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Merge pull request #23 from easyXAFS/master
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Transmission sample calculation bug fix; add molar_fraction to output of transmission_sample
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@newville
newville authored Jan 26, 2023
2 parents 433716d + 04ab4bb commit 056e8ee
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73 changes: 72 additions & 1 deletion python/tests/test_xray.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,9 @@
ionchamber_fluxes, XrayDB)


from xraydb.xray import chantler_data
from xraydb.xray import (chantler_data, formula_to_mass_fracs,
_validate_mass_fracs, mass_fracs_to_molar_fracs,
transmission_sample)

def test_atomic_data():
assert atomic_number('zn') == 30
Expand Down Expand Up @@ -634,3 +636,72 @@ def test_ionchamber_fluxes():

assert_allclose(ic4.transmitted/ic4.incident, 0.4928, rtol=0.01)
assert_allclose(ic4.incident, 2.7615e10, rtol=0.01)


def test_formula_to_mass_fracs():
mf1 = formula_to_mass_fracs('Fe2O3')
desired1 = {'Fe': 0.69943, 'O': 0.30056}
assert_allclose(mf1['Fe'], desired1['Fe'], rtol=0.001)
assert_allclose(mf1['O'], desired1['O'], rtol=0.001)
assert_allclose(sum(mf1.values()), 1.0, rtol=0.001)

mf2 = formula_to_mass_fracs({'Fe2O3':1, 'FeO':2})
desired2 = {'Fe': 0.7363, 'O': 0.2637}
assert_allclose(mf2['Fe'], desired2['Fe'], rtol=0.001)
assert_allclose(mf2['O'], desired2['O'], rtol=0.001)
assert_allclose(sum(mf2.values()), 1.0, rtol=0.001)


def test_validate_mass_fracs():
mf = _validate_mass_fracs({'Fe2O3': 0.75, 'FeO': 0.25})
desired = {'Fe': 0.7189, 'O': 0.2811}
assert_allclose(mf['Fe'], desired['Fe'], rtol=0.001)
assert_allclose(mf['O'], desired['O'], rtol=0.001)
assert_allclose(sum(mf.values()), 1.0, rtol=0.001)


def test_mass_fracs_to_molar_fracs():
"""Circular test for consistency formula->mass fracs
and vice versa."""
formula = {'Fe':1, 'FeO': 3}
mass_fracs = formula_to_mass_fracs(formula)
molar_fracs = mass_fracs_to_molar_fracs(mass_fracs)
assert_allclose(molar_fracs['Fe'], 4 / 7, rtol=0.001)
assert_allclose(molar_fracs['O'], 3 / 7, rtol=0.001)


def test_transmission_sample():
# Validate against Hephaestus result, see PR #16
result1 = transmission_sample(
sample='Fe2O3',
energy=7162,
absorp_total=1,
area=1,
density=5.24
)
assert_allclose(result1.mass_total_mg, 3.506, rtol=0.001)
assert_allclose(result1.absorption_length_um, 6.7, rtol=0.01)

# Validate against Hephaestus result, see PR #16
result2 = transmission_sample(
sample='Cu',
energy=9029,
absorp_total=1,
area=1,
density=8.94
)
assert_allclose(result2.mass_total_mg, 3.640, rtol=0.001)
assert_allclose(result2.absorption_length_um, 4.1, rtol=0.01)

