[Ifeffit] Fw: Re: Fit XANES spectra using Athena

Jenny Cai jennyh_cai at yahoo.ca
Sun Oct 26 01:12:29 CDT 2008

Sorry, Bruce.  I have to send it again to the group.  -Jenny

--- On Sun, 10/26/08, Jenny Cai <jennyh_cai at yahoo.ca> wrote:
From: Jenny Cai <jennyh_cai at yahoo.ca>
Subject: Re: [Ifeffit] Fit XANES spectra using Athena
To: "Bruce Ravel" <bravel at bnl.gov>
Received: Sunday, October 26, 2008, 2:08 AM

Hi everyone,

Thank you for your reply.

I understand the difference between peak fitting and linear combination fitting. It is like, If I don't know anything about my sample, peak fitting should be used. If I know the components of my sample, I can use linear combination. That is why I use peak fitting first, because I know very little about my sample. However, what I am thinking is that from the results of peak fitting, I know there may be some types of sulphur in my sample, and based on the peak positions, I can chose the standards for linear combination fitting.

I can't use linear combination fitting in the first place, because I don't exactly know what sulphur forms in my sample, and I may miss an important species if I chose the wrong standards. However, I still want to try linear combination after peak fitting, because I think the
 linear combination fitting may be more accurate than peak fitting. It uses the whole spectrum of the standard, while the peak fitting neglectes the effect of small features on the fitting. Does it make sense?

My samples are fluid coke and their activation products. They have reduced and oxidized sulphur species, more likely in organic forms. I have 26 standards covering the sulphur oxidation states from elemental sulphur to sulphate. Most of them are organic sulphur. 

Any more suggestions? Thank you!

Best regards,



--- On Fri, 10/24/08, Bruce Ravel <bravel at bnl.gov> wrote:
From: Bruce Ravel <bravel at bnl.gov>
Subject: Re: [Ifeffit] Fit XANES spectra using Athena
To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
Received: Friday,
 October 24, 2008, 9:06 AM

On Friday 24 October 2008 00:59:21 Jenny Cai wrote:
> Hello everyone,
> Sorry for bothering you again.
> I am using least-squares peak fit and linear combination fit to analyze my
> samples. I have spent tons of time on it, and it really makes me crazy.
> can't I get consistent results from these two methods?
> Please see the attached file. Both of these methods work well
> but linear combination fit always need more peaks than peak fit to get an
> 'ok' fitting. Should I stick on one method for all my samples, no
> what results the other one gives? It is confusing me so much. Could anyone
> help me out?


I think you are comparing apples and oranges.  I certainly think you
are looking for some correspondance between peak fitting and linear
combination fitting that
 probably does not exist.

When doing linear combination fitting, you are making the implicit
assumption that your data can be described in that way.  Suppose that
you go to the chemical cabinet and grab jars of 5 stable, non-reactive
chemicals.  Scoop out a spatula-full of each and mix them together
very well in ajar.  Then scoop out a bit of the mixture, spread it on
a piece of tape, and measure some XAS.  In that case, we certainly
expect LCF to work well.  The measured spectrum should be a linear
combination of the spectra from each of the 5 original materials in
proportion that has something to do with how many absorber atoms were
in each scoop.

Now suppose that you take a scoop of soil from a swamp.  You might
expect that your metal atom is distributed among oxide and sulfide
species.  You measure some xas on the swamp soil and on a library of
standards.  You may find that you can do LCF using some
 mixture of
oxides and sulfide, or you might not.  That may mean that you
neglected to consider an important standard, a carbide, for example.
*Or* it might mean that the oxides and sulfides in the real sample
include some kind of exotic organic species that isn't quite like the
standards you have available.  In the latter case, your LCF fit
results will be approximate in the best scenario.

So, you don't say anything about what sulfur species you are using as
standards, nor do you say anything about what the sample is.  Should
you expect a perfect fit from some number of standards?  Do you know
for a fact that your standard is simply a linear combination of
standards.  That is, should you expect the LCF to tell you what the
components *are* or should you expect the LCF to tell what the sample

As for the peak fitting, what do each of the line shapes mean
physically?  Chemically?  No XAS data
 is described by a single
Gaussian.  Neither is any XAS data described by a single arc-tangent.
So why should the number of lineshapes required to generate a
mathematical function that resembles your data be related to the
number of species you require in a linear combination fit?  You seem
to making yourself crazy based on the assumption that there is some
magical relationship between the six lineshapes you used in the peak
fitting and the number of standards you use in the linear combination

It seems to me that you would make yourself a lot less crazy if you
didn't cling to this unsubstantiated assumption.


 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:   
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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