How Artemis handle crystal structure data with partial occupancy in vorlanite (cubic CaUO4)
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
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
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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
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
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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participants (4)
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Christopher Patridge
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Dien.Li@srnl.doe.gov
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John J Rehr
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Matt Newville