Merge pull request #1639 from paulromano/isotopes-func

Add function for getting naturally-occurring isotopes

docs/source/pythonapi/data.rst

@@ -60,8 +60,10 @@ Core Functions
     :template: myfunction.rst
 
     atomic_mass
+    atomic_weight
     dose_coefficients
     gnd_name
+    isotopes
     linearize
     thin
     water_density

openmc/data/data.py

@@ -236,10 +236,8 @@ def atomic_mass(isotope):
         for element in ['C', 'Zn', 'Pt', 'Os', 'Tl']:
             isotope_zero = element.lower() + '0'
             _ATOMIC_MASS[isotope_zero] = 0.
-            for iso, abundance in NATURAL_ABUNDANCE.items():
-                if re.match(r'{}\d+'.format(element), iso):
-                    _ATOMIC_MASS[isotope_zero] += abundance * \
-                                                  _ATOMIC_MASS[iso.lower()]
+            for iso, abundance in isotopes(element):
+                _ATOMIC_MASS[isotope_zero] += abundance * _ATOMIC_MASS[iso.lower()]
 
     # Get rid of metastable information
     if '_' in isotope:
@@ -257,7 +255,7 @@ def atomic_weight(element):
     Parameters
     ----------
     element : str
-        Name of element, e.g. 'H', 'U'
+        Element symbol (e.g., 'H') or name (e.g., 'helium')
 
     Returns
     -------
@@ -266,9 +264,8 @@ def atomic_weight(element):
 
     """
     weight = 0.
-    for nuclide, abundance in NATURAL_ABUNDANCE.items():
-        if re.match(r'{}\d+'.format(element), nuclide):
-            weight += atomic_mass(nuclide) * abundance
+    for nuclide, abundance in isotopes(element):
+        weight += atomic_mass(nuclide) * abundance
     if weight > 0.:
         return weight
     else:
@@ -404,6 +401,41 @@ def gnd_name(Z, A, m=0):
         return '{}{}'.format(ATOMIC_SYMBOL[Z], A)
 
 
+def isotopes(element):
+    """Return naturally-occurring isotopes and their abundances
+
+    Parameters
+    ----------
+    element : str
+        Element symbol (e.g., 'H') or name (e.g., 'helium')
+
+    Returns
+    -------
+    list
+        A list of tuples of (isotope, abundance)
+
+    Raises
+    ------
+    ValueError
+        If the element name is not recognized
+
+    """
+    # Convert name to symbol if needed
+    if len(element) > 2:
+        symbol = ELEMENT_SYMBOL.get(element.lower())
+        if symbol is None:
+            raise ValueError('Element name "{}" not recognised'.format(element))
+        element = symbol
+
+    # Get the nuclides present in nature
+    result = []
+    for kv in sorted(NATURAL_ABUNDANCE.items()):
+        if re.match(r'{}\d+'.format(element), kv[0]):
+            result.append(kv)
+
+    return result
+
+
 def zam(name):
     """Return tuple of (atomic number, mass number, metastable state)
 

openmc/data/thermal.py

@@ -16,7 +16,7 @@ import openmc.checkvalue as cv
 from openmc.mixin import EqualityMixin
 from openmc.stats import Discrete, Tabular
 from . import HDF5_VERSION, HDF5_VERSION_MAJOR, endf
-from .data import K_BOLTZMANN, ATOMIC_SYMBOL, EV_PER_MEV, NATURAL_ABUNDANCE
+from .data import K_BOLTZMANN, ATOMIC_SYMBOL, EV_PER_MEV, isotopes
 from .ace import Table, get_table, Library
 from .angle_energy import AngleEnergy
 from .function import Tabulated1D, Function1D
@@ -722,10 +722,9 @@ class ThermalScattering(EqualityMixin):
                 else:
                     if element + '0' not in table.nuclides:
                         table.nuclides.append(element + '0')
-                    for isotope in sorted(NATURAL_ABUNDANCE):
-                        if re.match(r'{}\d+'.format(element), isotope):
-                            if isotope not in table.nuclides:
-                                table.nuclides.append(isotope)
+                    for isotope, _ in isotopes(element):
+                        if isotope not in table.nuclides:
+                            table.nuclides.append(isotope)
 
         return table
 

openmc/element.py

@@ -4,7 +4,8 @@ import re
 from xml.etree import ElementTree as ET
 
 import openmc.checkvalue as cv
-from openmc.data import NATURAL_ABUNDANCE, atomic_mass
+from openmc.data import NATURAL_ABUNDANCE, atomic_mass, \
+    isotopes as natural_isotopes
 
 
 class Element(str):
@@ -119,10 +120,7 @@ class Element(str):
             cv.check_greater_than('enrichment', enrichment, 0., equality=True)
 
         # Get the nuclides present in nature
-        natural_nuclides = set()
-        for nuclide in sorted(NATURAL_ABUNDANCE.keys()):
-            if re.match(r'{}\d+'.format(self), nuclide):
-                natural_nuclides.add(nuclide)
+        natural_nuclides = {name for name, abundance in natural_isotopes(self)}
 
         # Create dict to store the expanded nuclides and abundances
         abundances = OrderedDict()

tests/unit_tests/test_data_misc.py

@@ -84,6 +84,7 @@ def test_atomic_mass():
 
 def test_atomic_weight():
     assert openmc.data.atomic_weight('C') == 12.011115164864455
+    assert openmc.data.atomic_weight('carbon') == 12.011115164864455
     with pytest.raises(ValueError):
         openmc.data.atomic_weight('Qt')
 
@@ -106,6 +107,17 @@ def test_gnd_name():
     assert openmc.data.gnd_name(95, 242, 10) == ('Am242_m10')
 
 
+def test_isotopes():
+    hydrogen_isotopes = [('H1', 0.99984426), ('H2', 0.00015574)]
+    assert openmc.data.isotopes('H') == hydrogen_isotopes
+    assert openmc.data.isotopes('hydrogen') == hydrogen_isotopes
+    assert openmc.data.isotopes('Al') == [('Al27', 1.0)]
+    assert openmc.data.isotopes('Aluminum') == [('Al27', 1.0)]
+    assert openmc.data.isotopes('aluminium') == [('Al27', 1.0)]
+    with pytest.raises(ValueError):
+        openmc.data.isotopes('Чорнобиль')
+
+
 def test_zam():
     assert openmc.data.zam('H1') == (1, 1, 0)
     assert openmc.data.zam('Zr90') == (40, 90, 0)