from collections import OrderedDict
from collections.abc import Iterable
from copy import copy, deepcopy
from numbers import Real
import random
import numpy as np
import openmc
import openmc.checkvalue as cv
from .mixin import IDManagerMixin
from .plots import _SVG_COLORS
[docs]class Universe(IDManagerMixin):
"""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 : collections.OrderedDict
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 : 2-tuple of numpy.array
Lower-left and upper-right coordinates of an axis-aligned bounding box
of the universe.
"""
next_id = 1
used_ids = set()
def __init__(self, universe_id=None, name='', cells=None):
# Initialize Cell class attributes
self.id = universe_id
self.name = name
self._volume = None
self._atoms = {}
# Keys - Cell IDs
# Values - Cells
self._cells = OrderedDict()
if cells is not None:
self.add_cells(cells)
def __repr__(self):
string = 'Universe\n'
string += '{: <16}=\t{}\n'.format('\tID', self._id)
string += '{: <16}=\t{}\n'.format('\tName', self._name)
string += '{: <16}=\t{}\n'.format('\tCells', list(self._cells.keys()))
return string
@property
def name(self):
return self._name
@property
def cells(self):
return self._cells
@property
def volume(self):
return self._volume
@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:
# Infinite bounding box
return openmc.Intersection([]).bounding_box
@name.setter
def name(self, name):
if name is not None:
cv.check_type('universe name', name, str)
self._name = name
else:
self._name = ''
@volume.setter
def volume(self, volume):
if volume is not None:
cv.check_type('universe volume', volume, Real)
self._volume = volume
[docs] @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
[docs] 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 []
[docs] def plot(self, origin=(0., 0., 0.), width=(1., 1.), pixels=(200, 200),
basis='xy', color_by='cell', colors=None, seed=None,
**kwargs):
"""Display a slice plot of the universe.
To display or save the plot, call :func:`matplotlib.pyplot.show` or
:func:`matplotlib.pyplot.savefig`. In a Jupyter notebook, enabling the
matplotlib inline backend will show the plot inline.
Parameters
----------
origin : Iterable of float
Coordinates at the origin of the plot
width : Iterable of float
Width of the plot in each basis direction
pixels : Iterable of int
Number of pixels to use in each basis direction
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 : hashable object or None
Hashable object which is used to seed the random number generator
used to select colors. If None, the generator is seeded from the
current time.
**kwargs
All keyword arguments are passed to
:func:`matplotlib.pyplot.imshow`.
Returns
-------
matplotlib.image.AxesImage
Resulting image
"""
import matplotlib.pyplot as plt
# Seed the random number generator
if seed is not None:
random.seed(seed)
if colors is None:
# Create default dictionary if none supplied
colors = {}
else:
# Convert to RGBA if necessary
colors = copy(colors)
for obj, color in colors.items():
if isinstance(color, str):
if color.lower() not in _SVG_COLORS:
raise ValueError("'{}' is not a valid color."
.format(color))
colors[obj] = [x/255 for x in
_SVG_COLORS[color.lower()]] + [1.0]
elif len(color) == 3:
colors[obj] = list(color) + [1.0]
if basis == 'xy':
x_min = origin[0] - 0.5*width[0]
x_max = origin[0] + 0.5*width[0]
y_min = origin[1] - 0.5*width[1]
y_max = origin[1] + 0.5*width[1]
elif basis == 'yz':
# The x-axis will correspond to physical y and the y-axis will
# correspond to physical z
x_min = origin[1] - 0.5*width[0]
x_max = origin[1] + 0.5*width[0]
y_min = origin[2] - 0.5*width[1]
y_max = origin[2] + 0.5*width[1]
elif basis == 'xz':
# The y-axis will correspond to physical z
x_min = origin[0] - 0.5*width[0]
x_max = origin[0] + 0.5*width[0]
y_min = origin[2] - 0.5*width[1]
y_max = origin[2] + 0.5*width[1]
# Determine locations to determine cells at
x_coords = np.linspace(x_min, x_max, pixels[0], endpoint=False) + \
0.5*(x_max - x_min)/pixels[0]
y_coords = np.linspace(y_max, y_min, pixels[1], endpoint=False) - \
0.5*(y_max - y_min)/pixels[1]
