[Ifeffit] Using the amplitude reduction factor as alinearcombination fitting parameter

[Bruggeman Christophe]

XAFS fitting is sometimes a "puzzling world", but here's some more
clarification :-)

I indeed collected a series of spectra on FeS2, with varying conditions
such as equilibration time and geochemical parameters. The general
outlook of all these spectra are relatively similar, but some clear
differences can be noticed from both the XANES and EXAFS patterns and
the FTs. More precisely, based on these differences the samples can be
"categorised" from "more oxidised U" to "more reduced U", but no pure
end member is present anywhere in the samples. So, a first PCA was
performed on the samples themselves, taking the "most oxidised" and
"most reduced" as end member, and trying if the other samples could be
reproduced as a linear combination of these two end members. This proved
to be possible. 

Now for standards: I collected some scans of U standards, but it is very
difficult to have a standard which represents a pure end member in the
FeS2 samples. For example, my guess is that the "reduced U" resembles
uraninite, but given the fact that with such heterogeneous reduction on
FeS2 surface, it is more likely that UO2 nanocolloids are formed, a
crystalline uraninite standard can not be used as pure end member. 

Therefore, what I would like to do, is reproduce the FTs and EXAFS
spectra, starting from U standards, but adapting them (e.g. playing with
Debye-Waller factors), so that I would get a pure end member for the
FeS2 samples, then fix the parameters, and use the amplitude reduction
factor as a sort of linear combination fitting parameter to get an idea
of the amount of this pure end member in my samples.

Hopefully, this sheds some more light on the matter,
Thanks already for your interest,

Christophe




-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Frenkel,
Anatoly
Sent: dinsdag 29 april 2008 16:23
To: ifeffit at millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] Using the amplitude reduction factor as
alinearcombination fitting parameter

There are a few points in your description that puzzle me. Have you
collected not one but a series of spectra where some external condition
(e.g., temperature, concentration, time, pH etc) were varied? If not,
PCA cannot be used if only one spectrum was collected containing a
mixture of two species. Such spectrum would have only one component, of
course - itself. Next, assuming you did use PCA for a series of spectra,
without having XANES and/or EXAFS data of test compounds how were you
able to  deconvolute abstract components that PCA generates into the two
species that have meening of XANES or EXAFS data? Without test compounds
such deconvolution is not possible unless you used not PCA but a linear
combination fit of some sort... And, finally, if you used test compounds
that could be reliably reproduced by your 2 principal components, why do
you need to do anything else? They are your two species. 

Please clarify. 

Anatoly



----- Original Message -----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
<ifeffit-bounces at millenia.cars.aps.anl.gov>
To: ifeffit at millenia.cars.aps.anl.gov
<ifeffit at millenia.cars.aps.anl.gov>
Sent: Tue Apr 29 03:06:28 2008
Subject: [Ifeffit] Using the amplitude reduction factor as a
linearcombination fitting parameter

I have recently collected EXAFS spectra of uranium on a FeS2 surface.
Using principal component analysis of the XANES and k3-weighted EXAFS
spectra, I have found that there are two uranium species which compose
the spectra. As a first tentative guess, I believe these two uranium
species are uraninite (UO2(c)) and a uranyl species. I would like now to
fit the fourier transform functions (real parts and magnitudes) using
the theoretical paths and path degeneracies created by feff, and use the
amplitude reduction factor S02 as a fitting parameter to derive the
relative amounts of the two uranium species in my samples. 
 
Normally, this S02 is taken as a constant (between 0.7 and 1.0), and the
path degeneracies are fitted. So normally, S02 is not really a fitting
parameter (some papers derive it even with theoretical functions).
However, given the fact that S02 and N are completely correlated, I
think it is justified to use this approach. 
 
Can someone comment on this?
 
Many thanks in advance,
 
Christophe
 


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