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Fixed merge conflicts with develop

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Will Boyd 2015-07-26 16:09:15 -07:00
commit 4e6aca6028
331 changed files with 6506 additions and 222815 deletions
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305
openmc/material.py
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@ -1,10 +1,14 @@
from collections import MappingView
from collections import Iterable
from copy import deepcopy
from numbers import Real, Integral
import warnings
from xml.etree import ElementTree as ET
import sys
if sys.version_info[0] >= 3:
basestring = str
import openmc
from openmc.checkvalue import *
from openmc.checkvalue import check_type, check_value, check_greater_than
from openmc.clean_xml import *
@ -14,6 +18,7 @@ MATERIAL_IDS = []
# A static variable for auto-generated Material IDs
AUTO_MATERIAL_ID = 10000
def reset_auto_material_id():
global AUTO_MATERIAL_ID, MATERIAL_IDS
AUTO_MATERIAL_ID = 10000
@ -23,20 +28,36 @@ def reset_auto_material_id():
# Units for density supported by OpenMC
DENSITY_UNITS = ['g/cm3', 'g/cc', 'kg/cm3', 'at/b-cm', 'at/cm3', 'sum']
# ENDF temperatures
ENDF_TEMPS = np.array([300, 600, 700, 900, 1200, 1500])
# ENDF ZAIDs
ENDF_ZAIDS = np.array(['70c', '71c', '72c', '73c', '74c'])
# Constant for density when not needed
NO_DENSITY = 99999.
class Material(object):
"""A material composed of a collection of nuclides/elements that can be assigned
to a region of space.
Parameters
----------
material_id : int, optional
Unique identifier for the material. If not specified, an identifier will
automatically be assigned.
name : str, optional
Name of the material. If not specified, the name will be the empty
string.
Attributes
----------
id : int
Unique identifier for the material
density : float
Density of the material (units defined separately)
density_units : str
Units used for `density`. Can be one of 'g/cm3', 'g/cc', 'kg/cm3',
'atom/b-cm', 'atom/cm3', or 'sum'.
"""
def __init__(self, material_id=None, name=''):
# Initialize class attributes
self.id = material_id
self.name = name
@ -62,95 +83,75 @@ class Material(object):
# If specified, this file will be used instead of composition values
self._distrib_otf_file = None
@property
def id(self):
return self._id
@property
def name(self):
return self._name
@property
def density(self):
return self._density
@property
def density_units(self):
return self._density_units
@property
def convert_to_distrib_comps(self):
return self._convert_to_distrib_comps
@property
def distrib_otf_file(self):
return self._distrib_otf_file
@id.setter
def id(self, material_id):
global AUTO_MATERIAL_ID, MATERIAL_IDS
# If the Material already has an ID, remove it from global list
if hasattr(self, '_id') and not self._id is None:
if hasattr(self, '_id') and self._id is not None:
MATERIAL_IDS.remove(self._id)
if material_id is None:
self._id = AUTO_MATERIAL_ID
MATERIAL_IDS.append(AUTO_MATERIAL_ID)
AUTO_MATERIAL_ID += 1
# Check that the ID is an integer and wasn't already used
elif not is_integer(material_id):
msg = 'Unable to set a non-integer Material ' \
'ID {0}'.format(material_id)
raise ValueError(msg)
elif material_id in MATERIAL_IDS:
msg = 'Unable to set Material ID to {0} since a Material with ' \
'this ID was already initialized'.format(material_id)
raise ValueError(msg)
elif material_id < 0:
msg = 'Unable to set Material ID to {0} since it must be a ' \
'non-negative integer'.format(material_id)
raise ValueError(msg)
else:
check_type('material ID', material_id, Integral)
if material_id in MATERIAL_IDS:
msg = 'Unable to set Material ID to {0} since a Material with ' \
'this ID was already initialized'.format(material_id)
raise ValueError(msg)
check_greater_than('material ID', material_id, 0)
self._id = material_id
MATERIAL_IDS.append(material_id)
@name.setter
def name(self, name):
if not is_string(name):
msg = 'Unable to set name for Material ID={0} with a non-string ' \
'value {1}'.format(self._id, name)
raise ValueError(msg)
else:
self._name = name
check_type('name for Material ID={0}'.format(self._id),
name, basestring)
self._name = name
def set_density(self, units, density=NO_DENSITY):
"""Set the density of the material
if not is_float(density):
msg = 'Unable to set the density for Material ID={0} to a ' \
'non-floating point value {1}'.format(self._id, density)
raise ValueError(msg)
Parameters
----------
units : str
Physical units of density
density : float, optional
Value of the density. Must be specified unless units is given as
'sum'.
