[Ifeffit] Problems with fitting in ATHENA for XANES

Bruce Ravel bravel at anl.gov
Mon May 8 10:54:33 CDT 2006

Hi Pushan,

Well, it seems that no one bit on your questions and I am now back from my
trip to California, so I'll take a stab at this.

> I am the new user of XAFS method. Recently I obtained some data with
> XANES method.
> I have just started using ATHENA for my data analysis. I am using
> "Using ATHENA" document to learn the software.
> I have two  questions
> 1.For XANES, Which method is better for knowing unknown data with known
> standards: Peak fitting analysis or Linear combination analysis.
> I would like to get some comments from your experiences so far which
> works better if tried both for same type of data.

I don't see how I can answer this question in an objective way ;-)

I rarely find peak fitting to be useful.  I often find linear combination
analysis to be useful.

The caveat about linear combination fitting is that you need to have measured
an appropriate set of standards.  If you do not have the right standards, you
cannot do linear combination analysis effectively.  If you do, though, have a
good set of standards, LCF is a very powerful tool indeed.

The second caveat is that your problem needs to be well-suited for LCF.  As an
example of what I mean by that, consider the work in a paper that I just
submitted with a colleague.  In that paper, we report on the reduction of
Au(III) chloride to metallic gold via interactions with cyanobacteria.  Over
the course of tens of hours the gold(III) chloride is converted to gold(I)
sulfide then to colloidal gold.  We analyzed these data using LCF, fitting
those three species to spectra measured over the course of 10s of hours and
relating the fractions of the species to a reaction rate constant.  In that
case, LCF is perfect because the sample itself is a combination of standards
that we had measured.  The point here is that you need to have a reason to
believe that your sample is, in fact, a linear combination for LCF analysis to
be useful.

Peak fitting is often useful in a situation where the physical structure is
known only partially.  If some feature of the spectrum changes in response to
changes in some extrinsic parameter (polarization, temperature, or some such)
then peak fitting can be a good way to quantify that response.

My main problem with peak fitting is that it is hard to know how to interpret
the physical meaning of the line shapes used to do the fit.  That is, it may
not be clear how some Gaussian or Lorentzian used in the fit is related in a
meaningful way to the electronic or atomic structure of the material.

> 2. In the peak fit analysis, in literature related to my work it was
> mentioned that peak  modelled by 50%-50% combination of Gaussian and
> Lorentzian functions works better. Is it possible to do in ATHENA.?

Athena does not currently have a Voight or psuedo-Voight function.

As you can see (http://cars9.uchicago.edu/iffwiki/HoraeToDoList) improvements
to the peak fitting dialog are on my list of things to do.  I would like to
add a pseudo-Voight as well as some other lineshapes.  One thing that comes to
mind is that it would be nice to use the Cromer-Lieberman function rather than
an arc-tangent for the step part of the fit.


 Bruce Ravel  ---------------------------------------------- bravel at anl.gov

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007

 Argonne National Laboratory         phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USA                                fax: (1) 630 252 9793

 My homepage:    http://cars9.uchicago.edu/~ravel 
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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