from __future__ import annotations
import os
import typing
from collections import defaultdict
from copy import deepcopy
from collections.abc import Iterable
from pathlib import Path
import warnings
import lxml.etree as ET
import numpy as np
import openmc
import openmc._xml as xml
from .checkvalue import check_type, check_less_than, check_greater_than, PathLike
[docs]class Geometry:
"""Geometry representing a collection of surfaces, cells, and universes.
Parameters
----------
root : openmc.UniverseBase or Iterable of openmc.Cell, optional
Root universe which contains all others, or an iterable of cells that
should be used to create a root universe.
Attributes
----------
root_universe : openmc.UniverseBase
Root universe which contains all others
bounding_box : openmc.BoundingBox
Lower-left and upper-right coordinates of an axis-aligned bounding box
of the universe.
merge_surfaces : bool
Whether to remove redundant surfaces when the geometry is exported.
surface_precision : int
Number of decimal places to round to for comparing the coefficients of
surfaces for considering them topologically equivalent.
"""
def __init__(
self,
root: typing.Optional[openmc.UniverseBase] = None,
merge_surfaces: bool = False,
surface_precision: int = 10
):
self._root_universe = None
self._offsets = {}
self.merge_surfaces = merge_surfaces
self.surface_precision = surface_precision
if root is not None:
if isinstance(root, openmc.UniverseBase):
self.root_universe = root
else:
univ = openmc.Universe()
for cell in root:
univ.add_cell(cell)
self._root_universe = univ
@property
def root_universe(self) -> openmc.UniverseBase:
return self._root_universe
@root_universe.setter
def root_universe(self, root_universe):
check_type('root universe', root_universe, openmc.UniverseBase)
self._root_universe = root_universe
@property
def bounding_box(self) -> np.ndarray:
return self.root_universe.bounding_box
@property
def merge_surfaces(self) -> bool:
return self._merge_surfaces
@merge_surfaces.setter
def merge_surfaces(self, merge_surfaces):
check_type('merge surfaces', merge_surfaces, bool)
self._merge_surfaces = merge_surfaces
@property
def surface_precision(self) -> int:
return self._surface_precision
@surface_precision.setter
def surface_precision(self, surface_precision):
check_type('surface precision', surface_precision, int)
check_less_than('surface_precision', surface_precision, 16)
check_greater_than('surface_precision', surface_precision, 0)
self._surface_precision = surface_precision
[docs] def to_xml_element(self, remove_surfs=False) -> ET.Element:
"""Creates a 'geometry' element to be written to an XML file.
Parameters
----------
remove_surfs : bool
Whether or not to remove redundant surfaces from the geometry when
exporting
"""
# Find and remove redundant surfaces from the geometry
if remove_surfs:
warnings.warn("remove_surfs kwarg will be deprecated soon, please "
"set the Geometry.merge_surfaces attribute instead.")
self.merge_surfaces = True
if self.merge_surfaces:
self.remove_redundant_surfaces()
# Create XML representation
element = ET.Element("geometry")
self.root_universe.create_xml_subelement(element, memo=set())
# Sort the elements in the file
element[:] = sorted(element, key=lambda x: (
x.tag, int(x.get('id'))))
# Clean the indentation in the file to be user-readable
xml.clean_indentation(element)
xml.reorder_attributes(element) # TODO: Remove when support is Python 3.8+
return element
[docs] def export_to_xml(self, path='geometry.xml', remove_surfs=False):
"""Export geometry to an XML file.
Parameters
----------
path : str
Path to file to write. Defaults to 'geometry.xml'.
remove_surfs : bool
Whether or not to remove redundant surfaces from the geometry when
exporting
.. versionadded:: 0.12
"""
root_element = self.to_xml_element(remove_surfs)
# Check if path is a directory
p = Path(path)
if p.is_dir():
p /= 'geometry.xml'
# Write the XML Tree to the geometry.xml file
tree = ET.ElementTree(root_element)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
[docs] @classmethod
def from_xml_element(cls, elem, materials=None) -> Geometry:
"""Generate geometry from an XML element
Parameters
----------
elem : lxml.etree._Element
XML element
materials : openmc.Materials or None
Materials used to assign to cells. If None, an attempt is made to
generate it from the materials.xml file.
