[Ifeffit] Re: Problems with linear combination fitting S-XANES data in Athena

28 Jul 2025

      Good afternoon, Matt,

Thanks so much for the information. I was able to apply the settings you mentioned as a starting point in Athena, and now I am getting much better results. Still some tweaking to get the best background, but things are much better.

Re: reference spectra, I will discuss with my collaborator, but I don't think he will mind if anyone finds our data useful and would like to use it in a database. 🙂 From my perspective, it would be a highlight of this project! How would we go about doing this, if he agrees?

Kindest regards,
Julie

Julie Muretta, Ph.D.

Materials Testing Laboratory Manager

Center for Advanced Materials Processing (CAMP)

(406) 496-4808 | jmuretta@mtech.edu

[Montana Technological University]<https://urldefense.us/v3/__https://www.mtech.edu/__;!!G_uCfscf7eWS!YgUaDWSDN... >

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From: matt.newville--- via Ifeffit 
Sent: Sunday, July 27, 2025 8:27 AM
To: XAFS Analysis using Ifeffit 
Cc: matt.newville@gmail.com 
Subject: [Ifeffit] Re: Problems with linear combination fitting S-XANES data in Athena

Hi Julie, Sorry for the late reply. As Bruce and Bokky suggest, the ranges for pre-edge and normalization regions are not easy to automate over all energy ranges, and especially (for us, at least) at “tender” energies like the S K edge. This
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Hi Julie,

Sorry for the late reply. As Bruce and Bokky suggest, the ranges for pre-edge and normalization regions are not easy to automate over all energy ranges, and especially (for us, at least) at “tender” energies like the S K edge.  This partly because the automated E0 can move a lot compared to the energy range.    And for your project,  having a very short “normalization range” of only a few eV, can be unstable.

Reading this project into Larix, it does use a “Constant” for the normalization range.  So, the edge step does not go negative, even with the short normalization range.

If I were analyzing this data, I would probably start with putting all spectra to having E0=2472,  the pre-edge range to [-45, -15] (and Linear), and the post-edge range to [50, 150] and Constant.  For the “test mu” data, I would shorten the normalization range to [50, 100].

This project has some excellent S K-edge spectra on some standards, and a “test” spectrum that is “less good”.  To be clear: we do at my beamline and that is completely normal data with artefacts that we sometimes see too – and those standards are better than we ever measure (and, from browsing the CLS and ESRF ID21 databases, much better than “commonly measured”) and should be in some database ;).

--Matt

https://urldefense.us/v3/__https://xasdb.lightsource.ca/__;!!G_uCfscf7eWS!Yg... https://urldefense.us/v3/__https://xasdb.lightsource.ca/__;!!G_uCfscf7eWS!b7...

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I should say also that Larch and Larix probably have smarter ways of choosing initial parameters for the data reduction. Athena's initial guesses are pretty good for EXAFS data, but often do funny things (like you saw here) for data measured

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From: Ravel, Bruce via Ifeffit 
Date: Friday, July 25, 2025 at 12:49 PM
To: ifeffit@millenia.cars.aps.anl.gov 
Cc: Ravel, Bruce 
Subject: [Ifeffit] Re: Problems with linear combination fitting S-XANES data in Athena

I should say also that Larch and Larix probably have smarter ways of

choosing initial parameters for the data reduction.  Athena's initial

guesses are pretty good for EXAFS data, but often do funny things (like

you saw here) for data measured over a shorter energy range.

B

On 7/25/25 13:07, Ravel, Bruce wrote:
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Investigating further, it seems that the problem might instead be that
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you are putting too much faith in the default values for the various
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parameters used to process the data.  I mean this in the sense of the
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third paragraph of this page:
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https://urldefense.us/v3/__https://bruceravel.github.io/demeter/documents/At...https://urldefense.us/v3/__https:/bruceravel.github.io/demeter/documents/Ath...
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In short, you need to be more mindful of the values of the various
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processing parameters.  I am skeptical of the value of E0.  The values
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of the normalization parameters are certainly incorrect for this
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measurement, as is clear from the green and purple lines.  And when I
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click the orange normalization button, sure enough ... it plots the data
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inverted.
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Playing around just a bit with the parameters explained here:
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https://urldefense.us/v3/__https://bruceravel.github.io/demeter/documents/At...https://urldefense.us/v3/__https:/bruceravel.github.io/demeter/documents/Ath...
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and setting them to sensible values for your data completely fixes the
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problem.
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Professorial advice: don't just trust things, make sure you understand
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what is happening with your data.
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B
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On 7/24/25 16:28, Muretta, Julie via Ifeffit wrote:
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Hello, First of all, thank you all so very much for offering this
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platform to address XAS data processing!! It is wonderful to know it is
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available. I am having a problem using Athena "Linear Combination
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Fitting" with x-ray fluorescence
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Hello,
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First of all, thank you all so very much for offering this platform to
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address XAS data processing!! It is wonderful to know it is available.
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I am having a problem using Athena "Linear Combination Fitting" with x-
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ray fluorescence data from SSRL. Last year, we collected sulfur K-edge
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XANES data at SSRL, beamline 4-3 and processed them using SixPack
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(averaging 5 sweeps and normalization) and then used Athena to conduct
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linear combination fitting of the XANES region. It worked great!
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This year's data are presenting a problem when I get to the LCF step,
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however.  When I import the sample data .mu file into Athena and plot it
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by pressing the orange "E" button, the normalized spectrum looks like it
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should (albeit noisy and sometimes not the best data, but that is not
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Athena's fault). When I attempt to apply the Linear Combination Fitting
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algorithm, fitting a number of spectra from reference samples also
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collected _last year and this year_, Athena inverts the sample.mu
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spectrum (between -1 and 0 rather than 0 and 1). It does not invert old
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or new reference sample spectra. When I try this with old data, using
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old and new reference sample spectra, I do not have this problem. With
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the inverted sample spectrum, it often does not find a fit, but
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sometimes it does.
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Attached is an example Athena project file, the .mu file, and a plot of
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the output of a test fit, for your reference.
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I am hoping someone can please help me figure out why this is happening.
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I cannot see anything wrong, based on my limited experience, but
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hopefully it is something I have done wrong that can be easily corrected.
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Thank you in advance,
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Julie
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*Julie Muretta, Ph.D.*
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/Materials Testing Laboratory Manager/
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/Center for Advanced Materials Processing (CAMP)/
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_(406) 496-4808_ | jmuretta@mtech.edu
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--

  Bruce Ravel  ------------------------------------ bravel@bnl.gov

  National Institute of Standards and Technology

  Synchrotron Science Group at NSLS-II

  Lead Beamline Scientist, 6BM (BMM)

  Building 743, Room 114

  Upton NY, 11973

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