elif not units in DENSITY_UNITS:
msg = 'Unable to set the density for Material ID={0} with ' \
'units {1}'.format(self._id, units)
raise ValueError(msg)
"""
check_type('the density for Material ID={0}'.format(self._id),
density, Real)
check_value('density units', units, DENSITY_UNITS)
if density == NO_DENSITY and units is not 'sum':
msg = 'Unable to set the density Material ID={0} ' \
@ -161,45 +162,52 @@ class Material(object):
self._density = density
self._density_units = units
@distrib_otf_file.setter
def distrib_otf_file(self, filename):
# TODO: remove this when distributed materials are merged
warnings.warn('This feature is not yet implemented in a release ' \
warnings.warn('This feature is not yet implemented in a release '
'version of openmc')
if not is_string(filename) and not filename is None:
if not isinstance(filename, basestring) and filename is not None:
msg = 'Unable to add OTF material file to Material ID={0} with a ' \
'non-string name {1}'.format(self._id, filename)
raise ValueError(msg)
self._distrib_otf_file = filename
@convert_to_distrib_comps.setter
def convert_to_distrib_comps(self):
# TODO: remove this when distributed materials are merged
warnings.warn('This feature is not yet implemented in a release ' \
warnings.warn('This feature is not yet implemented in a release '
'version of openmc')
self._convert_to_distrib_comps = True
def add_nuclide(self, nuclide, percent, percent_type='ao'):
"""Add a nuclide to the material
Parameters
----------
nuclide : str or openmc.nuclide.Nuclide
Nuclide to add
percent : float
Atom or weight percent
percent_type : str
'ao' for atom percent and 'wo' for weight percent
"""
if not isinstance(nuclide, (openmc.Nuclide, str)):
msg = 'Unable to add a Nuclide to Material ID={0} with a ' \
'non-Nuclide value {1}'.format(self._id, nuclide)
raise ValueError(msg)
elif not is_float(percent):
elif not isinstance(percent, Real):
msg = 'Unable to add a Nuclide to Material ID={0} with a ' \
'non-floating point value {1}'.format(self._id, percent)
raise ValueError(msg)
elif not percent_type in ['ao', 'wo', 'at/g-cm']:
elif percent_type not in ['ao', 'wo', 'at/g-cm']:
msg = 'Unable to add a Nuclide to Material ID={0} with a ' \
'percent type {1}'.format(self._id, percent_type)
raise ValueError(msg)
@ -213,8 +221,15 @@ class Material(object):
self._nuclides[nuclide._name] = (nuclide, percent, percent_type)
def remove_nuclide(self, nuclide):
"""Remove a nuclide from the material
Parameters
----------
nuclide : openmc.nuclide.Nuclide
Nuclide to remove
"""
if not isinstance(nuclide, openmc.Nuclide):
msg = 'Unable to remove a Nuclide {0} in Material ID={1} ' \
@ -225,20 +240,31 @@ class Material(object):
if nuclide._name in self._nuclides:
del self._nuclides[nuclide._name]
def add_element(self, element, percent, percent_type='ao'):
"""Add a natural element to the material
Parameters
----------
element : openmc.element.Element
Element to add
percent : float
Atom or weight percent
percent_type : str
'ao' for atom percent and 'wo' for weight percent
"""
if not isinstance(element, openmc.Element):
msg = 'Unable to add an Element to Material ID={0} with a ' \
'non-Element value {1}'.format(self._id, element)
raise ValueError(msg)
if not is_float(percent):
if not isinstance(percent, Real):
msg = 'Unable to add an Element to Material ID={0} with a ' \
'non-floating point value {1}'.format(self._id, percent)
raise ValueError(msg)
if not percent_type in ['ao', 'wo']:
if percent_type not in ['ao', 'wo']:
msg = 'Unable to add an Element to Material ID={0} with a ' \
'percent type {1}'.format(self._id, percent_type)
raise ValueError(msg)