Returns
-------
openmc.Geometry
Geometry object
"""
mats = dict()
if materials is not None:
mats.update({str(m.id): m for m in materials})
mats['void'] = None
# Helper function for keeping a cache of Universe instances
universes = {}
def get_universe(univ_id):
if univ_id not in universes:
univ = openmc.Universe(univ_id)
universes[univ_id] = univ
return universes[univ_id]
# Get surfaces
surfaces = {}
periodic = {}
for surface in elem.findall('surface'):
s = openmc.Surface.from_xml_element(surface)
surfaces[s.id] = s
# Check for periodic surface
other_id = xml.get_text(surface, 'periodic_surface_id')
if other_id is not None:
periodic[s.id] = int(other_id)
# Apply periodic surfaces
for s1, s2 in periodic.items():
surfaces[s1].periodic_surface = surfaces[s2]
# Add any DAGMC universes
for e in elem.findall('dagmc_universe'):
dag_univ = openmc.DAGMCUniverse.from_xml_element(e)
universes[dag_univ.id] = dag_univ
# Dictionary that maps each universe to a list of cells/lattices that
# contain it (needed to determine which universe is the elem)
child_of = defaultdict(list)
for e in elem.findall('lattice'):
lat = openmc.RectLattice.from_xml_element(e, get_universe)
universes[lat.id] = lat
if lat.outer is not None:
child_of[lat.outer].append(lat)
for u in lat.universes.ravel():
child_of[u].append(lat)
for e in elem.findall('hex_lattice'):
lat = openmc.HexLattice.from_xml_element(e, get_universe)
universes[lat.id] = lat
if lat.outer is not None:
child_of[lat.outer].append(lat)
if lat.ndim == 2:
for ring in lat.universes:
for u in ring:
child_of[u].append(lat)
else:
for axial_slice in lat.universes:
for ring in axial_slice:
for u in ring:
child_of[u].append(lat)
for e in elem.findall('cell'):
c = openmc.Cell.from_xml_element(e, surfaces, mats, get_universe)
if c.fill_type in ('universe', 'lattice'):
child_of[c.fill].append(c)
# Determine which universe is the root by finding one which is not a
# child of any other object
for u in universes.values():
if not child_of[u]:
return cls(u)
else:
raise ValueError('Error determining root universe.')
[docs] @classmethod
def from_xml(
cls,
path: PathLike = 'geometry.xml',
materials: typing.Optional[typing.Union[PathLike, 'openmc.Materials']] = 'materials.xml'
) -> Geometry:
"""Generate geometry from XML file
Parameters
----------
path : PathLike, optional
Path to geometry XML file
materials : openmc.Materials or PathLike
Materials used to assign to cells. If PathLike, an attempt is made
to generate materials from the provided xml file.
Returns
-------
openmc.Geometry
Geometry object
"""
# Using str and os.PathLike here to avoid error when using just the imported PathLike
# TypeError: Subscripted generics cannot be used with class and instance checks
check_type('materials', materials, (str, os.PathLike, openmc.Materials))
if isinstance(materials, (str, os.PathLike)):
materials = openmc.Materials.from_xml(materials)
tree = ET.parse(path)
root = tree.getroot()
return cls.from_xml_element(root, materials)
[docs] def find(self, point) -> list:
"""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
"""
return self.root_universe.find(point)
[docs] def get_instances(self, paths) -> typing.Union[int, typing.List[int]]:
"""Return the instance number(s) for a cell/material in a geometry path.
The instance numbers are used as indices into distributed
material/temperature arrays and tally distribcell filter arrays.
Parameters
----------
paths : str or iterable of str
The path traversed through the CSG tree to reach a cell or material
instance. For example, 'u0->c10->l20(2,2,1)->u5->c5' would indicate
the cell instance whose first level is universe 0 and cell 10,
second level is lattice 20 position (2,2,1), and third level is
universe 5 and cell 5.
Returns
-------
int or list of int
Instance number(s) for the given path(s)
"""
# Make sure we are working with an iterable
return_list = (isinstance(paths, Iterable) and
not isinstance(paths, str))
path_list = paths if return_list else [paths]
indices = []
for p in path_list:
# Extract the cell id from the path
last_index = p.rfind('>')
last_path = p[last_index+1:]
uid = int(last_path[1:])
# Get corresponding cell/material
if last_path[0] == 'c':
obj = self.get_all_cells()[uid]
elif last_path[0] == 'm':
obj = self.get_all_materials()[uid]
# Determine index in paths array
try:
indices.append(obj.paths.index(p))
except ValueError:
indices.append(None)
return indices if return_list else indices[0]
[docs] def get_all_cells(self) -> typing.Dict[int, openmc.Cell]:
"""Return all cells in the geometry.
Returns
-------
dict
Dictionary mapping cell IDs to :class:`openmc.Cell` instances
"""
if self.root_universe is not None:
return self.root_universe.get_all_cells(memo=set())
else:
return {}
[docs] def get_all_universes(self) -> typing.Dict[int, openmc.Universe]:
"""Return all universes in the geometry.
Returns
-------
dict
Dictionary mapping universe IDs to :class:`openmc.Universe`
instances
"""
universes = {}
universes[self.root_universe.id] = self.root_universe
universes.update(self.root_universe.get_all_universes())
return universes
[docs] def get_all_materials(self) -> typing.Dict[int, openmc.Material]:
"""Return all materials within the geometry.
