def composition_from_formula(formula):
# Parse chemical formula
formulaData = CHEMICAL_FORMULA_PARSER.parseString(formula)
zs = []
atomicfractions = []
for symbol, atomicfraction in formulaData:
zs.append(ep.atomic_number(symbol=symbol))
atomicfractions.append(float(atomicfraction))
# Calculate total atomic mass
totalatomicmass = 0.0
for z, atomicfraction in zip(zs, atomicfractions):
atomicmass = ep.atomic_mass_kg_mol(z)
totalatomicmass += atomicfraction * atomicmass
# Create composition
composition = defaultdict(float)
for z, atomicfraction in zip(zs, atomicfractions):
atomicmass = ep.atomic_mass_kg_mol(z)
weightfraction = atomicfraction * atomicmass / totalatomicmass
composition[z] += weightfraction
return composition
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 * (ep.atomic_mass_kg_mol(z) * 1000.0) * (energy / 1000.0) ** 1.67) / \
(z ** 0.89 * (ep.mass_density_kg_m3(z) / 1000.0))
r += fraction / (dr * 1e-6)
return 1.0 / r;
def calculate_composition_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 / ep.atomic_mass_kg_mol(z)
totalfraction = sum(composition2.values())
for z, fraction in composition2.items():
composition2[z] = fraction / totalfraction
return defaultdict(float, composition2)
def testatomic_mass(self):
self.assertAlmostEqual(51.996000, ep.atomic_mass_kg_mol(24) * 1000.0)
def testatomic_mass(self):
self.assertAlmostEqual(51.996000, ep.atomic_mass_kg_mol(24) * 1000.0)
self.assertRaises(ValueError, self.ep.atomic_mass_kg_mol, 118)
def _export_geometry_substrate(self, options, geometry, outputdir, *args):
material = geometry.body.material
composition = sorted(material.composition.items(), key=itemgetter(0))
density_g_cm3 = material.density_kg_m3 / 1000.0
filepath = os.path.join(outputdir, options.name + '.MAT')
with open(filepath, 'wb') as fp:
# Header
# DELPHI: s:=6;Blockwrite(Matfile,Typ,6,f);Inc(Sum,f);
# 1st Byte: Type = 2 (homogenous bulk)
# 2nd Byte: NC = <nr. of elements> (amount of occurring formulae (compounds or elements))
# 3rd Byte: NZ = <nr. of elements>
# 4th Byte: NP = 0 (nr. of layers)
# 5th Byte: CU = 2 (1=at%, 2=wt%)
# 6th Byte: MU = 1 (not important for bulk; this is the unit for the layer thickness)
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', 0))
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', 1))
# Write length of element and element
# DELPHI:
# for i:=1 to Nc do begin
# l:=1+Length(Comp[i]);Inc(s,l);
# Blockwrite(Matfile,Comp[i,0],l,f);Inc(Sum,f);
# end;
for z, _wf in composition:
symbol = ep.symbol(z).upper()
fp.write(
struct.pack('b', len(symbol)) + symbol.encode('ascii'))
# Write molar mass
# DELPHI: l:=4*Nc;Inc(s,l);Blockwrite(Matfile,AC[1],l,f);Inc(Sum,f);
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
# Write atomic number
# DELPHI: Inc(s,NZ);Blockwrite(Matfile,Z[1],NZ,f);Inc(Sum,f);
for z, _wf in composition:
fp.write(struct.pack('b', z))
# Write molar mass
# DELPHI:
# l:=4*Nc+4;
# for i:=0 to NZ do begin
# Inc(s,l);BlockWrite(Matfile,GZ[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00') # Skip 4 bytes
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
for i, item in enumerate(composition):
z = item[0]
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
fp.write(b'\x00\x00\x00\x00' * i) # Skip 4 bytes
fp.write(struct.pack('f', 1.0 / mass))
fp.write(b'\x00\x00\x00\x00' *
(len(composition) - i - 1)) # Skip 4 bytes
# DELPHI: Inc(s,l);BlockWrite(Matfile,GM,l,f);Inc(Sum,f);
gs = [
wf / (ep.atomic_mass_kg_mol(z) * 1000.0)
for z, wf in composition
]
g0 = 1.0 / sum(gs)
fp.write(struct.pack('f', g0))
for g in gs:
fp.write(struct.pack('f', g))
# DELPHI:
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,GS[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00' * (len(composition) + 1))