@ -248,36 +274,58 @@ class Material(object):
self._elements[element._name] = (element, percent, percent_type)
def remove_element(self, element):
"""Remove a natural element from the material
Parameters
----------
element : openmc.element.Element
Element to remove
"""
# If the Material contains the Element, delete it
if element._name in self._elements:
del self._elements[element._name]
def add_s_alpha_beta(self, name, xs):
r"""Add an :math:`S(\alpha,\beta)` table to the material
if not is_string(name):
Parameters
----------
name : str
Name of the :math:`S(\alpha,\beta)` table
xs : str
Cross section identifier, e.g. '71t'
"""
if not isinstance(name, basestring):
msg = 'Unable to add an S(a,b) table to Material ID={0} with a ' \
'non-string table name {1}'.format(self._id, name)
raise ValueError(msg)
if not is_string(xs):
if not isinstance(xs, basestring):
msg = 'Unable to add an S(a,b) table to Material ID={0} with a ' \
'non-string cross-section identifier {1}'.format(self._id, xs)
raise ValueError(msg)
self._sab.append((name, xs))
def make_isotropic_in_lab(self):
for nuclide_name in self._nuclides:
self._nuclides[nuclide_name][0].make_isotropic_in_lab()
def get_all_nuclides(self):
"""Returns all nuclides in the material
Returns
-------
nuclides : dict
Dictionary whose keys are nuclide names and values are 2-tuples of
(nuclide, density)
"""
nuclides = {}
@ -288,9 +336,7 @@ class Material(object):
return nuclides
def _repr__(self):
string = 'Material\n'
string += '{0: <16}{1}{2}\n'.format('\tID', '=\t', self._id)
string += '{0: <16}{1}{2}\n'.format('\tName', '=\t', self._name)
@ -322,9 +368,7 @@ class Material(object):
return string
def get_nuclide_xml(self, nuclide, distrib=False):
def _get_nuclide_xml(self, nuclide, distrib=False):
xml_element = ET.Element("nuclide")
xml_element.set("name", nuclide[0]._name)
@ -334,7 +378,7 @@ class Material(object):
else:
xml_element.set("wo", str(nuclide[1]))
if not nuclide[0]._xs is None:
if nuclide[0]._xs is not None:
xml_element.set("xs", nuclide[0]._xs)
if not nuclide[0]._scattering is None:
@ -342,9 +386,7 @@ class Material(object):
return xml_element
def get_element_xml(self, element, distrib=False):
def _get_element_xml(self, element, distrib=False):
xml_element = ET.Element("element")
xml_element.set("name", str(element[0]._name))
@ -356,28 +398,31 @@ class Material(object):
return xml_element
def get_nuclides_xml(self, nuclides, distrib=False):
def _get_nuclides_xml(self, nuclides, distrib=False):
xml_elements = []
for nuclide in nuclides.values():
xml_elements.append(self.get_nuclide_xml(nuclide, distrib))
xml_elements.append(self._get_nuclide_xml(nuclide, distrib))
return xml_elements
def get_elements_xml(self, elements, distrib=False):
def _get_elements_xml(self, elements, distrib=False):
xml_elements = []
for element in elements.values():
xml_elements.append(self.get_element_xml(element, distrib))
xml_elements.append(self._get_element_xml(element, distrib))
return xml_elements
def get_material_xml(self):
"""Return XML representation of the material
Returns
-------
element : xml.etree.ElementTree.Element
XML element containing material data
"""
# Create Material XML element
element = ET.Element("material")
@ -393,19 +438,17 @@ class Material(object):
subelement.set("units", self._density_units)
if not self._convert_to_distrib_comps:
# Create nuclide XML subelements
subelements = self.get_nuclides_xml(self._nuclides)
subelements = self._get_nuclides_xml(self._nuclides)
for subelement in subelements:
element.append(subelement)
# Create element XML subelements
subelements = self.get_elements_xml(self._elements)
