One way to import the data is to use separate calcs, one with Ca and one with U. To get the mixed, you might alter the Feff file and replace some U with Ca and vice versa. There are many others who probably have a better method but this will at least get over the partial occupancy problem in Artemis. Chris ********************************************* Dr. Chris Patridge Assistant Professor Department of Chemistry SASE 315 D’Youville College 320 Porter Ave Buffalo, NY 14201 716-829-8096 patridgc@dyc.edu

On Apr 28, 2020, at 11:13 AM, "Dien.Li@srnl.doe.gov" wrote:

 HI, Matthew and Bruce and Carlo

As I want to fit a U L3-edge EXAFS spectrum using a crystal structure model of vorlanite (cubic CaUO4), I was not able to load the crystal structure data, with an error message of “could not input the data file because of partial occupancy” or something like this. I believe that the reason is that Ca and U are on the same site (coordination), and they are completely disordered, it is like (Ca,U)O2, a CaF2 structure, and the occupancy for each of Ca and U is 0.5. Is there any way to handling of such crystal structure data in Artemis? Please see the attached crystal data file in cif. Thank you so much for your instruction.

Dien Li Savannah River National Laboratory _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

Just a comment: typically the A and B atoms cluster with a given NN distribution function to help set the structure. In our experience the results from FEFF are often not very sensitive to the distribution but you can try a couple of sample distributions to check this.\ John On Tue, Apr 28, 2020 at 9:29 AM Matt Newville wrote:

Hi Dien,

Yes, basically Artemis / Atoms cannot handle partial occupancy for crystallographic sites because partial occupancy is not readily translated to a cluster of atoms. So, what you have to do is start with a CIF without fractional occupancy, say that has only Ca or only U in that site, and generate a cluster of atoms from it. Then, you can (and here, have to) edit that cluster of atoms to replace some of the Ca/U with U/Ca. Which ones, and how many, is up to you.

--Matt

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