns ------- element : xml.etree.ElementTree.Element XML element containing mesh data """ element = ET.Element("mesh") element.set("id", str(self._id)) element.set("type", "spherical") subelement = ET.SubElement(element, "r_grid") subelement.text = ' '.join(map(str, self.r_grid)) subelement = ET.SubElement(element, "theta_grid") subelement.text = ' '.join(map(str, self.theta_grid)) subelement = ET.SubElement(element, "phi_grid") subelement.text = ' '.join(map(str, self.phi_grid)) return element
[docs] @classmethod def from_xml_element(cls, elem): """Generate a spherical mesh from an XML element Parameters ---------- elem : xml.etree.ElementTree.Element XML element Returns ------- openmc.SphericalMesh Spherical mesh object """ mesh_id = int(get_text(elem, 'id')) mesh = cls(mesh_id) mesh.r_grid = [float(x) for x in get_text(elem, "r_grid").split()] mesh.theta_grid = [float(x) for x in get_text(elem, "theta_grid").split()] mesh.phi_grid = [float(x) for x in get_text(elem, "phi_grid").split()] return mesh
@property def volumes(self): """Return Volumes for every mesh cell Returns ------- volumes : Iterable of float Volumes """ self._volume_dim_check() V_r = np.diff(np.asarray(self.r_grid)**3 / 3) V_t = np.diff(-np.cos(self.theta_grid)) V_p = np.diff(self.phi_grid) return np.multiply.outer(np.outer(V_r, V_t), V_p)
[docs] def write_data_to_vtk(self, filename, datasets, volume_normalization=True): """Creates a VTK object of the mesh Parameters ---------- filename : str or pathlib.Path Name of the VTK file to write. datasets : dict Dictionary whose keys are the data labels and values are the data sets. volume_normalization : bool, optional Whether or not to normalize the data by the volume of the mesh elements. Defaults to True. Returns ------- vtk.vtkStructuredGrid the VTK object """ # create points pts_spherical = np.array( [ [r, theta, phi] for phi in self.phi_grid for theta in self.theta_grid for r in self.r_grid ] ) pts_cartesian = np.copy(pts_spherical) r, theta, phi = pts_spherical[:, 0], pts_spherical[:, 1], pts_spherical[:, 2] pts_cartesian[:, 0] = r * np.sin(phi) * np.cos(theta) pts_cartesian[:, 1] = r * np.sin(phi) * np.sin(theta) pts_cartesian[:, 2] = r * np.cos(phi) return super().write_data_to_vtk( points=pts_cartesian, filename=filename, datasets=datasets, volume_normalization=volume_normalization )
[docs]class UnstructuredMesh(MeshBase): """A 3D unstructured mesh .. versionadded:: 0.12 .. versionchanged:: 0.12.2 Support for libMesh unstructured meshes was added. Parameters ---------- filename : str or pathlib.Path Location of the unstructured mesh file library : {'moab', 'libmesh'} Mesh library used for the unstructured mesh tally mesh_id : int Unique identifier for the mesh name : str Name of the mesh length_multiplier: float Constant multiplier to apply to mesh coordinates Attributes ---------- id : int Unique identifier for the mesh name : str Name of the mesh filename : str Name of the file containing the unstructured mesh length_multiplier: float Multiplicative factor to apply to mesh coordinates library : {'moab', 'libmesh'} Mesh library used for the unstructured mesh tally output : bool Indicates whether or not automatic tally output should be generated for this mesh volumes : Iterable of float Volumes of the unstructured mesh elements centroids : numpy.ndarray Centroids of the mesh elements with array shape (n_elements, 3) vertices : numpy.ndarray Coordinates of the mesh vertices with array shape (n_elements, 3) .. versionadded:: 0.13.1 connectivity : numpy.ndarray Connectivity of the elements with array shape (n_elements, 8) .. versionadded:: 0.13.1 element_types : Iterable of integers Mesh element types .. versionadded:: 0.13.1 total_volume : float Volume of the unstructured mesh in total """ _UNSUPPORTED_ELEM = -1 _LINEAR_TET = 0 _LINEAR_HEX = 1 def __init__(self, filename, library, mesh_id=None, name='', length_multiplier=1.0): super().