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A suite of tools for handling surface science related data

Project description


A suite of tools for handling surface science related data. This project will contain tools for the following:

  • X-ray photoelectron spectroscopy (XPS)


  • Docmuentation (priority)

X-ray Photonelectron Spectroscopy


An example analyzing a Ge peak fit within CasaXPS.

from surfsci import xps

# Shortcut for the XPS machine at Dalhousie
# xps_mach = 'Dalhousie'
# mach = xps.mach_param[xps_mach]
mach = {
	'coef' : [0.9033, -4.0724, 5.0677, 1.1066],
	'scale'     : 0.01,
	'work_func' : 4.6,
hv = xps.photon_energy['Al']

# Pass energy [eV], found from XPS operator
pe = 30

sfwagner_Ge = xps.sf.Ge['3d'].area

data = xps.parser.CasaXPS('Ge_example.csv')

# Labels defined by user in CasaXPS fits
pk_lbl = 'Ge 3d'
be = data.binding_energy(pk_lbl)
area = data.area(pk_lbl)

ke = xps.kinetic_energy(be, hv, mach['work_func'])

t_fn = xps.transmission(ke, pe, mach['coef'], mach['scale'])
t_fn_wagner = 1/ke # Proportional to 1/KE

sf_mach = xps.sf_machine(sfwagner_Ge, t_fn, t_fn_wagner)

pk_corr = xps.peak_correction(area, sf_mach)

# NOTE Use the surfsci.xps.XPSPeak(...) helper for convienence
# analyzed_Ge = xps.XPSPeak(pk_lbl, be, area, sfwagner_Ge, hv, pe, mach)

# NOTE Returns pandas.DataFrame with all parameters calculated.
# The user can also query parameters individually
# df = analyzed_Ge.df()

Matrix Factor corrections

If using multple elements within a matrix (e.g. an alloy), you can utilize the surfsci.xps.matrix_factor function. You require the inelastic mean free path of electron scattering (imfp) of both species in bulk and the density, as well as the imfp of the matrix at the measured kinetic energies of both elements. For example, if you have two corrected peaks: pk_Mn_corr, and pk_Ge_corr. The imfp can be calculated using the TPP-2M equation for inelastic mean free path, found in the following reference:

S. Tanuma, C. J. Powel, D. R. Penn, Surf. Interf. Anal., Vol 21, 165 (1994)

from surfsci import xps
# pk_Mn_corr and pk_Ge_corr calculated as in the example above

# a is the kinetic energy used to determine imfp of Ge in Bulk
imfp_matrix_a = 21.17
imfp_Ge_a = 29.84
rho_Ge_a = 5.32

# b is the kinetic energy used to determine imfp of Mn in Bulk
imfp_matrix_b = 14.17
imfp_Mn_b = 14.87
rho_Mn_b = 7.43

mat_fact = xps.matrix_factor(imfp_Ge_a, imfp_Mn_b,
							 mfp_matrix_a, mfp_matrix_b,
							 rho_Ge_a, rho_Mn_b)
relative_pk_Ge_corr = (pk_Ge_corr/pk_Mn_corr)*mat_fact

# NOTE because Mn is used as the normalizing component we can use its
# corrected peak value directly, all other elements require the matrix
# factor correction
print('Ratios of Mn and Ge in MnGe matrix')
print('Mn : {:0.4e}'.format(pk_Mn_corr))
print('Ge : {:0.4e}'.format(relative_pk_Ge_corr))

sfwagner.{db,py}: Empirically derived set of atomic sensitivity factors for XPS

The data in Appendix 5 is reproduced and provided here for non-profit use with permission of the publisher John Wiley & Sons Ltd.

"Practical Surface Analysis by Auger and X-ray Photoelectron Spectroscopy", D. Briggs and M. P. Seah, Appendix 5, p511-514, Published by J. Wiley and Sons in 1983, ISBN 0-471-26279

Copyright (c) 1983 by John Wiley & Sons Ltd.

The original set of data first appeared in the following resource: C. D. Wagner, L. E. Davis, M. V. Zeller, J. A. Taylor, R. M. Raymond and L. H. Gale, Surf. Interface Anal., 3. 211 (1981)

Any use of this data must include the citations above in any work.

Electron Inelastic Mean Free Path (IMFP)

Electron IMFP can be calculated from using the Tanuma, Powel, Penn modified (TPP-2M) equation derived from equations (3), (4b,c,d,e) and (8) in the following reference:

S. Tanuma, C. J. Powel, D. R. Penn, Surf. Interf. Anal., Vol 21, 165 (1994)

For convienence the IMFP TPP-2M equation is located in surfsci.scatter and can be used as such:

from surfsci import scatter

# Mn example
kinetic_energy = 1000 # Can be calculated from surfsci.xps.kinetic_energy

rho = 7.43         # [g/cc]
Nv = 7             # valence electrons
M = 53.938         # atomic mass
bandgap_energy = 0 # [eV]

# Return SI units [m]
imfp_Mn = scatter.imfp_TPP2M(kinetic_energy, rho, M, Nv,
							 bandgap_energy, 'SI')

The value here can be used in the surfsci.xps.matrix_factor calculations outlined above.

Project details

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