[Ifeffit] Fitting on Athena

Bruce Ravel bravel at bnl.gov
Thu Sep 8 08:53:01 CDT 2011

On Wednesday, September 07, 2011 07:52:38 pm Niken Wijaya wrote:
> I think I have to clarify that I used MBACK to do the normalization 
> instead of ATHENA. This might as well explain why I got such a high 
> value of y-axis offset, why you think I did not choose the right 
> parameters for the "pre-edge" and "normalization range" and also why I 
> imported the data as normalized mu(E) rather than mu(E). As mentioned in 
> the manual, doing normalization in Athena is very subjective, tiny 
> difference in the point chosen for both the "pre-edge region" and 
> "normalization range" will result in different normalized spectra. Due 
> to lack of experience in processing XAFS spectra and noisy spectra 
> obtained, I was planning to eliminate this problem by using MBACK. My 
> initial plan was to combine the benefit I can get from both ATHENA and 
> MBACK. So, I did the normalization using MBACK, then do the 
> self-absorption correction and fit the normalized spectra in ATHENA. 
> However, looking at your comment, LCF in ATHENA requires edge-step 
> normalization, by saying that, does it mean that I cannot normalized my 
> spectra using MBACK then fit them in ATHENA?


So, you want to use MBACK because it is less subjective than Autobk.
How, then, do you then plan to do your self absorption correction in a
similarly and defensibly rigorous manner?  I am suspicious that you
have not thought this through very well.

Your original email suggested that you believed there to be a problem
with Athena.  A cursory examination of your work -- once you actually
did the favor of posting a project file -- made it clear to me that
you are not using the program correctly.  Indeed, in one of your
emails, you made it clear that you have never read the documentation.

I am unaware of a bug in Athena that precludes using data normalized
outside of Athena to do LCF within Athena.  That may not be the mornal
mode of operation, but it is a reasonable thing to want to do.  You
must take care to import the data correctly and verify that the form
of your data has been preserved before performing the LCF.  If you
expect the program to magically do what you want rather then observing
how the program actually behaves, it is unlikely that you will be
satisfied with the results.

Is it possible that there is a bug that precludes Athena from doing
this thing?  Of course.  A quick examination of the archives of this
mailing list should make it clear that my software is *way* less than
perfect.  So far, you have not given me any reason to belive that's
the case.



 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

 My homepage:    http://xafs.org/BruceRavel
 EXAFS software:  http://cars9.uchicago.edu/ifeffit/Demeter

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