Exemple #1
0
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
Exemple #2
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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
Exemple #3
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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)
Exemple #5
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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
Exemple #6
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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