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Merge pull request #1530 from Shimwell/develop
adding elements to a material from formula
This commit is contained in:
Paul Romano
GitHub
commit
a294172342
2 changed files with 191 additions and 4 deletions
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@ -1,9 +1,10 @@
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from collections import OrderedDict, defaultdict
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from collections import OrderedDict, defaultdict, Counter
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from collections.abc import Iterable
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from copy import deepcopy
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from numbers import Real, Integral
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from pathlib import Path
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import warnings
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import re
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from xml.etree import ElementTree as ET
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import numpy as np
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@ -588,6 +589,99 @@ class Material(IDManagerMixin):
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enrichment_type):
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self.add_nuclide(*nuclide)
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def add_elements_from_formula(self, formula, percent_type='ao', enrichment=None,
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enrichment_target=None, enrichment_type=None):
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"""Add a elements from a chemical formula to the material.
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Parameters
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----------
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formula : str
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Formula to add, e.g., 'C2O', 'C6H12O6', or (NH4)2SO4.
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Note this is case sensitive, elements must start with an uppercase
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character. Multiplier numbers must be integers.
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percent_type : {'ao', 'wo'}, optional
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'ao' for atom percent and 'wo' for weight percent. Defaults to atom
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percent.
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enrichment : float, optional
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Enrichment of an enrichment_target nuclide in percent (ao or wo).
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If enrichment_target is not supplied then it is enrichment for U235
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in weight percent. For example, input 4.95 for 4.95 weight percent
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enriched U. Default is None (natural composition).
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enrichment_target : str, optional
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Single nuclide name to enrich from a natural composition (e.g., 'O16')
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enrichment_type : {'ao', 'wo'}, optional
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'ao' for enrichment as atom percent and 'wo' for weight percent.
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Default is: 'ao' for two-isotope enrichment; 'wo' for U enrichment
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Notes
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-----
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General enrichment procedure is allowed only for elements composed of
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two isotopes. If `enrichment_target` is given without `enrichment`
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natural composition is added to the material.
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"""
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cv.check_type('formula', formula, str)
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if '.' in formula:
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msg = 'Non-integer multiplier values are not accepted. The ' \
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'input formula {} contains a "." character.'.format(formula)
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raise ValueError(msg)
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# Tokenizes the formula and check validity of tokens
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tokens = re.findall(r"([A-Z][a-z]*)(\d*)|(\()|(\))(\d*)", formula)
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for row in tokens:
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for token in row:
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if token.isalpha():
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if token == "n" or token not in openmc.data.ATOMIC_NUMBER:
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msg = 'Formula entry {} not an element symbol.' \
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.format(token)
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raise ValueError(msg)
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elif token not in ['(', ')', ''] and not token.isdigit():
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msg = 'Formula must be made from a sequence of ' \
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'element symbols, integers, and backets. ' \
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'{} is not an allowable entry.'.format(token)
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raise ValueError(msg)
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# Checks that the number of opening and closing brackets are equal
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if formula.count('(') != formula.count(')'):
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msg = 'Number of opening and closing brackets is not equal ' \
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'in the input formula {}.'.format(formula)
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raise ValueError(msg)
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# Checks that every part of the original formula has been tokenized
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for row in tokens:
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for token in row:
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formula = formula.replace(token, '', 1)
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if len(formula) != 0:
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msg = 'Part of formula was not successfully parsed as an ' \
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'element symbol, bracket or integer. {} was not parsed.' \
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.format(formula)
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raise ValueError(msg)
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# Works through the tokens building a stack
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mat_stack = [Counter()]
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for symbol, multi1, opening_bracket, closing_bracket, multi2 in tokens:
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if symbol:
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mat_stack[-1][symbol] += int(multi1 or 1)
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if opening_bracket:
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mat_stack.append(Counter())
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if closing_bracket:
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stack_top = mat_stack.pop()
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for symbol, value in stack_top.items():
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mat_stack[-1][symbol] += int(multi2 or 1) * value
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# Normalizing percentages
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percents = mat_stack[0].values()
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norm_percents = [float(i) / sum(percents) for i in percents]
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elements = mat_stack[0].keys()
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# Adds each element and percent to the material
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for element, percent in zip(elements, norm_percents):
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if enrichment_target is not None and element == re.sub(r'\d+$', '', enrichment_target):
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self.add_element(element, percent, percent_type, enrichment,
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enrichment_target, enrichment_type)
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else:
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self.add_element(element, percent, percent_type)
