[Ifeffit] No shift in XANES absorption peak
Disha Gupta
dsha.91 at gmail.com
Mon Jun 11 09:58:15 CDT 2018
Dear Claudia, Qingying Jia, Matt
Thank you so much for your responses :)
The shift in bond length I see is almost around 0.1-0.12 Angstrom, which is
not small enough to ignore. I think the coordination might be changing, if
not the oxidation state. I will redo the Artemis calculations with N as a
variable again to see if that helps. Because keeping my N constant actually
gave me pretty low Debye-Waller values and R factor was also below 5% so I
was assuming the fits were reliable.
I was also thinking maybe Mn is undergoing partial oxidation, however, in
bulk we do not see that change in the main XANES absorption peak. I am not
sure if that can be a possibility.
Thanks a lot again!
Kind Regards
Disha
Disha Gupta
Graduate Student
School of Materials Science and Engineering
Nanyang Technological University (NTU), Singapore
+65 84087404
DISHA001 at e.ntu.edu.sg
On Mon, Jun 11, 2018 at 10:14 PM, <ifeffit-request at millenia.cars.aps.anl.gov
> wrote:
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> Today's Topics:
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> 1. Re: Demeter on Windows 10 does not work (sikolen)
> 2. Re: No shift in XANES absorption peak (Claudia Schnohr)
> 3. Re: No shift in XANES absorption peak (Qingying Jia)
> 4. Re: Demeter on Windows 10 does not work (Matt Newville)
> 5. Re: No shift in XANES absorption peak (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Jun 2018 13:39:03 +0200
> From: sikolen <sikolen at jinr.ru>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Demeter on Windows 10 does not work
> Message-ID: <f70651f521390af9595e52ea564ba769 at jinr.ru>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Thanks Kathy,
>
> It seems the problem is really with the wrong path... Now I see how to
> fix it.
>
> Vadim
>
>
> On 2018-06-08 17:07, Kathy Dardenne wrote:
> > Dear Vadim,
> >
> > I am running myself Demeter 0.9.26, 64bit under win10 and do not have
> > such
> > trouble. But your description is similar to the problem occurring with
> > the
> > previous release of Demeter 0.9.26 pre2 (old path for gnuplot
> > executable in
> > ini file leading the same effect), did you download the actual version
> > for
> > Demeter 0.9.26? this later trouble is fixed and Demeter runs smoothly
> > with
> > win7 and win10.
> >
> > Kathy
> >
> > -----Message d'origine-----
> > De?: Ifeffit <ifeffit-bounces at millenia.cars.aps.anl.gov> De la part de
> > sikolen
> > Envoy??: vendredi 25 mai 2018 10:01
> > ??: ifeffit at millenia.cars.aps.anl.gov
> > Objet?: [Ifeffit] Demeter on Windows 10 does not work
> >
> >
> > Dear all,
> >
> > I've just changed my loving Windows-7 to the new Windows-10. I've
> > installed
> > Demeter (v.0.9.26, 64-bit), but it does not work: cmd-Windows appears
> > for
> > the a couple of seconds and disappears forever. Is it already known
> > problem
> > of the OS? Sorry, may be this question already appeared here, I just
> > missed
> > it.
> >
> > Vadim
> > --
> > ***********************************
> > Dr. Vadim Sikolenko
> > Senior Scientist
> > Frank Laboratory of Neutron Physics
> > Vadim.Sikolenko at jinr.ru
> > Skype: svadimm
> > **********************************
> > _______________________________________________
> > Ifeffit mailing list
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> >
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> --
> ***********************************
> Dr. Vadim Sikolenko
> Senior Scientist
> Frank Laboratory of Neutron Physics
> Vadim.Sikolenko at jinr.ru
> Skype: svadimm
> **********************************
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Jun 2018 14:56:22 +0200
> From: Claudia Schnohr <c.schnohr at uni-jena.de>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] No shift in XANES absorption peak
> Message-ID:
> <20180611145622.Horde.4UvsqRy3fmqp-P5XNJL1uln at webmail.uni-jena.de>
> Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes
>
> Dear Disha,
>
> In principle, yes, there can be a change of bond length without a
> notable change of the XANES. But it also depends on how large the bond
> length changes are that you observe.
