Hi Disha,

  For such a huge shit of bond distance, the corresponding lattice constant change should be readily seen by XRD. It will also shift the XANES edge slightly.

  Regards,

On Mon, Jun 11, 2018 at 10:58 AM, Disha Gupta <dsha.91@gmail.com> wrote:
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


On Mon, Jun 11, 2018 at 10:14 PM, <ifeffit-request@millenia.cars.aps.anl.gov> wrote:
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Today's Topics:

   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@jinr.ru>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
 Subject: Re: [Ifeffit] Demeter on Windows 10 does not work
Message-ID: <f70651f521390af9595e52ea564ba769@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@millenia.cars.aps.anl.gov> De la part de
> sikolen
> Envoy??: vendredi 25 mai 2018 10:01
> ??: ifeffit@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@jinr.ru
> Skype: svadimm
> **********************************
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
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 --
***********************************
Dr. Vadim Sikolenko
Senior Scientist
Frank Laboratory of Neutron Physics
Vadim.Sikolenko@jinr.ru
Skype: svadimm
**********************************


------------------------------

Message: 2
Date: Mon, 11 Jun 2018 14:56:22 +0200
From: Claudia Schnohr <c.schnohr@uni-jena.de>
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] No shift in XANES absorption peak
 Message-ID:
        <20180611145622.Horde.4UvsqRy3fmqp-P5XNJL1uln@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@gmail.com> ---------
      Datum: Mon, 11 Jun 2018 18:29:49 +0800
        Von: Disha Gupta <dsha.91@gmail.com>
Antwort an: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
    Betreff: Re: [Ifeffit] No shift in XANES absorption peak
         An: ifeffit@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@iit.edu>
> Date: Mon, Jun 11, 2018, 12:34
> Subject: Re: [Ifeffit] No shift in XANES absorption peak
> To: XAFS Analysis using Ifeffit <ifeffit@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@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
>
 > Disha Gupta
> Graduate Student
> School of Materials Science and Engineering
> Nanyang Technological University (NTU), Singapore
> +65 84087404
> DISHA001@e.ntu.edu.sg
>
>
 > On Mon, Jun 11, 2018 at 11:34 AM, Disha Gupta <dsha.91@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@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@hawk.iit.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] No shift in XANES absorption peak
 Message-ID:
        <CAJR6HVQPT6q_1_PhFNB2+mqWuZf+YjgqvJpYeaWg5j=h30Zp8w@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@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@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@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
 Subject: Re: [Ifeffit] Demeter on Windows 10 does not work
Message-ID:
        <CA+7ESborfschG-Ufvz6WE0APVw3=9LBSGj202B9v6Pcf39KRYA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Vadim,

On Mon, Jun 11, 2018 at 6:39 AM sikolen <sikolen@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@cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] No shift in XANES absorption peak
 Message-ID:
        <CA+7ESboo9DRJ-5mTnfokzOGpo3vjxr6mc1zMYGDBnQgpqVfrqQ@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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