Returns
-------
dict
Dictionary mapping material IDs to :class:`openmc.Material`
instances
"""
if self.root_universe is not None:
return self.root_universe.get_all_materials(memo=set())
else:
return {}
[docs] def get_all_material_cells(self) -> typing.Dict[int, openmc.Cell]:
"""Return all cells filled by a material
Returns
-------
dict
Dictionary mapping cell IDs to :class:`openmc.Cell` instances that
are filled with materials or distributed materials.
"""
material_cells = {}
for cell in self.get_all_cells().values():
if cell.fill_type in ('material', 'distribmat'):
if cell not in material_cells:
material_cells[cell.id] = cell
return material_cells
[docs] def get_all_material_universes(self) -> typing.Dict[int, openmc.Universe]:
"""Return all universes having at least one material-filled cell.
This method can be used to find universes that have at least one cell
that is filled with a material or is void.
Returns
-------
dict
Dictionary mapping universe IDs to :class:`openmc.Universe`
instances with at least one material-filled cell
"""
material_universes = {}
for universe in self.get_all_universes().values():
for cell in universe.cells.values():
if cell.fill_type in ('material', 'distribmat', 'void'):
if universe not in material_universes:
material_universes[universe.id] = universe
return material_universes
[docs] def get_all_lattices(self) -> typing.Dict[int, openmc.Lattice]:
"""Return all lattices defined
Returns
-------
dict
Dictionary mapping lattice IDs to :class:`openmc.Lattice` instances
"""
lattices = {}
for cell in self.get_all_cells().values():
if cell.fill_type == 'lattice':
if cell.fill.id not in lattices:
lattices[cell.fill.id] = cell.fill
return lattices
[docs] def get_all_surfaces(self) -> typing.Dict[int, openmc.Surface]:
"""
Return all surfaces used in the geometry
Returns
-------
dict
Dictionary mapping surface IDs to :class:`openmc.Surface` instances
"""
surfaces = {}
for cell in self.get_all_cells().values():
if cell.region is not None:
surfaces = cell.region.get_surfaces(surfaces)
return surfaces
def _get_domains_by_name(self, name, case_sensitive, matching, domain_type) -> list:
if not case_sensitive:
name = name.lower()
domains = []
func = getattr(self, f'get_all_{domain_type}s')
for domain in func().values():
domain_name = domain.name if case_sensitive else domain.name.lower()
if domain_name == name:
domains.append(domain)
elif not matching and name in domain_name:
domains.append(domain)
domains.sort(key=lambda x: x.id)
return domains
[docs] def get_materials_by_name(
self, name, case_sensitive=False, matching=False
) -> typing.List[openmc.Material]:
"""Return a list of materials with matching names.
Parameters
----------
name : str
The name to match
case_sensitive : bool
Whether to distinguish upper and lower case letters in each
material's name (default is False)
matching : bool
Whether the names must match completely (default is False)
Returns
-------
list of openmc.Material
Materials matching the queried name
"""
return self._get_domains_by_name(name, case_sensitive, matching, 'material')
[docs] def get_cells_by_name(
self, name, case_sensitive=False, matching=False
) -> typing.List[openmc.Cell]:
"""Return a list of cells with matching names.
Parameters
----------
name : str
The name to search match
case_sensitive : bool
Whether to distinguish upper and lower case letters in each
cell's name (default is False)
matching : bool
Whether the names must match completely (default is False)
Returns
-------
list of openmc.Cell
Cells matching the queried name
"""
return self._get_domains_by_name(name, case_sensitive, matching, 'cell')
[docs] def get_surfaces_by_name(
self, name, case_sensitive=False, matching=False
) -> typing.List[openmc.Surface]:
"""Return a list of surfaces with matching names.
.. versionadded:: 0.13.3
Parameters
----------
name : str
The name to search match
case_sensitive : bool
Whether to distinguish upper and lower case letters in each
surface's name (default is False)
matching : bool
Whether the names must match completely (default is False)
Returns
-------
list of openmc.Surface
Surfaces matching the queried name
"""
return self._get_domains_by_name(name, case_sensitive, matching, 'surface')
[docs] def get_cells_by_fill_name(
self, name, case_sensitive=False, matching=False
) -> typing.List[openmc.Cell]:
"""Return a list of cells with fills with matching names.