>
> I have studied a lot of semiconductor alloys, for example (In,Ga)P or
> Cu(In,Ga)Se2 where the Ga and In atoms share the same lattice site.
> They are always coordinated to four P or Se atoms, respectively, but
> the bond lengths change by 0.02 to 0.03 A because the size of the unit
> cell changes with In/Ga ratio. At the same time, the Ga and In XANES
> is completely unaffected by a change of the In/Ga ratio. If you are
> interested in this, you may have a look at Phys. Rev. B 85, 245204
> (2012), J. Appl. Phys. 116, 093703 (2014), or Appl. Phys. Rev. 2,
> 031304 (2015).
>
> This is just to say that, yes, in some special cases you can have a
> change of bond length without a change of XANES. There can be lot's of
> other things going on, too :)
>
> Cheers, Claudia
>
>
>
> ----- Nachricht von Disha Gupta <dsha.91 at gmail.com> ---------
> Datum: Mon, 11 Jun 2018 18:29:49 +0800
> Von: Disha Gupta <dsha.91 at gmail.com>
> Antwort an: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
> >
> Betreff: Re: [Ifeffit] No shift in XANES absorption peak
> An: ifeffit at millenia.cars.aps.anl.gov
>
>
> > Dear Dr Carlo
> >
> > The edges are almost identical. The pre-edge intensity change isn't that
> > significant I feel. I did the Artemis fittings with the coordination
> > numbers fixed. Maybe I can try varying the coordination numbers and see
> if
> > it gives a different result.
> > I have attached the images of the pre-edge and main peak.
> >
> >
> >
> >
> >
> > Thanks and Regards
> > Disha
> >
> >
> >
> >
> > From: Carlo Segre <segre at iit.edu>
> > Date: Mon, Jun 11, 2018, 12:34
> > Subject: Re: [Ifeffit] No shift in XANES absorption peak
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> >
> >
> >
> > Hi Disha:
> >
> > it would be good to see the XANES you are referring to. Are the edges
> > identical or do they change but not shift significantly? Is the
> > coordination number also constant? Generally, the bond distance will
> > change with oxidation state if the coordination number is constant but if
> > the coordination number changes, then there could be a change in bond
> > length too.
> >
> > Cheers,
> >
> > Carlo
> >
> >
> > On Mon, 11 Jun 2018, Disha Gupta wrote:
> >
> >> Dear All
> >>
> >> Firstly, I would like to say sorry if I have missed out on this
> discussion
> >> before but it would be great if you could help me out.
> >> I have been analyzing some Mn K-edge XAS data for some battery
> materials.
> >> While the XANES data shows no shift in the main absorption peak which
> > means
> >> that there is no oxidation change happening, however, when I am fitting
> > the
> >> data in Artemis, I can see a shift in the bond lengths suggesting an
> >> oxidation change. Is it possible that bond lengths change even though
> > XANES
> >> spectra show no change?
> >>
> >>
> >> Thank you and Kind Regards
> >> Disha
> >>
> >
> > --
> > Carlo U. Segre -- Duchossois Leadership Professor of Physics
> > Interim Chair, Department of Chemistry
> > Director, Center for Synchrotron Radiation Research and Instrumentation
> > Illinois Institute of Technology
> > Voice: 312.567.3498 Fax: 312.567.3494
> > segre at iit.edu http://phys.iit.edu/~segre segre at debian.org
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
> >
> > Disha Gupta
> > Graduate Student
> > School of Materials Science and Engineering
> > Nanyang Technological University (NTU), Singapore
> > +65 84087404
> > DISHA001 at e.ntu.edu.sg
> >
> >
> > On Mon, Jun 11, 2018 at 11:34 AM, Disha Gupta <dsha.91 at gmail.com> wrote:
> >
> >> Dear All
> >>
> >> Firstly, I would like to say sorry if I have missed out on this
> discussion
> >> before but it would be great if you could help me out.
