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OpenMC/openmc/universe.py

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import math
from abc import ABC, abstractmethod
from collections.abc import Iterable
from numbers import Integral, Real
from pathlib import Path
from tempfile import TemporaryDirectory
import warnings
import h5py
import lxml.etree as ET
import numpy as np
import openmc
import openmc.checkvalue as cv
from ._xml import get_text
from .checkvalue import check_type, check_value
from .mixin import IDManagerMixin
from .surface import _BOUNDARY_TYPES
class UniverseBase(ABC, IDManagerMixin):
"""A collection of cells that can be repeated.
Attributes
----------
id : int
Unique identifier of the universe
name : str
Name of the universe
"""
next_id = 1
used_ids = set()
def __init__(self, universe_id=None, name=''):
# Initialize Universe class attributes
self.id = universe_id
self.name = name
self._volume = None
self._atoms = {}
# Keys - Cell IDs
# Values - Cells
self._cells = {}
def __repr__(self):
string = 'Universe\n'
string += '{: <16}=\t{}\n'.format('\tID', self._id)
string += '{: <16}=\t{}\n'.format('\tName', self._name)
return string
@property
def name(self):
return self._name
@name.setter
def name(self, name):
if name is not None:
cv.check_type('universe name', name, str)
self._name = name
else:
self._name = ''
@property
def volume(self):
return self._volume
@volume.setter
def volume(self, volume):
if volume is not None:
cv.check_type('universe volume', volume, Real)
self._volume = volume
def add_volume_information(self, volume_calc):
"""Add volume information to a universe.
Parameters
----------
volume_calc : openmc.VolumeCalculation
Results from a stochastic volume calculation
"""
if volume_calc.domain_type == 'universe':
if self.id in volume_calc.volumes:
self._volume = volume_calc.volumes[self.id].n
self._atoms = volume_calc.atoms[self.id]
else:
raise ValueError(
'No volume information found for this universe.')
else:
raise ValueError('No volume information found for this universe.')
def get_all_universes(self):
"""Return all universes that are contained within this one.
Returns
-------
universes : dict
Dictionary whose keys are universe IDs and values are
:class:`Universe` instances
"""
# Append all Universes within each Cell to the dictionary
universes = {}
for cell in self.get_all_cells().values():
universes.update(cell.get_all_universes())
return universes
@abstractmethod
def create_xml_subelement(self, xml_element, memo=None):
"""Add the universe xml representation to an incoming xml element
Parameters
----------
xml_element : lxml.etree._Element
XML element to be added to
memo : set or None
A set of object id's representing geometry entities already
written to the xml_element. This parameter is used internally
and should not be specified by users.
Returns
-------
None
"""
@abstractmethod
def _partial_deepcopy(self):
"""Deepcopy all parameters of an openmc.UniverseBase object except its cells.
This should only be used from the openmc.UniverseBase.clone() context.
"""
def clone(self, clone_materials=True, clone_regions=True, memo=None):
"""Create a copy of this universe with a new unique ID, and clones
all cells within this universe.
Parameters
----------
clone_materials : bool
Whether to create separates copies of the materials filling cells
contained in this universe.
clone_regions : bool
Whether to create separates copies of the regions bounding cells
contained in this universe.
memo : dict or None
A nested dictionary of previously cloned objects. This parameter
is used internally and should not be specified by the user.
Returns
-------
clone : openmc.Universe
The clone of this universe
"""
if memo is None:
memo = {}
# If no memoize'd clone exists, instantiate one
if self not in memo:
clone = self._partial_deepcopy()
# Clone all cells for the universe clone
clone._cells = {}
for cell in self._cells.values():
clone.add_cell(cell.clone(clone_materials, clone_regions,
memo))
# Memoize the clone
memo[self] = clone
return memo[self]
class Universe(UniverseBase):
"""A collection of cells that can be repeated.
Parameters
----------
universe_id : int, optional
Unique identifier of the universe. If not specified, an identifier will
automatically be assigned
name : str, optional
Name of the universe. If not specified, the name is the empty string.
cells : Iterable of openmc.Cell, optional
Cells to add to the universe. By default no cells are added.
