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

Anatoly Frenkel frenkel at bnl.gov
Sun Oct 26 10:05:44 CDT 2008



Here are some links to the work of A. Vairavamurthy who did extensive
research on sulfur speciation, that may help:






The good resource for many issues on sulfur speciation are original articles
by Pickering (1998) and Vairavamurthy (1998).


I think, putting it conservatively, you can use peak fitting to find the
mixing fractions of each charge state of S, and you can use LCF to get a
better idea of what functional groups each is in, which is obviously not the
same (several functional groups may have S in the same state).






From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Jenny Cai
Sent: Sunday, October 26, 2008 2:12 AM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Fw: Re: Fit XANES spectra using Athena


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

 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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