> >> I have been analyzing some Mn K-edge XAS data for some battery
> materials.
> >> While the XANES data shows no shift in the main absorption peak which
> means
> >> that there is no oxidation change happening, however, when I am fitting
> the
> >> data in Artemis, I can see a shift in the bond lengths suggesting an
> >> oxidation change. Is it possible that bond lengths change even though
> XANES
> >> spectra show no change?
> >>
> >>
> >> Thank you and Kind Regards
> >> Disha
> >>
>
>
> ----- Ende der Nachricht von Disha Gupta <dsha.91 at gmail.com> -----
>
>
>
> --
> PD Dr. Claudia S. Schnohr
> Institut f?r Festk?rperphysik
> Friedrich-Schiller-Universit?t Jena
> Max-Wien-Platz 1
> D-07743 Jena
> Germany
>
> Tel: +49 3641 947333
> Fax: +49 3641 947302
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 11 Jun 2018 09:59:23 -0400
> From: Qingying Jia <qjia at hawk.iit.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] No shift in XANES absorption peak
> Message-ID:
> <CAJR6HVQPT6q_1_PhFNB2+mqWuZf+YjgqvJpYeaWg5j=h30Zp8w at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Disha,
>
> The shift in bond distance in this case, is not necessarily associated
> with the change of oxidation state. It can be simply caused by the
> insertion/removal of Li/Na or whatever depending on your battery type
> during the charge/discharge, which sometimes changes the oxidation state of
> Mn slightly, sometimes doesn't.
>
> Regards,
>
> On Sun, Jun 10, 2018 at 11:34 PM, Disha Gupta <dsha.91 at gmail.com> wrote:
>
> > Dear All
> >
> > Firstly, I would like to say sorry if I have missed out on this
> discussion
> > before but it would be great if you could help me out.
> > I have been analyzing some Mn K-edge XAS data for some battery materials.
> > While the XANES data shows no shift in the main absorption peak which
> means
> > that there is no oxidation change happening, however, when I am fitting
> the
> > data in Artemis, I can see a shift in the bond lengths suggesting an
> > oxidation change. Is it possible that bond lengths change even though
> XANES
> > spectra show no change?
> >
> >
> > Thank you and Kind Regards
> > Disha
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at 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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> >
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> ------------------------------
>
> Message: 4
> Date: Mon, 11 Jun 2018 09:05:25 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Demeter on Windows 10 does not work
> Message-ID:
> <CA+7ESborfschG-Ufvz6WE0APVw3=9LBSGj202B9v6Pcf39KRYA at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Vadim,
>
> On Mon, Jun 11, 2018 at 6:39 AM sikolen <sikolen at jinr.ru> wrote:
>
> > Thanks Kathy,
> >
> > It seems the problem is really with the wrong path... Now I see how to
> > fix it.
> >
> >
> ?Can you please let us know which path was wrong and what you did? Your
> solution might be helpful to others....
>
> Thanks,
>
> --Matt
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> ------------------------------
>
> Message: 5
> Date: Mon, 11 Jun 2018 09:12:51 -0500
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] No shift in XANES absorption peak
> Message-ID:
> <CA+7ESboo9DRJ-5mTnfokzOGpo3vjxr6mc1zMYGDBnQg
> pqVfrqQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Disha,
>
> How big are the distance changes you are seeing? Like Carlo mentioned,
> there is a close connection between the set of (bond distance, coordination
> number, valence). See, for example, the very successful Bond Valence
> Model (https://en.wikipedia.org/wiki/Bond_valence_method). But in an
> abstract sense, coordination number and valence are discrete, while values
> for bond distance are continuous. So, there is some range of bond
> distances over which the valence does not change
>
> --Matt Newville
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