June 2018 - Ifeffit - millenia.cars.aps.anl.gov

Restrain
by ABDUL AHAD 14 Jun '18

14 Jun '18

Hi all, i have query regarding restrain. suppose i have single scattering path which is equal to lattice parameter. Now i also have multi-scattering path with Reff equal to the same single scattering path. Now my question is, Is it correct to constraint the all path of same reff to equal delt_r, Because i think in magnitude they must lie on same R but different in phase (different frequency component). thanks -- ** *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a <a_ahad.rs(a)amu.ac.in>bdulahad.phy(a)gmail.com <bdulahad.phy(a)gmail.com>*

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Decision of Enot and model
by ABDUL AHAD 12 Jun '18

12 Jun '18

hi all, i have some questions to experts. if i have cif file to any compound say ZnO and i fitted the exafs data with it. Now the question is if i wish to fit the doped ZnO with the same cif and the same Enot then it shows large value of delta to fit. The question is have i look for different Enot or i have to change the cif for the doped one. Note i m talking about the main peak fit that only contain the Zn and O not the doped element. Is there any limit of delta for bond length? i think it should be small. Thanks in advance -- ** *A. Ahad* *--------------------* *Abdul Ahad* Junior Research Fellow *Dept of Physics* *Aligarh Muslim University* *Aligarh 202002 (U.P.), India* *http://www.researcherid.com/rid/G-8198-2018 <http://www.researcherid.com/rid/G-8198-2018>* *Email: a <a_ahad.rs(a)amu.ac.in>bdulahad.phy(a)gmail.com <bdulahad.phy(a)gmail.com>*

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Re: [Ifeffit] No shift in XANES absorption peak
by Disha Gupta 12 Jun '18

12 Jun '18

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(a)e.ntu.edu.sg On Mon, Jun 11, 2018 at 10:14 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov > wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: 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(a)jinr.ru> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter on Windows 10 does not work > Message-ID: <f70651f521390af9595e52ea564ba769(a)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(a)millenia.cars.aps.anl.gov> De la part de > > sikolen > > Envoy??: vendredi 25 mai 2018 10:01 > > ??: ifeffit(a)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(a)jinr.ru > > Skype: svadimm > > ********************************** > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > -- > *********************************** > Dr. Vadim Sikolenko > Senior Scientist > Frank Laboratory of Neutron Physics > Vadim.Sikolenko(a)jinr.ru > Skype: svadimm > ********************************** > > > ------------------------------ > > Message: 2 > Date: Mon, 11 Jun 2018 14:56:22 +0200 > From: Claudia Schnohr <c.schnohr(a)uni-jena.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] No shift in XANES absorption peak > Message-ID: > <20180611145622.Horde.4UvsqRy3fmqp-P5XNJL1uln(a)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(a)gmail.com> --------- > Datum: Mon, 11 Jun 2018 18:29:49 +0800 > Von: Disha Gupta <dsha.91(a)gmail.com> > Antwort an: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > > > Betreff: Re: [Ifeffit] No shift in XANES absorption peak > An: ifeffit(a)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(a)iit.edu> > > Date: Mon, Jun 11, 2018, 12:34 > > Subject: Re: [Ifeffit] No shift in XANES absorption peak > > To: XAFS Analysis using Ifeffit <ifeffit(a)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(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)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(a)e.ntu.edu.sg > > > > > > On Mon, Jun 11, 2018 at 11:34 AM, Disha Gupta <dsha.91(a)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(a)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(a)hawk.iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)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(a)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(a)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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Re: [Ifeffit] No shift in XANES absorption peak
by Disha Gupta 11 Jun '18

11 Jun '18

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(a)iit.edu> Date: Mon, Jun 11, 2018, 12:34 Subject: Re: [Ifeffit] No shift in XANES absorption peak To: XAFS Analysis using Ifeffit <ifeffit(a)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(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org _______________________________________________ Ifeffit mailing list Ifeffit(a)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(a)e.ntu.edu.sg On Mon, Jun 11, 2018 at 11:34 AM, Disha Gupta <dsha.91(a)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 >

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Demeter on Windows 10 does not work
by sikolen 11 Jun '18

11 Jun '18

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(a)jinr.ru Skype: svadimm **********************************

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No shift in XANES absorption peak
by Disha Gupta 11 Jun '18

11 Jun '18

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

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Interpreting old XANES data with missing standards
by Don Baker 08 Jun '18

08 Jun '18

Hello All, First let me apologize if the question below is inappropriate for this group, but I don't know of a better set of experts that I can ask. So, here is some background: I have some old S K-edge XANES data from NSLS X15B for S-bearing silicate glasses that was collected by a Ph.D. student who decided to leave for a good job rather than finishing their degree. During my current sabbatical year I have been looking at the data and reading papers on the topic. I think that I now understand, at least qualitatively, the changes in the spectra as a function of iron concentration in the glasses, but to perform quantitative modelling I need XANES spectra of MgS and CaS, which we did not think to collect all those years ago. I have searched for XANES spectra of MgS and CaS on the CARS XAFS Data Library and on the XAFS Database at IIT without success. I am unaware of other databases available. Now for for my questions: 1. Does anyone know of a XANES database that contains MgS and CaS spectra? (Or did I miss it in the databases I searched?) 2. If I cannot find measured MgS and CaS spectra, what do you think about using calculated spectra (e.g., Zheng et al.,2012, NPJ Computational Materials, 12 -- which uses FEFF) for quantitative modelling? And information, ideas, and suggestions that you may have will be appreciated. Wishing you all the best from a spring morning in Montreal, Don -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University

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FEFF question
by Loges, Anselm G 06 Jun '18

06 Jun '18

Hi everyone, not exactly an ifeffit question, but maybe someone knows. Since I am for ome reason unable to install ifeffit or demeter on certain Linux computers (others with the same distribution and same settings work fine), I have been trying to install FEFF8-lite. However, on the downloadpage: http://monalisa.phys.washington.edu/feff/Bin-Source-feff8Lite/Bin-Source.ht… the link for the Linux binary is dead and when I try to compile from source using gfortran it does not work and throws "Error: Two main PROGRAMs at (1) and (2)". A quick look in the code reveals that none of the subroutines etc. are ended explicitly by name but only by an anonymous "end", making debugging this problem in the source a colossal nightmare in a 52951 line source file. This also likely explains where the error comes from in the first place, since lack of explicitness is the mother of portability problems. I'm wondering: has anyone had success installing FEFF8-lite or compiling from source? If so, with what compiler? Or is there a working Linux binary wandering about the interwebs, which I have not found? I have also tried using Matt Newvilles package on Github: https://github.com/xraypy/feff85exafs but no luck there either. This one complains about a python package named "larch" being missing, making me think it wants a preexisting a Larch installation. Installing FEFF8L should not require Larch, only the other way round (possibly), right? I'm lost and thankful for any and all help! Best regards, Anselm

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