[Ifeffit] Peakfitting CeO2 data in Athena

Thu Dec 8 13:05:20 CST 2016

Hi Stephanie,
Typically, LCA fitting is done for the more widely applied speciation
analysis while Gaussian fitting is done to obtain quantitative pre-edge
information: a) metal-ligand covalency and b)ligand-field splitting and
metal 3d-4p mixing.

LCA
In the context of S K-edge XANES, LCA is tricky- the very detailed
structure you see in S XANES is almost always electronic in nature and can
be correlated to molecular orbital in the molecule. The correlation of DFT
derived MO energy level to metal and ligand pre-edges has exploded in the
last decade and very good correlations can be obtained. In such cases the
peaks actually do have meaning. I attach a paper on simple S compounds
where the match with theory is rather good.

This paper also talks a bit about why unknown LCA is BAD idea. Because
small structural perturbations can lead to large changes in the S XANES the
concept of "standards" is dangerous. Unless you know what you have in your
mixture.

If you are doing LCA for metal K-edges, you are mostly matching the
"Structural" part of the XANES (post edge) and not the "electronic" part
(restricted to pre-edges and to the low rising-edge). Therefore metal
K-edge LCA still makes sense and gives reasonable results.

Gaussian Fitting
Gaussian fitting only makes sense for the pre-edge region. Anything
post-edge or higher is pure speculation and you are doing so to obtain a
good background function for the pre-edge region, where all the
quantitative analysis rests. I attach on Fe K-pre-edge analysis, which
basically fits a random function to the edge-region and treats it for
background purposes. No quantitative/meaningful information can be (yet)
obtained from such gaussian fitting. Take a look at the power of pre-edge
analysis as shown in the Westre paper.

Hope this helps,
Best,
-Riti Sarangi

On Thu, Dec 8, 2016 at 9:06 AM, Stephanie Laga <stephanie.laga at yale.edu>
wrote:

