[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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