Attributes
----------
id : int
Unique identifier of the universe
name : str
Name of the universe
cells : dict
Dictionary whose keys are cell IDs and values are :class:`Cell`
instances
volume : float
Volume of the universe in cm^3. This can either be set manually or
calculated in a stochastic volume calculation and added via the
:meth:`Universe.add_volume_information` method.
bounding_box : openmc.BoundingBox
Lower-left and upper-right coordinates of an axis-aligned bounding box
of the universe.
"""
def __init__(self, universe_id=None, name='', cells=None):
super().__init__(universe_id, name)
if cells is not None:
self.add_cells(cells)
def __repr__(self):
string = super().__repr__()
string += '{: <16}=\t{}\n'.format('\tGeom', 'CSG')
string += '{: <16}=\t{}\n'.format('\tCells', list(self._cells.keys()))
return string
@property
def cells(self):
return self._cells
@property
def bounding_box(self):
regions = [c.region for c in self.cells.values()
if c.region is not None]
if regions:
return openmc.Union(regions).bounding_box
else:
return openmc.BoundingBox.infinite()
@classmethod
def from_hdf5(cls, group, cells):
"""Create universe from HDF5 group
Parameters
----------
group : h5py.Group
Group in HDF5 file
cells : dict
Dictionary mapping cell IDs to instances of :class:`openmc.Cell`.
Returns
-------
openmc.Universe
Universe instance
"""
universe_id = int(group.name.split('/')[-1].lstrip('universe '))
cell_ids = group['cells'][()]
# Create this Universe
universe = cls(universe_id)
# Add each Cell to the Universe
for cell_id in cell_ids:
universe.add_cell(cells[cell_id])
return universe
def find(self, point):
"""Find cells/universes/lattices which contain a given point
Parameters
----------
point : 3-tuple of float
Cartesian coordinates of the point
Returns
-------
list
Sequence of universes, cells, and lattices which are traversed to
find the given point
"""
p = np.asarray(point)
for cell in self._cells.values():
if p in cell:
if cell.fill_type in ('material', 'distribmat', 'void'):
return [self, cell]
elif cell.fill_type == 'universe':
if cell.translation is not None:
p -= cell.translation
if cell.rotation is not None:
p[:] = cell.rotation_matrix.dot(p)
return [self, cell] + cell.fill.find(p)
else:
return [self, cell] + cell.fill.find(p)
return []
# default kwargs that are passed to plt.legend in the plot method below.
_default_legend_kwargs = {'bbox_to_anchor': (
1.05, 1), 'loc': 2, 'borderaxespad': 0.0}
def plot(self, origin=None, width=None, pixels=40000,
basis='xy', color_by='cell', colors=None, seed=None,
openmc_exec='openmc', axes=None, legend=False, axis_units='cm',
legend_kwargs=_default_legend_kwargs, outline=False,
**kwargs):
"""Display a slice plot of the universe.
Parameters
----------
origin : iterable of float
Coordinates at the origin of the plot. If left as None,
universe.bounding_box.center will be used to attempt to ascertain
the origin with infinite values being replaced by 0.
width : iterable of float
Width of the plot in each basis direction. If left as none then the
universe.bounding_box.width() will be used to attempt to
ascertain the plot width. Defaults to (10, 10) if the bounding_box
contains inf values
pixels : Iterable of int or int
If iterable of ints provided then this directly sets the number of
pixels to use in each basis direction. If int provided then this
sets the total number of pixels in the plot and the number of
pixels in each basis direction is calculated from this total and
the image aspect ratio.
basis : {'xy', 'xz', 'yz'}
The basis directions for the plot
color_by : {'cell', 'material'}
Indicate whether the plot should be colored by cell or by material
colors : dict
Assigns colors to specific materials or cells. Keys are instances of
:class:`Cell` or :class:`Material` and values are RGB 3-tuples, RGBA
4-tuples, or strings indicating SVG color names. Red, green, blue,
and alpha should all be floats in the range [0.0, 1.0], for example:
.. code-block:: python
# Make water blue
water = openmc.Cell(fill=h2o)
universe.plot(..., colors={water: (0., 0., 1.))
seed : int
Seed for the random number generator
openmc_exec : str
Path to OpenMC executable.
axes : matplotlib.Axes
Axes to draw to
.. versionadded:: 0.13.1
legend : bool
Whether a legend showing material or cell names should be drawn
.. versionadded:: 0.14.0
legend_kwargs : dict
Keyword arguments passed to :func:`matplotlib.pyplot.legend`.
