from collections import OrderedDict, defaultdict
from collections.abc import Iterable
from copy import deepcopy
from pathlib import Path
from xml.etree import ElementTree as ET
import numpy as np
import openmc
import openmc._xml as xml
from openmc.checkvalue import check_type
[docs]class Geometry(object):
"""Geometry representing a collection of surfaces, cells, and universes.
Parameters
----------
root : openmc.Universe 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.Universe
Root universe which contains all others
bounding_box : 2-tuple of numpy.array
Lower-left and upper-right coordinates of an axis-aligned bounding box
of the universe.
"""
def __init__(self, root=None):
self._root_universe = None
self._offsets = {}
if root is not None:
if isinstance(root, openmc.Universe):
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):
return self._root_universe
@property
def bounding_box(self):
return self.root_universe.bounding_box
@root_universe.setter
def root_universe(self, root_universe):
check_type('root universe', root_universe, openmc.Universe)
self._root_universe = root_universe
[docs] def export_to_xml(self, path='geometry.xml'):
"""Export geometry to an XML file.
Parameters
----------
path : str
Path to file to write. Defaults to 'geometry.xml'.
"""
# Create XML representation
root_element = ET.Element("geometry")
self.root_universe.create_xml_subelement(root_element)
# Sort the elements in the file
root_element[:] = sorted(root_element, key=lambda x: (
x.tag, int(x.get('id'))))
# Clean the indentation in the file to be user-readable
xml.clean_indentation(root_element)
# 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(cls, path='geometry.xml', materials=None):
"""Generate geometry from XML file
Parameters
----------
path : str, optional
Path to geometry XML file
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
"""
# 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]
tree = ET.parse(path)
root = tree.getroot()
# Get surfaces
surfaces = {}
periodic = {}
for surface in root.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]
# Dictionary that maps each universe to a list of cells/lattices that
# contain it (needed to determine which universe is the root)
child_of = defaultdict(list)
for elem in root.findall('lattice'):
lat = openmc.RectLattice.from_xml_element(elem, 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 elem in root.findall('hex_lattice'):
lat = openmc.HexLattice.from_xml_element(elem, 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)
# Create dictionary to easily look up materials
if materials is None:
filename = Path(path).parent / 'materials.xml'
materials = openmc.Materials.from_xml(str(filename))
mats = {str(m.id): m for m in materials}
mats['void'] = None
for elem in root.findall('cell'):
c = openmc.Cell.from_xml_element(elem, 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] 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
"""
return self.root_universe.find(point)
[docs] def get_instances(self, paths):
"""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):
"""Return all cells in the geometry.
Returns
-------
collections.OrderedDict
Dictionary mapping cell IDs to :class:`openmc.Cell` instances
"""
if self.root_universe is not None:
return self.root_universe.get_all_cells()
else:
return []
[docs] def get_all_universes(self):
"""Return all universes in the geometry.
Returns
-------
collections.OrderedDict
Dictionary mapping universe IDs to :class:`openmc.Universe`
instances
"""
universes = OrderedDict()
universes[self.root_universe.id] = self.root_universe
universes.update(self.root_universe.get_all_universes())
return universes
[docs] def get_all_materials(self):
"""Return all materials within the geometry.
Returns
-------
collections.OrderedDict
Dictionary mapping material IDs to :class:`openmc.Material`
instances
"""
return self.root_universe.get_all_materials()
[docs] def get_all_material_cells(self):
"""Return all cells filled by a material
Returns
-------
collections.OrderedDict
Dictionary mapping cell IDs to :class:`openmc.Cell` instances that
are filled with materials or distributed materials.
"""
material_cells = OrderedDict()
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):
"""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
-------
collections.OrderedDict
Dictionary mapping universe IDs to :class:`openmc.Universe`
instances with at least one material-filled cell
"""
material_universes = OrderedDict()
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):
"""Return all lattices defined
Returns
-------
collections.OrderedDict
Dictionary mapping lattice IDs to :class:`openmc.Lattice` instances
"""
lattices = OrderedDict()
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):
"""
Return all surfaces used in the geometry
Returns
-------
collections.OrderedDict
Dictionary mapping surface IDs to :class:`openmc.Surface` instances
"""
surfaces = OrderedDict()
for cell in self.get_all_cells().values():
surfaces = cell.region.get_surfaces(surfaces)
return surfaces
[docs] def get_materials_by_name(self, name, case_sensitive=False, matching=False):
"""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
"""
if not case_sensitive:
name = name.lower()
all_materials = self.get_all_materials().values()
materials = set()
for material in all_materials:
material_name = material.name
if not case_sensitive:
material_name = material_name.lower()
if material_name == name:
materials.add(material)
elif not matching and name in material_name:
materials.add(material)
return sorted(materials, key=lambda x: x.id)
[docs] def get_cells_by_name(self, name, case_sensitive=False, matching=False):
"""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
"""
if not case_sensitive:
name = name.lower()
all_cells = self.get_all_cells().values()
cells = set()
for cell in all_cells:
cell_name = cell.name
if not case_sensitive:
cell_name = cell_name.lower()
if cell_name == name:
cells.add(cell)
elif not matching and name in cell_name:
cells.add(cell)
return sorted(cells, key=lambda x: x.id)
[docs] def get_cells_by_fill_name(self, name, case_sensitive=False, matching=False):
"""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):
"""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
"""
if not case_sensitive:
name = name.lower()
all_universes = self.get_all_universes().values()
universes = set()
for universe in all_universes:
universe_name = universe.name
if not case_sensitive:
universe_name = universe_name.lower()
if universe_name == name:
universes.add(universe)
elif not matching and name in universe_name:
universes.add(universe)
return sorted(universes, key=lambda x: x.id)
[docs] def get_lattices_by_name(self, name, case_sensitive=False, matching=False):
"""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
"""
if not case_sensitive:
name = name.lower()
all_lattices = self.get_all_lattices().values()
lattices = set()
for lattice in all_lattices:
lattice_name = lattice.name
if not case_sensitive:
lattice_name = lattice_name.lower()
if lattice_name == name:
lattices.add(lattice)
elif not matching and name in lattice_name:
lattices.add(lattice)
return sorted(lattices, key=lambda x: x.id)
[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):
"""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