# Validate against XAFSmass result, see PR #16
result3 = transmission_sample(
sample={'Fe': 0.05, 'SiO2': -1},
energy=7162,
absorp_total=2.6,
area=1.33,
density=2.65
)
assert_allclose(result3.mass_components_mg['Fe'], 2.58, rtol=0.03)
assert_allclose(result3.absorbance_steps['Fe'], 0.706, rtol=0.06)
assert_allclose(result3.mass_total_mg, 51.7, rtol=0.02)
assert_allclose(result3.thickness_mm, 0.1466, rtol=0.02)
64 changes: 38 additions & 26 deletions python/xraydb/xray.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
TransmissionSample = namedtuple('TransmissionSample', ('energy_eV',
'absorp_total',
'mass_fractions',
'molar_fractions',
'absorbance_steps',
'area_cm2',
'mass_total_mg',
Expand Down Expand Up @@ -1197,6 +1198,8 @@ def transmission_sample(sample, energy, absorp_total=2.6, area=1,
`mass_fractions` mass fractions of elements
`molar_fractions` molar fractions of elements
`absorbance_steps` absorbance steps of each element in the sample
`area (cm^2)` area, if specified
Expand Down Expand Up @@ -1229,10 +1232,14 @@ def transmission_sample(sample, energy, absorp_total=2.6, area=1,
'Fe': 0.05,
'Si': 0.4440648769202603,
'O': 0.5059351230797396},
molar_fractions={
'Fe': 0.018525564495838743,
'Si': 0.3271581451680538,
'O': 0.6543162903361075},
absorbance_steps={
'Fe': 0.6692395733146204,
'Si': 1.297403071978392e-06,
'O': 3.386553723091669e-07},
'Fe': 0.6692395963328747,
'Si': 1.6477111496690233e-06,
'O': 4.3017044962086656e-07},
area_cm2=1.33,
mass_total_mg=51.05953690489308,
mass_components_mg={
Expand All @@ -1241,8 +1248,7 @@ def transmission_sample(sample, energy, absorp_total=2.6, area=1,
'O': 25.832813088371587},
density=None,
thickness_mm=None,
absorption_length_um=None
)
absorption_length_um=None)
>>> transmission_sample(
sample='Fe2O3',
Expand All @@ -1257,9 +1263,12 @@ def transmission_sample(sample, energy, absorp_total=2.6, area=1,
mass_fractions={
'Fe': 0.6994307614270416,
'O': 0.3005692385729583},
molar_fractions={
'Fe': 0.4,
'O': 0.6},
absorbance_steps={
'Fe': 2.2227981005407176,
'O': 4.7769571901536886e-08},
'Fe': 2.2227981769930585,
'O': 6.067837661326302e-08},
area_cm2=1.33,
mass_total_mg=12.123291571370844,
mass_components_mg={
Expand Down Expand Up @@ -1316,6 +1325,7 @@ def transmission_sample(sample, energy, absorp_total=2.6, area=1,
energy_eV=energy,
absorp_total=absorp_total,
mass_fractions=sample,
molar_fractions=mass_fracs_to_molar_fracs(sample),
absorbance_steps=absorbance_steps,
area_cm2=area,
mass_total_mg=mass_total,
Expand Down Expand Up @@ -1361,8 +1371,9 @@ def formula_to_mass_fracs(formula):
return mass_fracs


def mass_fracs_to_formula(mass_fracs):
"""Calculate molecular formula from a given mass fractions of elements.
def mass_fracs_to_molar_fracs(mass_fracs):
"""Calculate molar fractions from a given mass fractions of elements.
Result is normalized to one.
Args:
mass_fracs (dict): mass fractions of elements
Expand All @@ -1371,22 +1382,18 @@ def mass_fracs_to_formula(mass_fracs):
dict with fields of each element and values of their coefficients
Example:
>>> mass_fracs_to_formula({'Fe': 0.7, 'SiO2': -1})
>>> mass_fracs_to_molar_fracs({'Fe': 0.7, 'SiO2': -1})
{
'Fe': 0.012534694242994,
'Si': 0.004993092888171364,
'O': 0.009986185776342726
'Fe': 0.4555755828186302,
'Si': 0.18147480572712324,
'O': 0.3629496114542464
}
"""
mass_fracs = _validate_mass_fracs(mass_fracs)
masses = {}
for el, _ in mass_fracs.items():
parsed = chemparse(el)
masses[el] = sum([atomic_mass(el) * c for el, c in parsed.items()])

coeffs = {k: mass_fracs[k] / masses[k] for k in mass_fracs.keys()}

return coeffs
molar_fracs = {el: fr / atomic_mass(el) for el, fr in mass_fracs.items()}
total = sum(molar_fracs.values())
molar_fracs = {el: fr / total for el, fr in molar_fracs.items()}
return molar_fracs


def _validate_mass_fracs(mass_fracs):
Expand All @@ -1401,14 +1408,19 @@ def _validate_mass_fracs(mass_fracs):
assert len(unknown) == 1, 'Multiple unknown weight percentages'
mass_fracs[unknown[0]] = 1 - sum({k:v for k, v in mass_fracs.items() if k != unknown[0]}.values())
else:
compare = abs(sum([v for v in mass_fracs.values()]) - 1) < 1e-4
compare = abs(sum(mass_fracs.values()) - 1) < 1e-4
if not compare:
raise RuntimeError("Mass fractions do not add up to one.")

simplified_mass_fracs = {}
for comp, frac in mass_fracs.items():
parsed = chemparse(comp)
parsed_sum = sum([atomic_mass(el) * c for el, c in parsed.items()])
for el, c in parsed.items():
simplified_mass_fracs[el] = atomic_mass(el) * c / parsed_sum * frac
elements = chemparse(comp)
element_masses = {el: atomic_mass(el) * c for el, c in elements.items()}
for el, c in elements.items():
contribution = element_masses[el] / sum(element_masses.values()) * frac
if el not in simplified_mass_fracs:
simplified_mass_fracs[el] = contribution
else:
simplified_mass_fracs[el] += contribution
assert abs(sum(simplified_mass_fracs.values()) - 1) < 1e-4, "Validation failed, calculated mass fractions do not add up to one."
return simplified_mass_fracs

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