.. versionadded:: 0.14.0
outline : bool
Whether outlines between color boundaries should be drawn
.. versionadded:: 0.14.0
axis_units : {'km', 'm', 'cm', 'mm'}
Units used on the plot axis
.. versionadded:: 0.14.0
**kwargs
Keyword arguments passed to :func:`matplotlib.pyplot.imshow`
Returns
-------
matplotlib.axes.Axes
Axes containing resulting image
"""
import matplotlib.image as mpimg
import matplotlib.patches as mpatches
import matplotlib.pyplot as plt
# Determine extents of plot
if basis == 'xy':
x, y = 0, 1
xlabel, ylabel = f'x [{axis_units}]', f'y [{axis_units}]'
elif basis == 'yz':
x, y = 1, 2
xlabel, ylabel = f'y [{axis_units}]', f'z [{axis_units}]'
elif basis == 'xz':
x, y = 0, 2
xlabel, ylabel = f'x [{axis_units}]', f'z [{axis_units}]'
bb = self.bounding_box
# checks to see if bounding box contains -inf or inf values
if np.isinf(bb.extent[basis]).any():
if origin is None:
origin = (0, 0, 0)
if width is None:
width = (10, 10)
else:
if origin is None:
# if nan values in the bb.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(bb.center)
if width is None:
bb_width = bb.width
x_width = bb_width['xyz'.index(basis[0])]
y_width = bb_width['xyz'.index(basis[1])]
width = (x_width, y_width)
if isinstance(pixels, int):
aspect_ratio = width[0] / width[1]
pixels_y = math.sqrt(pixels / aspect_ratio)
pixels = (int(pixels / pixels_y), int(pixels_y))
axis_scaling_factor = {'km': 0.00001, 'm': 0.01, 'cm': 1, 'mm': 10}
x_min = (origin[x] - 0.5*width[0]) * axis_scaling_factor[axis_units]
x_max = (origin[x] + 0.5*width[0]) * axis_scaling_factor[axis_units]
y_min = (origin[y] - 0.5*width[1]) * axis_scaling_factor[axis_units]
y_max = (origin[y] + 0.5*width[1]) * axis_scaling_factor[axis_units]
with TemporaryDirectory() as tmpdir:
model = openmc.Model()
model.geometry = openmc.Geometry(self)
if seed is not None:
model.settings.plot_seed = seed
# Determine whether any materials contains macroscopic data and if
# so, set energy mode accordingly
for mat in self.get_all_materials().values():
if mat._macroscopic is not None:
model.settings.energy_mode = 'multi-group'
break
# Create plot object matching passed arguments
plot = openmc.Plot()
plot.origin = origin
plot.width = width
plot.pixels = pixels
plot.basis = basis
plot.color_by = color_by
if colors is not None:
plot.colors = colors
model.plots.append(plot)
# Run OpenMC in geometry plotting mode
model.plot_geometry(False, cwd=tmpdir, openmc_exec=openmc_exec)
# Read image from file
img_path = Path(tmpdir) / f'plot_{plot.id}.png'
if not img_path.is_file():
img_path = img_path.with_suffix('.ppm')
img = mpimg.imread(str(img_path))
# Create a figure sized such that the size of the axes within
# exactly matches the number of pixels specified
if axes is None:
px = 1/plt.rcParams['figure.dpi']
fig, axes = plt.subplots()
axes.set_xlabel(xlabel)
axes.set_ylabel(ylabel)
params = fig.subplotpars
width = pixels[0]*px/(params.right - params.left)
height = pixels[1]*px/(params.top - params.bottom)
fig.set_size_inches(width, height)
if outline:
# Combine R, G, B values into a single int
rgb = (img * 256).astype(int)
image_value = (rgb[..., 0] << 16) + \
(rgb[..., 1] << 8) + (rgb[..., 2])
axes.contour(
image_value,
origin="upper",
colors="k",
linestyles="solid",
linewidths=1,
levels=np.unique(image_value),
extent=(x_min, x_max, y_min, y_max),
)
# add legend showing which colors represent which material
# or cell if that was requested
if legend:
if plot.colors == {}:
raise ValueError("Must pass 'colors' dictionary if you "
"are adding a legend via legend=True.")