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def add_s_alpha_beta(self, name, fraction=1.0):
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r"""Add an :math:`S(\alpha,\beta)` table to the material
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@ -1,8 +1,11 @@
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from collections import defaultdict
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import pytest
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import openmc
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import openmc.examples
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import openmc.model
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import openmc.stats
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import openmc.examples
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import pytest
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def test_attributes(uo2):
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@ -58,6 +61,97 @@ def test_elements_by_name():
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assert a._nuclides == b._nuclides
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assert b._nuclides == c._nuclides
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def test_add_elements_by_formula():
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"""Test adding elements from a formula"""
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# testing the correct nuclides and elements are added to a material
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m = openmc.Material()
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m.add_elements_from_formula('Li4SiO4')
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# checking the ratio of elements is 4:1:4 for Li:Si:O
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elem = defaultdict(float)
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for nuclide, adens in m.get_nuclide_atom_densities().values():
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if nuclide.startswith("Li"):
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elem["Li"] += adens
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if nuclide.startswith("Si"):
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elem["Si"] += adens
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if nuclide.startswith("O"):
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elem["O"] += adens
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total_number_of_atoms = 9
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assert elem["Li"] == pytest.approx(4./total_number_of_atoms)
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assert elem["Si"] == pytest.approx(1./total_number_of_atoms)
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assert elem["O"] == pytest.approx(4/total_number_of_atoms)
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# testing the correct nuclides are added to the Material
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ref_dens = {'Li6': 0.033728, 'Li7': 0.410715,
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'Si28': 0.102477, 'Si29': 0.0052035, 'Si30': 0.0034301,
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'O16': 0.443386, 'O17': 0.000168}
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nuc_dens = m.get_nuclide_atom_densities()
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for nuclide in ref_dens:
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assert nuc_dens[nuclide][1] == pytest.approx(ref_dens[nuclide], 1e-2)
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# testing the correct nuclides are added to the Material when enriched
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m = openmc.Material()
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m.add_elements_from_formula('Li4SiO4',
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enrichment=60.,
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enrichment_target='Li6')
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ref_dens = {'Li6': 0.2666, 'Li7': 0.1777,
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'Si28': 0.102477, 'Si29': 0.0052035, 'Si30': 0.0034301,
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'O16': 0.443386, 'O17': 0.000168}
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nuc_dens = m.get_nuclide_atom_densities()
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for nuclide in ref_dens:
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assert nuc_dens[nuclide][1] == pytest.approx(ref_dens[nuclide], 1e-2)
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# testing the use of brackets
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m = openmc.Material()
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m.add_elements_from_formula('Mg2(NO3)2')
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# checking the ratio of elements is 2:2:6 for Mg:N:O
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elem = defaultdict(float)
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for nuclide, adens in m.get_nuclide_atom_densities().values():
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if nuclide.startswith("Mg"):
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elem["Mg"] += adens
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if nuclide.startswith("N"):
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elem["N"] += adens
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if nuclide.startswith("O"):
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elem["O"] += adens
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total_number_of_atoms = 10
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assert elem["Mg"] == pytest.approx(2./total_number_of_atoms)
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assert elem["N"] == pytest.approx(2./total_number_of_atoms)
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assert elem["O"] == pytest.approx(6/total_number_of_atoms)
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# testing the correct nuclides are added when brackets are used
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ref_dens = {'Mg24': 0.157902, 'Mg25': 0.02004, 'Mg26': 0.022058,
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'N14': 0.199267, 'N15': 0.000732,
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'O16': 0.599772, 'O17': 0.000227}
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nuc_dens = m.get_nuclide_atom_densities()
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for nuclide in ref_dens:
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assert nuc_dens[nuclide][1] == pytest.approx(ref_dens[nuclide], 1e-2)
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# testing non integer multiplier results in a value error
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m = openmc.Material()
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with pytest.raises(ValueError):
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m.add_elements_from_formula('Li4.2SiO4')
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# testing lowercase elements results in a value error
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m = openmc.Material()
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with pytest.raises(ValueError):
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m.add_elements_from_formula('li4SiO4')
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# testing lowercase elements results in a value error
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m = openmc.Material()
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with pytest.raises(ValueError):
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m.add_elements_from_formula('Li4Sio4')
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# testing incorrect character in formula results in a value error
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m = openmc.Material()
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with pytest.raises(ValueError):
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m.add_elements_from_formula('Li4$SiO4')
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# testing unequal opening and closing brackets
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m = openmc.Material()
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with pytest.raises(ValueError):
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m.add_elements_from_formula('Fe(H2O)4(OH)2)')
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def test_density():
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m = openmc.Material()
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for unit in ['g/cm3', 'g/cc', 'kg/m3', 'atom/b-cm', 'atom/cm3']:
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@ -264,4 +358,3 @@ def test_mix_materials():
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assert m3.density == pytest.approx(dens3)
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assert m4.density == pytest.approx(dens4)
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assert m5.density == pytest.approx(dens5)
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