EXAFS

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Data Analysis

Setting up

Install feff. Follow the link for instructions.

Install the full 'Demeter' package, that includes the 'Athena' program. It only works well in Windows 64-bits. https://bruceravel.github.io/demeter/

Pre-processing

For each structure you want to analyze:

• Create a folder.
• Put the VASP output in that folder.
• Convert the structure to a .cif file.
• Convert the .cif to feff.inp using this page: http://millenia.cars.aps.anl.gov/webatoms/. If that page is offline, open Artemis (part of Demeter package, you need to do this in Windows), file, open project or data, pick your cif file.
• In the webatoms page or in Artemis, select the edge, select feff6_element style, and select the atom that will be the center of the analysis. In Artemis, clic in "Run Atoms". It will generate a file that contains something like this:

(...)
POTENTIALS
*   ipot   Z  element        l_scmt  l_fms   stoichiometry
    0     26     Fe           2       2       0.001
    1     6      C            1       1       64
    2     7      N            1       1       4


ATOMS                  * this list contains 71 atoms
*   x          y          z     ipot tag           distance
   0.00000    0.00000    0.00000  0  Fe70          0.00000
  -1.82232   -0.51126   -0.02496  2  N69.1         1.89285
  -0.46930    1.83344   -0.04068  2  N67.1         1.89298
   1.82348    0.51118   -0.03720  2  N66.1         1.89414
   0.46853   -1.83477   -0.04752  2  N68.1         1.89424
  -2.56146    0.65484   -0.06360  1  C17.1         2.64460
   1.84706   -1.89028   -0.09876  1  C33.1         2.64472
   2.56107   -0.65476   -0.08652  1  C34.1         2.64486
  -1.84924    1.89065   -0.07752  1  C18.1         2.64580
(...) 

• Save that file as feff.inp and place it in the folder where you are runnig your analysis.
• Be sure that all elements listed in POTENTIALS (ipot) appear in ATOMS (ipot).
• If there is an element missing in ATOMS, remove the respective entry (full line) in POTENTIALS.
• The list of ipot in POTENTIALS must be continuous and start from 0. If you have a discontinuity (i.e. 0, 1, 3, 4), you must change the ipot numbers both in POTENTIALS and ATOMS (i.e. 3=>2 and 4=>3).

Processing

Run sequentially these commands on a terminal; feff must be already installed. More information can be found in INSTALL.md, inside the feff85exafs-master folder.

feff8l_rdinp
feff8l_pot
feff8l_xsph
feff8l_pathfinder
feff8l_genfmt
feff8l_ff2x

Post-processing

These steps should be followed in Athena, from your Virtual machine.

• Open Athena.
• Import chi.dat.
• Select chi(k) as data type.
• Click in "replot".
• Select the element and edge. (i.e., Pd, K-edge).
• Edit k-range [3.0;14.0], dK=1.
• Select plotting k-weights: 3.
• Apply a forward Fourier transform.
• Change plot to R-space, Magnitude-Magnitude. Select and unselect "real part" to update the graph. This will generate a plot |chi(R)| in Å^(-4) as a function of the radial distance in Å.
• To change the units of chi(R), change the k-weights.
• In the main window, clic on file > save current group as > chi(R).
• Save the file as .dat inside your Windows virtual machine. Then move to the shared folder to do the analysis.
• You can now do a fancy plot in Origin, showing the chi(R) data you got from Athena.