if color_by == "cell":
expected_key_type = openmc.Cell
else:
expected_key_type = openmc.Material
patches = []
for key, color in plot.colors.items():
if isinstance(key, int):
raise TypeError(
"Cannot use IDs in colors dict for auto legend.")
elif not isinstance(key, expected_key_type):
raise TypeError(
"Color dict key type does not match color_by")
# this works whether we're doing cells or materials
label = key.name if key.name != '' else key.id
# matplotlib takes RGB on 0-1 scale rather than 0-255. at
# this point PlotBase has already checked that 3-tuple
# based colors are already valid, so if the length is three
# then we know it just needs to be converted to the 0-1
# format.
if len(color) == 3 and not isinstance(color, str):
scaled_color = (
color[0]/255, color[1]/255, color[2]/255)
else:
scaled_color = color
key_patch = mpatches.Patch(color=scaled_color, label=label)
patches.append(key_patch)
axes.legend(handles=patches, **legend_kwargs)
# Plot image and return the axes
axes.imshow(img, extent=(x_min, x_max, y_min, y_max), **kwargs)
return axes
def add_cell(self, cell):
"""Add a cell to the universe.
Parameters
----------
cell : openmc.Cell
Cell to add
"""
if not isinstance(cell, openmc.Cell):
msg = f'Unable to add a Cell to Universe ID="{self._id}" since ' \
f'"{cell}" is not a Cell'
raise TypeError(msg)
cell_id = cell.id
if cell_id not in self._cells:
self._cells[cell_id] = cell
def add_cells(self, cells):
"""Add multiple cells to the universe.
Parameters
----------
cells : Iterable of openmc.Cell
Cells to add
"""
if not isinstance(cells, Iterable):
msg = f'Unable to add Cells to Universe ID="{self._id}" since ' \
f'"{cells}" is not iterable'
raise TypeError(msg)
for cell in cells:
self.add_cell(cell)
def remove_cell(self, cell):
"""Remove a cell from the universe.
Parameters
----------
cell : openmc.Cell
Cell to remove
"""
if not isinstance(cell, openmc.Cell):
msg = f'Unable to remove a Cell from Universe ID="{self._id}" ' \
f'since "{cell}" is not a Cell'
raise TypeError(msg)
# If the Cell is in the Universe's list of Cells, delete it
self._cells.pop(cell.id, None)
def clear_cells(self):
"""Remove all cells from the universe."""
self._cells.clear()
def get_nuclides(self):
"""Returns all nuclides in the universe
Returns
-------
nuclides : list of str
List of nuclide names
"""
nuclides = []
# Append all Nuclides in each Cell in the Universe to the dictionary
for cell in self.cells.values():
for nuclide in cell.get_nuclides():
if nuclide not in nuclides:
nuclides.append(nuclide)
return nuclides
def get_nuclide_densities(self):
"""Return all nuclides contained in the universe
Returns
-------
nuclides : dict
Dictionary whose keys are nuclide names and values are 2-tuples of
(nuclide, density)
"""
nuclides = {}
if self._atoms:
volume = self.volume
for name, atoms in self._atoms.items():
nuclide = openmc.Nuclide(name)
density = 1.0e-24 * atoms.n/volume # density in atoms/b-cm
nuclides[name] = (nuclide, density)
else:
raise RuntimeError(
'Volume information is needed to calculate microscopic cross '
f'sections for universe {self.id}. This can be done by running '
'a stochastic volume calculation via the '
'openmc.VolumeCalculation object')
return nuclides
def get_all_cells(self, memo=None):
"""Return all cells that are contained within the universe
Returns
-------
cells : dict
Dictionary whose keys are cell IDs and values are :class:`Cell`
instances
"""
cells = {}
if memo and self in memo:
return cells
if memo is not None:
memo.add(self)
# Add this Universe's cells to the dictionary
cells.update(self._cells)
# Append all Cells in each Cell in the Universe to the dictionary
for cell in self._cells.values():
cells.update(cell.get_all_cells(memo))
return cells
def get_all_materials(self, memo=None):
"""Return all materials that are contained within the universe
Returns
-------
materials : dict
Dictionary whose keys are material IDs and values are
:class:`Material` instances
"""
materials = {}
# Append all Cells in each Cell in the Universe to the dictionary
cells = self.get_all_cells(memo)
for cell in cells.values():
materials.update(cell.get_all_materials(memo))
return materials
def create_xml_subelement(self, xml_element, memo=None):
# Iterate over all Cells
for cell in self._cells.values():
# If the cell was already written, move on
if memo and cell in memo:
continue
if memo is not None:
memo.add(cell)
# Create XML subelement for this Cell
cell_element = cell.create_xml_subelement(xml_element, memo)
# Append the Universe ID to the subelement and add to Element
cell_element.set("universe", str(self._id))
xml_element.append(cell_element)
def _determine_paths(self, path='', instances_only=False):
"""Count the number of instances for each cell in the universe, and
record the count in the :attr:`Cell.num_instances` properties."""
