def test_expand_elements2():
"""Inspired by #86"""
natmat = Material({'C': 1.0})
expmat = natmat.expand_elements()
afrac = expmat.to_atom_frac()
assert_almost_equal(data.natural_abund(60120000), afrac[60120000])
assert_almost_equal(data.natural_abund(60130000), afrac[60130000])
def test_expand_elements2():
"""Inspired by #86"""
natmat = Material({'C': 1.0})
expmat = natmat.expand_elements()
afrac = expmat.to_atom_frac()
assert_almost_equal(data.natural_abund(60120000), afrac[60120000])
assert_almost_equal(data.natural_abund(60130000), afrac[60130000])
def test_natural_abund_excited_state():
# initialize natural_abund_map
gnd = 902320000
excited = gnd + 1
data.natural_abund(gnd)
# excited state should not be in the map yet
assert_equal(data.natural_abund_map.get(excited), None)
nabund = data.natural_abund(excited)
assert_equal(nabund, data.natural_abund_map.get(excited))
def test_natural_abund_excited_state():
# initialize natural_abund_map
gnd = 902320000
excited = gnd + 1
data.natural_abund(gnd)
# excited state should not be in the map yet
assert_equal(data.natural_abund_map.get(excited), None)
nabund = data.natural_abund(excited)
assert_equal(nabund, data.natural_abund_map.get(excited))
def test_natural_abund_excited_state():
# set the datapath to nonsense so we call, the cpp data version
orig = pyne_conf.NUC_DATA_PATH
pyne_conf.NUC_DATA_PATH = b"bobbobhonkeytonk"
# initialize natural_abund_map
gnd = 902320000
excited = gnd + 42
data.natural_abund(gnd)
# excited state should not be in the map yet
assert_true(excited not in data.natural_abund_map)
nabund = data.natural_abund(excited)
assert_equal(nabund, data.natural_abund_map.get(excited))
pyne_conf.NUC_DATA_PATH = orig
def make_elements():
"""Make natural elemental materials based on isotopic abundances.
Returns
-------
eltsdict : dict from str to pyne.material.Material
Natural elements as materials.
"""
natural_abund("H1") # initialize natural_abund_map
# get rid of elemental total abundances and empty isotopic abundances
abunds_no_trivial = [abund for abund in natural_abund_map.items() if
nucname.anum(abund[0]) != 0 and abund[1] != 0]
sorted_abunds = sorted(abunds_no_trivial)
grouped_abunds = groupby(sorted_abunds, lambda abund: nucname.znum(abund[0]))
# filter out 111, 113, 115, 117, 118 - the ones with no names
elts = (Material(dict(abunds), metadata={"name": nucname.name(zz)})
for zz, abunds in grouped_abunds if zz in nucname.zz_name.keys())
eltsdict = dict(((elt.metadata["name"], elt) for elt in elts))
return eltsdict
def make_elements():
"""Makes natural elemental materials based on isotopic abundances."""
habund = natural_abund('H')
for name, zz in nucname.name_zz.items():
elemental_mats[name] = {}
for nuc, abund in natural_abund_map.items():
if 0 == nuc%10000 or abund == 0.0:
continue
zz = nuc/10000
if zz not in nucname.zz_name:
continue
name = nucname.zz_name[zz]
elemental_mats[name][nuc] = abund
def grab_materials_compendium(location="materials_compendium.csv"):
"""Parses data from a materials compendium csv file.
Parameters
----------
location : str
The file to read in compendium from.
Returns
-------
mats : list of pyne.material.Material
The materials in the compendium.
"""
natural_abund("H1") # initialize natural_abund_map
if sys.version_info[0] > 2:
f = open(location, "r", newline="", encoding="utf-8")
else:
f = open(location, "rb")
reader = csv.reader(f, delimiter=",", quotechar='"')
lines = list(filter(is_comp_matname_or_density, reader))
mats = parse_materials({}, lines)
f.close()
return mats
def grab_materials_compendium(location='materials_compendium.csv'):
"""Parses data from a materials compendium csv file.
Parameters
----------
location : str
The file to read in compendium from.
Returns
-------
mats : list of pyne.material.Material
The materials in the compendium.
"""
natural_abund("H1") # initialize natural_abund_map
if sys.version_info[0] > 2:
f = open(location, 'r', newline='', encoding="utf-8")
else:
f = open(location, 'rb')
reader = csv.reader(f, delimiter=',', quotechar='"')
lines = list(filter(is_comp_matname_or_density, reader))
mats = parse_materials({}, lines)
f.close()
return mats
def findPeaks(energyList=[],
energyUncertainty=[],
intensityList=[],
intensityUncertainty=[]):
"""Finds relevant 'peak' elements in a spectra.
Args:
energyList: energies associated with an intensity peak in our
dataset.
energyUncertainty: uncertainties of energy values (in order).
intensityList: The spectrum of intensities in our dataset.
intensityUncertainty: The uncertainties of intensity peaks (in
order) of dataset
"""
#initialize
posEl = []
counts = 0
bestCount = 0
bestElement = 'FirstRun'
abundance = 0.0
bCE = []
bAE = []
bA = []
bC = []
bCEN = []
bAEN = []
bAN = []
bCN = []
#for each energy, find the parents associated with that energy
posEl = findParents(energyList, energyUncertainty)
for element in posEl:
counts = 0
#find all intensities associated with this element
intensities = data.gamma_photon_intensity(element)
#find unicode name of element
name = nucname.name(element)
#count number of intensity peaks that this set has in common
#with this element
counts = countIntensityPeaks(intensities, intensityList,
intensityUncertainty)
#calculate relative counts and natural abundance
counts = 1.0 * counts / len(intensities)
abundance = data.natural_abund(element)
#update lists
addToLists(bC, bA, bCE, bAE, bCN, bAN, bCEN, bAEN, counts, abundance,
name, element)
checkAbundanceLists(abundance, name, bA, bAE, bAN, element, bAEN)
checkCountsLists(abundance, name, element, bCE, bC, bCN, bCEN, counts)
if (counts > bestCount and abundance > 0.0 and abundance < 1.0
and name[-1] != 'M'):
num = getNum(name)
if bestElement == 'FirstRun':
bestCount = counts
bestElement = name
counts = 0
elif num < getNum(bestElement):
bestCount = counts
bestElement = name
counts = 0
elif data.natural_abund(bestElement) < abundance:
bestCount = counts
bestElement = name
counts = 0
presentInfo(bestElement, bAN, bAEN)