[Ifeffit] Larch Energy calibration

Christopher Patridge patridge at buffalo.edu
Fri Mar 5 10:58:12 CST 2021 

Valerie,

What type of energy range are you looking at?  How far back do samples go?  

Chris

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Dr Christopher Patridge
Associate Professor 
Dept of Chemistry
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> On Mar 5, 2021, at 11:06 AM, Schoepfer, Valerie <valerie.schoepfer at usask.ca> wrote:
> 
> Hi Matt,
> 
> The backstory is that I'm trying to find which standards will define my samples, so I am pulling standards from different beamlines and years to get a basic linear combination fit, to run new standards myself when I have more beamtime.  
> 
> I'm able to do it in Athena- where you more or less:
> 1. Assign E0 to the first peak in the first derivative of your standard reference foil. 
> 2. Calibrate one standard reference foil to the theoretical edge energy.
> 3. Ensure E0 is right/adjust E0 for all samples and sample foils.
> 4. Align reference foils to the standard reference foil, because the foil will pull the sample with it.
> 
> But in Larch, maybe I'm unsure about the groups function?  I'm not convinced the reference foils 'follow' the sample spectra. 
> If the reference and samples aren't tied together, how do you align samples when your energies are off because of different beamlines or years or people not as careful to calibrate the beamline energy? 
> My first thought was using the first derivative peak of your sample, but if your edge energy shifts because of oxidation state changes, what do you use then?
> 
> 
> I'm still trying to form my question, so let me know if this still doesn't make much sense. 
> 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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