univ_path = path + f'u{self.id}'
for cell in self.cells.values():
cell_path = f'{univ_path}->c{cell.id}'
fill = cell._fill
fill_type = cell.fill_type
# If universe-filled, recursively count cells in filling universe
if fill_type == 'universe':
fill._determine_paths(cell_path + '->', instances_only)
# If lattice-filled, recursively call for all universes in lattice
elif fill_type == 'lattice':
latt = fill
# Count instances in each universe in the lattice
for index in latt._natural_indices:
latt_path = '{}->l{}({})->'.format(
cell_path, latt.id, ",".join(str(x) for x in index))
univ = latt.get_universe(index)
univ._determine_paths(latt_path, instances_only)
else:
if fill_type == 'material':
mat = fill
elif fill_type == 'distribmat':
mat = fill[cell._num_instances]
else:
mat = None
if mat is not None:
mat._num_instances += 1
if not instances_only:
mat._paths.append(f'{cell_path}->m{mat.id}')
# Append current path
cell._num_instances += 1
if not instances_only:
cell._paths.append(cell_path)
def _partial_deepcopy(self):
"""Clone all of the openmc.Universe object's attributes except for its cells,
as they are copied within the clone function. This should only to be
used within the openmc.UniverseBase.clone() context.
"""
clone = openmc.Universe(name=self.name)
clone.volume = self.volume
return clone
class DAGMCUniverse(UniverseBase):
"""A reference to a DAGMC file to be used in the model.
.. versionadded:: 0.13.0
Parameters
----------
filename : str
Path to the DAGMC file used to represent this universe.
universe_id : int, optional
Unique identifier of the universe. If not specified, an identifier will
automatically be assigned.
name : str, optional
Name of the universe. If not specified, the name is the empty string.
auto_geom_ids : bool
Set IDs automatically on initialization (True) or report overlaps in ID
space between CSG and DAGMC (False)
auto_mat_ids : bool
Set IDs automatically on initialization (True) or report overlaps in ID
space between OpenMC and UWUW materials (False)
Attributes
----------
id : int
Unique identifier of the universe
name : str
Name of the universe
filename : str
Path to the DAGMC file used to represent this universe.
auto_geom_ids : bool
Set IDs automatically on initialization (True) or report overlaps in ID
space between CSG and DAGMC (False)
auto_mat_ids : bool
Set IDs automatically on initialization (True) or report overlaps in ID
space between OpenMC and UWUW materials (False)
bounding_box : openmc.BoundingBox
Lower-left and upper-right coordinates of an axis-aligned bounding box
of the universe.
.. versionadded:: 0.13.1
material_names : list of str
Return a sorted list of materials names that are contained within the
DAGMC h5m file. This is useful when naming openmc.Material() objects
as each material name present in the DAGMC h5m file must have a
matching openmc.Material() with the same name.
.. versionadded:: 0.13.2
n_cells : int
The number of cells in the DAGMC model. This is the number of cells at
runtime and accounts for the implicit complement whether or not is it
present in the DAGMC file.
.. versionadded:: 0.13.2
n_surfaces : int
The number of surfaces in the model.
