Using XrayDB from Python

The wrappers/python directly contains a Python module for XrayDB. This module gives a higher-level wrapping of the XrayDB, including the conversion of data from json-encoded data to numpy arrays. The module requires the json, numpy, and sqlalchemy modules, and can be installed with:

python setup.py install

XrayDB module

To use the XrayDB from python, create an instance, and start using it:

>>> from xraydb import XrayDB
>>> xdb = XrayDB()
>>> xdb.xray_edge('Ag', 'K')
XrayEdge(edge=25514.0, fyield=0.821892, jump_ratio=6.334)

Table of XrayDB methods for Atomic and X-ray data for the elements. calculate and return some element-specific properties, given the element symbol or atomic number. Most data extends to Z=98 (Cf), but much data for elements with atomic number > 92 (U) may not be available, and may not be very reliable when provided. Except where noted, the data comes from Elam et al.

XrayDB method description
XrayDB.atomic_number() atomic number from symbol
XrayDB.atomic_number() atomic number from symbol
XrayDB.symbol() atomic symbol from number
XrayDB.molar_mass() atomic mass
XrayDB.density() density of pure element
XrayDB.xray_edge() xray edge data for a particular element and edge
XrayDB.xray_edges() dictionary of all X-ray edges data for an element
XrayDB.xray_lines() dictionary of all X-ray emission line data for an element
XrayDB.xray_line_strengths() absolute line strength in cm^2/gr for all available lines
XrayDB.mu_elam() absorption cross sectionm photo-electric or total
XrayDB.cross_section_elam() photo-electric, coherent, or incoherent cross sections.
XrayDB.corehole_width() core level width for an element and edge ()
XrayDB.f0() elastic scattering factor (Waasmaier and Kirfel )
XrayDB.f0_ions() list of valid "ions" for f0() (Waasmaier and Kirfel )
XrayDB.chantler_energies() energies of tabulation for Chantler data (Chantler )
XrayDB.f1_chantler() \(f'(E)\) anomalous scattering factor (Chantler )
XrayDB.f2_chantler() \(f"(E)\) anomalous scattering factor (Chantler )
XrayDB.mu_chantler() absorption cross section (Chantler )
class xraydb.XrayDB(dbname='xraydb.sqlite', read_only=True)

Database of Atomic and X-ray Data

This XrayDB object gives methods to access the Atomic and X-ray data in th SQLite3 database xraydb.sqlite.

Much of the data in this database comes from the compilation of Elam, Ravel, and Sieber, with additional data from Chantler, and other sources. See the documention and bibliography for a complete listing.

atomic_number(element)

return element's atomic number

Parameters:element (string or int) -- atomic number or symbol
Returns:atomic number
Return type:integer
symbol(element)

return element symbol

Parameters:element (string or int) -- atomic number or symbol
Returns:element symbol
Return type:string
molar_mass(element)

return molar mass of element

Parameters:element (string or int) -- atomic number or symbol
Returns:molar mass of element in amu
Return type:float
density(element)

return density of pure element

Parameters:element (string or int) -- atomic number or symbol
Returns:density of element in gr/cm^3
Return type:float
xray_edges(element)

returns dictionary of X-ray absorption edge energy (in eV), fluorescence yield, and jump ratio for an element.

Parameters:element (string or int) -- atomic number or symbol
Returns:
keys of edge (iupac symbol), and values of
XrayEdge namedtuple of (energy, fyield, edge_jump))
Return type:dictionary

References

Elam, Ravel, and Sieber.

xray_edge(element, edge)

returns XrayEdge for an element and edge

Parameters:
  • element (string or int) -- atomic number or symbol
  • edge (string) -- X-ray edge
Returns:

namedtuple of (energy, fyield, edge_jump))
Return type:

XrayEdge

Example

>>> xdb = XrayDB()
>>> xdb.xray_edge('Co', 'K')
XrayEdge(edge=7709.0, fyield=0.381903, jump_ratio=7.796)

References

Elam, Ravel, and Sieber.

xray_lines(element, initial_level=None, excitation_energy=None)

returns dictionary of X-ray emission lines of an element, with

Parameters:
  • initial_level (string or list/tuple of string) -- initial level(s) to limit output.
  • excitation_energy (float) -- energy of excitation, limit output those excited by X-rays of this energy (in eV).
Returns:

keys of lines (iupac symbol), values of Xray Lines
Return type:

dictionary

Notes

if both excitation_energy and initial_level are given, excitation_level will limit output

Example

>>> xdb = XrayDB()
>>> for key, val in xdb.xray_lines('Ga', 'K').items():
>>>      print(key, val)
'Ka3', XrayLine(energy=9068.0, intensity=0.000326203, initial_level=u'K', final_level=u'L1')
'Ka2', XrayLine(energy=9223.8, intensity=0.294438, initial_level=u'K', final_level=u'L2')
'Ka1', XrayLine(energy=9250.6, intensity=0.57501, initial_level=u'K', final_level=u'L3')
'Kb3', XrayLine(energy=10263.5, intensity=0.0441511, initial_level=u'K', final_level=u'M2')
'Kb1', XrayLine(energy=10267.0, intensity=0.0852337, initial_level=u'K', final_level=u'M3')
'Kb5', XrayLine(energy=10348.3, intensity=0.000841354, initial_level=u'K', final_level=u'M4,5')

