[Ifeffit] problem with importing data between version of artemis
Baker, Leslie
lbaker at uidaho.edu
Tue May 14 10:00:25 CDT 2013
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 at millenia.cars.aps.anl.gov [mailto:ifeffit-bounces at 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 at 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
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