def from_formula(formula):
# Parse chemical formula
formulaData = CHEMICAL_FORMULA_PARSER.parseString(formula)
zs = []
atomicfractions = []
for symbol, atomicfraction in formulaData:
zs.append(pyxray.element_atomic_number(symbol))
atomicfractions.append(float(atomicfraction))
# Calculate total atomic mass
totalatomicmass = 0.0
for z, atomicfraction in zip(zs, atomicfractions):
atomicmass = pyxray.element_atomic_weight(z)
totalatomicmass += atomicfraction * atomicmass
# Create composition
composition = defaultdict(float)
for z, atomicfraction in zip(zs, atomicfractions):
atomicmass = pyxray.element_atomic_weight(z)
weightfraction = atomicfraction * atomicmass / totalatomicmass
composition[z] += weightfraction
return composition
def convert_atomic_to_mass_fractions(atomic_fractions):
"""
Converts an atomic fraction :class:`dict` to a mass fraction :class:`dict`.
Args:
atomic_fractions (dict): atomic fraction :class:`dict`.
The composition is specified by a dictionary.
The keys are atomic numbers and the values atomic fractions.
No wildcard are accepted.
"""
# Calculate total atomic mass
atomic_masses = {}
total_atomic_mass = 0.0
for z, atomic_fraction in atomic_fractions.items():
atomic_mass = pyxray.element_atomic_weight(z)
atomic_masses[z] = atomic_mass
total_atomic_mass += atomic_fraction * atomic_mass
# Create mass fraction
mass_fractions = {}
for z, atomic_fraction in atomic_fractions.items():
mass_fractions[
z] = atomic_fraction * atomic_masses[z] / total_atomic_mass
return mass_fractions
def read_material(cls, fileobj):
"""
Reads a PENELOPE generated material file (.mat).
:arg fileobj: file object opened with read access
"""
first_line = fileobj.readline().strip()
assert first_line[:8] == 'PENELOPE'
line = fileobj.readline()
_label, value = line.split()
name = value.strip()
line = fileobj.readline()
_label, value = line.split('=')
value, _unit = value.split()
density_g_per_cm3 = float(value)
line = fileobj.readline()
_label, value = line.split('=')
element_count = int(value)
composition = {}
totalatomicmass = 0.0
for _ in range(element_count):
line = fileobj.readline()
part_z, part_af = line.split(',')
_label, value = part_z.split('=')
z = int(value)
_label, value = part_af.split('=')
atomicfraction = float(value)
atomicmass = atomicfraction * pyxray.element_atomic_weight(z)
composition[z] = atomicmass
totalatomicmass += atomicmass
for z, atomicmass in composition.items():
composition[z] = atomicmass / totalatomicmass
line = fileobj.readline()
_label, value = line.split('=')
value, _unit = value.split()
mean_excitation_energy_eV = float(value)
line = fileobj.readline()
label, _value = line.split('=')
assert label.strip() == 'Number of oscillators'
line = fileobj.readline()
_, value1, _, value2, _, _ = line.split()
oscillator_strength_fcb = float(value1)
oscillator_energy_wcb_eV = float(value2)
return cls(name, composition, density_g_per_cm3,
mean_excitation_energy_eV, oscillator_strength_fcb,
oscillator_energy_wcb_eV)
def kanaya_okayama(composition, energy):
"""
Returns the electron range (in meters).
:arg composition: composition in weight fraction.
The composition is specified by a dictionary.
The keys are the atomic numbers and the values are the weight fractions
between ]0.0, 1.0].
:type composition: :class:`dict`
:arg energy: beam energy in eV
"""
r = 0.0
for z, fraction in composition.items():
dr = (0.0276 * pyxray.element_atomic_weight(z) * (energy / 1000.0) ** 1.67) / \
(z ** 0.89 * pyxray.element_mass_density_g_per_cm3(z))
r += fraction / (dr * 1e-6)
return 1.0 / r
def to_atomic(composition):
"""
Returns a composition :class:`dict` where the values are atomic fractions.
:arg composition: composition in weight fraction.
The composition is specified by a dictionary.
The key are atomic numbers and the values weight fractions.
No wildcard are accepted.
:type composition: :class:`dict`
"""
composition2 = {}
for z, weightfraction in composition.items():
composition2[z] = weightfraction / pyxray.element_atomic_weight(z)
totalfraction = sum(composition2.values())
for z, fraction in composition2.items():
try:
composition2[z] = fraction / totalfraction
except ZeroDivisionError:
composition2[z] = 0.0
return defaultdict(float, composition2)
def convert_atomic_to_mass_fractions(atomic_fractions):
"""
Converts an atomic fraction :class:`dict` to a mass fraction :class:`dict`.
Args:
atomic_fractions (dict): atomic fraction :class:`dict`.
The composition is specified by a dictionary.
The keys are atomic numbers and the values atomic fractions.
No wildcard are accepted.
"""
# Calculate total atomic mass
atomic_masses = {}
total_atomic_mass = 0.0
for z, atomic_fraction in atomic_fractions.items():
atomic_mass = pyxray.element_atomic_weight(z)
atomic_masses[z] = atomic_mass
total_atomic_mass += atomic_fraction * atomic_mass
# Create mass fraction
mass_fractions = {}
for z, atomic_fraction in atomic_fractions.items():
mass_fractions[z] = atomic_fraction * atomic_masses[z] / total_atomic_mass
return mass_fractions
def convert_mass_to_atomic_fractions(mass_fractions):
"""
Converts a mass fraction :class:`dict` to an atomic fraction :class:`dict`.
Args:
mass_fractions (dict): mass fraction :class:`dict`.
The composition is specified by a dictionary.
The keys are atomic numbers and the values weight fractions.
No wildcard are accepted.
"""
atomic_fractions = {}
for z, mass_fraction in mass_fractions.items():
atomic_fractions[z] = mass_fraction / pyxray.element_atomic_weight(z)
total_fraction = sum(atomic_fractions.values())
for z, fraction in atomic_fractions.items():
try:
atomic_fractions[z] = fraction / total_fraction
except ZeroDivisionError:
atomic_fractions[z] = 0.0
return atomic_fractions
def convert_mass_to_atomic_fractions(mass_fractions):
"""
Converts a mass fraction :class:`dict` to an atomic fraction :class:`dict`.
Args:
mass_fractions (dict): mass fraction :class:`dict`.
The composition is specified by a dictionary.
The keys are atomic numbers and the values weight fractions.
No wildcard are accepted.
"""
atomic_fractions = {}
for z, mass_fraction in mass_fractions.items():
atomic_fractions[z] = mass_fraction / pyxray.element_atomic_weight(z)
total_fraction = sum(atomic_fractions.values())
for z, fraction in atomic_fractions.items():
try:
atomic_fractions[z] = fraction / total_fraction
except ZeroDivisionError:
atomic_fractions[z] = 0.0
return atomic_fractions