Dear Valerie
Which Fe standards are you looking to compare?
I have a large collection of Fe references collected from the SuperXAS beamline
all relatively recently and are all calibrated using Fe reference foil measured
simultaneously.
Using a Si(111) monochromator:
Fe2O3
Fe3C
Fe5C2
Fe3O4
FeO
Ferrihydrite
Goethite
Lepidrocrite
FeCl3.xH2O
FeCl2
FeSO4
FeAmmoniumSulfate
Fe_Nitrate
Using Si(311) monochromator:
FeO
Fe2O3
Geothite
Lepidrocrite
Ferrihydrite
FeIII_Hexacyanoferrate
Fephthalocyanine
Fetetraohenylporphyrine
FePhenanthroline
Fephthalocyanine chloride
FeII_Hexacyanoferrate
FeBisglycinate
FeAmmoniumSulfate
Fe2EDTA
Fe3EDTA
The monochromator crystal choice affects the shape of the XANES due to the
relative energy resolution of the crystal.
Regards
Adam
__________________________________________
Paul Scherrer Institut
Adam Hugh Clark
WLGA/129
Forschungsstrasse 111
5232 Villigen PSI
Schweiz
Telefon: +41 56 310 41 51
E-Mail: adam.cl...@psi.ch
-----Original Message-----
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Today's Topics:
1. Re: Larch Energy calibration (Schoepfer, Valerie)
2. Re: Larch Energy calibration (Christopher Patridge)
----------------------------------------------------------------------
Message: 1
Date: Fri, 5 Mar 2021 16:06:22 +0000
From: "Schoepfer, Valerie" <valerie.schoep...@usask.ca>
To: "ifeffit@millenia.cars.aps.anl.gov"
<ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Larch Energy calibration
Message-ID:
<ytbpr01mb27659005c1015912348ba93894...@ytbpr01mb2765.canprd01.prod.outlook.com>
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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
-----Original Message-----
From: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> On Behalf Of
ifeffit-requ...@millenia.cars.aps.anl.gov
Sent: Thursday, March 4, 2021 12:00 PM
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Subject: Ifeffit Digest, Vol 217, Issue 3
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Today's Topics:
1. Re: Larch energy calibration (Matt Newville)
----------------------------------------------------------------------
Message: 1
Date: Wed, 3 Mar 2021 18:38:24 -0600
From: Matt Newville <newvi...@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Larch energy calibration
Message-ID:
<ca+7esbrgytdjidl4x+rcuei+dfml3duyg-r2r-fhffeqshs...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi Valerie,
On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie <
valerie.schoep...@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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Message: 2
Date: Fri, 5 Mar 2021 11:58:12 -0500
From: Christopher Patridge <patri...@buffalo.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Larch Energy calibration
Message-ID: <fa915b3b-177c-4c6b-9750-020cd1361...@buffalo.edu>
Content-Type: text/plain; charset="us-ascii"
Valerie,
What type of energy range are you looking at? How far back do samples go?
Chris
**********************************************
Dr Christopher Patridge
Associate Professor
Dept of Chemistry
SASE 315
716-829-8096 | patri...@dyc.edu
www.dyc.edu <http://www.dyc.edu/>
Social: Twitter <http://www.twitter.com/drpatridgc>
> On Mar 5, 2021, at 11:06 AM, Schoepfer, Valerie <valerie.schoep...@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
>
>
> -----Original Message-----
> From: Ifeffit <ifeffit-boun...@millenia.cars.aps.anl.gov> On Behalf Of
> ifeffit-requ...@millenia.cars.aps.anl.gov
> Sent: Thursday, March 4, 2021 12:00 PM
> To: ifeffit@millenia.cars.aps.anl.gov
> Subject: Ifeffit Digest, Vol 217, Issue 3
>
> CAUTION: External to USask. Verify sender and use caution with links
> and attachments. Forward suspicious emails to phish...@usask.ca
>
>
> 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-requ...@millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> ifeffit-ow...@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: Larch energy calibration (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Mar 2021 18:38:24 -0600
> From: Matt Newville <newvi...@cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Larch energy calibration
> Message-ID:
>
> <ca+7esbrgytdjidl4x+rcuei+dfml3duyg-r2r-fhffeqshs...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Valerie,
>
> On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie <
> valerie.schoep...@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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