.. versionadded:: 0.13.2
"""
def __init__(self,
filename,
universe_id=None,
name='',
auto_geom_ids=False,
auto_mat_ids=False):
super().__init__(universe_id, name)
# Initialize class attributes
self.filename = filename
self.auto_geom_ids = auto_geom_ids
self.auto_mat_ids = auto_mat_ids
def __repr__(self):
string = super().__repr__()
string += '{: <16}=\t{}\n'.format('\tGeom', 'DAGMC')
string += '{: <16}=\t{}\n'.format('\tFile', self.filename)
return string
@property
def bounding_box(self):
with h5py.File(self.filename) as dagmc_file:
coords = dagmc_file['tstt']['nodes']['coordinates'][()]
lower_left_corner = coords.min(axis=0)
upper_right_corner = coords.max(axis=0)
return openmc.BoundingBox(lower_left_corner, upper_right_corner)
@property
def filename(self):
return self._filename
@filename.setter
def filename(self, val):
cv.check_type('DAGMC filename', val, (Path, str))
self._filename = val
@property
def auto_geom_ids(self):
return self._auto_geom_ids
@auto_geom_ids.setter
def auto_geom_ids(self, val):
cv.check_type('DAGMC automatic geometry ids', val, bool)
self._auto_geom_ids = val
@property
def auto_mat_ids(self):
return self._auto_mat_ids
@auto_mat_ids.setter
def auto_mat_ids(self, val):
cv.check_type('DAGMC automatic material ids', val, bool)
self._auto_mat_ids = val
@property
def material_names(self):
dagmc_file_contents = h5py.File(self.filename)
material_tags_hex = dagmc_file_contents['/tstt/tags/NAME'].get(
'values')
material_tags_ascii = []
for tag in material_tags_hex:
candidate_tag = tag.tobytes().decode().replace('\x00', '')
# tags might be for temperature or reflective surfaces
if candidate_tag.startswith('mat:'):
# removes first 4 characters as openmc.Material name should be
# set without the 'mat:' part of the tag
material_tags_ascii.append(candidate_tag[4:])
return sorted(set(material_tags_ascii))
def get_all_cells(self, memo=None):
return {}
def get_all_materials(self, memo=None):
return {}
def _n_geom_elements(self, geom_type):
"""
Helper function for retrieving the number geometric entities in a DAGMC
file
Parameters
----------
geom_type : str
The type of geometric entity to count. One of {'Volume', 'Surface'}. Returns
the runtime number of voumes in the DAGMC model (includes implicit complement).
Returns
-------
int
Number of geometry elements of the specified type
"""
cv.check_value('geometry type', geom_type, ('volume', 'surface'))
def decode_str_tag(tag_val):
return tag_val.tobytes().decode().replace('\x00', '')
dagmc_filepath = Path(self.filename).resolve()
with h5py.File(dagmc_filepath) as dagmc_file:
category_data = dagmc_file['tstt/tags/CATEGORY/values']
category_strs = map(decode_str_tag, category_data)
n = sum([v == geom_type.capitalize() for v in category_strs])
# check for presence of an implicit complement in the file and
# increment the number of cells if it doesn't exist
if geom_type == 'volume':
name_data = dagmc_file['tstt/tags/NAME/values']
name_strs = map(decode_str_tag, name_data)
if not sum(['impl_complement' in n for n in name_strs]):
n += 1
return n
@property
def n_cells(self):
return self._n_geom_elements('volume')
@property
def n_surfaces(self):
return self._n_geom_elements('surface')
def create_xml_subelement(self, xml_element, memo=None):
if memo and self in memo:
return
if memo is not None:
memo.add(self)
# Set xml element values
dagmc_element = ET.Element('dagmc_universe')
dagmc_element.set('id', str(self.id))
if self.auto_geom_ids:
dagmc_element.set('auto_geom_ids', 'true')
if self.auto_mat_ids:
dagmc_element.set('auto_mat_ids', 'true')
dagmc_element.set('filename', str(self.filename))
xml_element.append(dagmc_element)
def bounding_region(
self,
bounded_type: str = 'box',
boundary_type: str = 'vacuum',
starting_id: int = 10000,
padding_distance: float = 0.
):
"""Creates a either a spherical or box shaped bounding region around
the DAGMC geometry.
.. versionadded:: 0.13.1
Parameters
----------
bounded_type : str
The type of bounding surface(s) to use when constructing the region.
