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Hi Matthew,

Larix and its CIF Parser (based on pymatgen) can help turn such a CIF file into feff.inp files. For sites with multiple fractional occupations, the feff.inp generated will try to be randomly filled according to those fractions. Of course, with small numbers of neighboring atoms it never perfectly reflects the occupations, but it does tend to give a good guess of atoms of each species in the correct coordination sphere.

>From Larix, one can go to the "Feff" Menu, then "Browse CIF Structures, Run Feff" to bring up its CIF Browser page. This will have ~20,000 CIFs from the AmMin database, but you can import most other CIF files. The one you attached imports without trouble.

Pymatgen is a little odd in assigning equivalent sites, so it identifies 6 Ni/Al sites here (4 for Ni1, 2 for Ni2). Anyway, selecting each of those generates the two attached Feff files. This CIF Browser will also run Feff for you for these files, with each run being in a different folder, and so easy to import into Larix's Feffit Page. The feff_Ni1.inp file has some Ni and Al in the Ni/Al sites at 2.85 and 3.34 Ang. Similarly, the feff_Ni2.inp file has some Ni and some Al at the Ni/Al site at 3.34 Ang.

If you want even more randomness, you could also make a tweak to the settings and re-generate feff.inp repeatedly. But since there are not many sites and the structure is pretty uniform, just having Ni1-Ni, Ni1-Al, Ni2-Ni, and Ni2-Ni and applying the fractional occupation in the fit is the simpler thing to do (and also allow testing of things like are these occupations random at a local level or is there some preferential ordering.

Cheers,

--Matt

From: Ifeffit <ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of matthew marcus <mamarcus@lbl.gov>
Sent: Friday, July 12, 2024 1:10 PM
To: 'XAFS Analysis using Ifeffit' <ifeffit@millenia.cars.aps.anl.gov>
Cc: Min-Jae <MinJaeKim@lbl.gov>
Subject: [Ifeffit] Modeling a spinel structure with fractional occupancy

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A colleague want to fit EXAFS on a NiAl2O4-based material (I don't have 
the details).  As shown in the attached CIF, Ni (the central atom) is 
distributed 60-40 between the 1 and 2 sites, and Al 20-80.  I imagine 
that to model this, I'll need to somehow generate feff.inp files, one 
centered around Ni1 and one Ni2, each with neighboring atoms randomly 
chosen according to the site occupancies.  Does anyone have a good idea 
or tool with which to do this?  I'd rather not have to write a program 
to do that, but will if it's necessary.
	mam