Parameters
----------
name : str
The name to match
case_sensitive : bool
Whether to distinguish upper and lower case letters in each
cell's name (default is False)
matching : bool
Whether the names must match completely (default is False)
Returns
-------
list of openmc.Cell
Cells with fills matching the queried name
"""
if not case_sensitive:
name = name.lower()
cells = set()
for cell in self.get_all_cells().values():
names = []
if cell.fill_type in ('material', 'universe', 'lattice'):
names.append(cell.fill.name)
elif cell.fill_type == 'distribmat':
for mat in cell.fill:
if mat is not None:
names.append(mat.name)
for fill_name in names:
if not case_sensitive:
fill_name = fill_name.lower()
if fill_name == name:
cells.add(cell)
elif not matching and name in fill_name:
cells.add(cell)
return sorted(cells, key=lambda x: x.id)
[docs] def get_universes_by_name(
self, name, case_sensitive=False, matching=False
) -> typing.List[openmc.Universe]:
"""Return a list of universes with matching names.
Parameters
----------
name : str
The name to match
case_sensitive : bool
Whether to distinguish upper and lower case letters in each
universe's name (default is False)
matching : bool
Whether the names must match completely (default is False)
Returns
-------
list of openmc.Universe
Universes matching the queried name
"""
return self._get_domains_by_name(name, case_sensitive, matching, 'universe')
[docs] def get_lattices_by_name(
self, name, case_sensitive=False, matching=False
) -> typing.List[openmc.Lattice]:
"""Return a list of lattices with matching names.
Parameters
----------
name : str
The name to match
case_sensitive : bool
Whether to distinguish upper and lower case letters in each
lattice's name (default is False)
matching : bool
Whether the names must match completely (default is False)
Returns
-------
list of openmc.Lattice
Lattices matching the queried name
"""
return self._get_domains_by_name(name, case_sensitive, matching, 'lattice')
[docs] def remove_redundant_surfaces(self) -> typing.Dict[int, openmc.Surface]:
"""Remove and return all of the redundant surfaces.
Uses surface_precision attribute of Geometry instance for rounding and
comparing surface coefficients.
.. versionadded:: 0.12
Returns
-------
redundant_surfaces
Dictionary whose keys are the ID of a redundant surface and whose
values are the topologically equivalent :class:`openmc.Surface`
that should replace it.
"""
# Get redundant surfaces
redundancies = defaultdict(list)
for surf in self.get_all_surfaces().values():
coeffs = tuple(round(surf._coefficients[k],
self.surface_precision)
for k in surf._coeff_keys)
key = (surf._type,) + coeffs
redundancies[key].append(surf)
redundant_surfaces = {replace.id: keep
for keep, *redundant in redundancies.values()
for replace in redundant}
if redundant_surfaces:
# Iterate through all cells contained in the geometry
for cell in self.get_all_cells().values():
# Recursively remove redundant surfaces from regions
if cell.region:
cell.region.remove_redundant_surfaces(redundant_surfaces)
return redundant_surfaces
[docs] def determine_paths(self, instances_only=False):
"""Determine paths through CSG tree for cells and materials.
This method recursively traverses the CSG tree to determine each unique
path that reaches every cell and material. The paths are stored in the
:attr:`Cell.paths` and :attr:`Material.paths` attributes.
Parameters
----------
instances_only : bool, optional
If true, this method will only determine the number of instances of
each cell and material.
"""
# (Re-)initialize all cell instances to 0
for cell in self.get_all_cells().values():
cell._paths = []
cell._num_instances = 0
for material in self.get_all_materials().values():
material._paths = []
material._num_instances = 0
# Recursively traverse the CSG tree to count all cell instances
self.root_universe._determine_paths(instances_only=instances_only)
[docs] def clone(self) -> Geometry:
"""Create a copy of this geometry with new unique IDs for all of its
enclosed materials, surfaces, cells, universes and lattices."""
clone = deepcopy(self)
clone.root_universe = self.root_universe.clone()
return clone
[docs] def plot(self, *args, **kwargs):
"""Display a slice plot of the geometry.
.. versionadded:: 0.14.0
Parameters
----------
origin : iterable of float
Coordinates at the origin of the plot. If left as None then the
bounding box center will be used to attempt to ascertain the origin.
Defaults to (0, 0, 0) if the bounding box is not finite
width : iterable of float
Width of the plot in each basis direction. If left as none then the
bounding box width will be used to attempt to ascertain the plot
width. Defaults to (10, 10) if the bounding box is not finite
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::
# 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
legend : bool
Whether a legend showing material or cell names should be drawn
legend_kwargs : dict
Keyword arguments passed to :func:`matplotlib.pyplot.legend`.
outline : bool
Whether outlines between color boundaries should be drawn
axis_units : {'km', 'm', 'cm', 'mm'}
Units used on the plot axis
**kwargs
Keyword arguments passed to :func:`matplotlib.pyplot.imshow`
Returns
-------
matplotlib.axes.Axes
Axes containing resulting image
"""
return self.root_universe.plot(*args, **kwargs)