__init__(mesh_id, name) self.filename = filename self._volumes = None self._n_elements = None self._conectivity = None self._vertices = None self.library = library self._output = False self.length_multiplier = length_multiplier @property def filename(self): return self._filename @filename.setter def filename(self, filename): cv.check_type('Unstructured Mesh filename', filename, (str, Path)) self._filename = filename @property def library(self): return self._library @library.setter def library(self, lib): cv.check_value('Unstructured mesh library', lib, ('moab', 'libmesh')) self._library = lib @property def size(self): return self._size @size.setter def size(self, size): cv.check_type("Unstructured mesh size", size, Integral) self._size = size @property def output(self): return self._output @output.setter def output(self, val): cv.check_type("Unstructured mesh output value", val, bool) self._output = val @property def volumes(self): """Return Volumes for every mesh cell if populated by a StatePoint file Returns ------- volumes : numpy.ndarray Volumes """ return self._volumes @volumes.setter def volumes(self, volumes): cv.check_type("Unstructured mesh volumes", volumes, Iterable, Real) self._volumes = volumes @property def total_volume(self): return np.sum(self.volumes) @property def centroids(self): return self._centroids @property def vertices(self): return self._vertices @property def connectivity(self): return self._connectivity @property def element_types(self): return self._element_types @property def centroids(self): return np.array([self.centroid(i) for i in range(self.n_elements)]) @property def n_elements(self): if self._n_elements is None: raise RuntimeError("No information about this mesh has " "been loaded from a statepoint file.") return self._n_elements @n_elements.setter def n_elements(self, val): cv.check_type('Number of elements', val, Integral) self._n_elements = val @property def length_multiplier(self): return self._length_multiplier @length_multiplier.setter def length_multiplier(self, length_multiplier): cv.check_type("Unstructured mesh length multiplier", length_multiplier, Real) self._length_multiplier = length_multiplier @property def dimension(self): return (self.n_elements,) @property def n_dimension(self): return 3 def __repr__(self): string = super().__repr__() string += '{: <16}=\t{}\n'.format('\tFilename', self.filename) string += '{: <16}=\t{}\n'.format('\tMesh Library', self.library) if self.length_multiplier != 1.0: string += '{: <16}=\t{}\n'.format('\tLength multiplier', self.length_multiplier) return string
[docs] def centroid(self, bin): """Return the vertex averaged centroid of an element Parameters ---------- bin : int Bin ID for the returned centroid Returns ------- numpy.ndarray x, y, z values of the element centroid """ conn = self.connectivity[bin] coords = self.vertices[conn] return coords.mean(axis=0)
[docs] def write_vtk_mesh(self, **kwargs): """Map data to unstructured VTK mesh elements. .. deprecated:: 0.13 Use :func:`UnstructuredMesh.write_data_to_vtk` instead. Parameters ---------- filename : str or pathlib.Path Name of the VTK file to write. datasets : dict Dictionary whose keys are the data labels and values are the data sets. volume_normalization : bool Whether or not to normalize the data by the volume of the mesh elements """ warnings.warn( "The 'UnstructuredMesh.write_vtk_mesh' method has been renamed " "to 'write_data_to_vtk' and will be removed in a future version " " of OpenMC.", FutureWarning ) self.write_data_to_vtk(**kwargs)
