Difference between revisions of "X-Ray Absorption Spectra"

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(Presentation of Spectra)
 
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[https://github.com/materialsproject/fireworks Fireworks] packages for the generation of the input/output files for the calculations and for the workflow  
 
[https://github.com/materialsproject/fireworks Fireworks] packages for the generation of the input/output files for the calculations and for the workflow  
 
execution management respectively.
 
execution management respectively.
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 +
These results are intended to be semi-quantitative in that corrections, such as edge shifts and Debye-Waller damping, have not been included.
  
 
=Presentation of Spectra=
 
=Presentation of Spectra=
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See MP's database builder repository [https://github.com/materialsproject/emmet/ Emmet] (<code>emmet.feff.builders.xas</code> module) for details.
 
See MP's database builder repository [https://github.com/materialsproject/emmet/ Emmet] (<code>emmet.feff.builders.xas</code> module) for details.
 
=Format of Downloaded Data=
 
 
The downloaded data for each element contains the output produced by the FEFF calculation for all the symmetrically unique sites in the structure.
 
And each one of those data contains the following fields:
 
 
'input_parameters': the FEFF input settings used in the computation of the spectrum.
 
'xas_id': unique id for each spectrum, e.g. 'mp-505011-28-XANES-K'.
 
'spectrum_type': type of XAS e.g. 'XANES'.
 
'edge': absorption edge e.g. 'K'.
 
'mp_id': mp id of the structure.
 
'absorbing_atom': site index of the absorbing site in the structure.
 
'structure': the structure in dictionary format.
 
'spectrum': array of shape (100, 6) where each column means the following(in that order):
 
''Energy(eV), Energy with respect to the Fermi level(eV),  Wavenumber,  mu(total absorption coefficient),  mu0(the background absorption coefficient), chi(normalized finestructure)
 
''
 
  
 
=References=
 
=References=
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Smidt, B. Bocklund, M. Horton, J. Dagdalen, B. Wood, Z. Liu, J. Neaton, S. P. Ong, K. Persson,
 
Smidt, B. Bocklund, M. Horton, J. Dagdalen, B. Wood, Z. Liu, J. Neaton, S. P. Ong, K. Persson,
 
A. Jain, Atomate: A High-Level Interface to Generate, Execute, and Analyze Computational
 
A. Jain, Atomate: A High-Level Interface to Generate, Execute, and Analyze Computational
Materials Science Workflows, Computational Materials Science (submitted), 2017
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Materials Science Workflows, Computational Materials Science (accepted), 2017

Latest revision as of 18:27, 30 September 2017

Methodology

All the spectra(only K-edge XANES currently) were computed using the FEFF code. For each structure, spectra were computed with each symmetrically unique site in the structure as the absorbing site. The workflow used for the calculations can be found in the open source comprehensive materials science workflow package, Atomate in the atomate.feff namespace. The package leverages Pymatgen and Fireworks packages for the generation of the input/output files for the calculations and for the workflow execution management respectively.

These results are intended to be semi-quantitative in that corrections, such as edge shifts and Debye-Waller damping, have not been included.

Presentation of Spectra

The computed absorption coefficient for an element in the given structure is set to the absorption coefficient averaged over all the sites in the structure with that element.

See MP's database builder repository Emmet (emmet.feff.builders.xas module) for details.

References

K. Mathew, J. H. Montoya, A. Faghaninia, S. Dwarakanath, M. Aykol, H. Tang, I. Chu, T. Smidt, B. Bocklund, M. Horton, J. Dagdalen, B. Wood, Z. Liu, J. Neaton, S. P. Ong, K. Persson, A. Jain, Atomate: A High-Level Interface to Generate, Execute, and Analyze Computational Materials Science Workflows, Computational Materials Science (accepted), 2017