Re: [Ifeffit] Ifeffit Digest, Vol 217, Issue 6

Dear Valerie Sorry! I don't know where I got the idea that it was Fe, I was probably working on Fe data at the time of writing. Having looked back I can see Mo. "I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting." For Mo I also have some standards, maybe these would be helpful for you. These are all calibrated with the first derivative of the Mo foil and so are consistent with each other. Although measured on a different monochromator, the likely would serve well to compare the edge position to make sure the calibration is done consistently for the standards you have from the canadian light source to give some idea of if things are reliable. Si(111): Mo MoO2 MoO3 Fe2Mo3O12 Mo2C NiMoO4 Adam __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark@psi.ch ________________________________ From: Ifeffit on behalf of ifeffit-request@millenia.cars.aps.anl.gov Sent: Tuesday, March 9, 2021 7:00:01 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 6 Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Re. Larch Energy Calibration (Mangold, Stefan (IPS)) 2. Re: Larch Energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Mar 2021 11:20:38 +0000 From: "Mangold, Stefan (IPS)" To: "Schoepfer, Valerie" Cc: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Re. Larch Energy Calibration Message-ID: <45116D6C-9314-4822-8E1B-7FB929333D72@kit.edu> Content-Type: text/plain; charset="utf-8" Dear Valerie, The reason why I'm currently not using Larch for my data-evaluation chain is, that I didn?t found some features (like energy calibration; not as I use it; like Calibration of references, absorption and fluorescence spectra in one group) in Larch, which I need for my data evaluation process. They might be there, but I didn?t found them. for the XANES data evaluation your energy region might be a bit to short to fit a good background to the data. Anyway you have to fine-tune the parameters to reach a good background fit in the XANES region. While the automatic process in Athena produces quite good results for a lot of absorption edges, one has to be careful not add artefacts to the data in the XANES. Best regards Stefan

Am 08.03.2021 um 14:17 schrieb Schoepfer, Valerie :

Hi Chris and Adam,

I'm actually looking at Mo, so the energy range is from about 19800 through 20200 eV on a Si(220) monochromator. (But thank you for your Fe offer!) The standards seem to be all from the Canadian Light Source, but going as far back as 2013... I'm not looking to make the LCF perfect at this point, but it does seem like the deeper I go, the less confident I am that I have the correct standards.

I'm doing alright in Athena with respect to the process, its just that I can't get Larch to align properly. I'll probably just use Athena for data prep, Larch just seemed nice to learn. But then in Athena I run into trouble with incorrect standards. One thing after another, you know?

Thanks- Valerie

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Today's Topics:

1. Re: Larch energy calibration (Matt Newville)

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Message: 1 Date: Wed, 3 Mar 2021 18:38:24 -0600 From: Matt Newville To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Larch energy calibration Message-ID: Content-Type: text/plain; charset="utf-8"

Hi Valerie,

On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer@usask.ca> wrote:

...

Hi,

I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting.

Right now, which is likely wrong, I?m calibrating the energy of a standard to the theoretical edge, then auto-aligning the samples to the standard. But how do reference foils fit in here? Reference foils don?t seem to be tied to the sample like they are in Athena. Should I be manually aligning?

Is there a general guidance or work flow?

It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question.

For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime.

If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every measurement - that would indicate a serious problem. So, I think you should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable?

I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead of time. I'm sure that leads to a bias in the software. I guess I forgot that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration.

Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient?

--Matt