References

Elam, Ravel, and Sieber.

xray_line_strengths(element, excitation_energy=None)

return the absolute line strength in cm^2/gr for all available lines

Parameters:
  • element (string or int) -- Atomic symbol or number for element
  • excitation_energy (float) -- incident energy, in eV
Returns:

elemental line with fluorescence cross section in cm2/gr.
Return type:

dictionary

References

Elam, Ravel, and Sieber.

ck_probability(element, initial, final, total=True)

return Coster-Kronig transition probability for an element and initial/final levels

Parameters:
  • element (string or int) -- Atomic symbol or number for element
  • initial (string) -- initial level
  • final (string) -- final level
  • total (bool) -- whether to return total or partial probability
Returns:

transition probability
Return type:

float

Example

>>> xdb = XrayDB()
>>> xdb.CK_probability('Cu', 'L1', 'L3', total=True)
0.681

References

Elam, Ravel, and Sieber.

corehole_width(element, edge)

returns core hole width for an element and edge

Parameters:
  • element (string, integer) -- atomic number or symbol for element
  • edge (string) -- edge for hole.
Returns:

corehole width in eV.
Return type:

float

References

Keski-Rahkonen and Krause

cross_section_elam(element, energies, kind='photo')

returns Elam Cross Section values for an element and energies

Parameters:
  • element (string or int) -- atomic number or symbol for element
  • energies (float or ndarray) -- energies (in eV) to calculate cross-sections
  • kind (string) -- one of 'photo', 'coh', and 'incoh' for photo-absorption, coherent scattering, and incoherent scattering cross sections, respectively. Default is 'photo'.
Returns:

ndarray of scattering data

References

Elam, Ravel, and Sieber.

mu_elam(element, energies, kind='total')

returns attenuation cross section for an element at energies (in eV)

Parameters:
  • element (string or int) -- atomic number or symbol for element
  • energies (float or ndarray) -- energies (in eV) to calculate cross-sections
  • kind (string) -- one of 'photo' or 'total' for photo-electric or total attenuation, respectively. Default is 'total'.
Returns:

ndarray of scattering values in units of cm^2/gr

References

Elam, Ravel, and Sieber.

chantler_energies(element, emin=0, emax=1000000000.0)

return array of energies (in eV) at which data is tabulated in the Chantler tables for a particular element.

Parameters:
  • element (string or int) -- atomic number or symbol
  • emin (float) -- minimum energy (in eV) [0]
  • emax (float) -- maximum energy (in eV) [1.e9]
Returns:

energies
Return type:

ndarray

References

Chantler

f1_chantler(element, energy, **kws)

returns f1 -- real part of anomalous X-ray scattering factor for selected input energy (or energies) in eV.

Parameters:
  • element (string or int) -- atomic number or symbol
  • energy (float or ndarray) -- energies (in eV).
Returns:

real part of anomalous scattering factor
Return type:

ndarray

References

Chantler

f2_chantler(element, energy, **kws)

returns f2 -- imaginary part of anomalous X-ray scattering factor for selected input energy (or energies) in eV.

Parameters:
  • element (string or int) -- atomic number or symbol
  • energy (float or ndarray) -- energies (in eV).
Returns:

imaginary part of anomalous scattering factor
Return type:

ndarray

References

Chantler

mu_chantler(element, energy, incoh=False, photo=False)

returns X-ray mass attenuation coefficient, mu/rho in cm^2/gr for selected input energy (or energies) in eV. default is to return total attenuation coefficient.

Parameters:
  • element (string or int) -- atomic number or symbol
  • energy (float or ndarray) -- energies (in eV).
  • photo (bool) -- return only the photo-electric contribution [False]
  • incoh (bool) -- return only the incoherent contribution [False]
Returns:

mass attenuation coefficient in cm^2/gr
Return type:

ndarray

References

Chantler

f0_ions(element=None)

return list of ion names supported for the .f0() function.

Parameters:element (string, int, pr None) -- atomic number, symbol, or ionic symbol of scattering element.
Returns:
if element is None, all 211 ions are returned.
if element is not None, the ions for that element are returned
Return type:list

Example

>>> xdb = XrayDB()
>>> xdb.f0_ions('Fe')
['Fe', 'Fe2+', 'Fe3+']

Notes

Z values from 1 to 98 (and symbols 'H' to 'Cf') are supported.

References

Waasmaier and Kirfel

f0(ion, q)

return f0(q) -- elastic X-ray scattering factor from Waasmaier and Kirfel

Parameters:
  • ion (string, int, or None) -- atomic number, symbol or ionic symbol of scattering element.
  • q (float, list, ndarray) -- value(s) of q for scattering factors
Returns:

elastic scattering factors
Return type:

ndarray

Example

>>> xdb = XrayDB()
>>> xdb.f0('Fe', range(10))
array([ 25.994603  ,   6.55945765,   3.21048827,   1.65112769,
         1.21133507,   1.0035555 ,   0.81012185,   0.61900285,
         0.43883403,   0.27673021])

Notes

q = sin(theta) / lambda, where theta = incident angle, and lambda = X-ray wavelength

References

Waasmaier and Kirfel