> Thank you Matthew and Matt for your responses. Sorry if these are silly
> questions...so then does that mean arctan and gaussian shouldn't be used
> together?
>
> What was meant by "it does not inherently include any understanding of
> what that peak is"? That these functions aren't representative of the
> processes occuring because the single electronic assumption doesn't hold
> anymore...ie there are many electron effects once we get in the EXAFS
> region?
>
> And if I am primarily looking at XANES, I don't need to be worried about
> the initial EXAFS region right?
>
> On Thu, Dec 8, 2016 at 10:48 AM, Matthew Marcus <mamarcus at lbl.gov> wrote:
>
>> The usual justification for using gaussians for peaks, aside from "it
>> works" is that there's inhomogeneous broadening over and above the
>> lifetime.  The usual justification for using an arctan for the step is
>> exactly the opposite.  Instrument broadening is often taken to be
>> gaussian.  Net result:  A (pseudo)Voight for peaks often works.  One
>> issue is what to do about the post-white-line peaks, which sometimes
>> are viewed as the first EXAFS wiggles.  Manceau has a nice paper about
>> S XANES  (I don't have the ref handy right now) in which he goes
>> through peak fitting and evaluates its uniqueness.
>>    mam
>>
>> On Thu, Dec 8, 2016 at 5:40 AM, Matt Newville
>> <newville at cars.uchicago.edu> wrote:
>> > Hi Stephanie,
>> >
>> >
>> >
>> > On Wed, Dec 7, 2016 at 12:33 PM, Stephanie Laga <
>> stephanie.laga at yale.edu>
>> > wrote:
>> >>
>> >> Dear all,
>> >>
>> >> I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS
>> data.
>> >> I have been using moved the peak fitting function in Athena to model
>> the
>> >> XANES with an arctan background function and a series of gaussians.
>> >>
>> >> Looking through the literature I haven't seen too many specifics to
>> using
>> >> this approach (rationale for choosing the widths of peaks or how to
>> define
>> >> the background function). Similarly, doesn't seem to be much rationale
>> for
>> >> choosing a 4 vs 5 peak fit for the XANES.
>> >>
>> >> My main question is then...1) Is there a rational for picking the
>> >> background function, specifically the height and width (can I let the
>> height
>> >> vary or should I be keeping a constant arctan through all samples)?
>> >>
>> >> Any advice is greatly appreciated!
>> >>
>> >> Stephanie
>> >>
>> >
>> > Matthew answered quickly, but sort of changed the subject, suggesting a
>> > different analysis (LSQ) and then discussing some of the pitfalls of
>> that
>> > approach.  Your original question is still worth discussing.
>> >
>> > There is not a whole lot of justification in using one particular shape
>> for
>> > the background.  A step broadened as arctan, error function are common
>> and
>> > seem to work well. Each has some theoretical explanation in that the
>> > integral of a series of Lorentzian gives an arc-tangent function while
>> the
>> > integral of a series of Gaussians will give the error function. (If
>> this is
>> > wrong, can someone please correct?).  If you think as the above edge
>> > spectrum as a series of finely spaced individual transitions, then these
>> > functions have some justification.    Whether it actually works well in
>> > detail on a particular spectrum is a separate question.   FWIW, I've
>> also
>> > seen people use (successfully) a single, very broad Lorentzian for the
>> "main
>> > edge".
>> >
>> > The use of Lorentzians, Gaussians, Voigts, and PseudoVoigts is somewhat
>> more
>> > justified in that those are how you would expect a single electronic
>> > transition to appear, especially broadened in the way(s) you'd expect a
>> > monochromatic X-ray beam to be energy broadened.  Using such functions
>> is
>> > essentially asserting that there is a single electronic transition at
>> that
>> > energy, and you want to know it's size and shape.  This is not wrong,
>> but it
>> > does not inherently include any understanding of what that peak is. For
>> > pre-edge peaks, it's pretty well-justified, and works pretty well.  For
>> > peaks on or after the main edge or "white line", it's less justified
>> because
>> > we know that EXAFS-like effects can be important.
>> >
>> > The biggest dangers in the peak-fitting approach are:
>> >    1) one always gets an answer, and that is rarely "no, this is not the
>> > right model to use".  In fairness, most linear algebra methods used for
>> > XANES analysis or really most other spectroscopies have the same
>> feature.
>> >    2) interpretation of the results can be challenging, or at least it
>> is
>> > hard to know when they are misleading.  Again, most linear algebra
>> methods
>> > used for XANES analysis or really most other spectroscopies have the
>> same
>> > feature.
>> >    3) it can sort of willfully ignore other parts of the spectra.  In
>> > fairness, we all do this sort of thing all the time.
>> >
>> > Hope that helps.  Peak fitting is not exactly "theoretical XANES
>> analysis",
>> > but it is not always done in an ad-hoc manner out of ignorance either.
>> >
>> > Linear algebra techniques are completely justified too.
>> >
>> > Hope that helps,
>> >
>> > --Matt Newville
>> >
>> >
>> >
>> > _______________________________________________
>> > Ifeffit mailing list
>> > Ifeffit at millenia.cars.aps.anl.gov
>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia
>> .cars.aps.anl.gov_mailman_listinfo_ifeffit&d=CwICAg&c=-d
>> g2m7zWuuDZ0MUcV7Sdqw&r=UZ6LahCCy9yRGAvO8QDSWFzQq7a3vkDZfWzr2
>> SslhiE&m=1Dl796heiYduL4EDzxeWdcjHhaDpvCGzN-gt3GQjKtQ&s=iJtvu
>> bKegs7Ku7dPBbetFqQS3BGu_LEpD2iDIRnLVpk&e=
>> > Unsubscribe: https://urldefense.proofpoint.
>> com/v2/url?u=http-3A__millenia.cars.aps.anl.gov_mailman_
>> options_ifeffit&d=CwICAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=UZ6LahCC
>> y9yRGAvO8QDSWFzQq7a3vkDZfWzr2SslhiE&m=1Dl796heiYduL4EDzxeWdc
>> jHhaDpvCGzN-gt3GQjKtQ&s=FXCHDGbIdIGP3_1IjIkriL6-8jZe_v4iEjOfJUMnUl0&e=
>> >
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia
>> .cars.aps.anl.gov_mailman_listinfo_ifeffit&d=CwICAg&c=-d
>> g2m7zWuuDZ0MUcV7Sdqw&r=UZ6LahCCy9yRGAvO8QDSWFzQq7a3vkDZfWzr2
>> SslhiE&m=1Dl796heiYduL4EDzxeWdcjHhaDpvCGzN-gt3GQjKtQ&s=iJtvu
>> bKegs7Ku7dPBbetFqQS3BGu_LEpD2iDIRnLVpk&e=
>> Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=http-3A__millenia
>> .cars.aps.anl.gov_mailman_options_ifeffit&d=CwICAg&c=-dg
>> 2m7zWuuDZ0MUcV7Sdqw&r=UZ6LahCCy9yRGAvO8QDSWFzQq7a3vkDZfWzr2S
>> slhiE&m=1Dl796heiYduL4EDzxeWdcjHhaDpvCGzN-gt3GQjKtQ&s=
>> FXCHDGbIdIGP3_1IjIkriL6-8jZe_v4iEjOfJUMnUl0&e=
>>
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20161208/ca1bb856/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 2008_Sarangi_ICA.pdf
Type: application/pdf
Size: 601689 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20161208/ca1bb856/attachment-0002.pdf>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Westre.pdf
Type: application/pdf
Size: 592424 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20161208/ca1bb856/attachment-0003.pdf>