def material_mu(name, energy, density=None, kind='total', _larch=None):
"""
material_mu(name, energy, density=None, kind='total')
return X-ray attenuation length (in 1/cm) for a material by name or formula
arguments
---------
name: chemical formul or name of material from materials list.
energy: energy or array of energies in eV
density: material density (gr/cm^3). If None, and material is a
known material, that density will be used.
kind: 'photo' or 'total' (default) for whether to
return photo-absorption or total cross-section.
returns
-------
mu, absorption length in 1/cm
notes
-----
1. material names are not case sensitive,
chemical compounds are case sensitive.
2. mu_elam() is used for mu calculation.
example
-------
>>> print material_mu('H2O', 10000.0)
5.32986401658495
"""
_materials = get_materials(_larch)
formula = None
mater = _materials.get(name.lower(), None)
if mater is not None:
formula, density = mater
else:
for key, val in _materials.items():
if name.lower() == val[0].lower(): # match formula
formula, density = val
break
# default to using passed in name as a formula
if formula is None:
formula = name
if density is None:
raise Warning('material_mu(): must give density for unknown materials')
mass_tot, mu = 0.0, 0.0
for elem, frac in chemparse(formula).items():
mass = frac * atomic_mass(elem, _larch=_larch)
mu += mass * mu_elam(elem, energy, kind=kind, _larch=_larch)
mass_tot += mass
return density*mu/mass_tot
def material_mu(name, energy, density=None, kind='total', _larch=None):
"""
material_mu(name, energy, density=None, kind='total')
return X-ray attenuation length (in 1/cm) for a material by name or formula
arguments
---------
name: chemical formul or name of material from materials list.
energy: energy or array of energies in eV
density: material density (gr/cm^3). If None, and material is a
known material, that density will be used.
kind: 'photo' or 'total' (default) for whether to
return photo-absorption or total cross-section.
returns
-------
mu, absorption length in 1/cm
notes
-----
1. material names are not case sensitive,
chemical compounds are case sensitive.
2. mu_elam() is used for mu calculation.
example
-------
>>> print(material_mu('H2O', 10000.0))
5.32986401658495
"""
_materials = get_materials(_larch)
formula = None
mater = _materials.get(name.lower(), None)
if mater is not None:
formula, density = mater
else:
for key, val in _materials.items():
if name.lower() == val[0].lower(): # match formula
formula, density = val
break
# default to using passed in name as a formula
if formula is None:
formula = name
if density is None:
raise Warning('material_mu(): must give density for unknown materials')
mass_tot, mu = 0.0, 0.0
for elem, frac in chemparse(formula).items():
mass = frac * atomic_mass(elem, _larch=_larch)
mu += mass * mu_elam(elem, energy, kind=kind, _larch=_larch)
mass_tot += mass
return density * mu / mass_tot
def xray_delta_beta(material, density, energy, photo_only=False, _larch=None):
"""
return anomalous components of the index of refraction for a material,
using the tabulated scattering components from Chantler.
arguments:
----------
material: chemical formula ('Fe2O3', 'CaMg(CO3)2', 'La1.9Sr0.1CuO4')
density: material density in g/cm^3
energy: x-ray energy in eV
photo_only: boolean for returning photo cross-section component only
if False (default), the total cross-section is returned
returns:
---------
(delta, beta, atlen)
where
delta : real part of index of refraction
beta : imag part of index of refraction
atlen : attenuation length in cm
These are the anomalous scattering components of the index of refraction:
n = 1 - delta - i*beta = 1 - lambda**2 * r0/(2*pi) Sum_j (n_j * fj)
Adapted for Larch from code by Yong Choi
"""
lamb_cm = 1.e-8 * PLANCK_HC / energy # lambda in cm
elements = []
for symbol, number in chemparse(material).items():
elements.append((number, Scatterer(symbol, energy, _larch=_larch)))
total_mass, delta, beta_photo, beta_total = 0, 0, 0, 0
for (number, scat) in elements:
weight = density*number*AVOGADRO
delta += weight * scat.f1
beta_photo += weight * scat.f2
beta_total += weight * scat.f2*(scat.mu_total/scat.mu_photo)
total_mass += number * scat.mass
scale = lamb_cm * lamb_cm * R_ELECTRON_CM / (2*pi * total_mass)
delta = delta * scale
beta = beta_total * scale
if photo_only:
beta = beta_photo * scale
return delta, beta, lamb_cm/(4*pi*beta)
def xray_delta_beta(material, density, energy, photo_only=False, _larch=None):
"""
return anomalous components of the index of refraction for a material,
using the tabulated scattering components from Chantler.
