Exporting XANES data as a .csv file

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Kumar Jena

13 Apr 2023 13 Apr '23

3:52 a.m.

Dear, all, I am a new XAS user. I have done preprocessing of my data in Athena and have been trying to export the XANES data as a .csv file. I would like to fit the pre-peak region to pseudo-Voigt line shapes to extract approximate relative intensities of various transitions (A1, A2, A3, and B). Attached is a screenshot from an article for your reference ( https://doi.org/10.1021/jp981644k). Is it possible to do so in Athena? Any help would be appreciated. Kind regards, Kumar [image: image.png] -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email.

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Carlo Segre

13 Apr 13 Apr

4:14 a.m.

New subject: [Ext] Exporting XANES data as a .csv file

It is possible with the Peak Fit menu item however, you might wish to try xraylarch instead as it has a lot of useful tools for peak fitting of this kind. Carlo On Wed, Apr 12, 2023 at 10:53 PM Kumar Jena wrote:

...

Dear, all, I am a new XAS user. I have done preprocessing of my data in Athena and have been trying to export the XANES data as a .csv file. I would like to fit the pre-peak region to pseudo-Voigt line shapes to extract approximate relative intensities of various transitions (A1, A2, A3, and B). Attached is a screenshot from an article for your reference ( https://doi.org/10.1021/jp981644k).

Is it possible to do so in Athena?

Any help would be appreciated. Kind regards, Kumar

[image: image.png] -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email. _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org

Kumar Jena

4:21 a.m.

New subject: [Ext] Exporting XANES data as a .csv file

Thank you, Prof. Segre. I appreciate your fast response. Kind regards, Kumar On Thu, 13 Apr 2023 at 16:15, Carlo Segre wrote:

...

It is possible with the Peak Fit menu item however, you might wish to try xraylarch instead as it has a lot of useful tools for peak fitting of this kind.

Carlo

On Wed, Apr 12, 2023 at 10:53 PM Kumar Jena wrote:

...
Dear, all, I am a new XAS user. I have done preprocessing of my data in Athena and have been trying to export the XANES data as a .csv file. I would like to fit the pre-peak region to pseudo-Voigt line shapes to extract approximate relative intensities of various transitions (A1, A2, A3, and B). Attached is a screenshot from an article for your reference ( https://doi.org/10.1021/jp981644k).

Is it possible to do so in Athena?

Any help would be appreciated. Kind regards, Kumar

[image: image.png] -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email. _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- Carlo U. Segre (he/him) -- Duchossois Leadership Professor of Physics Professor of Materials Science & Engineering Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* ***THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email.

Matt Newville

12:05 p.m.

Hi Kumar, Just to echo Carlo's suggestion, you can import the Athena project into XAS Viewer and do the pre-edge peak fitting there. Pre-edge peak fitting is really significantly better in XAS Viewer than in Athena. There are more lineshapes available (including a non-pseudo Voigt) choices, and you can place upper/lower bounds on each variable in the fit. The Pre-Edge Peak panel starts by wanting to define a "baseline" function describing the main edge -- typically a line + a Lorentzian, and then you can add peaks from there. There is a video on using this at https://www.youtube.com/watch?v=bd7PgaDpVc0 On Wed, Apr 12, 2023 at 10:53 PM Kumar Jena wrote:

...

Dear, all, I am a new XAS user. I have done preprocessing of my data in Athena and have been trying to export the XANES data as a .csv file. I would like to fit the pre-peak region to pseudo-Voigt line shapes to extract approximate relative intensities of various transitions (A1, A2, A3, and B). Attached is a screenshot from an article for your reference ( https://doi.org/10.1021/jp981644k).

Is it possible to do so in Athena?

Any help would be appreciated. Kind regards, Kumar

[image: image.png] -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email. _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411

Kumar Jena

12:43 p.m.

Hi Matt, Thank you for taking time to reply. Really appreciate it. And the video lecture is super helpful. Kind regards, Kumar On Fri, 14 Apr 2023, 12:08 am Matt Newville, wrote:

...

Hi Kumar,

Just to echo Carlo's suggestion, you can import the Athena project into XAS Viewer and do the pre-edge peak fitting there. Pre-edge peak fitting is really significantly better in XAS Viewer than in Athena. There are more lineshapes available (including a non-pseudo Voigt) choices, and you can place upper/lower bounds on each variable in the fit. The Pre-Edge Peak panel starts by wanting to define a "baseline" function describing the main edge -- typically a line + a Lorentzian, and then you can add peaks from there.

There is a video on using this at https://www.youtube.com/watch?v=bd7PgaDpVc0

On Wed, Apr 12, 2023 at 10:53 PM Kumar Jena wrote:

...
Dear, all, I am a new XAS user. I have done preprocessing of my data in Athena and have been trying to export the XANES data as a .csv file. I would like to fit the pre-peak region to pseudo-Voigt line shapes to extract approximate relative intensities of various transitions (A1, A2, A3, and B). Attached is a screenshot from an article for your reference ( https://doi.org/10.1021/jp981644k).

Is it possible to do so in Athena?

Any help would be appreciated. Kind regards, Kumar

[image: image.png] -- [image: University of Auckland (UOA) - WEGO-ITN] *Kumar Debajyoti Jena* *M.Tech (IIT Kanpur)* *Ph.D. Student* Department of Chemical and Materials Engineering Faculty of Engineering The University of Auckland Mob: *(+64) 225155447* *THERE IS NO PLAN*ET *B*. Please think of the environment before you print this email. _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- --Matt Newville <newville at cars.uchicago.edu> 630-327-7411 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Carlo Segre
Kumar Jena
Matt Newville