# Initialize output image in RGBA format. Flip the pixels from
# traditional (x, y) to (y, x) used in graphics.
img = np.zeros((pixels[1], pixels[0], 4))
for i, x in enumerate(x_coords):
for j, y in enumerate(y_coords):
if basis == 'xy':
path = self.find((x, y, origin[2]))
elif basis == 'yz':
path = self.find((origin[0], x, y))
elif basis == 'xz':
path = self.find((x, origin[1], y))
if len(path) > 0:
try:
if color_by == 'cell':
obj = path[-1]
elif color_by == 'material':
if path[-1].fill_type == 'material':
obj = path[-1].fill
else:
continue
except AttributeError:
continue
if obj not in colors:
colors[obj] = (random.random(), random.random(),
random.random(), 1.0)
img[j, i, :] = colors[obj]
# Display image
return plt.imshow(img, extent=(x_min, x_max, y_min, y_max),
interpolation='nearest', **kwargs)
[docs] 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 = 'Unable to add a Cell to Universe ID="{0}" since "{1}" is not ' \
'a Cell'.format(self._id, cell)
raise TypeError(msg)
cell_id = cell.id
if cell_id not in self._cells:
self._cells[cell_id] = cell
[docs] 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 = 'Unable to add Cells to Universe ID="{0}" since "{1}" is not ' \
'iterable'.format(self._id, cells)
raise TypeError(msg)
for cell in cells:
self.add_cell(cell)
[docs] 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 = 'Unable to remove a Cell from Universe ID="{0}" since "{1}" is ' \
'not a Cell'.format(self._id, cell)
raise TypeError(msg)
# If the Cell is in the Universe's list of Cells, delete it
self._cells.pop(cell.id, None)
[docs] def clear_cells(self):
"""Remove all cells from the universe."""
self._cells.clear()
[docs] 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
[docs] def get_nuclide_densities(self):
"""Return all nuclides contained in the universe
Returns
-------
nuclides : collections.OrderedDict
Dictionary whose keys are nuclide names and values are 2-tuples of
(nuclide, density)
"""
nuclides = OrderedDict()
if self._atoms is not None:
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 '
'sections for universe {}. This can be done by running a '
'stochastic volume calculation via the '
'openmc.VolumeCalculation object'.format(self.id))
return nuclides
[docs] def get_all_cells(self, memo=None):
"""Return all cells that are contained within the universe
Returns
-------
cells : collections.OrderedDict
Dictionary whose keys are cell IDs and values are :class:`Cell`
instances
"""
cells = OrderedDict()
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
[docs] def get_all_materials(self, memo=None):
"""Return all materials that are contained within the universe
Returns
-------
materials : collections.OrderedDict
Dictionary whose keys are material IDs and values are
:class:`Material` instances
"""
materials = OrderedDict()
# 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
[docs] def get_all_universes(self):
"""Return all universes that are contained within this one.
Returns
-------
universes : collections.OrderedDict
Dictionary whose keys are universe IDs and values are
:class:`Universe` instances
"""
# Append all Universes within each Cell to the dictionary
universes = OrderedDict()
for cell in self.get_all_cells().values():
universes.update(cell.get_all_universes())
return universes
[docs] 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 nemoize'd clone exists, instantiate one
if self not in memo:
clone = deepcopy(self)
clone.id = None
# Clone all cells for the universe clone
clone._cells = OrderedDict()
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]
[docs] def create_xml_subelement(self, xml_element, memo=None):
"""Add the universe xml representation to an incoming xml element
Parameters
----------
xml_element : xml.etree.ElementTree.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
"""
# 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 + 'u{}'.format(self.id)
for cell in self.cells.values():
cell_path = '{}->c{}'.format(univ_path, 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('{}->m{}'.format(cell_path, mat.id))
# Append current path
cell._num_instances += 1
if not instances_only:
cell._paths.append(cell_path)