Difference between revisions of "X-Ray Absorption Spectra"

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=Methodology=
 
=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  
+
All the spectra(only K-edge XANES currently) were computed using the [http://leonardo.phys.washington.edu/index-feffproject.html FEFF] code. For each structure, spectra were computed with each symmetrically unique site  
in the structure as the absorbing 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, [https://github.com/hackingmaterials/atomate Atomate]. The package leverages [https://github.com/materialsproject/pymatgen Pymatgen] and
 +
[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.  
  
 
=Presentation of Spectra=
 
=Presentation of Spectra=
  
The spectrum for element in the given structure is set to the average of all the spectra for that element in the structure.  
+
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.  
Note: The downloaded data is
 
  
 
=Format of Downloaded Data=
 
=Format of Downloaded Data=
  
The downloaded data contains the following fields:  
+
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 setting used in the computation of the spectrum
+
'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'
+
'xas_id': unique id for each spectrum, e.g. 'mp-505011-28-XANES-K'.
'spectrum_type': type of XAS e.g. 'XANES'   
+
'spectrum_type': type of XAS e.g. 'XANES'.
'edge': e.g. 'K'
+
  'edge': absorption edge e.g. 'K'.
'mp_id': mp id of the structure .
+
'mp_id': mp id of the structure.
'absorbing_atom': site index of the absorbing site in the structure
+
'absorbing_atom': site index of the absorbing site in the structure.
 
  'structure': the structure in dictionary format.
 
  'structure': the structure in dictionary format.
'spectrum': list of shape (100, 5) where each column means the following respectively:  
+
'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)
+
''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=
  
=External Links=
+
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 (submitted), 2017

Revision as of 14:35, 18 July 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. 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.

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.

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

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 (submitted), 2017