[Ifeffit] Re. Larch Energy Calibration

Mangold, Stefan (IPS) stefan.mangold at kit.edu
Tue Mar 9 05:20:38 CST 2021


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 <valerie.schoepfer at usask.ca>:
> 
> 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:
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>   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 <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Larch energy calibration
> Message-ID:
>        <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Valerie,
> 
> On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer at 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
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