Hi Shaofeng, feff, because I suppose you stacked in this moment of paths' calculations, is not suitable for partial occupancy. There are already few discussions and tutorial about it (see below) - try to find something about doping. In principle the partial occupancy and doping can be in the same way calculated. I do not know what you want to do, but my first suggestion would be - calculate FEFF paths with full occupation, and later in Artemis change the parameter N (no. of degeneracy) to desired and for desired paths. you can have a look also here https://www.google.pl/#sclient=psy-ab&q=doping+%2B[ifeffit]&oq=doping+%2B[ifeffit]&gs_l=hp.3...5371.10248.2.10875.5.5.0.0.0.0.144.526.1j4.5.0...0.0...1c.1.9.hp.e9ABLCClltg&psj=1&bav=on.2,or.r_cp.r_qf.&bvm=bv.45512109,d.Yms&fp=c9abf273936dad2e&biw=1024&bih=470 https://www.google.pl/#sclient=psy-ab&q=partial+occupancy+%2B[ifeffit]&oq=partial+occupancy+%2B[ifeffit]&gs_l=hp.3...31481.34165.3.34414.17.17.0.0.0.3.122.1277.13j4.17.0...0.0...1c.1.9.hp.kamqDtF1aTI&psj=1&bav=on.2,or.r_cp.r_qf.&bvm=bv.45512109,d.Yms&fp=c9abf273936dad2e&biw=1024&bih=470 kicaj W dniu 13-04-23 04:54, Shaofeng Wang pisze:

Hi Bruce, I want to use a crystal structure file to calculate the path. But the software remind me it can not use crystal data whick has sites of partial occupancy. How can I solve this problem. See the file in attachment. Shaofeng

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Hi Bruce, Thanks for your concern. I just simply modified the site_occupancy to 1. I don’t know if my method is correct, but I did get path from feff calculation. Shaofeng From: Ravel, Bruce Sent: Tuesday, April 23, 2013 11:04 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] artemis can not use a cif file Shaofeng, What have you tried so far to address your problem? B -------------------------------------------------------------------------------- From: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] on behalf of Shaofeng Wang [wangshaofeng@iae.ac.cn] Sent: Monday, April 22, 2013 10:54 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] artemis can not use a cif file Hi Bruce, I want to use a crystal structure file to calculate the path. But the software remind me it can not use crystal data whick has sites of partial occupancy. How can I solve this problem. See the file in attachment. Shaofeng -------------------------------------------------------------------------------- _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

On Monday, May 13, 2013 04:19:05 PM Bruce Ravel wrote:

I agree that the fits are being evaluated slightly differently in the old and new versions of the code. As you say, best fit values and statistical parameters are somewhat different. I am not sure I agree that they are "nowhere near similar", but the disrepancy is much larger than a mere numerical difference. I am not yet clear what is going on, but I am looking into it.

More info: the behavior on my linux machine is differnt from Windows. The difference in the fit result is subtle on Linux and quite enormous on Windows. I am not sure which part of that confuses me more. I'll keep looking into it. 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

Bruce, I have also seen a difference between old and new Artemis, but I have one additional bit of information that may be useful: in my case the good fit is decidedly from the new version. I have tried to reproduce fits in Artemis that someone else made in WinXAS. The samples included some well-characterized published mineral standards, for which the WinXAS fit agreed with the published model. I could not reproduce these fits with the old Artemis - sometimes the fit would zoom off to something unphysical, but often it would settle on something plausible but different. We never found a satisfactory explanation for this behavior. Redoing the same work in Demeter Artemis, I can consistently reproduce the WinXAS fits. I did not import the old files; I built new ones, but used the same data and feff input files as before. I am working in Windows, but it's been pretty much the same under three different operating systems (XP, Vista, 7). I am having trouble finding the old fit files to attach, but I could probably reconstruct them if it would be helpful to you to see another example of this behavior. Leslie Baker -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Monday, May 13, 2013 1:19 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with importing data between version of artemis Georges, Sorry for the lengthy delay. Beamline, travel, etc -- I just haven't had a chance to look into software issues until this week. I agree that the fits are being evaluated slightly differently in the old and new versions of the code. As you say, best fit values and statistical parameters are somewhat different. I am not sure I agree that they are "nowhere near similar", but the disrepancy is much larger than a mere numerical difference. I am not yet clear what is going on, but I am looking into it. If I may comment a bit more broadly on the project you sent me, I have some concerns about your fitting model. I would not agree that your fit is "good" using either version of Artemis. Or perhaps I should say that you and I may not have the same expectation of what "good fit" means. The central problem in your fitting model is that you are using the same parameter for sigma^2 for all your paths, which include O, C, and N atoms spread over a distance range from 1.69 A to 2.03 A. Similarly, you use the same deltaR parameter for all four paths. I understand that you have rather limited information (although you have usable data out to at least 13 invAng), but I don't really accept your constraint that the O atom at 1.69 should have the same sigma^2 as the N atom at 2.04. My intuition tells me that the short O atom should be very tightly bound to the tungsten absorber. Consequently, the O should have a much smaller sigma^2 than the N. So, I question whether your model is defensible, thus I dispute that the one fit is "good" while the other is "bad". That said, they are significantly different. You have uncovered a problem that needs to be figured out and fixed. I'll keep you posted. B On Monday, April 22, 2013 04:05:46 PM Georges Siddiqi wrote:

Hi All,

I've done a fit in the old version of Artemis (0.8.014), and wanted to import this fit into the new version of artemis (demeter 0.9.15) that I have to play around with it a bit more.

The problem is, when I import the the "old-style artemis project", and do the same fit, the values, and fit itself are nowhere near similar to what i got with the old version of Artemis.

what is the cause of this discrepancy? As far as I can tell from double checking all the fitting parameters, windows, variables, etc, they are all exactly the same. Even if I try to just do a summation in the new version with my best-fit values from the old version, the fit is completely different.

Previously when I was importing fits between versions I had no issues whatsoever.

I've attached the artemis project file (W EXAFS.apj) that gives me a good fit in the old version, and a poor fit in the new version.

thanks, georges

-- 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