[docs] def write_data_to_vtk(self, filename=None, datasets=None, volume_normalization=True): """Map data to unstructured VTK mesh elements. Parameters ---------- filename : str or pathlib.Path Name of the VTK file to write datasets : dict Dictionary whose keys are the data labels and values are numpy appropriately sized arrays of the data volume_normalization : bool Whether or not to normalize the data by the volume of the mesh elements """ import vtk from vtk.util import numpy_support as nps if self.connectivity is None or self.vertices is None: raise RuntimeError('This mesh has not been ' 'loaded from a statepoint file.') if filename is None: filename = f'mesh_{self.id}.vtk' writer = vtk.vtkUnstructuredGridWriter() writer.SetFileName(str(filename)) grid = vtk.vtkUnstructuredGrid() vtk_pnts = vtk.vtkPoints() vtk_pnts.SetData(nps.numpy_to_vtk(self.vertices)) grid.SetPoints(vtk_pnts) n_skipped = 0 elems = [] for elem_type, conn in zip(self.element_types, self.connectivity): if elem_type == self._LINEAR_TET: elem = vtk.vtkTetra() elif elem_type == self._LINEAR_HEX: elem = vtk.vtkHexahedron() elif elem_type == self._UNSUPPORTED_ELEM: n_skipped += 1 else: raise RuntimeError(f'Invalid element type {elem_type} found') for i, c in enumerate(conn): if c == -1: break elem.GetPointIds().SetId(i, c) elems.append(elem) if n_skipped > 0: warnings.warn(f'{n_skipped} elements were not written because ' 'they are not of type linear tet/hex') for elem in elems: grid.InsertNextCell(elem.GetCellType(), elem.GetPointIds()) # check that datasets are the correct size datasets_out = [] if datasets is not None: for name, data in datasets.items(): if data.shape != self.dimension: raise ValueError(f'Cannot apply dataset "{name}" with ' f'shape {data.shape} to mesh {self.id} ' f'with dimensions {self.dimension}') if volume_normalization: for name, data in datasets.items(): if np.issubdtype(data.dtype, np.integer): warnings.warn(f'Integer data set "{name}" will ' 'not be volume-normalized.') continue data /= self.volumes # add data to the mesh for name, data in datasets.items(): datasets_out.append(data) arr = vtk.vtkDoubleArray() arr.SetName(name) arr.SetNumberOfTuples(data.size) for i in range(data.size): arr.SetTuple1(i, data.flat[i]) grid.GetCellData().AddArray(arr) writer.SetInputData(grid) writer.Write()
[docs] @classmethod def from_hdf5(cls, group): mesh_id = int(group.name.split('/')[-1].lstrip('mesh ')) filename = group['filename'][()].decode() library = group['library'][()].decode() mesh = cls(filename, library, mesh_id=mesh_id) vol_data = group['volumes'][()] mesh.volumes = np.reshape(vol_data, (vol_data.shape[0],)) mesh.n_elements = mesh.volumes.size vertices = group['vertices'][()] mesh._vertices = vertices.reshape((-1, 3)) connectivity = group['connectivity'][()] mesh._connectivity = connectivity.reshape((-1, 8)) mesh._element_types = group['element_types'][()] if 'length_multiplier' in group: mesh.length_multiplier = group['length_multiplier'][()] return mesh
[docs] def to_xml_element(self): """Return XML representation of the mesh Returns ------- element : xml.etree.ElementTree.Element XML element containing mesh data """ element = ET.Element("mesh") element.set("id", str(self._id)) element.set("type", "unstructured") element.set("library", self._library) subelement = ET.SubElement(element, "filename") subelement.text = str(self.filename) if self._length_multiplier != 1.0: element.set("length_multiplier", str(self.length_multiplier)) return element
[docs] @classmethod def from_xml_element(cls, elem): """Generate unstructured mesh object from XML element Parameters ---------- elem : xml.etree.ElementTree.Element XML element Returns ------- openmc.UnstructuredMesh UnstructuredMesh generated from an XML element """ mesh_id = int(get_text(elem, 'id')) filename = get_text(elem, 'filename') library = get_text(elem, 'library') length_multiplier = float(get_text(elem, 'length_multiplier', 1.0)) return cls(filename, library, mesh_id, '', length_multiplier)