Options include a single spherical surface (sphere) or a rectangle
made from six planes (box).
boundary_type : str
Boundary condition that defines the behavior for particles hitting
the surface. Defaults to vacuum boundary condition. Passed into the
surface construction.
starting_id : int
Starting ID of the surface(s) used in the region. For bounded_type
'box', the next 5 IDs will also be used. Defaults to 10000 to reduce
the chance of an overlap of surface IDs with the DAGMC geometry.
padding_distance : float
Distance between the bounding region surfaces and the minimal
bounding box. Allows for the region to be larger than the DAGMC
geometry.
Returns
-------
openmc.Region
Region instance
"""
check_type('boundary type', boundary_type, str)
check_value('boundary type', boundary_type, _BOUNDARY_TYPES)
check_type('starting surface id', starting_id, Integral)
check_type('bounded type', bounded_type, str)
check_value('bounded type', bounded_type, ('box', 'sphere'))
bbox = self.bounding_box.expand(padding_distance, True)
if bounded_type == 'sphere':
radius = np.linalg.norm(bbox.upper_right - bbox.center)
bounding_surface = openmc.Sphere(
surface_id=starting_id,
x0=bbox.center[0],
y0=bbox.center[1],
z0=bbox.center[2],
boundary_type=boundary_type,
r=radius,
)
return -bounding_surface
if bounded_type == 'box':
# defines plane surfaces for all six faces of the bounding box
lower_x = openmc.XPlane(bbox[0][0], surface_id=starting_id)
upper_x = openmc.XPlane(bbox[1][0], surface_id=starting_id+1)
lower_y = openmc.YPlane(bbox[0][1], surface_id=starting_id+2)
upper_y = openmc.YPlane(bbox[1][1], surface_id=starting_id+3)
lower_z = openmc.ZPlane(bbox[0][2], surface_id=starting_id+4)
upper_z = openmc.ZPlane(bbox[1][2], surface_id=starting_id+5)
region = +lower_x & -upper_x & +lower_y & -upper_y & +lower_z & -upper_z
for surface in region.get_surfaces().values():
surface.boundary_type = boundary_type
return region
def bounded_universe(self, bounding_cell_id=10000, **kwargs):
"""Returns an openmc.Universe filled with this DAGMCUniverse and bounded
with a cell. Defaults to a box cell with a vacuum surface however this
can be changed using the kwargs which are passed directly to
DAGMCUniverse.bounding_region().
Parameters
----------
bounding_cell_id : int
The cell ID number to use for the bounding cell, defaults to 10000 to reduce
the chance of overlapping ID numbers with the DAGMC geometry.
Returns
-------
openmc.Universe
Universe instance
"""
bounding_cell = openmc.Cell(
fill=self, cell_id=bounding_cell_id, region=self.bounding_region(**kwargs))
return openmc.Universe(cells=[bounding_cell])
@classmethod
def from_hdf5(cls, group):
"""Create DAGMC universe from HDF5 group
Parameters
----------
group : h5py.Group
Group in HDF5 file
Returns
-------
openmc.DAGMCUniverse
DAGMCUniverse instance
"""
id = int(group.name.split('/')[-1].lstrip('universe '))
fname = group['filename'][()].decode()
name = group['name'][()].decode() if 'name' in group else None
out = cls(fname, universe_id=id, name=name)
out.auto_geom_ids = bool(group.attrs['auto_geom_ids'])
out.auto_mat_ids = bool(group.attrs['auto_mat_ids'])
return out
@classmethod
def from_xml_element(cls, elem):
"""Generate DAGMC universe from XML element
Parameters
----------
elem : lxml.etree._Element
`<dagmc_universe>` element
Returns
-------
openmc.DAGMCUniverse
DAGMCUniverse instance
"""
id = int(get_text(elem, 'id'))
fname = get_text(elem, 'filename')
out = cls(fname, universe_id=id)
name = get_text(elem, 'name')
if name is not None:
out.name = name
out.auto_geom_ids = bool(elem.get('auto_geom_ids'))
out.auto_mat_ids = bool(elem.get('auto_mat_ids'))
return out
def _partial_deepcopy(self):
"""Clone all of the openmc.DAGMCUniverse object's attributes except for
its cells, as they are copied within the clone function. This should
only to be used within the openmc.UniverseBase.clone() context.
"""
clone = openmc.DAGMCUniverse(name=self.name, filename=self.filename)
clone.volume = self.volume
clone.auto_geom_ids = self.auto_geom_ids
clone.auto_mat_ids = self.auto_mat_ids
return clone
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