arguments:
----------
material: chemical formula ('Fe2O3', 'CaMg(CO3)2', 'La1.9Sr0.1CuO4')
density: material density in g/cm^3
energy: x-ray energy in eV
photo_only: boolean for returning photo cross-section component only
if False (default), the total cross-section is returned
returns:
---------
(delta, beta, atlen)
where
delta : real part of index of refraction
beta : imag part of index of refraction
atlen : attenuation length in cm
These are the anomalous scattering components of the index of refraction:
n = 1 - delta - i*beta = 1 - lambda**2 * r0/(2*pi) Sum_j (n_j * fj)
Adapted for Larch from code by Yong Choi
"""
lamb_cm = 1.e-8 * PLANCK_HC / energy # lambda in cm
elements = []
for symbol, number in chemparse(material).items():
elements.append((number, Scatterer(symbol, energy, _larch=_larch)))
total_mass, delta, beta_photo, beta_total = 0, 0, 0, 0
for (number, scat) in elements:
weight = density*number*AVOGADRO
delta += weight * scat.f1
beta_photo += weight * scat.f2
beta_total += weight * scat.f2*(scat.mu_total/scat.mu_photo)
total_mass += number * scat.mass
scale = lamb_cm * lamb_cm * R_ELECTRON_CM / (2*pi * total_mass)
delta = delta * scale
beta = beta_total * scale
if photo_only:
beta = beta_photo * scale
return delta, beta, lamb_cm/(4*pi*beta)
def material_mu_components(name,
energy,
density=None,
kind='total',
_larch=None):
"""material_mu_components: absorption coefficient (in 1/cm) for a compound
arguments
---------
name: material name or compound formula
energy: energy or array of energies at which to calculate mu
density: compound density in gr/cm^3
kind: cross-section to use ('total', 'photo') for mu_elam())
returns
-------
dictionary of data for constructing mu per element,
with elements 'mass' (total mass), 'density', and
'elements' (list of atomic symbols for elements in material).
For each element, there will be an item (atomic symbol as key)
with tuple of (stoichiometric fraction, atomic mass, mu)
larch> material_mu_components('quartz', 10000)
{'Si': (1, 28.0855, 33.879432430185062), 'elements': ['Si', 'O'],
'mass': 60.0843, 'O': (2.0, 15.9994, 5.9528248152970837), 'density': 2.65}
"""
_materials = get_materials(_larch)
mater = _materials.get(name.lower(), None)
if mater is None:
formula = name
if density is None:
raise Warning(
'material_mu(): must give density for unknown materials')
else:
formula, density = mater
out = {'mass': 0.0, 'density': density, 'elements': []}
for atom, frac in chemparse(formula).items():
mass = atomic_mass(atom, _larch=_larch)
mu = mu_elam(atom, energy, kind=kind, _larch=_larch)
out['mass'] += frac * mass
out[atom] = (frac, mass, mu)
out['elements'].append(atom)
return out
def material_mu_components(name, energy, density=None, kind='total',
_larch=None):
"""material_mu_components: absorption coefficient (in 1/cm) for a compound
arguments
---------
name: material name or compound formula
energy: energy or array of energies at which to calculate mu
density: compound density in gr/cm^3
kind: cross-section to use ('total', 'photo') for mu_elam())
returns
-------
dictionary of data for constructing mu per element,
with elements 'mass' (total mass), 'density', and
'elements' (list of atomic symbols for elements in material).
For each element, there will be an item (atomic symbol as key)
with tuple of (stoichiometric fraction, atomic mass, mu)
larch> material_mu_components('quartz', 10000)
{'Si': (1, 28.0855, 33.879432430185062), 'elements': ['Si', 'O'],
'mass': 60.0843, 'O': (2.0, 15.9994, 5.9528248152970837), 'density': 2.65}
"""
_materials = get_materials(_larch)
mater = _materials.get(name.lower(), None)
if mater is None:
formula = name
if density is None:
raise Warning('material_mu(): must give density for unknown materials')
else:
formula, density = mater
out = {'mass': 0.0, 'density': density, 'elements':[]}
for atom, frac in chemparse(formula).items():
mass = atomic_mass(atom, _larch=_larch)
mu = mu_elam(atom, energy, kind=kind, _larch=_larch)
out['mass'] += frac*mass
out[atom] = (frac, mass, mu)
out['elements'].append(atom)
return out