# DELPHI:
# l:=4*NP+4;Inc(s,l);Blockwrite(Matfile,ML[0],l,f);Inc(Sum,f);
fp.write(b'\x00\x00\x00\x00')
# DELPHI: Inc(s,l);Blockwrite(Matfile,rho[0],l,f);Inc(Sum,f);
fp.write(struct.pack('f', density_g_cm3))
# DELPHI:
# l:=NC+1;
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,PC[i],l,f);Inc(Sum,f);
# end;
fp.write(struct.pack('b', len(composition)))
fp.write(b'\x00' * len(composition))
# DELPHI: Inc(s,l);BlockWrite(Matfile,PM,l,f);Inc(Sum,f);
fp.write(struct.pack('b', len(composition)))
for i in range(len(composition)):
fp.write(struct.pack('b', i + 1))
return filepath
def _export_geometry_substrate(self, options, geometry, outputdir, *args):
material = geometry.body.material
composition = sorted(material.composition.items(), key=itemgetter(0))
density_g_cm3 = material.density_kg_m3 / 1000.0
filepath = os.path.join(outputdir, options.name + '.MAT')
with open(filepath, 'wb') as fp:
# Header
# DELPHI: s:=6;Blockwrite(Matfile,Typ,6,f);Inc(Sum,f);
# 1st Byte: Type = 2 (homogenous bulk)
# 2nd Byte: NC = <nr. of elements> (amount of occurring formulae (compounds or elements))
# 3rd Byte: NZ = <nr. of elements>
# 4th Byte: NP = 0 (nr. of layers)
# 5th Byte: CU = 2 (1=at%, 2=wt%)
# 6th Byte: MU = 1 (not important for bulk; this is the unit for the layer thickness)
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', len(composition)))
fp.write(struct.pack('b', 0))
fp.write(struct.pack('b', 2))
fp.write(struct.pack('b', 1))
# Write length of element and element
# DELPHI:
# for i:=1 to Nc do begin
# l:=1+Length(Comp[i]);Inc(s,l);
# Blockwrite(Matfile,Comp[i,0],l,f);Inc(Sum,f);
# end;
for z, _wf in composition:
symbol = ep.symbol(z).upper()
fp.write(struct.pack('b', len(symbol)) + symbol.encode('ascii'))
# Write molar mass
# DELPHI: l:=4*Nc;Inc(s,l);Blockwrite(Matfile,AC[1],l,f);Inc(Sum,f);
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
# Write atomic number
# DELPHI: Inc(s,NZ);Blockwrite(Matfile,Z[1],NZ,f);Inc(Sum,f);
for z, _wf in composition:
fp.write(struct.pack('b', z))
# Write molar mass
# DELPHI:
# l:=4*Nc+4;
# for i:=0 to NZ do begin
# Inc(s,l);BlockWrite(Matfile,GZ[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00') # Skip 4 bytes
for z, _wf in composition:
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
for i, item in enumerate(composition):
z = item[0]
mass = ep.atomic_mass_kg_mol(z) * 1000.0
fp.write(struct.pack('f', mass))
fp.write(b'\x00\x00\x00\x00' * i) # Skip 4 bytes
fp.write(struct.pack('f', 1.0 / mass))
fp.write(b'\x00\x00\x00\x00' * (len(composition) - i - 1)) # Skip 4 bytes
# DELPHI: Inc(s,l);BlockWrite(Matfile,GM,l,f);Inc(Sum,f);
gs = [wf / (ep.atomic_mass_kg_mol(z) * 1000.0) for z, wf in composition]
g0 = 1.0 / sum(gs)
fp.write(struct.pack('f', g0))
for g in gs:
fp.write(struct.pack('f', g))
# DELPHI:
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,GS[i],l,f);Inc(Sum,f);
# end;
fp.write(b'\x00\x00\x00\x00' * (len(composition) + 1))
# DELPHI:
# l:=4*NP+4;Inc(s,l);Blockwrite(Matfile,ML[0],l,f);Inc(Sum,f);
fp.write(b'\x00\x00\x00\x00')
# DELPHI: Inc(s,l);Blockwrite(Matfile,rho[0],l,f);Inc(Sum,f);
fp.write(struct.pack('f', density_g_cm3))
# DELPHI:
# l:=NC+1;
# for i:=0 to NP do begin
# Inc(s,l);BlockWrite(Matfile,PC[i],l,f);Inc(Sum,f);
# end;
fp.write(struct.pack('b', len(composition)))
fp.write(b'\x00' * len(composition))
# DELPHI: Inc(s,l);BlockWrite(Matfile,PM,l,f);Inc(Sum,f);
fp.write(struct.pack('b', len(composition)))
for i in range(len(composition)):
fp.write(struct.pack('b', i + 1))
return filepath
def testatomic_mass(self):
self.assertAlmostEqual(51.996000, ep.atomic_mass_kg_mol(24) * 1000.0)
def testatomic_mass(self):
self.assertAlmostEqual(51.996000, ep.atomic_mass_kg_mol(24) * 1000.0)
self.assertRaises(ValueError, self.ep.atomic_mass_kg_mol, 118)
