Editing 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.