subelements = self._get_elements_xml(self._elements)
for subelement in subelements:
element.append(subelement)
else:
subelement = ET.SubElement(element, "compositions")
comps = []
@ -418,29 +461,24 @@ class Material(object):
raise ValueError(msg)
comps.append(per)
if self._distrib_otf_file is None:
# Create values and units subelements
subsubelement = ET.SubElement(subelement, "values")
subsubelement.text = ' '.join([str(c) for c in comps])
subsubelement = ET.SubElement(subelement, "units")
subsubelement.text = dist_per_type
else:
# Specify the materials file
subsubelement = ET.SubElement(subelement, "otf_file_path")
subsubelement.text = self._distrib_otf_file
# Create nuclide XML subelements
subelements = self.get_nuclides_xml(self._nuclides, distrib=True)
for subelement_nuc in subelements:
subelement.append(subelement_nuc)
# Create element XML subelements
subelements = self.get_elements_xml(self._elements, distrib=True)
subelements = self._get_elements_xml(self._elements, distrib=True)
for subelement_ele in subelements:
subelement.append(subelement_ele)
@ -454,31 +492,41 @@ class Material(object):
class MaterialsFile(object):
"""Materials file used for an OpenMC simulation. Corresponds directly to the
materials.xml input file.
Attributes
----------
default_xs : str
The default cross section identifier applied to a nuclide when none is
specified
"""
def __init__(self):
# Initialize MaterialsFile class attributes
self._materials = []
self._default_xs = None
self._materials_file = ET.Element("materials")
@property
def default_xs(self):
return self._default_xs
@default_xs.setter
def default_xs(self, xs):
if not is_string(xs):
msg = 'Unable to set default xs to a non-string value'.format(xs)
raise ValueError(msg)
check_type('default xs', xs, basestring)
self._default_xs = xs
def add_material(self, material):
"""Add a material to the file.
Parameters
----------
material : Material
Material to add
"""
if not isinstance(material, Material):
msg = 'Unable to add a non-Material {0} to the ' \
@ -487,19 +535,33 @@ class MaterialsFile(object):
self._materials.append(material)
def add_materials(self, materials):
"""Add multiple materials to the file.
if not isinstance(materials, (tuple, list, MappingView)):
Parameters
----------
materials : tuple or list of Material
Materials to add
"""
if not isinstance(materials, Iterable):
msg = 'Unable to create OpenMC materials.xml file from {0} which ' \
'is not a Python tuple/list'.format(materials)
'is not iterable'.format(materials)
raise ValueError(msg)
for material in materials:
self.add_material(material)
def remove_material(self, material):
"""Remove a material from the file
def remove_materials(self, material):
Parameters
----------
material : Material
Material to remove
"""
if not isinstance(material, Material):
msg = 'Unable to remove a non-Material {0} from the ' \
@ -509,26 +571,25 @@ class MaterialsFile(object):
self._materials.remove(material)
def make_isotropic_in_lab(self):
for material in self._materials:
materials.make_isotropic_in_lab()
def create_material_subelements(self):
def _create_material_subelements(self):
subelement = ET.SubElement(self._materials_file, "default_xs")
if not self._default_xs is None:
if self._default_xs is not None:
subelement.text = self._default_xs
for material in self._materials:
xml_element = material.get_material_xml()
self._materials_file.append(xml_element)
def export_to_xml(self):
"""Create a materials.xml file that can be used for a simulation.
self.create_material_subelements()
"""
self._create_material_subelements()
# Clean the indentation in the file to be user-readable
sort_xml_elements(self._materials_file)