Hi Bruce, Matt, Fantastic! Many thanks for your help, I will try that and will let you know. Best wishes, Adriana :) -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: 03 July 2012 13:55 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with fit in pyrite structure with Se substitution On Tuesday, July 03, 2012 09:26:38 AM Adriana Matamoros Veloza wrote:
In both projects the data corresponds to Se edge (no sulphur). Selenium data was collected on natural pyrite grains. When Se associates to pyrite, it is normally inferred that Se substituted sulphur within the pyrite structure. Both elements are chemically very similar. Looking at selenium as the core atom, we want to see if it is possible to get the chemical environment related to pyrite (Se-S, Se-Fe bonds). In natural environments if substitution of sulphur with selenium occurs the proportion is rather than low (perhaps maximum 1% of the population of sulphur atoms). So, in that case we are expecting to get data that fit to the pyrite structure taking Se as the core atom. For that reason, the Feff calculations were made with the crystal structure of pyrite with sulphur as the core atom and used Se edge instead. Is that making any sense?
I understand what you are trying to do, but what you actually did isn't very sensible. If Se is the central atom in the experiment, Se must be the central atom in the Feff calculation. The central atom phase shift (see http://leonardo.phys.washington.edu/feff/wiki/index.php?title=FEFF_Variables) for Se is very different from S. If you get that so wrong, it will have a profound impact on the evaluation of E0 and DeltaR. Here's a snippet from the feff input that you used: POTENTIALS * ipot Z tag 0 16 S 1 26 Fe 2 16 S ATOMS * this list contains 170 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 1.25695 1.25695 1.25695 2 S1.1 2.17711 -2.08047 0.62848 0.62848 1 Fe1.1 2.26237 0.62848 -2.08047 0.62848 1 Fe1.1 2.26237 0.62848 0.62848 -2.08047 1 Fe1.1 2.26237 It needs to be edited to read POTENTIALS * ipot Z tag 0 34 Se 1 26 Fe 2 16 S ATOMS * this list contains 170 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Se 0.00000 1.25695 1.25695 1.25695 2 S1.1 2.17711 -2.08047 0.62848 0.62848 1 Fe1.1 2.26237 0.62848 -2.08047 0.62848 1 Fe1.1 2.26237 0.62848 0.62848 -2.08047 1 Fe1.1 2.26237 The truly important change was to change the Z for potential 0 from 16 to 34. That tells Feff that the central atom is Se. The other two edits help Artemis help you understand the calculation. This illustrates an aspect of how Artemis works. In principle, it should not be necessary to press the "Run Atoms" button then to press the "Run Feff" button in order to make a Feff calculation happen. In many situation, those two buttons are pushed in quick succession, making the second button press seemingly unnecessary. There are, however, many analysis situations where it is useful for the user to pause between the two button presses and ponder feff's input data. In this case, you need to change the absorber to deal with the situation of having measured XAS at the edge of the dopant. Try that. I suspect your analysis will make more sense. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit