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

Re: [Ifeffit] sigma^2 values for multiple scattering paths
by Scott Calvin 06 Oct '10

06 Oct '10

Although I agree with the main points that Bruce makes, I do want to comment on one piece: On Oct 6, 2010, at 7:03 AM, Bruce Ravel wrote: > . > > In no case can I understand a physical explanation for the the MS > sigma^2 being smaller than for the SS. Actually, there is a physical situation where something like that can occur, although it sounds like it's not the one that Han Sen has. Consider an absorbing atom rattling around in a relatively fixed cage or lattice. And then consider a linear (or near-linear) arrangement: S1 -- A -- S2 One multiple scattering path that can sometimes have a sizable contribution is A --> S1 --> S2 --> A. This path will have a sigma^2 that is a bit larger than the single-scattering path S1 --> S2 --> S1, because of the perpendicular component of the motion of A. But it's quite frequently the case that S1 --> S2 --> S1 is not modeled in a fit, because the S edge is not measured. On the other hand, the single scattering paths A --> S1 --> A and A -- > S2 --> A ARE included in the fit. Those two have high sigma^2's, because A is rattling around a lot. Under that circumstance, a multiple-scattering path included in the fit may indeed have a lower sigma^2 than the single-scattering paths included in the fit. The moral, of course, is that it's not hard to think physically about what sigma^2 means for a multiple scattering path. If one appears to have an "unphysically" small sigma2, then the explanation is probably one of the ones given by Bruce or Shelly. One more thought on this. How much does it change your fit, Han Sen, if you set the sigma^2 for the multiple-scattering path to some "reasonable" value. If the scientific information you want from your fit is not sensitive to exactly what sigma^2 the MS path gets, and is not significantly different when given a "reasonable" value than when allowed to find its "best-fit" value, then there's probably no need to resolve the issue. In my experience, this is often the case with low- amplitude MS paths: the fit is improved by their inclusion, but may not be particularly sensitive to the details of their path parameters. --Scott Calvin Sarah Lawrence College

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More than 256 paths on Mac OS 10.5?
by Scott Calvin 06 Oct '10

06 Oct '10

Hi all, Do any of you have a version of Ifeffit compiled for Mac OS 10.5 that allows more than 256 paths? --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Shelly Kelly/Bruce Ravel); Re: Ifeffit Digest, Vol 92, Issue 2
by Han Sen Soo 06 Oct '10

06 Oct '10

Hello Shelly and Bruce, Thank you both for replying. I was wondering if there was some obvious reason that I missed. But you're both right, I think I will try to re-orientate the paths to make them more linear and then try the Debye and Einstein models. I may be back for more before I conclude that its bad data quality... Thank you again! han sen On Oct 6, 2010, at 7:02 AM, 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: Ifeffit Digest, Vol 92, Issue 1 (Elsa Sileo) > 2. sigma^2 values for multiple scattering paths (Han Sen Soo) > 3. More than 256 paths on Mac OS 10.5? (Scott Calvin) > 4. Re: sigma^2 values for multiple scattering paths (Shelly Kelly) > 5. Re: sigma^2 values for multiple scattering paths (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 5 Oct 2010 20:58:03 +0000 (GMT) > From: Elsa Sileo <e_sileo(a)yahoo.es> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 92, Issue 1 > Message-ID: <532560.26796.qm(a)web27807.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks Shelly, > ? > now atoms is running beautifully!!! > ? > Elsa > ? > > --- El s?b, 2/10/10, ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> escribi?: > > > De: ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> > Asunto: Ifeffit Digest, Vol 92, Issue 1 > Para: ifeffit(a)millenia.cars.aps.anl.gov > Fecha: s?bado, 2 de octubre, 2010 14:00 > > > 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. Incorrect distances obtaines from Scorodite CIF file (Elsa Sileo) > ???2. Re: Incorrect distances obtaines from Scorodite CIF file > ? ? ? (Shelly Kelly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Oct 2010 17:06:28 +0000 (GMT) > From: Elsa Sileo <e_sileo(a)yahoo.es> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Incorrect distances obtaines from Scorodite CIF > ??? file > Message-ID: <957578.81901.qm(a)web27807.mail.ukl.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Shelly, thanks?for your answer to the Eo aligment. > Now I am attaching the the scorodite CIF?file because I get incorrect As-Fe distances when I use it to obtain the feff path. > I hope someone has the answer, > ? > Elsa > ? > > > ? ? ? >

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sigma^2 values for multiple scattering paths
by Han Sen Soo 06 Oct '10

06 Oct '10

Hello, I briefly read through the FAQ about this but I'm not sure if it answers my question. Are there situations where the sigma^2 for a multiple scattering path can be smaller than the direct paths? So small that they're on the order of 0.001-0.003 for a degeneracy of 12 such paths? I'm working on a fitting model that does not work well with additional shells but it looks almost perfect with a multiple scattering path included. I'm skeptical however, because of the small sigma^2 values. I am also not discounting the fact that the data quality may be poor. But I would appreciate any physical reasons for small sigma^2 values. Thanks! han sen

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Re: [Ifeffit] Ifeffit Digest, Vol 92, Issue 1
by Elsa Sileo 05 Oct '10

05 Oct '10

Thanks Shelly, now atoms is running beautifully!!! Elsa --- El sáb, 2/10/10, ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> escribió: De: ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Asunto: Ifeffit Digest, Vol 92, Issue 1 Para: ifeffit(a)millenia.cars.aps.anl.gov Fecha: sábado, 2 de octubre, 2010 14:00 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. Incorrect distances obtaines from Scorodite CIF file (Elsa Sileo) 2. Re: Incorrect distances obtaines from Scorodite CIF file (Shelly Kelly) ---------------------------------------------------------------------- Message: 1 Date: Fri, 1 Oct 2010 17:06:28 +0000 (GMT) From: Elsa Sileo <e_sileo(a)yahoo.es> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Incorrect distances obtaines from Scorodite CIF file Message-ID: <957578.81901.qm(a)web27807.mail.ukl.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear Shelly, thanks?for your answer to the Eo aligment. Now I am attaching the the scorodite CIF?file because I get incorrect As-Fe distances when I use it to obtain the feff path. I hope someone has the answer, ? Elsa ?

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Incorrect distances obtaines from Scorodite CIF file
by Elsa Sileo 01 Oct '10

01 Oct '10

Dear Shelly, thanks for your answer to the Eo aligment. Now I am attaching the the scorodite CIF file because I get incorrect As-Fe distances when I use it to obtain the feff path. I hope someone has the answer, Elsa

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Interatomic distances from feff paths
by Elsa E. Sileo 01 Oct '10

01 Oct '10

I am trying to use the following CIF files to generate the feff path at the As edge: 1- 'Iron(III) arsenate(V) dihydrate', Scorodite, H4 As Fe O6'; space group P c a b; number 61; orthorhombic and 2. Iron(III) tris(dihydrogenarsenate) pentahydrate Kaatialaite, Fe (H2 As O4)3 (H2 O)5, P 1 21/n 1, number 14; monoclinic and in both cases, after running Feff, I obtain distances Fe-As that are not real. For instance in scorodite I find a distance As-Fe = 1,71 A. How can I overcome this problem? Thanks, Elsa At 14:00 30/09/2010, you 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: Ifeffit Digest, Vol 91, Issue 28 (Matt Newville) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 30 Sep 2010 11:28:28 -0500 >From: Matt Newville <newville(a)cars.uchicago.edu> >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28 >Message-ID: > <AANLkTinRMxoi2ANd=H=a+Bir5FRG0rruw_UPYy53sfCE(a)mail.gmail.com> >Content-Type: text/plain; charset=ISO-8859-1 > >Hi Elsa, > >On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo <e_sileo(a)yahoo.es> wrote: > > > > Dear Matt, > > > > I have to perform EXAFS analysis, and when I tried to fit the first > > shell, I found deltaE0 values of about 8 eV. Following the paper of > > Kelly et al (Analysis of soils and minerals using X-ray absorption > > spectroscopy. In Methods of soil analysis, Part 5: Mineralogical > > methods; 2008; pp 446) I fitted the first shell obtaining values for > > deltaE0, sigma^2; delta R and amplitude. Then, using the obtained > > values, and making deltaE0=0, I got the theoretical signal. > >Why is important to have a theoretical spectra with deltaE0=0? > > > When I compare the experimental and theoretical spectrum I see a mismatch > > between the position of the nodes at low wavenumbers. > >Yes, that is what E0 does. > > > Having done this, how I have to proceed to correct the experimental > > data in order to obtain smalller delta E0 values? > >I think what you are trying to do (though I don't understand why) is >to adjust E0 for the experimental data so that the fit to a particular >theoretical standard gives deltaE0 close to zero. If so, you want to >adjust E0 in the background subtraction. If you change E0 by 8eV >there, you should end up with a deltaE0 in the fit that is close to >zero. > >Hope that helps, > >--Matt > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 91, Issue 30 >*************************************** > > >No virus found in this incoming message. >Checked by AVG - www.avg.com >Version: 8.5.445 / Virus Database: 271.1.1/3168 >- Release Date: 09/30/10 06:34:00 Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 30
by Elsa E. Sileo 30 Sep '10

30 Sep '10

Thanks Matt, now I realize that I can directly change de Eo in the Athena window, Elsa At 14:00 30/09/2010, you 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: Ifeffit Digest, Vol 91, Issue 28 (Matt Newville) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 30 Sep 2010 11:28:28 -0500 >From: Matt Newville <newville(a)cars.uchicago.edu> >To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >Subject: Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28 >Message-ID: > <AANLkTinRMxoi2ANd=H=a+Bir5FRG0rruw_UPYy53sfCE(a)mail.gmail.com> >Content-Type: text/plain; charset=ISO-8859-1 > >Hi Elsa, > >On Thu, Sep 30, 2010 at 10:33 AM, Elsa Sileo <e_sileo(a)yahoo.es> wrote: > > > > Dear Matt, > > > > I have to perform EXAFS analysis, and when I tried to fit the first > > shell, I found deltaE0 values of about 8 eV. Following the paper of > > Kelly et al (Analysis of soils and minerals using X-ray absorption > > spectroscopy. In Methods of soil analysis, Part 5: Mineralogical > > methods; 2008; pp 446) I fitted the first shell obtaining values for > > deltaE0, sigma^2; delta R and amplitude. Then, using the obtained > > values, and making deltaE0=0, I got the theoretical signal. > >Why is important to have a theoretical spectra with deltaE0=0? > > > When I compare the experimental and theoretical spectrum I see a mismatch > > between the position of the nodes at low wavenumbers. > >Yes, that is what E0 does. > > > Having done this, how I have to proceed to correct the experimental > > data in order to obtain smalller delta E0 values? > >I think what you are trying to do (though I don't understand why) is >to adjust E0 for the experimental data so that the fit to a particular >theoretical standard gives deltaE0 close to zero. If so, you want to >adjust E0 in the background subtraction. If you change E0 by 8eV >there, you should end up with a deltaE0 in the fit that is close to >zero. > >Hope that helps, > >--Matt > > >------------------------------ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >End of Ifeffit Digest, Vol 91, Issue 30 >*************************************** > > >No virus found in this incoming message. >Checked by AVG - www.avg.com >Version: 8.5.445 / Virus Database: 271.1.1/3168 >- Release Date: 09/30/10 06:34:00 Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Ifeffit Digest, Vol 91, Issue 28
by Elsa Sileo 30 Sep '10

30 Sep '10

Dear Matt, I have to perform EXAFS analysis, and when I tried to fit the first shell, I found deltaE0 values of about 8 eV. Following the paper of Kelly et al (Analysis of soils and minerals using X-ray absorption spectroscopy. In Methods of soil analysis, Part 5: Mineralogical methods; 2008; pp 446) I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, using the obtained values, and making deltaE0=0, I got the theoretical signal. When I compare the experimental and theoretical spectrum I see a mismatch between the position of the nodes at low wavenumbers. Having done this, how I have to proceed to correct the experimental data in order to obtain smalller delta E0 values? Thanks in advance, Elsa --- El mié, 29/9/10, ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> escribió: De: ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Asunto: Ifeffit Digest, Vol 91, Issue 28 Para: ifeffit(a)millenia.cars.aps.anl.gov Fecha: miércoles, 29 de septiembre, 2010 14:00 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: Aligning Energy scales (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 28 Sep 2010 12:55:15 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Aligning Energy scales Message-ID: <AANLkTima_bGt5OO=K-Vb-0aRGwb9AC_W6BcBLwgCAg4t(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear Elsa, It sounds like you want to adjust the data chi(k) so that deltaE0 is 0 in a fit. Is that correct, or are you trying to do something else (say, align the XANES)? If that assumption is correct, you want to change the E0 used to extract chi(k) from the experimental spectra -- the E0 of the background subtraction. That is what sets k for the data. If that's not clear or not the right question, let us know, --Matt On Mon, Sep 27, 2010 at 2:00 PM, Elsa E. Sileo <sileo(a)qi.fcen.uba.ar> wrote: > I need to align a measured spectra to a theoretically calculated spectra. > I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and > amplitude. > Then, using the obtained values, and making deltaE0=0, I got the theoretical > signal. > But I do not know how to use this last theoretical fit to align the spectra. > Can somebody help me? > > Thanks, > > Elsa > > > Dra. Elsa E. Sileo > Solidos Inorganicos > INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA > Int. G?iraldes 2160, Pabell?n 2, Piso 3, Ciudad Universitaria - C1428EHA > CABA - Argentina > Tel: (54 11) 4576 3380 ext. 113 > Fax: (54 11) 4576 3341 > e-mail: sileo(a)qi.fcen.uba.ar > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 91, Issue 28 *************************************** ns

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EXAFS spectrum of Fe foil (fcc)
by KONG Quingyu 30 Sep '10

30 Sep '10

Dear All, Does anyone has an EXAFS spectrum of gama Fe foil, or Fe foil spectrum measured at high temperature (more than 1000 degree). If you have this measurement, would you please send me a copy of the data. I would like to compare with our recent measured EXAFS spectrum. Thanks a lot in advance, Sincerely, Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ************************************

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Aligning Energy scales
by Elsa E. Sileo 28 Sep '10

28 Sep '10

I need to align a measured spectra to a theoretically calculated spectra. I fitted the first shell obtaining values for deltaE0, sigma^2; delta R and amplitude. Then, using the obtained values, and making deltaE0=0, I got the theoretical signal. But I do not know how to use this last theoretical fit to align the spectra. Can somebody help me? Thanks, Elsa Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] iXAFS 3.0.3 for Mac OS X (Brandon Reese)
by Brugger, Joel (SAM) 23 Sep '10

23 Sep '10

Hi Brandon, Did you actually test the python module (i.e. Use python scripting to control arthemis?) On 10.6.4, I've obtain the following error: bash-3.2$ python Python 2.6.1 (r261:67515, Dec 17 2009, 00:59:15) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import math >>> import Ifeffit >>> iff = Ifeffit.Ifeffit() failed to load ifeffit library libifeffit.dylib /usr/local/share/ifeffit/:/opt/intel/Compiler/11.1/089/bin/intel64:/opt/local/bin:/opt/local/sbin:/Volumes/iXAFS3.0/iXAFS.app/Contents/Resources/local/bin:/opt/intel/Compiler/11.1/089/bin/intel64:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Applications/iXAFS.app/Contents/Resources/local/bin:/Users/joelb/Desktop/Molecular Dynamics/nwchem-5.1-MACX-Darwin-gfortran-i386/bin/:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Users/joelb/Desktop/Molecular Dynamics/nwchem-5.1-MACX-Darwin-gfortran-i386/bin/:/Applications/iXAFS.app/Contents/Resources/local/lib:/Applications/iXAFS.app/Contents/Resources/local/bin Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 80, in __init__ raise ImportError('Cannot load ifeffit library') ImportError: Cannot load ifeffit library . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh is in my .profile and is loaded. Indeed, invoking libifeffit.dylib from the command line 'works': bash-3.2$ libifeffit.dylib bash: /Applications/iXAFS.app/Contents/Resources/local/lib/libifeffit.dylib: cannot execute binary file bash-3.2$ ls -l libifeffit.dylib -rwxr-xr-x 1 joelb admin 1500676 12 Sep 00:07 libifeffit.dylib So close! Godd news last: we did not try python scripting on another machine, but IFEFFIT appears to run perfectly on 10.5 now - thanks Matt (champagne cork noise). Joel & Barbara

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iXAFS 3.0.3 for Mac OS X
by Matt Newville 21 Sep '10

21 Sep '10

Hi All, OK, sorry for the delay, but I think that http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.3.dmg should now work well for both Mac OS X 10.6 and 10.5. That is, all the applications launch for me on a 10.6.5 machine and a 10.5.8 machine, and seem to work as expected. I'll try this on a PowerPC machine within the next couple days. I didn't include the Python module in this installer (I forgot), but put it at http://cars9.uchicago.edu/~ifeffit/src/IfeffitPython-2.0.1.tar.gz This *should* work now, but then I thought the last one was going to work too. It might be best to run this through the Ifeffit Shell, or to be extra careful in setting the environment to source the /..../iXAFS.app/Contents/Resources/local/bin/iff_init.sh As always, any feedback on what works and what doesn't would be greatly appreciated. Cheers, --Matt

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Space group notation
by Abhijeet Gaur 21 Sep '10

21 Sep '10

Hi all, I am trying to generate the theoretical model of a compound in Artemis. The compound crystallizes in the triclinic space group I1ˉ. As superscript and subscript cannot be given, I tried the notations like I-1, I1-, I1_, but it is showing the message "Invalid space group". I read the tutorial on "Atoms", still not able to resolve the problem. Please help. With regards Abhijeet Gaur

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Re: [Ifeffit] XasPerlBundle problems
by Joshua Kas 20 Sep '10

20 Sep '10

Hi Matt, Thanks for the suggestion. I tried removing the file /usr/lib/perl5/5.10.X/CPAN/Config.pm, but no luck. Finally, I wrote my own bash script which just went through each of the modules listed in XasPerlBundle.pm and did cpan -i $module This seems to have worked fine, although I only tested startup of artemis/athena. Cheers, Josh Kas On Mon, Sep 20, 2010 at 10:00 AM, <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. iXAFS 3.0.3 for Mac OS X (Matt Newville) > 2. Re: XasPerlBundle problems (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 19 Sep 2010 12:46:31 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] iXAFS 3.0.3 for Mac OS X > Message-ID: > <AANLkTin2OXBe79nM8=gr7sFY2CBGT=o5y8UAvfxfVUNV(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi All, > > OK, sorry for the delay, but I think that > http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.3.dmg<http://cars9.uchicago.edu/%7Eifeffit/src/iXAFS3.0.3.dmg> > > should now work well for both Mac OS X 10.6 and 10.5. That is, all > the applications launch for me on a 10.6.5 machine and a 10.5.8 > machine, and seem to work as expected. I'll try this on a PowerPC > machine within the next couple days. > > I didn't include the Python module in this installer (I forgot), but put it > at > http://cars9.uchicago.edu/~ifeffit/src/IfeffitPython-2.0.1.tar.gz<http://cars9.uchicago.edu/%7Eifeffit/src/IfeffitPython-2.0.1.tar.gz> > > This *should* work now, but then I thought the last one was going to > work too. It might be best to run this through the Ifeffit Shell, or > to be extra careful in setting the environment to source the > /..../iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > As always, any feedback on what works and what doesn't would be > greatly appreciated. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Sun, 19 Sep 2010 19:58:04 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: joshua jason kas <hebhop(a)u.washington.edu>, Bruce Ravel > <bravel(a)bnl.gov>, XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XasPerlBundle problems > Message-ID: > <AANLkTik7OwOBWoTb_V3GTG1i5sU+3_FLo+eicY5qP8aD(a)mail.gmail.com<AANLkTik7OwOBWoTb_V3GTG1i5sU%2B3_FLo%2BeicY5qP8aD(a)mail.gmail.com> > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Josh, > > > Hi Matt, > > Thanks for the quick response. I did run the command from within the > horae > > install directory, and the file XasPerlBundle.pm is in the Bundle > directory, > > i.e., > > > > verrocchio.phys #] pwd > > /tmp/horae-070 > > verrocchio.phys #] ls > > . Bundle INSTALL aug build_private libperlxray > > .. CPAN INSTALL_not_root build horae > > verrocchio.phys #] ls Bundle/ > > . .. XasPerlBundle.pm > > verrocchio.phys #] perl -MCPAN -e'install Bundle::XasPerlBundle' > > CPAN: Storable loaded ok > > Going to read /CPAN/Metadata > > Database was generated on Fri, 17 Sep 2010 18:28:36 GMT > > CPAN: LWP::UserAgent loaded ok > > Fetching with LWP: > > http://www.perl.com/CPAN/authors/01mailrc.txt.gz > > Going to read /CPAN/source/authors/01mailrc.txt.gz > > Fetching with LWP: > > http://www.perl.com/CPAN/modules/02packages.details.txt.gz > > Going to read /CPAN/source/modules/02packages.details.txt.gz > > Database was generated on Sat, 18 Sep 2010 17:59:57 GMT > > > > There's a new CPAN.pm version (v1.9402) available! > > [Current version is v1.7602] > > You might want to try > > install Bundle::CPAN > > reload cpan > > without quitting the current session. It should be a seamless upgrade > > while we are running... > > > > Fetching with LWP: > > http://www.perl.com/CPAN/modules/03modlist.data.gz > > Going to read /CPAN/source/modules/03modlist.data.gz > > Going to write /CPAN/Metadata > > Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. > > Try the command > > > > i /Bundle::XasPerlBundle/ > > > > to find objects with matching identifiers. > > I had similar troubles on Mac OS X, I think possibly due to a bad > CPAN/Config.pm file (that is, /usr/lib/perl5/5.10.X/CPAN/Config.pm). > Among other things, I was also seeing CPAN trying to use /CPAN/ as its > root directory -- that can't be very good. > > I think this could be related to the MyConfig.pm in Bruce's > distribution, which has > 'cpan_home' => File::Spec->catfile($ENV{__INSTALLING_BRPERL}, "CPAN"), > > but I haven't tested this carefully. > > Anyway, I would suggest blowing away the CPAN/CONFIG.pm file and > starting over. I think that will use a '.cpan' folder in your home > directory for CPAN stuff, and that might fix it. > > If that doesn't help, hopefully Bruce will have more insight. > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 91, Issue 23 > *************************************** >

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Re: [Ifeffit] XasPerlBundle problems
by Matt Newville 20 Sep '10

20 Sep '10

Hi Josh, > Hi Matt, > Thanks for the quick response. I did run the command from within the horae > install directory, and the file XasPerlBundle.pm is in the Bundle directory, > i.e., > > verrocchio.phys #] pwd > /tmp/horae-070 > verrocchio.phys #] ls > . Bundle INSTALL aug build_private libperlxray > .. CPAN INSTALL_not_root build horae > verrocchio.phys #] ls Bundle/ > . .. XasPerlBundle.pm > verrocchio.phys #] perl -MCPAN -e'install Bundle::XasPerlBundle' > CPAN: Storable loaded ok > Going to read /CPAN/Metadata > Database was generated on Fri, 17 Sep 2010 18:28:36 GMT > CPAN: LWP::UserAgent loaded ok > Fetching with LWP: > http://www.perl.com/CPAN/authors/01mailrc.txt.gz > Going to read /CPAN/source/authors/01mailrc.txt.gz > Fetching with LWP: > http://www.perl.com/CPAN/modules/02packages.details.txt.gz > Going to read /CPAN/source/modules/02packages.details.txt.gz > Database was generated on Sat, 18 Sep 2010 17:59:57 GMT > > There's a new CPAN.pm version (v1.9402) available! > [Current version is v1.7602] > You might want to try > install Bundle::CPAN > reload cpan > without quitting the current session. It should be a seamless upgrade > while we are running... > > Fetching with LWP: > http://www.perl.com/CPAN/modules/03modlist.data.gz > Going to read /CPAN/source/modules/03modlist.data.gz > Going to write /CPAN/Metadata > Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. > Try the command > > i /Bundle::XasPerlBundle/ > > to find objects with matching identifiers. I had similar troubles on Mac OS X, I think possibly due to a bad CPAN/Config.pm file (that is, /usr/lib/perl5/5.10.X/CPAN/Config.pm). Among other things, I was also seeing CPAN trying to use /CPAN/ as its root directory -- that can't be very good. I think this could be related to the MyConfig.pm in Bruce's distribution, which has 'cpan_home' => File::Spec->catfile($ENV{__INSTALLING_BRPERL}, "CPAN"), but I haven't tested this carefully. Anyway, I would suggest blowing away the CPAN/CONFIG.pm file and starting over. I think that will use a '.cpan' folder in your home directory for CPAN stuff, and that might fix it. If that doesn't help, hopefully Bruce will have more insight. --Matt

1 0

Help with Artemis fit
by Han Sen Soo 19 Sep '10

19 Sep '10

Hello, I'm a post-doc at LBL and I recently attended the XAFS Summer School at IIT. I just started trying to fit some data on titanium sites embedded in amorphous silica and I was hoping to get some advice on how to improve my fit. My first objective is to get an idea of the coordination number of Ti, and I'm trying to do this in Artemis by using the parameter N as my S0^2 and letting the amplitude of S0^2 vary. I'm not sure if this is appropriate? A problem I am encountering is that the physically reasonable fits look visually unacceptable. I am just trying to fit the first Ti-O shell initially and plan to work on the 2nd shell subsequently. The R space fit for the first shell has 2 peaks that are about 0.3 Å apart at 1.2 and 1.5 Å (uncorrected). With only 1 shell of O atoms at a distance I found for similar materials, a reasonable fit was found (including background fitting) but the amplitude of the fit at the 1.5 Å peak is too high while the amplitude at the 1.2 Å peak is too low. I naively tried to improve the fit by adding a 2nd shell at a shorter distance and tried different combinations of distances 0.02 Å apart, but I consistently find that the sigma^2 values for one or both shells become negative. I also realized that the resolution of the data may not be sufficient to distinguish shells that are less than 0.2 Å apart, which is what I am expecting based on data on similar materials. I have attached a pdf image of one of the bad fits. My question then is, should I not try to improve the fit and accept the 1 shell fit, or am I mis-interpreting the fit and are there ways I can introduce the 2nd shell without having an unphysical model (the main problem being the negative sigma^2)? Thanks for reading and any suggestions! han sen

2 1

Re: [Ifeffit] XasPerlBundle problems
by Joshua Kas 18 Sep '10

18 Sep '10

Hi Matt, Thanks for the quick response. I did run the command from within the horae install directory, and the file XasPerlBundle.pm is in the Bundle directory, i.e., verrocchio.phys #] pwd /tmp/horae-070 verrocchio.phys #] ls . Bundle INSTALL aug build_private libperlxray .. CPAN INSTALL_not_root build horae verrocchio.phys #] ls Bundle/ . .. XasPerlBundle.pm verrocchio.phys #] perl -MCPAN -e'install Bundle::XasPerlBundle' CPAN: Storable loaded ok Going to read /CPAN/Metadata Database was generated on Fri, 17 Sep 2010 18:28:36 GMT CPAN: LWP::UserAgent loaded ok Fetching with LWP: http://www.perl.com/CPAN/authors/01mailrc.txt.gz Going to read /CPAN/source/authors/01mailrc.txt.gz Fetching with LWP: http://www.perl.com/CPAN/modules/02packages.details.txt.gz Going to read /CPAN/source/modules/02packages.details.txt.gz Database was generated on Sat, 18 Sep 2010 17:59:57 GMT There's a new CPAN.pm version (v1.9402) available! [Current version is v1.7602] You might want to try install Bundle::CPAN reload cpan without quitting the current session. It should be a seamless upgrade while we are running... Fetching with LWP: http://www.perl.com/CPAN/modules/03modlist.data.gz Going to read /CPAN/source/modules/03modlist.data.gz Going to write /CPAN/Metadata Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. Try the command i /Bundle::XasPerlBundle/ to find objects with matching identifiers. Could there be something wrong with my installation of CPAN that would cause this behavior? Cheers, Josh Kas On Sat, Sep 18, 2010 at 10:00 AM, <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: XasPerlBundle problems (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Sep 2010 16:32:53 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XasPerlBundle problems > Message-ID: > <AANLkTi=tDjqnmBT8nhWZ0VtAMrvyZTSdvHLPePmR0iYu(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Josh, > > That cpan command should be done from the horae install directory. Saying > > perl -MCPAN -e 'install Bundle::XXX' > > is looking for the file named XXX.pm (which simply contains a list of > Perl modules) > in the directory Bundle/. I think that if it can't find that, then > it goes to look on-line. > > Cheers, > > --Matt > > > On Fri, Sep 17, 2010 at 3:24 PM, Joshua Kas <joshua.j.kas(a)gmail.com> > wrote: > > Hi, > > I'm trying to install horae on RHEL5 and I'm having trouble getting the > > prerequisites from CPAN. IFEFFIT installed fine, but when I try to > install > > ARTEMIS/ATHENA I have the following problem: > > > > verrocchio.phys #] perl -MCPAN -e 'install Bundle::XasPerlBundle' > > CPAN: Storable loaded ok > > Going to read /CPAN/Metadata > > ? Database was generated on Fri, 17 Sep 2010 18:28:36 GMT > > Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. > > Try the command > > > > ??? i /Bundle::XasPerlBundle/ > > > > to find objects with matching identifiers. > > > > This was after becoming root, then copying the CPAN/MyConfig.pm file to > > ~/.cpan/CPAN/. > > I am using the mose recent version of the horae tarball, i.e., horae-070. > > I'm out of ideas for now. > > Thanks very much for any help. > > Josh Kas > > > > On Fri, Sep 17, 2010 at 10:00 AM, > > <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: Bkg removal problem (Alfred Hummer) > >> ? 2. Mathematical expressions for the path parameters in ? ? ? Fitting > >> ? ? ?(sumitk(a)barc.gov.in) > >> ? 3. Re: Mathematical expressions for the path parameters in > >> ? ? ?Fitting (Shelly Kelly) > >> ? 4. Re: Mathematical expressions for the path parameters in > >> ? ? ?Fitting (Brandon Reese) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Thu, 16 Sep 2010 19:58:53 +0200 > >> From: Alfred Hummer <alfred.hummer(a)univie.ac.at> > >> To: ifeffit(a)millenia.cars.aps.anl.gov > >> Subject: Re: [Ifeffit] Bkg removal problem > >> Message-ID: <4C925ADD.90306(a)univie.ac.at> > >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >> > >> > >> Thx for the detailed answer. Helped me a lot. > >> Also tested it with other programs using smoothed splines, leading to > >> similar results. > >> > >> And you are right, I don't expect a peak at about 1A in the FT. The > >> first peak at 1.5A in the FT should represent a mixed 1st shell of 3O/3N > >> atoms at about 2A distance. > >> > >> best regards Alfred > >> > >> > >> Am 15.09.2010 19:00, schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > >> > 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: Bkg removal problem (Bruce Ravel) > >> > > >> > > >> > ---------------------------------------------------------------------- > >> > > >> > Message: 1 > >> > Date: Tue, 14 Sep 2010 14:07:55 -0400 > >> > From: Bruce Ravel<bravel(a)bnl.gov> > >> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > >> > Subject: Re: [Ifeffit] Bkg removal problem > >> > Message-ID:<201009141407.55193.bravel(a)bnl.gov> > >> > Content-Type: Text/Plain; ?charset="iso-8859-1" > >> > > >> > > >> > Alfred, > >> > > >> > I certainly encourage you to look at Shelly's book chapter. It's very > >> > useful. > >> > > >> > The question you ask is one that we hear frequently on this mailing > >> > list. ?I don't mean anything bad by saying that -- in fact, it's an > >> > excellent question that every practitioner of XAS needs to come to > >> > terms with early on in his or her XAS career. ?Indeed, I am pleased > >> > that you are insightful enough to recognize your confusion and wise > >> > enough to ask for help. > >> > > >> > That said, I am a bit weary of answering questions about Rbkg on the > >> > mailing list. ?Yours ain't the first! ;-) > >> > > >> > Rather than answering here, I decided to write up a wiki page on the > >> > topic. ?That way, I'll have something to point to the next time > >> > someone asks about Rbkg. > >> > > >> > Here it is: > >> > ? ?http://xafs.org/TheoryAnalysis/BackgroundRemovalWithAutobk > >> > > >> > Hope it helps, > >> > B > >> > > >> > > >> > On Friday 10 September 2010 10:25:50 am Shelly Kelly wrote: > >> >> Hi Alfred: > >> >> > >> >> You should take a look at my book chapter. I go through a lot of > >> >> details on how to remove the background. If you want a copy just send > >> >> me an email directly and I'll send you a pdf. > >> >> > >> >> Cheers, > >> >> Shelly > >> >> exafs(a)netzero.com > >> >> > >> >> On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer > >> >> > >> >> <alfred.hummer(a)univie.ac.at> ?wrote: > >> >>> Hello, > >> >>> > >> >>> Currently I am working on a Ga XAS spectrum. > >> >>> I'm trying to extract the EXAFS data but I'm not sure if the > >> >>> background > >> >>> function is right, or how to set the right values. > >> >>> > >> >>> I played around with different setting for kmin and Rbkg. > >> >>> So far I know that Rbkg defines the cutoff for the bkg frequencies > in > >> >>> the > >> >>> FT optimization and setting it to high leads to loss in information, > >> >>> as > >> >>> more high frequencies are included in the bkg. > >> >>> > >> >>> I also read that it is advisable to exclude strong white lines from > >> >>> the > >> >>> spline range (increasing kmin?). Would this a strategy in my case? > >> >>> > >> >>> I attached the project file. > >> >>> > >> >>> Maybe someone has a clue. The more I tried the bigger my > uncertainty. > >> >>> > >> >>> best regards > >> >>> > >> >>> Alfred > >> >>> > >> >>> > >> >>> _______________________________________________ > >> >>> Ifeffit mailing list > >> >>> Ifeffit(a)millenia.cars.aps.anl.gov > >> >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> >> > >> >> _______________________________________________ > >> >> Ifeffit mailing list > >> >> Ifeffit(a)millenia.cars.aps.anl.gov > >> >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> >> > >> > > >> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Fri, 17 Sep 2010 11:31:34 +0530 > >> From: sumitk(a)barc.gov.in > >> To: ifeffit(a)millenia.cars.aps.anl.gov > >> Subject: [Ifeffit] Mathematical expressions for the path parameters in > >> ? ? ? ?Fitting > >> Message-ID: > >> ? ? ? ?<edb6390523394cc867a1b7e12aa03d81.squirrel(a)bts.barc.gov.in> > >> Content-Type: text/plain;charset=UTF-8 > >> > >> Hello, > >> In EXAFS data modeling carried out by fitting excercise, we develop > >> mathematical expressions for ?different path parametrs as functions of a > >> smaller set of fitting parameters that can be adjusted to achieve to > best > >> fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > >> different environmentally relevent mineral oxides. In conection of this > i > >> also analysed some reference standard compounds. In developing > expression > >> for different path parameters, though i developed the expressions using > my > >> own ?understanding and taking help from one of Shelly's tutorial > regarding > >> SnO2 case, i am not confident. Basically SS2, and deltaE expressions > >> puzzle me. > >> Could someone help me in understanding basic approach in developing > their > >> expressions(for reference Eu2O3 structure could be taken). > >> Regards, > >> Sumit > >> > >> > >> > >> > >> > >> ------------------------------ > >> > >> Message: 3 > >> Date: Fri, 17 Sep 2010 10:40:14 -0500 > >> From: Shelly Kelly <dr.sdkelly(a)gmail.com> > >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >> Subject: Re: [Ifeffit] Mathematical expressions for the path > >> ? ? ? ?parameters in ? Fitting > >> Message-ID: > >> ? ? ? ?<AANLkTim40RLMwFRFm1JN0becDx7MM7Lthqmw_xu=Jsk-(a)mail.gmail.com> > >> Content-Type: text/plain; charset=ISO-8859-1 > >> > >> Hi Sumit: > >> > >> There are a lot of different ways to constrain the EXAFS parameters in > >> a fitting model. Mostly they are determined by physically meaningful > >> relationships or through trial and error of "what works". I just sent > >> you my book chapter and you will find detailed discussion on many of > >> the common constraints in there. Another good place to look is in the > >> literature to find out what people have done for systems similar to > >> yours. > >> > >> HTH, > >> Shelly > >> > >> On Fri, Sep 17, 2010 at 1:01 AM, ?<sumitk(a)barc.gov.in> wrote: > >> > Hello, > >> > In EXAFS data modeling carried out by fitting excercise, we develop > >> > mathematical expressions for ?different path parametrs as functions of > a > >> > smaller set of fitting parameters that can be adjusted to achieve to > >> > best > >> > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > >> > different environmentally relevent mineral oxides. In conection of > this > >> > i > >> > also analysed some reference standard compounds. In developing > >> > expression > >> > for different path parameters, though i developed the expressions > using > >> > my > >> > own ?understanding and taking help from one of Shelly's tutorial > >> > regarding > >> > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > >> > puzzle me. > >> > Could someone help me in understanding basic approach in developing > >> > their > >> > expressions(for reference Eu2O3 structure could be taken). > >> > Regards, > >> > Sumit > >> > > >> > > >> > > >> > _______________________________________________ > >> > Ifeffit mailing list > >> > Ifeffit(a)millenia.cars.aps.anl.gov > >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > >> > >> > >> > >> ------------------------------ > >> > >> Message: 4 > >> Date: Fri, 17 Sep 2010 10:54:21 -0600 > >> From: Brandon Reese <bjreese(a)gmail.com> > >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >> Subject: Re: [Ifeffit] Mathematical expressions for the path > >> ? ? ? ?parameters in ? Fitting > >> Message-ID: > >> ? ? ? ?<AANLkTikQG0L=-QWp_EX51XSuOYvN7_JZvESh5o9LSDp6(a)mail.gmail.com> > >> Content-Type: text/plain; charset="iso-8859-1" > >> > >> Hi Shelly, > >> > >> I am also looking into different ways to constrain my EXAFS fits. ?If > you > >> wouldn't mind, I would also be very interested in a copy of your book > >> chapter. > >> > >> Thanks, > >> Brandon > >> > >> On Fri, Sep 17, 2010 at 9:40 AM, Shelly Kelly <dr.sdkelly(a)gmail.com> > >> wrote: > >> > >> > Hi Sumit: > >> > > >> > There are a lot of different ways to constrain the EXAFS parameters in > >> > a fitting model. Mostly they are determined by physically meaningful > >> > relationships or through trial and error of "what works". I just sent > >> > you my book chapter and you will find detailed discussion on many of > >> > the common constraints in there. Another good place to look is in the > >> > literature to find out what people have done for systems similar to > >> > yours. > >> > > >> > HTH, > >> > Shelly > >> > > >> > On Fri, Sep 17, 2010 at 1:01 AM, ?<sumitk(a)barc.gov.in> wrote: > >> > > Hello, > >> > > In EXAFS data modeling carried out by fitting excercise, we develop > >> > > mathematical expressions for ?different path parametrs as functions > of > >> > > a > >> > > smaller set of fitting parameters that can be adjusted to achieve to > >> > > best > >> > > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed > on > >> > > different environmentally relevent mineral oxides. In conection of > >> > > this i > >> > > also analysed some reference standard compounds. In developing > >> > > expression > >> > > for different path parameters, though i developed the expressions > >> > > using > >> > my > >> > > own ?understanding and taking help from one of Shelly's tutorial > >> > regarding > >> > > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > >> > > puzzle me. > >> > > Could someone help me in understanding basic approach in developing > >> > > their > >> > > expressions(for reference Eu2O3 structure could be taken). > >> > > Regards, > >> > > Sumit > >> > > > >> > > > >> > > > >> > > _______________________________________________ > >> > > Ifeffit mailing list > >> > > Ifeffit(a)millenia.cars.aps.anl.gov > >> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > > >> > > >> > _______________________________________________ > >> > Ifeffit mailing list > >> > Ifeffit(a)millenia.cars.aps.anl.gov > >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > >>

1 0

XasPerlBundle problems
by Joshua Kas 17 Sep '10

17 Sep '10

Hi, I'm trying to install horae on RHEL5 and I'm having trouble getting the prerequisites from CPAN. IFEFFIT installed fine, but when I try to install ARTEMIS/ATHENA I have the following problem: verrocchio.phys #] perl -MCPAN -e 'install Bundle::XasPerlBundle' CPAN: Storable loaded ok Going to read /CPAN/Metadata Database was generated on Fri, 17 Sep 2010 18:28:36 GMT Warning: Cannot install Bundle::XasPerlBundle, don't know what it is. Try the command i /Bundle::XasPerlBundle/ to find objects with matching identifiers. This was after becoming root, then copying the CPAN/MyConfig.pm file to ~/.cpan/CPAN/. I am using the mose recent version of the horae tarball, i.e., horae-070. I'm out of ideas for now. Thanks very much for any help. Josh Kas On Fri, Sep 17, 2010 at 10:00 AM, <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: Bkg removal problem (Alfred Hummer) > 2. Mathematical expressions for the path parameters in Fitting > (sumitk(a)barc.gov.in) > 3. Re: Mathematical expressions for the path parameters in > Fitting (Shelly Kelly) > 4. Re: Mathematical expressions for the path parameters in > Fitting (Brandon Reese) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 16 Sep 2010 19:58:53 +0200 > From: Alfred Hummer <alfred.hummer(a)univie.ac.at> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Bkg removal problem > Message-ID: <4C925ADD.90306(a)univie.ac.at> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Thx for the detailed answer. Helped me a lot. > Also tested it with other programs using smoothed splines, leading to > similar results. > > And you are right, I don't expect a peak at about 1A in the FT. The > first peak at 1.5A in the FT should represent a mixed 1st shell of 3O/3N > atoms at about 2A distance. > > best regards Alfred > > > Am 15.09.2010 19:00, schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > > 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: Bkg removal problem (Bruce Ravel) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 14 Sep 2010 14:07:55 -0400 > > From: Bruce Ravel<bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Bkg removal problem > > Message-ID:<201009141407.55193.bravel(a)bnl.gov> > > Content-Type: Text/Plain; charset="iso-8859-1" > > > > > > Alfred, > > > > I certainly encourage you to look at Shelly's book chapter. It's very > > useful. > > > > The question you ask is one that we hear frequently on this mailing > > list. I don't mean anything bad by saying that -- in fact, it's an > > excellent question that every practitioner of XAS needs to come to > > terms with early on in his or her XAS career. Indeed, I am pleased > > that you are insightful enough to recognize your confusion and wise > > enough to ask for help. > > > > That said, I am a bit weary of answering questions about Rbkg on the > > mailing list. Yours ain't the first! ;-) > > > > Rather than answering here, I decided to write up a wiki page on the > > topic. That way, I'll have something to point to the next time > > someone asks about Rbkg. > > > > Here it is: > > http://xafs.org/TheoryAnalysis/BackgroundRemovalWithAutobk > > > > Hope it helps, > > B > > > > > > On Friday 10 September 2010 10:25:50 am Shelly Kelly wrote: > >> Hi Alfred: > >> > >> You should take a look at my book chapter. I go through a lot of > >> details on how to remove the background. If you want a copy just send > >> me an email directly and I'll send you a pdf. > >> > >> Cheers, > >> Shelly > >> exafs(a)netzero.com > >> > >> On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer > >> > >> <alfred.hummer(a)univie.ac.at> wrote: > >>> Hello, > >>> > >>> Currently I am working on a Ga XAS spectrum. > >>> I'm trying to extract the EXAFS data but I'm not sure if the background > >>> function is right, or how to set the right values. > >>> > >>> I played around with different setting for kmin and Rbkg. > >>> So far I know that Rbkg defines the cutoff for the bkg frequencies in > the > >>> FT optimization and setting it to high leads to loss in information, as > >>> more high frequencies are included in the bkg. > >>> > >>> I also read that it is advisable to exclude strong white lines from the > >>> spline range (increasing kmin?). Would this a strategy in my case? > >>> > >>> I attached the project file. > >>> > >>> Maybe someone has a clue. The more I tried the bigger my uncertainty. > >>> > >>> best regards > >>> > >>> Alfred > >>> > >>> > >>> _______________________________________________ > >>> Ifeffit mailing list > >>> Ifeffit(a)millenia.cars.aps.anl.gov > >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > > > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Sep 2010 11:31:34 +0530 > From: sumitk(a)barc.gov.in > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Mathematical expressions for the path parameters in > Fitting > Message-ID: > <edb6390523394cc867a1b7e12aa03d81.squirrel(a)bts.barc.gov.in> > Content-Type: text/plain;charset=UTF-8 > > Hello, > In EXAFS data modeling carried out by fitting excercise, we develop > mathematical expressions for different path parametrs as functions of a > smaller set of fitting parameters that can be adjusted to achieve to best > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > different environmentally relevent mineral oxides. In conection of this i > also analysed some reference standard compounds. In developing expression > for different path parameters, though i developed the expressions using my > own understanding and taking help from one of Shelly's tutorial regarding > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > puzzle me. > Could someone help me in understanding basic approach in developing their > expressions(for reference Eu2O3 structure could be taken). > Regards, > Sumit > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 17 Sep 2010 10:40:14 -0500 > From: Shelly Kelly <dr.sdkelly(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Mathematical expressions for the path > parameters in Fitting > Message-ID: > <AANLkTim40RLMwFRFm1JN0becDx7MM7Lthqmw_xu=Jsk-(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Sumit: > > There are a lot of different ways to constrain the EXAFS parameters in > a fitting model. Mostly they are determined by physically meaningful > relationships or through trial and error of "what works". I just sent > you my book chapter and you will find detailed discussion on many of > the common constraints in there. Another good place to look is in the > literature to find out what people have done for systems similar to > yours. > > HTH, > Shelly > > On Fri, Sep 17, 2010 at 1:01 AM, <sumitk(a)barc.gov.in> wrote: > > Hello, > > In EXAFS data modeling carried out by fitting excercise, we develop > > mathematical expressions for ?different path parametrs as functions of a > > smaller set of fitting parameters that can be adjusted to achieve to best > > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > > different environmentally relevent mineral oxides. In conection of this i > > also analysed some reference standard compounds. In developing expression > > for different path parameters, though i developed the expressions using > my > > own ?understanding and taking help from one of Shelly's tutorial > regarding > > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > > puzzle me. > > Could someone help me in understanding basic approach in developing their > > expressions(for reference Eu2O3 structure could be taken). > > Regards, > > Sumit > > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 17 Sep 2010 10:54:21 -0600 > From: Brandon Reese <bjreese(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Mathematical expressions for the path > parameters in Fitting > Message-ID: > <AANLkTikQG0L=-QWp_EX51XSuOYvN7_JZvESh5o9LSDp6(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Shelly, > > I am also looking into different ways to constrain my EXAFS fits. If you > wouldn't mind, I would also be very interested in a copy of your book > chapter. > > Thanks, > Brandon > > On Fri, Sep 17, 2010 at 9:40 AM, Shelly Kelly <dr.sdkelly(a)gmail.com> > wrote: > > > Hi Sumit: > > > > There are a lot of different ways to constrain the EXAFS parameters in > > a fitting model. Mostly they are determined by physically meaningful > > relationships or through trial and error of "what works". I just sent > > you my book chapter and you will find detailed discussion on many of > > the common constraints in there. Another good place to look is in the > > literature to find out what people have done for systems similar to > > yours. > > > > HTH, > > Shelly > > > > On Fri, Sep 17, 2010 at 1:01 AM, <sumitk(a)barc.gov.in> wrote: > > > Hello, > > > In EXAFS data modeling carried out by fitting excercise, we develop > > > mathematical expressions for different path parametrs as functions of > a > > > smaller set of fitting parameters that can be adjusted to achieve to > best > > > fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on > > > different environmentally relevent mineral oxides. In conection of this > i > > > also analysed some reference standard compounds. In developing > expression > > > for different path parameters, though i developed the expressions using > > my > > > own understanding and taking help from one of Shelly's tutorial > > regarding > > > SnO2 case, i am not confident. Basically SS2, and deltaE expressions > > > puzzle me. > > > Could someone help me in understanding basic approach in developing > their > > > expressions(for reference Eu2O3 structure could be taken). > > > Regards, > > > Sumit > > > > > > > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

2 1

Mathematical expressions for the path parameters in Fitting
by sumitk＠barc.gov.in 17 Sep '10

17 Sep '10

Hello, In EXAFS data modeling carried out by fitting excercise, we develop mathematical expressions for different path parametrs as functions of a smaller set of fitting parameters that can be adjusted to achieve to best fit to the data. I am carrying out EXAFS analysis of Eu(III) sorbed on different environmentally relevent mineral oxides. In conection of this i also analysed some reference standard compounds. In developing expression for different path parameters, though i developed the expressions using my own understanding and taking help from one of Shelly's tutorial regarding SnO2 case, i am not confident. Basically SS2, and deltaE expressions puzzle me. Could someone help me in understanding basic approach in developing their expressions(for reference Eu2O3 structure could be taken). Regards, Sumit

3 3

Re: [Ifeffit] Bkg removal problem
by Alfred Hummer 16 Sep '10

16 Sep '10

Thx for the detailed answer. Helped me a lot. Also tested it with other programs using smoothed splines, leading to similar results. And you are right, I don't expect a peak at about 1A in the FT. The first peak at 1.5A in the FT should represent a mixed 1st shell of 3O/3N atoms at about 2A distance. best regards Alfred Am 15.09.2010 19:00, schrieb ifeffit-request(a)millenia.cars.aps.anl.gov: > 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: Bkg removal problem (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 Sep 2010 14:07:55 -0400 > From: Bruce Ravel<bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Bkg removal problem > Message-ID:<201009141407.55193.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > > Alfred, > > I certainly encourage you to look at Shelly's book chapter. It's very > useful. > > The question you ask is one that we hear frequently on this mailing > list. I don't mean anything bad by saying that -- in fact, it's an > excellent question that every practitioner of XAS needs to come to > terms with early on in his or her XAS career. Indeed, I am pleased > that you are insightful enough to recognize your confusion and wise > enough to ask for help. > > That said, I am a bit weary of answering questions about Rbkg on the > mailing list. Yours ain't the first! ;-) > > Rather than answering here, I decided to write up a wiki page on the > topic. That way, I'll have something to point to the next time > someone asks about Rbkg. > > Here it is: > http://xafs.org/TheoryAnalysis/BackgroundRemovalWithAutobk > > Hope it helps, > B > > > On Friday 10 September 2010 10:25:50 am Shelly Kelly wrote: >> Hi Alfred: >> >> You should take a look at my book chapter. I go through a lot of >> details on how to remove the background. If you want a copy just send >> me an email directly and I'll send you a pdf. >> >> Cheers, >> Shelly >> exafs(a)netzero.com >> >> On Fri, Sep 10, 2010 at 8:42 AM, Alfred Hummer >> >> <alfred.hummer(a)univie.ac.at> wrote: >>> Hello, >>> >>> Currently I am working on a Ga XAS spectrum. >>> I'm trying to extract the EXAFS data but I'm not sure if the background >>> function is right, or how to set the right values. >>> >>> I played around with different setting for kmin and Rbkg. >>> So far I know that Rbkg defines the cutoff for the bkg frequencies in the >>> FT optimization and setting it to high leads to loss in information, as >>> more high frequencies are included in the bkg. >>> >>> I also read that it is advisable to exclude strong white lines from the >>> spline range (increasing kmin?). Would this a strategy in my case? >>> >>> I attached the project file. >>> >>> Maybe someone has a clue. The more I tried the bigger my uncertainty. >>> >>> best regards >>> >>> Alfred >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >

1 0

Bkg removal problem
by Alfred Hummer 14 Sep '10

14 Sep '10

Hello, Currently I am working on a Ga XAS spectrum. I'm trying to extract the EXAFS data but I'm not sure if the background function is right, or how to set the right values. I played around with different setting for kmin and Rbkg. So far I know that Rbkg defines the cutoff for the bkg frequencies in the FT optimization and setting it to high leads to loss in information, as more high frequencies are included in the bkg. I also read that it is advisable to exclude strong white lines from the spline range (increasing kmin?). Would this a strategy in my case? I attached the project file. Maybe someone has a clue. The more I tried the bigger my uncertainty. best regards Alfred

3 2

changing valence state
by JeongEunSuk 11 Sep '10

11 Sep '10

Hi all I want to change valence state for XANES calculation in FEFF , from Co2+ to Co3+ Is it possible in FEFF?

1 0

(Reposted) K-space vs R-spce fitting
by Lezama Pacheco, Juan Salvador 11 Sep '10

11 Sep '10

Hi Matt: Thanks so much for your answer. Let's see if I can make it more clear this time. Should dk have an effect on the actual fit, if it is performed in k-space? As I said, I found out that by changing dk (in k space) (keeping (kmin,kmax) constant) values change around 15%, so that tells me the actual fitting range is (kmin-dk/2,kmax+dk/2) is that so? Juan

2 1

Hi ! I am PHD student in Taiwan.
by clo 11 Sep '10

11 Sep '10

Dear joly: I am PHD student at deparment of physics of National Sun Yat-Sen University in Taiwan. I have some problems about DOS simulation by using Feff. 1.I want to compare the simulation result with the LDA+"U" calculation, Could you give some suggestions for presentation the "U" potential part by Feff? thank you for your help Chun Pin Wu

1 0

K-space vs R-spce fitting
by Lezama Pacheco, Juan Salvador 11 Sep '10

11 Sep '10

Dear All: First of all, nicely done you guys! This is indeed a set great of tools the community really appreciates it and I have been putting into heavy use. I have and issue though that has been making me scratch my head from time to time. I've been trying to figure out the feature of k-space and R-space fitting "relationship" for Ifeffit. I usually work out my fits in k-space although I have to admit that R-space fitting in combined approach will definitely be valuable. Now, as I am trying to work some data for Uranium (namely uranyl acetate standard) I am a little bit confused on the real independency of k-space and R-space fitting. This comes from the fact that even if I specified the fitting range in k (fitting in k space), the dk value seems to have an effect in the current fit values (changing as large as 15%). I understand the issue if the actual fitting range is then (kmin-dk/2,kmax+dk/2) but is this the case? Then what is the real relationship-independency between k-space and R-space fitting? For q-space that is of course another story. For the record I am using ixafs 1.2 on Mac OS X 10.5.8. Perl distribution seems to crash "unexpectedly" every time I tried the new 3.0.2, but that is another story in another thread... Thanks so much again Juan S Lezama

2 2

Bkg fit in Artemis
by hemantha aranwela 10 Sep '10

10 Sep '10

Hi All, I like to understand the way how the background fitting is done in Artemis. How the background functions are obtained (or defined)? How do we use the bkg fit in analyzing the data? I have a good idea about how Athena does the bkg reduction. But have no clue in case of Artemis. I would appreciate if somebody can direct me to an article written on this or can give a brief introduction about it. Thanks. Aranwela

3 2

iXAFS & python scripting
by Brugger, Joel (SAM) 09 Sep '10

09 Sep '10

Hi Matt, Actually we did run . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh (I was just wondering if it was still required). Hopefully the following output will be clearer than my prose. Line 5 in "iff = Ifeffit.Ifeffit()". The problem seems to be access to "/Users/Newville/Codes/ifeffit/local/share/ifeffit" while running Ifeffit.Ifeffit(). Thanks! Joel + Barb Last login: Fri Sep 10 08:14:26 on ttys004 JoelMacBook-Silver:~ joelb$ echo $PATH /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin JoelMacBook-Silver:~ joelb$ . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh JoelMacBook-Silver:~ joelb$ echo $PATH /Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin JoelMacBook-Silver:~ joelb$ cd /Users/joelb/data_ifeffit/APS-April08-Pascal/python JoelMacBook-Silver:python joelb$ python aps-12p9mLiCl.py failed to load ifeffit library libifeffit.dylib /Users/Newville/Codes/ifeffit/local/share/ifeffit:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin Traceback (most recent call last): File "aps-12p9mLiCl.py", line 5, in <module> iff = Ifeffit.Ifeffit() File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 79, in __init__ raise ImportError('Cannot load ifeffit library') ImportError: Cannot load ifeffit library JoelMacBook-Silver:python joelb$ echo $PATH /Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin ________________________________________ ------------------------------ Message: 4 Date: Thu, 9 Sep 2010 10:12:09 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "barbara.etschmann(a)adelaide.edu.au" <barbara.etschmann(a)adelaide.edu.au> Subject: Re: [Ifeffit] IXAFS3.0.2 and python scripting Message-ID: <AANLkTikYLAwnRcwZWNK+yBL0Byp7NgxNJ=Zrn_v3V56M(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Joel and Barb, Ah, sorry. I believe you need to do . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh in the shell prior to running python, or add this to your bash .profile file. It would be better if the setup procedure detected that it was on a Mac and set the environment up automatically. I'll work on that (and on the build for10.5). --Matt > Works great on 10.6 for us too. Thanks a million times, and fingers crossed for finding the error in 10.5 ! > > We tried the python scripting, but apparently a /Users/Newville still lurks in there. > > Running the aps-12p9mLiCl.py ?script > > 1. #!/usr/bin/python > 2. > 3. import math > 4. import Ifeffit > 5. iff = Ifeffit.Ifeffit() > > gives the following error: > > bash-3.2$ python aps-12p9mLiCl.py > ?failed to load ifeffit library ?libifeffit.dylib > /Users/Newville/Codes/ifeffit/local/share/ifeffit:/opt/local/bin:/opt/local/sbin:/opt/pgi/osx86/10.4/bin:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Applications/iXAFS.app/Contents/Resources/local/bin > Traceback (most recent call last): > ?File "aps-12p9mLiCl.py", line 5, in <module> > ? ?iff = Ifeffit.Ifeffit() > ?File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 79, in __init__ > ? ?raise ImportError('Cannot load ifeffit library') > ImportError: Cannot load ifeffit library > > > I tried to add /Applications/iXAFS.app/Contents/Resources/local/lib to PATH (there's a libifeffit.dylib there), but that did not help. > > Also notice that my PATH variables have been duplicated. This happens because I still have '. /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh' in my '.profile'. Do I need to keep this? If so, it would be nice to fix iff_init.sh too :-) > > Thanks, > > Joel + Barb >

1 0

atoms input file
by mohamed sobhy 09 Sep '10

09 Sep '10

Dear I would like to fit the signal from (U0.8Ce0.2)O2, so I tried to put Ce in the same position of U but all atoms generated files give no Ce in the scattering paths and some fitting give negative amplitude values. Could you help me with the Atoms input file? Mohamed

3 3

IXAFS3.0.2 and python scripting
by Brugger, Joel (SAM) 09 Sep '10

09 Sep '10

Dear Matt, Works great on 10.6 for us too. Thanks a million times, and fingers crossed for finding the error in 10.5 ! We tried the python scripting, but apparently a /Users/Newville still lurks in there. Running the aps-12p9mLiCl.py script 1. #!/usr/bin/python 2. 3. import math 4. import Ifeffit 5. iff = Ifeffit.Ifeffit() gives the following error: bash-3.2$ python aps-12p9mLiCl.py failed to load ifeffit library libifeffit.dylib /Users/Newville/Codes/ifeffit/local/share/ifeffit:/opt/local/bin:/opt/local/sbin:/opt/pgi/osx86/10.4/bin:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Applications/iXAFS.app/Contents/Resources/local/bin:/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/usr/X11R6/bin:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/usr/local/lib:/Users/joelb/Desktop/FitYK/:/usr/local/lib/:/sw/lib/:/sw/include/readline/:/unix/Molecular Dynamics/moldy-2.16e:/Users/joelb/Public/XDS/XDS-OSX_Intel:/Users/joelb/Desktop/fdmnes:/Applications/iXAFS.app/Contents/Resources/local/bin Traceback (most recent call last): File "aps-12p9mLiCl.py", line 5, in <module> iff = Ifeffit.Ifeffit() File "/Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py", line 79, in __init__ raise ImportError('Cannot load ifeffit library') ImportError: Cannot load ifeffit library I tried to add /Applications/iXAFS.app/Contents/Resources/local/lib to PATH (there's a libifeffit.dylib there), but that did not help. Also notice that my PATH variables have been duplicated. This happens because I still have '. /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh' in my '.profile'. Do I need to keep this? If so, it would be nice to fix iff_init.sh too :-) Thanks, Joel + Barb ________________________________________ Today's Topics: 1. Re: iXAFS3.0.2 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Sep 2010 11:36:06 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] iXAFS3.0.2 Message-ID: <AANLkTinmG5RGjBwj5eX5yui2JQo_nEP+1JJuMMdWPndh(a)mail.gmail.com> Content-Type: text/plain; charset=windows-1252 Hi Brandon, Thanks for the report. I've seen the same errors on the only system I have access to running 10.5.something: All the executable programs (perl, ifeffit) report the same dyld error. I thought these messages were perhaps because I had built a "universal binary" that included x86_64 and i386, so I rebuilt for i386 but not x86_64, hoping that would solve the problem. But it didn't. I've looked into a little bit more (if anyone knows more, please let me know!!), and believe the issue may be solved by adding compiler flags of -mmacosx-version-min=10.5 -isysroot /Developer/SDKs/MacOSX10.5u.sdk I have not tried this yet, but will try to get this rebuilt in the next day or two. Sorry for the trouble. FWIW, I still get results I don't understand on PPC, where ifeffit and artemis run but hephaestus are artemis do not.... isn't that amazing? --Matt

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iXAFS3.0.2
by Matt Newville 08 Sep '10

08 Sep '10

Hi All, OK, I put a next attempt for a Mac distribution at http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.2.dmg which should have some improvements. I believe this should work on 10.6 without issue -- I tested it on one other system at work, and everything launched without trouble. The Python module should now install well. With earlier attempts, I still had problems with a 10.5 machine, and suspected something wrong with i386 v x86_64. So I rebuilt everything (including perl) to be for i386 and ppc architectures, but not x86_64. In fact, I noticed some Aquaterm-related issues that also seemed x86_64 v i386, and went back to using (and including in the distribution) the standard issue Aquaterm1.0.1 that has i386 and ppc binaries, but not x86_64. Thus, iXAFS3.0.2 has no x86_64 binaries. For one thing, this makes the image "only" 60Mb. I could not find suitable 10.5 or PowerPC machines at work, but will test later today. For PPC, the iXAFS launcher application is now universal, and runs on PPC (G4) machine. With an earlier incarnation (when x86_64 was still included) I could run the Ifeffit shell and Athena. Unfortunately, both Artemis and Hephaestus failed to load with dyld: lazy symbol binding failed: Symbol not found: ___gcc_gmul Referenced from: ....local/bin/perl Expected in: /usr/lib/libSystem.B.dylib Hephaestus showed a splash screen, Artemis did not. I grepped out all the 'use' statements from Hephaestus, and these can all be loaded. In addition, all '*.bundle" files (Perl's binaries) claim to be universal binaries (including ppc). I don't really know what to make of this, but will try again with the latest build. Any feedback on what works and what doesn't would be greatly appreciated. Cheers, --Matt On Mon, Sep 6, 2010 at 11:06 AM, Jeff Terry <terryj(a)iit.edu> wrote: > Hi All, > > Looks like it works now on intel machines.. > I can run ifeffit from the iXAFS shell. > > The iXAFS app is not universal though, it is Intel only. > > Nice job Matt. > > Jeff > > > On Sep 6, 2010, at 10:17 AM, Matt Newville wrote: > >> Hi Joel, All, >> >> Yes, sorry for that. I'm still learning how to do this. Here's the >> latest news (some progress, incomplete): >> >> With Jeff's earlier message I looked into and solved at least one of >> the problems: that /Users/Newville/Codes/ifeffit/local/bin/perl >> was all over the place and expected. Of course, this worked when I >> tested it on my own machine!! I also found an issue with png >> support. >> >> I put a 3.0.1 dmg with these changes at >> http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.1.dmg >> >> I believe this may work on 10.6 systems. >> >> I tried this on a 10.5.7, i386 system (Julie's). The main iXAFS app >> runs, but I unfortunately get 'dyld' loading errors for all >> executables (including perl and ifeffit). I do not understand this, >> as thhe executables are definitely listed as "universal", ut I suspect >> it is a x86_64 v i386 issue. If anyone does understand this, please >> let me know. FWIW, the machine I'm building on is less than 3 months >> old, so I think it's x86_64, but 'arch' and 'uname -p' report i386. >> On the build machine, running >> arch -x86_64 ifeffit >> runs fine. >> arch -i386 ifeffit >> runs, but Aquaterm does not generate a plot (using PGPLOT_DEV=/XS does >> generate a plot with both settings). So my sense is that my box is >> really x86_64, but reports i386 and this may be causing trouble on >> real i386 machines. >> >> What's stranger is that I also tried this on a very old G4 powerpc, >> running 10.5. Here the iXAFS.app does not run, and indeed >> the iXAFS executable (iXAFS.app/Contents/MacOS/iXAFS) is indeed i386 >> only. But, the ifeffit application DOES RUN(!!!) on this machine. >> Perl runs too, but it appears I forgot to rebuild Ifeffit.pm for perl >> after some change for png support because >> perl -e 'use Ifeffit' still complains about png support. This is >> fixable. I'll look into making the iXAFS launcher application be >> universal. >> >> The python problem is definitely fixable too -- sorry for such poor testing! >> >> If you or Jeff or someone else wants to try this v3.0.1 out, that >> would be fine, but there are definitely "known problems". I'll make >> a v3.0.2 with the perl and python fixes today. I'll look into the >> i386 v x86_64 issues too, but that will take some research... >> >> Cheers, >> >> --Matt >> >> On Mon, Sep 6, 2010 at 7:34 AM, Brugger, Joel (SAM) >> <Joel.Brugger(a)samuseum.sa.gov.au> wrote: >>> Hi Matt, >>> >>> Not much luck with iXAFS3.0 so far. >>> >>> Under 10.5.8 (two macbooks), iXAFS crashes at startup. >>> >>> Under 10.6.4 (macbook pro), IXAFS opens, but clicking on athena/Artemis/Hephaestus only opens an X11 terminal. >>> >>> I think that somehow the installer expects perl to live in /Users/Newville/: >>> >>> $ pwd >>> /Applications/iXAFS.app/Contents/Resources/local/bin >>> b$ artemis >>> -bash: /Applications/iXAFS.app/Contents/Resources/local/bin/artemis: /Users/Newville/Codes/ifeffit/local//bin/perl: bad interpreter: No such file or directory >>> $ >>> >>> >>> >>> I also tried to install python, but something must be wrong with setup.py since files are copied to /Users/Newville. I now have such an inhabitant on my HD thanks to sudo, but even then the install failed. See details below. >>> >>> Hope it’s nothing traumatic! >>> >>> Thanks, JOEL >>> >>> >>> >>> JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ python setup.py install >>> running install >>> running build >>> running build_py >>> creating build >>> creating build/lib >>> creating build/lib/Ifeffit >>> copying lib/__init__.py -> build/lib/Ifeffit >>> copying lib/Ifeffit.py -> build/lib/Ifeffit >>> copying lib/ifeffit_config.py -> build/lib/Ifeffit >>> copying lib/shell.py -> build/lib/Ifeffit >>> running install_lib >>> creating /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/__init__.py -> /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/Ifeffit.py -> /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/ifeffit_config.py -> /Library/Python/2.6/site-packages/Ifeffit >>> copying build/lib/Ifeffit/shell.py -> /Library/Python/2.6/site-packages/Ifeffit >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/__init__.py to __init__.pyc >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py to Ifeffit.pyc >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/ifeffit_config.py to ifeffit_config.pyc >>> byte-compiling /Library/Python/2.6/site-packages/Ifeffit/shell.py to shell.pyc >>> running install_data >>> creating /Users/Newville >>> error: could not create '/Users/Newville': Permission denied >>> >>> >>> Running as SUDO: >>> >>> JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ sudo python setup.py install >>> Password: >>> running install >>> running build >>> running build_py >>> running install_lib >>> running install_data >>> creating /Users/Newville >>> creating /Users/Newville/Codes >>> creating /Users/Newville/Codes/ifeffit >>> creating /Users/Newville/Codes/ifeffit/local >>> creating /Users/Newville/Codes/ifeffit/local/bin >>> error: can't copy 'ifeffit_shell.py': doesn't exist or not a regular file >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

2 2

PhD Positions in Spectroscopy and Microscopy
by Matthias Bauer 07 Sep '10

07 Sep '10

Dear ifeffit mailing list users, the group of Prof. Grunwaldt at the Institute for Chemical Technology and Polymer Chemistry of the Karlsruher Insitute of Technology and myself are seeking for PhD Positions in Spectroscopy and Microscopy Karlsruhe Institute of Technology (KIT) is the result of the merger of the University of Karlsruhe and the Research Center, Karlsruhe. It is a unique institution in Germany, which combines the mission of a university with that of a large-scale research center of the Helmholtz Association. With 8000 employees and an annual budget of EUR 650 million, KIT is one of the largest research and edu-cation institutions worldwide. We are a establishing a new research group at the Institute for Technical Chemistry and Polymer Chemistry (ICTP) of the Karlsruhe Institute of Technology (KIT) in Southern Germany with focus on in situ spectroscopy, exhaust gas catalysis, biomass conversion and fine chemical processes. We combine effective catalyst preparation with profound spectroscopic knowledge of the catalysts and are therefore a highly interdisciplinary group. Presently, we have a number of open positions for enthusiastic Ph.D. students at the interface of physical, technical and solid state chemistry as well as in the field of chemical engineering and materials science. The work typically lasts over a period of 3 years. The salary will be according to E13/2, also depending on your professional and personal qualification. Open positions are presently available with focus on In situ spectroscopy of catalysts X-ray microscopy of heterogeneous catalysts Enthusiastic applicants with good English and/or German language knowledge should contact Prof. Dr. Jan-Dierk Grunwaldt (grunwaldt(a)kit.edu) or Dr. Matthias Bauer (matthias.bauer(a)kit.edu) for further information or visit the homepage http://www.itcp.uni-karlsruhe.de and www.grunwaldt.eu. KIT is pursuing a gender equality policy. Women are therefore particularly encouraged to apply. If qualified, handicapped applicants will be preferred. Please send your application including a CV, reference letters and publication list until 30.09.2010 to the Karlsruhe Institute of Technologie (KIT), Institute for Chemical Technology and Polymer Chemistry, Prof. Dr. Jan-Dierk Grunwaldt, Kaiserstr. 12, D-76131 Karlsruhe. Thanks for your attention and best regards, matthias bauer

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opening: Postdoctoral Fellow in Operando Spectroscopy
by Matthias Bauer 07 Sep '10

07 Sep '10

Dear ifeffit mailing list users, the group of Prof. Grunwaldt at the Institute for Chemical Technology and Polymer Chemistry of the Karlsruher Insitute of Technology is seeking for a Postdoctoral Fellow in Operando Spectroscopy Karlsruhe Institute of Technology (KIT) is the result of the merger of the University of Karlsruhe and the Research Center, Karlsruhe. It is a unique institution in Germany, which combines the mission of a university with that of a large-scale research center of the Helmholtz Association. With 8000 employees and an annual budget of EUR 650 million, KIT is one of the largest research and education institutions worldwide. The Institute for Technical Chemistry and Polymer Chemistry (ICTP) of the Karlsruhe Institute of Technology (KIT) in Southern Germany has an exciting opportunity for a Postdoctoral Fellow in Operando Spectroscopy for in situ characterization of heterogeneous catalysts in our catalysis laboratories at synchrotron radiation sources. Are you interested to work at the interface of physical chemistry and questions relevant to catalysis? The position is focused on the physico-chemical characterization of catalysts, mainly the identification and characterization of the active catalytic sites by means of X-ray absorption spectroscopy in combination with other spectroscopic methods like UV/Vis, FTIR and Raman techniques. The development of spectroscopic measurement cells as well as the realization of the according infrastructure are highly relevant for this work, which will be conducted in close cooperation with synchrotron radiation facilities such as ANKA (Karlsruhe), DESY (Hamburg), ESRF (Grenoble), and SLS (Switzerland). A PhD in chemistry, physics, chemical engineering or a related scientific field is a prerequisite for this position. Knowledge and experience with spectroscopic methods, mainly X-ray absorption in combination with other techniques, in catalysis is mandatory. Enthusiastic applicants with good English language knowledge should contact Prof. Dr. Jan-Dierk Grunwaldt (grunwaldt(a)kit.edu) for further information or visit the homepage http://www.itcp.uni-karlsruhe.de. KIT is pursuing a gender equality policy. Women are therefore particularly encouraged to apply. If qualified, handicapped applicants will be preferred. Please send your application including a CV, reference letters and publication list until 30.09.2010 to the Karlsruhe Institute of Technologie (KIT), Institute for Chemical Technology and Polymer Chemistry, Prof. Dr. Jan-Dierk Grunwaldt, Kaiserstr. 12, D-76131 Karlsruhe. On behalf of Prof. Grunwaldt, Matthias Bauer

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Re: [Ifeffit] XANES calculations
by Joshua Kas 06 Sep '10

06 Sep '10

Hi Jeong Eun Suk, FEFF doesn't come with any fitting program, but there is a program called FitIt developed by G. Smolentsev which is available for fitting XANES and can be used with FEFF or FDMNES. You can find FitIt at http://www.nano.sfedu.ru/fitit.html Cheers, Josh Kas > > > Thank Josha > > I already read the letter which you introduced but I misunderstood. > > can I ask a question? > > Other progrems like FDMNES are possibe to fit to experiment data. > > can I fit theory obtained from FEFF to experiment data like EXAFS? > > I couldn't have heard that from other users and I also didn't find fitting > parameters in FEFF. > > > > > > Date: Sat, 4 Sep 2010 10:36:48 -0700 > From: joshua.j.kas(a)gmail.com > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] XANES calculation > > Hi Jeong Eun Suk, > FEFF doesn't use basis functions. There is a truncation in angular > momentum, but the XANES is calculated by first calculating the Green's > function using multiple scattering theory. The Green's function is expanded > in terms of an angular momentum basis about each atom, and radial solutions > are numerical. Muffin tin potentials are used in FEFF8 and there is no > option for full potential calculations at present. For more information on > multiple scattering theory, > see for example > > Multiple scattering in solids By Antonios Gonis, > > > or > > > Theoretical approaches to x-ray absorption fine structure > J. J. Rehr and R. C. Albers > Rev. Mod. Phys. 72, 621 (2000) > > > Cheers, > Josh > On Sat, Sep 4, 2010 at 10:00 AM, < > 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. iXAFS for Mac OS X (Matt Newville) > 2. Re: iXAFS for Mac OS X (Matt Newville) > 3. Re: iXAFS for Mac OS X (Jeff Terry) > 4. XANES calculation (JeongEunSuk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Sep 2010 22:08:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTinSvabP-Z5ARvxYO4Gh6xMTrF_sErC=ykxUFdcR(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > With help from Ken McIvor and Jeff Terry, I've built a new version of > iXAFS for Mac OS X. This version should be considered experimental, > but for the brave and/or foolhardy please try it out and let us know > how it works. This version offers the latest versions of Athena, > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > meant to be universal (for x86_64, i386, and ppc), though I have not > fully tested this. > > The download is fairly large (~74Mb), mostly because it includes a > full distribution of Perl built right in (so it doesn't interfere with > the system Perl). It also provides a "complete" Unix shell-like > environment that can be used for those who need it. For example, a > python module is included that can be installed. > > The disk image is at > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > able to be installed by dragging the iXAFS application to any folder. > > To use the Unix shell, you'd put > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > in your .profile or from a bash Terminal command prompt (assuming you > installed to /Applications/). To install the Python module, first > run iff_init.sh above, then > copy and unpack > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > and run 'python setup.py install'. > > Again, this should be considered a beta release. Please be willing to > look for and report problems. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Fri, 3 Sep 2010 22:11:36 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTiku48seVpa5HTaW30_hiB7-Lap7u79zt0yFVQ3v(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Sorry for the typo. The download is at > http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg > > --Matt > > On Fri, Sep 3, 2010 at 10:08 PM, Matt Newville > <newville(a)cars.uchicago.edu> wrote: > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, ?I've built a new version of > > iXAFS for Mac OS X. ?This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. ? ?It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). ?It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. ?For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg ? This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > ? . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). ?To ?install the Python module, ?first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. ?Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 3 Sep 2010 22:38:23 -0500 > From: Jeff Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: <06727371-5AD2-401E-9EEF-0D981144D0E8(a)iit.edu> > Content-Type: text/plain; charset=us-ascii > > Hi All, > > If you have been using the iXAFS Shell for command line access, note that > it is currently not working in this version. > > Jeff > > On Sep 3, 2010, at 10:08 PM, Matt Newville wrote: > > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, I've built a new version of > > iXAFS for Mac OS X. This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). To install the Python module, first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Sat, 4 Sep 2010 13:03:21 +0900 > From: JeongEunSuk <eunsuk1986(a)hotmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XANES calculation > Message-ID: <BLU151-w31DB451074575B1BBF5E5EDA8E0(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > > Hi all > > I calculated XANES by using FEFF8.0. > > The manuel of FEFF8.0 demonstrates that basis functions of angular momentum > in each atom is used to calculate SCF potential and FMS. > > I know some codes use special basis functions of angular momentum like the > set of Slater-Type Orbital, contracted Gaussian-type function to describe > molecule or solid . > > Does anybody know what kinds of basis function is used in FEFF8.0 to > calculate SCF and FMS? > > and how can I know the contribution of each basis function? > > Finally, I read FEFF8.0 uses overlapped sherical muffin-tin(MT) to > calculate XANES. > > Is the non-muffin tin calculation impossible In FEFF8.0? > >

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iXAFS3.0 - not much luck so far
by Brugger, Joel (SAM) 06 Sep '10

06 Sep '10

Hi Matt, Not much luck with iXAFS3.0 so far. Under 10.5.8 (two macbooks), iXAFS crashes at startup. Under 10.6.4 (macbook pro), IXAFS opens, but clicking on athena/Artemis/Hephaestus only opens an X11 terminal. I think that somehow the installer expects perl to live in /Users/Newville/: $ pwd /Applications/iXAFS.app/Contents/Resources/local/bin b$ artemis -bash: /Applications/iXAFS.app/Contents/Resources/local/bin/artemis: /Users/Newville/Codes/ifeffit/local//bin/perl: bad interpreter: No such file or directory $ I also tried to install python, but something must be wrong with setup.py since files are copied to /Users/Newville. I now have such an inhabitant on my HD thanks to sudo, but even then the install failed. See details below. Hope it’s nothing traumatic! Thanks, JOEL JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ python setup.py install running install running build running build_py creating build creating build/lib creating build/lib/Ifeffit copying lib/__init__.py -> build/lib/Ifeffit copying lib/Ifeffit.py -> build/lib/Ifeffit copying lib/ifeffit_config.py -> build/lib/Ifeffit copying lib/shell.py -> build/lib/Ifeffit running install_lib creating /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/__init__.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/Ifeffit.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/ifeffit_config.py -> /Library/Python/2.6/site-packages/Ifeffit copying build/lib/Ifeffit/shell.py -> /Library/Python/2.6/site-packages/Ifeffit byte-compiling /Library/Python/2.6/site-packages/Ifeffit/__init__.py to __init__.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/Ifeffit.py to Ifeffit.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/ifeffit_config.py to ifeffit_config.pyc byte-compiling /Library/Python/2.6/site-packages/Ifeffit/shell.py to shell.pyc running install_data creating /Users/Newville error: could not create '/Users/Newville': Permission denied Running as SUDO: JoelMacBook-Silver:IfeffitPython-2.0.0 joelb$ sudo python setup.py install Password: running install running build running build_py running install_lib running install_data creating /Users/Newville creating /Users/Newville/Codes creating /Users/Newville/Codes/ifeffit creating /Users/Newville/Codes/ifeffit/local creating /Users/Newville/Codes/ifeffit/local/bin error: can't copy 'ifeffit_shell.py': doesn't exist or not a regular file

3 2

Re: [Ifeffit] XANES calculation
by Joshua Kas 05 Sep '10

05 Sep '10

Hi Jeong Eun Suk, FEFF doesn't use basis functions. There is a truncation in angular momentum, but the XANES is calculated by first calculating the Green's function using multiple scattering theory. The Green's function is expanded in terms of an angular momentum basis about each atom, and radial solutions are numerical. Muffin tin potentials are used in FEFF8 and there is no option for full potential calculations at present. For more information on multiple scattering theory, see for example Multiple scattering in solids By Antonios Gonis, or Theoretical approaches to x-ray absorption fine structure<http://rmp.aps.org/abstract/RMP/v72/i3/p621_1> J. J. Rehr and R. C. Albers Rev. Mod. Phys. 72, 621 (2000) Cheers, Josh On Sat, Sep 4, 2010 at 10:00 AM, <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. iXAFS for Mac OS X (Matt Newville) > 2. Re: iXAFS for Mac OS X (Matt Newville) > 3. Re: iXAFS for Mac OS X (Jeff Terry) > 4. XANES calculation (JeongEunSuk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Sep 2010 22:08:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTinSvabP-Z5ARvxYO4Gh6xMTrF_sErC=ykxUFdcR(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > With help from Ken McIvor and Jeff Terry, I've built a new version of > iXAFS for Mac OS X. This version should be considered experimental, > but for the brave and/or foolhardy please try it out and let us know > how it works. This version offers the latest versions of Athena, > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > meant to be universal (for x86_64, i386, and ppc), though I have not > fully tested this. > > The download is fairly large (~74Mb), mostly because it includes a > full distribution of Perl built right in (so it doesn't interfere with > the system Perl). It also provides a "complete" Unix shell-like > environment that can be used for those who need it. For example, a > python module is included that can be installed. > > The disk image is at > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > able to be installed by dragging the iXAFS application to any folder. > > To use the Unix shell, you'd put > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > in your .profile or from a bash Terminal command prompt (assuming you > installed to /Applications/). To install the Python module, first > run iff_init.sh above, then > copy and unpack > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > and run 'python setup.py install'. > > Again, this should be considered a beta release. Please be willing to > look for and report problems. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Fri, 3 Sep 2010 22:11:36 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: > <AANLkTiku48seVpa5HTaW30_hiB7-Lap7u79zt0yFVQ3v(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Sorry for the typo. The download is at > http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg > > --Matt > > On Fri, Sep 3, 2010 at 10:08 PM, Matt Newville > <newville(a)cars.uchicago.edu> wrote: > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, ?I've built a new version of > > iXAFS for Mac OS X. ?This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. ? ?It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). ?It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. ?For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg ? This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > ? . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). ?To ?install the Python module, ?first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. ?Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 3 Sep 2010 22:38:23 -0500 > From: Jeff Terry <terryj(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] iXAFS for Mac OS X > Message-ID: <06727371-5AD2-401E-9EEF-0D981144D0E8(a)iit.edu> > Content-Type: text/plain; charset=us-ascii > > Hi All, > > If you have been using the iXAFS Shell for command line access, note that > it is currently not working in this version. > > Jeff > > On Sep 3, 2010, at 10:08 PM, Matt Newville wrote: > > > Hi Folks, > > > > With help from Ken McIvor and Jeff Terry, I've built a new version of > > iXAFS for Mac OS X. This version should be considered experimental, > > but for the brave and/or foolhardy please try it out and let us know > > how it works. This version offers the latest versions of Athena, > > Artemis, and Hephaestus, and the latest version of Ifeffit. It is > > meant to be universal (for x86_64, i386, and ppc), though I have not > > fully tested this. > > > > The download is fairly large (~74Mb), mostly because it includes a > > full distribution of Perl built right in (so it doesn't interfere with > > the system Perl). It also provides a "complete" Unix shell-like > > environment that can be used for those who need it. For example, a > > python module is included that can be installed. > > > > The disk image is at > > http://car9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be > > able to be installed by dragging the iXAFS application to any folder. > > > > To use the Unix shell, you'd put > > . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh > > > > in your .profile or from a bash Terminal command prompt (assuming you > > installed to /Applications/). To install the Python module, first > > run iff_init.sh above, then > > copy and unpack > > > /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz > > and run 'python setup.py install'. > > > > Again, this should be considered a beta release. Please be willing to > > look for and report problems. > > > > Cheers, > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Sat, 4 Sep 2010 13:03:21 +0900 > From: JeongEunSuk <eunsuk1986(a)hotmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XANES calculation > Message-ID: <BLU151-w31DB451074575B1BBF5E5EDA8E0(a)phx.gbl> > Content-Type: text/plain; charset="ks_c_5601-1987" > > > Hi all > > I calculated XANES by using FEFF8.0. > > The manuel of FEFF8.0 demonstrates that basis functions of angular momentum > in each atom is used to calculate SCF potential and FMS. > > I know some codes use special basis functions of angular momentum like the > set of Slater-Type Orbital, contracted Gaussian-type function to describe > molecule or solid . > > Does anybody know what kinds of basis function is used in FEFF8.0 to > calculate SCF and FMS? > > and how can I know the contribution of each basis function? > > Finally, I read FEFF8.0 uses overlapped sherical muffin-tin(MT) to > calculate XANES. > > Is the non-muffin tin calculation impossible In FEFF8.0? > >

2 1

XANES calculation
by JeongEunSuk 04 Sep '10

04 Sep '10

Hi all I calculated XANES by using FEFF8.0. The manuel of FEFF8.0 demonstrates that basis functions of angular momentum in each atom is used to calculate SCF potential and FMS. I know some codes use special basis functions of angular momentum like the set of Slater-Type Orbital, contracted Gaussian-type function to describe molecule or solid . Does anybody know what kinds of basis function is used in FEFF8.0 to calculate SCF and FMS? and how can I know the contribution of each basis function? Finally, I read FEFF8.0 uses overlapped sherical muffin-tin(MT) to calculate XANES. Is the non-muffin tin calculation impossible In FEFF8.0?

1 0

iXAFS for Mac OS X
by Matt Newville 04 Sep '10

04 Sep '10

Hi Folks, With help from Ken McIvor and Jeff Terry, I've built a new version of iXAFS for Mac OS X. This version should be considered experimental, but for the brave and/or foolhardy please try it out and let us know how it works. This version offers the latest versions of Athena, Artemis, and Hephaestus, and the latest version of Ifeffit. It is meant to be universal (for x86_64, i386, and ppc), though I have not fully tested this. The download is fairly large (~74Mb), mostly because it includes a full distribution of Perl built right in (so it doesn't interfere with the system Perl). It also provides a "complete" Unix shell-like environment that can be used for those who need it. For example, a python module is included that can be installed. The disk image is at http://cars9.uchicago.edu/~ifeffit/src/iXAFS3.0.dmg This should be able to be installed by dragging the iXAFS application to any folder. To use the Unix shell, you'd put . /Applications/iXAFS.app/Contents/Resources/local/bin/iff_init.sh in your .profile or from a bash Terminal command prompt (assuming you installed to /Applications/). To install the Python module, first run iff_init.sh above, then copy and unpack /Applications/iXAFS.app/Contents/Resources/local/extras/IfeffitPython-2.0.0.tar.gz and run 'python setup.py install'. Again, this should be considered a beta release. Please be willing to look for and report problems. Cheers, --Matt

2 2

Re: [Ifeffit] Fwd: Methods to break correlations
by Bruce Ravel 01 Sep '10

01 Sep '10

On Tuesday 31 August 2010 06:49:36 pm you wrote: > I just noticed my reply to your message with a little more detail on my > error with the SSRL plugin did not post to the mailing list, so here is a > little more detail (with a few pictures). Thanks again (to you and all the > other users on the mailing list) for all of the tips for updating iXAfS, it > looks like I started a spark that got a bunch of folks pounding away at > their command lines. > Brandon, The most useful thing you sent me was a copy of the data that triggered the problem. With it, I was able to figure out what was going on. It turns out that version 2.0 of the SSRL XAS Data Collector stores its binary data differently from earlier versions. Who knew? Certainly not me! This difference was such that the data, as interpreted by the Athena plugin, were severely corrupted in a way that lead to Athena feeding very strange data to Ifeffit. Fortunately, Sam Webb once again came to the rescue. Suspecting that the problem would be something like this, I downloaded Sam's latest source code for SixPack and found the place where he imports SSRL binary data. Armed with Sam's knowledge, I was able to fix the SSRLB plugin. Sam, it seems that I owe you yet another beer the next time I see you. At this rate, it's going to be quite a bar tab. So .... grab the version of the plugin that I just committed to the svn repository: http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… Drop this new version in place on top of the old one wherever it sits on your computer. Try again and let me know if this fixes the problem. It worked for me on the data file you sent. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0

Manual update to iXAFS
by Paul Fons 31 Aug '10

31 Aug '10

Hi Bruce, Regards from a far too hot Japan, Thanks for the update suggestions for iXAFS Bruce. I managed to get it to work, but I found a couple of problems. 1. There is another intermediate directory in your steps (3,4,5), e.g. " /Applications/iXAFS/Contents/Resources/bin" should read " /Applications/iXAFS/Contents/Resources/Horae/bin" The intermediate directory Horae is missing in each case. 2. SVN is installed by default on the Mac. When I tried to run the mkartemis.pl and friends after downloading the latest svn release, however, I found that the rc.pl files were missing. How does one generate these from the svn files? I used a rc.pl from a horae-70 release I had around and it apparently worked. 3. The version numbers in the SVN release conflict within the files from the SVN (at least when following the procedure you mentioned above). Some of the files from the SVN release have (ArtemisLog) $VERSION set to 0.8.014 while others (e.g. Group.pm had $VERSION = "0.0.8.061"). This triggers an error in the athena and artemis of a version mismatch. I "fixed" this by disabling the check, as the logic of the versioning is not very clear from a simple examination of the files. What should the "$VERSION" string (and any other version related strings) be set to in each of the files? In any case it work, but it sure would be nice to have a nice new official release! paul

4 5

Re: [Ifeffit] Methods to break correlations
by Brandon Reese 31 Aug '10

31 Aug '10

Hi Bruce, Thanks for the tip on updating iXAFS, I will give that a try. As to the plugin not working on Athena, apologies about the vagueness. I have tried to open the file using iXAFS (ifeffit v.1.2.10, Athena v.0.8.054) and received the attached error message. After clicking 'ok' Athena remains open. I have also tried to open the same data file on Parallels running WinXP SP3 using the standard *.exe installer (ifeffit v.1.2.11c, Athena v.0.8.061) and received the attached error message. After clicking 'ok' for the windows error, Athena quits (leaving the plot window open). According to the header of the file it was collected using "SSRL - EXAFS Data Collector 2.0". I have tried several combination's which plug-ins are selected and it didn't seem to make a difference. Thanks for the tips Brandon On Mon, Aug 30, 2010 at 11:00 AM, <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: Methods to break correlations (Bruce Ravel) > 2. Re: Methods to break correlations (Bruce Ravel) > 3. Re: Residual EXAFS spectra (Bruce Ravel) > 4. Re: Methods to break correlations (Jeff Terry) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Aug 2010 10:08:13 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <201008301008.13700.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > > Does anyone have an Athena plugin for the SSRL data Collector > > v2.0? The SSRL plugins available make the program crash when I try and > use > > them. (moderators, let me know if these questions should have been in a > > separate posting) > > > > Here is the SSRL binary plugin from the svn repository > > > http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… > > And here is the one for data files that have been converted to ascii > > > http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… > > They should be placed in $HOME/.horae/Ifeffit/Plugins/Filetype/Athena/ > > > > I am willing to take a look at the problem you are seeing, but "it > crashes" doesn't give me much to work with. Obviously the plugins > worked for me otherwise I would not have considered them ready for > release. You need to provide some clue as to what the problem is. > Either supply a data file that triggers the problem or by cut and > paste what gets written after starting Athena in a terminal window or > (preferably) both. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 2 > Date: Mon, 30 Aug 2010 10:11:06 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: Jeff Terry <terryj(a)iit.edu> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <201008301011.06685.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > > I am running iXAFS 2.1 b1, is there any way to update the > > Athena/Artemis versions, or would I have to an source install? > > That is actually a question I need to know the answer to as well. In > fact, our group's post-doc has the same question, so I plan to look > into it this week. (Since I did not make the iXAFS package, I am not > 100% clear on how it works -- which is actually true of most things on > a Mac!) > > I believe the answer is yes, but I'll let you know what I know more. > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Aug 2010 10:20:02 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Residual EXAFS spectra > Message-ID: <201008301020.02497.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Monday 30 August 2010 09:57:09 am Bruce Ravel wrote: > > > Hi all, > > > I am doing an EXAFS spectra analysis of Eu(III) sorbed on mineral > oxides. > > > In course of this, I came across a lierature article(Geochimica et > > > cosmochimica Acta 64(16),2737,2000.) where a residual spectra (denoting > a > > > particular shell) was generated after subtracting four other different > > > paths contribution from the EXAFS spectra(k3.chi(k)). This procedure > was > > > adopted to identify and isolate different paths/shells informations > > > available in the EXAFS spectra. As the paper doesnot explain about the > > > procedure, I am little confused whether the author has adopted just the > > > linear subtraction methodology(i.e, sum of few selected paths minus the > > > original spectra) in creating the residual spectra or some other > > > mathematical approach. > > > > The caption to figure 5 in the article you cite says: > > > > "Residual EXAFS (produced by subtraction of U=Oax, U-Oeq, U-C, and > > U-U shells) ..." > > > > Seems pretty clear to me that what they show is the Fourier transform of > > > > data_chi(k) - sum_of_specified_paths(k) > > > > B > > > > Ummm... of course, I meant to say that the subtraction is done after > performing some kind of a fit to determine values of the parameters > affecting the paths included in the sum. > > Now I'll editorialize a bit ... the advantage of analyzing a > difference spectrum of this sort is that a small part of the data that > might get "lost" in the full fit gets emphasized. The disadvantage -- > and a big one at that -- is that you loose the ability to evaluate > correlations between the parameters of the fit to the residual and the > parameters that were used to determine the sum of paths used to make > the residual. Consequently, doing an analysis of the residual > spectrum requires a high level of confidence in the parameters used > for the subtracted paths. In my experience, that level of confidence > is rarely defensible. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 4 > Date: Mon, 30 Aug 2010 09:47:58 -0500 > From: Jeff Terry <terryj(a)iit.edu> > To: Bruce Ravel <bravel(a)bnl.gov> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <FA839956-699F-4DB8-88FE-3B5E17E3AAAA(a)iit.edu> > Content-Type: text/plain; charset=us-ascii > > iXAFS originally started out as a wrapper to launch the individual > programs. At that time, it was a simple matter to replace any of the > individual programs. Ken McIvor has improved iXAFS so that it now builds > universal projects but has perl code embedded. This makes it more difficult > to update. > > That said there is a directory structure within iXAFS and I would guess > that replacing the individual programs would work. I make no guarantees > though as I am not sure of all the changes that Ken has made since I > initially wrote the cocoa wrapper. > > Jeff > > Sent from my iPhone > > On Aug 30, 2010, at 9:11 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > >> I am running iXAFS 2.1 b1, is there any way to update the > >> Athena/Artemis versions, or would I have to an source install? > > > > That is actually a question I need to know the answer to as well. In > > fact, our group's post-doc has the same question, so I plan to look > > into it this week. (Since I did not make the iXAFS package, I am not > > 100% clear on how it works -- which is actually true of most things on > > a Mac!) > > > > I believe the answer is yes, but I'll let you know what I know more. > > > > B > > > > > > -- > > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > > Building 535A > > Upton NY, 11973 > > > > My homepage: http://xafs.org/BruceRavel > > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 90, Issue 24 > *************************************** >

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Methods to break correlations
by Brandon Reese 30 Aug '10

30 Aug '10

Hi all, I am performing EXAFS measurements on amorphous Indium Zinc Oxide (In and Zn edges) thin films and have a question about methods to break correlations. We have the films grown at several compositions ranging from 50/50 to 90/10 (In/Zn wt.%). We expect these films to display first NN shells very similar to their pure oxide cases, but the are interested in changes to the next-NN shells. I was wondering if folks on the mailing had some good references on multiple data set fits using doping fractions to break correlations. Would it be worth doing temperature dependent (or perhaps just cold) measurements to try and break correlations that way? Another couple unrelated questions... I am running iXAFS 2.1 b1, is there any way to update the Athena/Artemis versions, or would I have to an source install? Does anyone have an Athena plugin for the SSRL data Collector v2.0? The SSRL plugins available make the program crash when I try and use them. (moderators, let me know if these questions should have been in a separate posting) Regards, Brandon

3 4

Residual EXAFS spectra
by sumitk＠barc.gov.in 30 Aug '10

30 Aug '10

Hi all, I am doing an EXAFS spectra analysis of Eu(III) sorbed on mineral oxides. In course of this, I came across a lierature article(Geochimica et cosmochimica Acta 64(16),2737,2000.) where a residual spectra (denoting a particular shell) was generated after subtracting four other different paths contribution from the EXAFS spectra(k3.chi(k)). This procedure was adopted to identify and isolate different paths/shells informations available in the EXAFS spectra. As the paper doesnot explain about the procedure, I am little confused whether the author has adopted just the linear subtraction methodology(i.e, sum of few selected paths minus the original spectra) in creating the residual spectra or some other mathematical approach. Any one having experience in this analysis will please repond to my problem. I would also like to know the best way to identify different shells contribution in the EXAFs spectra. Thanking in advance Sumit Kumar Scientific officer Radiochemistry Division Bhabha Atomic Research Centre Mumbai India-400 085. Phone: +91-22-2559 0640.

2 2

Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 21
by Jatinkumar Rana 30 Aug '10

30 Aug '10

Dear Dominik, Thank you so much for your reply. However, i am not able to understand the logic behind removal of following atoms from Feff.inp file as mentioned by you **In principle, after running ATOMS, you just need to remove atoms from the generated feff.inp file so that the occupancy is correct. I.e., in this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1, 1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding those which are too close to other atoms. The FEFF output might help, so try deleting preferentially those causing FEFF to fail.** can you please give me the idea behind doing that and is it physically defendable to do such changes ?? Looking forward to your reply.. Best regards, Jatin On 27.08.2010 14:00, 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: Help with cif file (Dominik Samuelis) > 2. catalysis workshop at the karlsruher synchrotron ANKA > (Matthias Bauer) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 27 Aug 2010 10:09:05 +0200 > From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help with cif file > Message-ID:<4C7772A1.2000307(a)fkf.mpg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Jatin, > > in your original cif file, you have site occupancies as low as 0.5 (Cr1 > site) and 0.358 (P62). Just setting them to 1 will not help, because > ATOMS assumes them to be unity anyway. > > For such a complicated unit cell, the typical recipe with using > prototypical structures of course does not help, just because there is > not a simple prototype structure for arrojadite. > > In principle, after running ATOMS, you just need to remove atoms from > the generated feff.inp file so that the occupancy is correct. I.e., in > this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1, > 1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding > those which are too close to other atoms. The FEFF output might help, so > try deleting preferentially those causing FEFF to fail. > > Another solution might be loading the structure's cif file into a > structure editor such as DIAMOND. There, you can then check the bond > distance histograms and delete atoms accordingly. At the end, just > export the data in xyz format and use this as the atom positions list in > the feff.inp file. > > Regards, > Dominik > > > > On 20.08.2010 09:30, Jatinkumar Rana wrote: > >> Dear Dominic, Dear Bruce, >> >> I am also facing the same problem as experienced by Kleper. I am working >> on the EXAFS analysis of Arrojadite mineral. We have refined the >> strucutre using neutron diffraction to get crystallographic information >> which can be fed to ATOMS. The original .cif file contains the >> fractional occupancy so ATOMS give similar error report as mentioned by >> Kleper. After reading your post, i changed all site occupancy to 1 and >> then run ATOMS but still it gives me the error report. >> >> Can anybody tell me, why ATOMS report error ? >> >> I have attached both original .cif file (with fractional occupancy) and >> modified .cif file (all site occupancy = 1). I have EXAFS spectrum at Fe >> and Mn K-edge. >> >> Looking forward to your answer. >> >> Thanks a lot in advance... >> >> Best regards, >> Jatin >> >> >> >> >> >> On 18.08.2010 19:00, 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: Help with cif file (Dominik Samuelis) >>> 2. Re: Help with cif file (Bruce Ravel) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Wed, 18 Aug 2010 08:36:03 +0200 >>> From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> >>> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] Help with cif file >>> Message-ID:<01A98ED5-00FE-4875-989A-C7663E57BF97(a)fkf.mpg.de> >>> Content-Type: text/plain; charset=iso-8859-1 >>> >>> Dear Kleper, >>> >>> even though I haven't tested it in detail, I'm sure the errors come >>> from the fact that ATOMS cannot handle site occupancies other than >>> unity. If you have a look in the cif file, you can see that both W >>> (0.23) and Ti (0.54) have a fractional occupancy: >>> >>> loop_ >>> _atom_site_label >>> _atom_site_type_symbol >>> _atom_site_symmetry_multiplicity >>> _atom_site_Wyckoff_symbol >>> _atom_site_fract_x >>> _atom_site_fract_y >>> _atom_site_fract_z >>> _atom_site_occupancy >>> _atom_site_attached_hydrogens >>> _atom_site_calc_flag >>> W1 W4+ 4 e 0. 0. 0.0564(2) 0.23 0 d >>> Ti1 Ti4+ 2 a 0. 0. 0. 0.54 0 d >>> O1 O2- 4 f 0.3007(6) 0.3007(6) 0. 1. 0 d >>> >>> To get it working, you need to use the prototypical structure (e.g. >>> TiO2) without mixed sites as ATOMS input. In the feff.inp file, you >>> can then change 46 out of 100 Ti atoms to W (5 out of 10 should be ok >>> as well for a smaller cluster). Don't forget to add the appropriate >>> POTENTIALS line for W to the feff.inp. The small shift of the W atoms >>> away from the Ti positions then could be handled by some additional >>> delR parameter for the W paths during fitting. >>> >>> All the best, >>> Dominik >>> >>> >>> Am 17.08.2010 um 15:27 schrieb Kleper Rocha: >>> >>> >>>> Please, >>>> >>>> Could someone help me with the cif file attached, get from the >>>> www.crystallographic.net shearch with the terms Ti, W, O. When I try >>>> to run the Feff the following message appears. >>>> >>>> "Feff 6L.02 >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 1 2 >>>> 1 0.00000 0.00000 0.00000 >>>> 2 0.00000 0.00000 -0.16378 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 1 3 >>>> 1 0.00000 0.00000 0.00000 >>>> 3 0.00000 0.00000 -0.32756 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 2 3 >>>> 2 0.00000 0.00000 -0.16378 >>>> 3 0.00000 0.00000 -0.32756 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 10 11 >>>> 10 0.00000 0.00000 2.57634 >>>> 11 0.00000 0.00000 2.74012 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 10 12 >>>> 10 0.00000 0.00000 2.57634 >>>> 12 0.00000 0.00000 2.90390 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 11 12 >>>> 11 0.00000 0.00000 2.74012 >>>> 12 0.00000 0.00000 2.90390 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 13 14 >>>> 13 0.00000 0.00000 -2.90390 >>>> 14 0.00000 0.00000 -3.06768 >>>> Run continues... >>>> Titanium tungsten oxide (0.54/0.46/2) >>>> Ti.54 W.46 O2 >>>> O2 Ti0.54 W0.46 >>>> Peters, E. >>>> Ueber ein niedervalentes Titan-Wolframoxid: Ti0,54 W0,46 O2 >>>> Calculating potentials and phases... >>>> free atom potential and density for atom type 0 >>>> free atom potential and density for atom type 1 >>>> free atom potential and density for atom type 2 >>>> free atom potential and density for atom type 3 >>>> overlapped potential and density for unique potential 0 >>>> overlapped potential and density for unique potential 1 >>>> overlapped potential and density for unique potential 2 >>>> overlapped potential and density for unique potential 3 >>>> muffin tin radii and interstitial parameters >>>> >>>> >>>> This warning indicates a problem in the Atoms list. For some >>>> reason you have atoms that are separated by than 0.93 Angstroms >>>> (or 1.75 Rydberg). >>>> >>>> This may be due to the presence of hydrogen atoms in your feff.inp >>>> file, in which case this is an innocuous warning and may be ignored. >>>> >>>> However, this may indicate a problem constructing the Atoms >>>> list. The most common cause of this problem is a mistake in the >>>> crystallographic data used on the Atoms page. You may have >>>> incorrect values for lattice constants or angles or incorrect >>>> values for site coordinates. You may need a shift vector to move >>>> the lattice into its standard setting. >>>> >>>> Please be aware that Atoms works with 5 digits of precision. >>>> Thus, if you have a site with a coordinate of 1/3, you should use >>>> either "1/3" or "0.33333" on the Atoms page. Using insufficient >>>> precision, say "0.333" is a common cause of this error message. >>>> >>>> Artemis has continued on the possibility that the warning is >>>> caused by hydrogen atoms, but be warned that the feff.inp may >>>> require your attention." >>>> >>>> Thanks in advance. >>>> >>>> >>>> >>>> Kleper de Oliveira Rocha >>>> >>>> <O2 Ti0.54 W0.46.cif>_______________________________________________ >>>> Ifeffit mailing list >>>> Ifeffit(a)millenia.cars.aps.anl.gov >>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>>> >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > >

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catalysis workshop at the karlsruher synchrotron ANKA
by Matthias Bauer 27 Aug '10

27 Aug '10

Dear mailing list users, on behalf of the organising committee I would like to announce a workshop on catalysis at the Karlsruher synchrotron ANKA, please find attached the programm. Best regards, Matthias Bauer Workshop "Shining synchrotron light on catalysts - Needs and opportunities for the future" October 8th 2010 in Karlsruhe, Germany Catalysis is playing a major role in chemical industries considering that more than 90% of all chemical products have seen at least in one step a catalyst. With the challenges which we presently meet in fossil energy resources and CO2-emission, environmental catalysis and pharmaceuticals catalysis is one of the key areas. Rapid catalyst development by a rational approach requires a detailed understanding of their structure, where synchrotron light has significantly contributed in the past and will be even more powerful in the future. This is falling into the new developments also at ANKA with the establishment of a strengthened catalysis focus. During the workshop the needs and opportunities at synchrotron radiation sources will be discussed. Morning Session 1 8.30 Welcome (Tilo Baumbach, KIT Karlsruhe and Jan-Dierk Grunwaldt, KIT Karlsruhe) 8.40 9.00 Stefan Mangold (KIT, Karlsruhe) Spectroscopy and related techniques at ANKA 9.00 - 9.30 Anatoly Frenkel (NLSL, Brookhaven) "Multiple Length Scales in Nanocatalysts Probed in a Single Synchrotron Experiment: The Combined use of XAFS, XRD and DAFS" 9.30 10.00 Marc Newton (ESRF, Grenoble) "In situ hard X-ray studies of the dynamic behaviour of heterogeneous catalysts" 10.00 - 10.20 Ursula Bentrup (LIKAT, Rostock) Online monitoring of molybdate catalyst precursor synthesis and conditioning by coupled X-ray scattering and optical spectroscopic methods 10.20 - 10.40 Coffee Morning Session 2 10.40 11.10 Moniek Trompp (University of Southampton) 'Molecules in action - Developments in X-ray spectroscopy' 11.10 11.40 Anna Puig Molina (Haldor Topsøe, Lyngby) Synchrotron Radiation for Industrial Catalysis 11.40 - 12.10 Ronald Frahm (Universität Wuppertal) State of the art Quick-EXAFS: Applications in Catalysis 12.10 12.30 Olga Safonova (ESRF, Grenoble) Catalysis at SNBL and SLS 12.30 13.30 Lunch Future Developments 13.30 - 14.00 Wolfgang Caliebe (HASYLAB, Hamburg) Hard X-Ray Spectroscopy and Catalysis at DESY - Presence and Future 14.00 14.20 Jan-Dierk Grunwaldt (KIT, Karlsruhe) Shining X-rays on catalysts at ANKA: Present and Future 14.20 15.00 Discussion on Catalysis activities at ANKA and synchrotrons in general (Stefan Mangold, Matthias Bauer, Jan-Dierk Grunwaldt) Meeting site: The meeting will take place at the Akademie Hotel Karlsruhe (http://www.akademiehotel-karlsruhe.de/) Am Rüppurrer Schloß 40, 76199 Karlsruhe More info: http://anka.iss.kit.edu/english/448.php Admittance fee: Free of charge, but please register since the number of seats may be limited Organized by: Matthias Bauer, Jan-Dierk Grunwaldt, Stefan Mangold

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Re: [Ifeffit] Help with cif file
by Jatinkumar Rana 27 Aug '10

27 Aug '10

Dear Dominic, Dear Bruce, I am also facing the same problem as experienced by Kleper. I am working on the EXAFS analysis of Arrojadite mineral. We have refined the strucutre using neutron diffraction to get crystallographic information which can be fed to ATOMS. The original .cif file contains the fractional occupancy so ATOMS give similar error report as mentioned by Kleper. After reading your post, i changed all site occupancy to 1 and then run ATOMS but still it gives me the error report. Can anybody tell me, why ATOMS report error ? I have attached both original .cif file (with fractional occupancy) and modified .cif file (all site occupancy = 1). I have EXAFS spectrum at Fe and Mn K-edge. Looking forward to your answer. Thanks a lot in advance... Best regards, Jatin On 18.08.2010 19:00, 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: Help with cif file (Dominik Samuelis) > 2. Re: Help with cif file (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Aug 2010 08:36:03 +0200 > From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help with cif file > Message-ID:<01A98ED5-00FE-4875-989A-C7663E57BF97(a)fkf.mpg.de> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Kleper, > > even though I haven't tested it in detail, I'm sure the errors come from the fact that ATOMS cannot handle site occupancies other than unity. If you have a look in the cif file, you can see that both W (0.23) and Ti (0.54) have a fractional occupancy: > > loop_ > _atom_site_label > _atom_site_type_symbol > _atom_site_symmetry_multiplicity > _atom_site_Wyckoff_symbol > _atom_site_fract_x > _atom_site_fract_y > _atom_site_fract_z > _atom_site_occupancy > _atom_site_attached_hydrogens > _atom_site_calc_flag > W1 W4+ 4 e 0. 0. 0.0564(2) 0.23 0 d > Ti1 Ti4+ 2 a 0. 0. 0. 0.54 0 d > O1 O2- 4 f 0.3007(6) 0.3007(6) 0. 1. 0 d > > To get it working, you need to use the prototypical structure (e.g. TiO2) without mixed sites as ATOMS input. In the feff.inp file, you can then change 46 out of 100 Ti atoms to W (5 out of 10 should be ok as well for a smaller cluster). Don't forget to add the appropriate POTENTIALS line for W to the feff.inp. The small shift of the W atoms away from the Ti positions then could be handled by some additional delR parameter for the W paths during fitting. > > All the best, > Dominik > > > Am 17.08.2010 um 15:27 schrieb Kleper Rocha: > > >> Please, >> >> Could someone help me with the cif file attached, get from the www.crystallographic.net shearch with the terms Ti, W, O. When I try to run the Feff the following message appears. >> >> "Feff 6L.02 >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 1 2 >> 1 0.00000 0.00000 0.00000 >> 2 0.00000 0.00000 -0.16378 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 1 3 >> 1 0.00000 0.00000 0.00000 >> 3 0.00000 0.00000 -0.32756 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 2 3 >> 2 0.00000 0.00000 -0.16378 >> 3 0.00000 0.00000 -0.32756 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 10 11 >> 10 0.00000 0.00000 2.57634 >> 11 0.00000 0.00000 2.74012 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 10 12 >> 10 0.00000 0.00000 2.57634 >> 12 0.00000 0.00000 2.90390 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 11 12 >> 11 0.00000 0.00000 2.74012 >> 12 0.00000 0.00000 2.90390 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 13 14 >> 13 0.00000 0.00000 -2.90390 >> 14 0.00000 0.00000 -3.06768 >> Run continues... >> Titanium tungsten oxide (0.54/0.46/2) >> Ti.54 W.46 O2 >> O2 Ti0.54 W0.46 >> Peters, E. >> Ueber ein niedervalentes Titan-Wolframoxid: Ti0,54 W0,46 O2 >> Calculating potentials and phases... >> free atom potential and density for atom type 0 >> free atom potential and density for atom type 1 >> free atom potential and density for atom type 2 >> free atom potential and density for atom type 3 >> overlapped potential and density for unique potential 0 >> overlapped potential and density for unique potential 1 >> overlapped potential and density for unique potential 2 >> overlapped potential and density for unique potential 3 >> muffin tin radii and interstitial parameters >> >> >> This warning indicates a problem in the Atoms list. For some >> reason you have atoms that are separated by than 0.93 Angstroms >> (or 1.75 Rydberg). >> >> This may be due to the presence of hydrogen atoms in your feff.inp >> file, in which case this is an innocuous warning and may be ignored. >> >> However, this may indicate a problem constructing the Atoms >> list. The most common cause of this problem is a mistake in the >> crystallographic data used on the Atoms page. You may have >> incorrect values for lattice constants or angles or incorrect >> values for site coordinates. You may need a shift vector to move >> the lattice into its standard setting. >> >> Please be aware that Atoms works with 5 digits of precision. >> Thus, if you have a site with a coordinate of 1/3, you should use >> either "1/3" or "0.33333" on the Atoms page. Using insufficient >> precision, say "0.333" is a common cause of this error message. >> >> Artemis has continued on the possibility that the warning is >> caused by hydrogen atoms, but be warned that the feff.inp may >> require your attention." >> >> Thanks in advance. >> >> >> >> Kleper de Oliveira Rocha >> >> <O2 Ti0.54 W0.46.cif>_______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >

2 1

Strange problems with Artemis
by Jatinkumar Rana 27 Aug '10

27 Aug '10

Dear users, I am facing a strange problem with Artemis and i don't know how to get rid of it. I hope any expert in the mailing lists would help me solving this problem. I have EXAFS data on Fe and Mn K-edge for Arrojadite mineral. Since the crystal structure of this mineral is not known we did neutron diffraction to refine the structure. To support the neutron diffraction results, we planned to do EXAFS on this mineral (Fe and Mn k-edge). We have around 8 different atomic species (i.e. Na,K,Fe,Mn,Al,Cr,O,P) in the mineral and some of the sites are fractionally occupied. Since ATOMS can not handle more than 7 potentials and site occupancy other than unity i have made following changes : 1) replaced Cr with Al, mainly because Cr is present in a few ppm only (relative importance). 2) set all site occupancy to 1 Even after doing the above changes, i got following error message when i run FEFF ************** Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 20 11 -3.01973 -0.20361 1.44233 20 -3.54653 -0.05083 0.83053 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 46 62 46 -0.40014 -0.20361 5.03633 62 0.12666 -0.05083 5.64813 Run continues... Sodium Potassium Aluminium Chromium Iron Manganese Phosphate Hydrate Al Cr Fe7.53 H2 K1.21 Mn6 Na3 O50 P12 Kallfa\&s, Christoph Crystal structure, chemical composition and thermal behaviour of arrojadite Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 free atom potential and density for atom type 4 free atom potential and density for atom type 5 free atom potential and density for atom type 6 free atom potential and density for atom type 7 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 overlapped potential and density for unique potential 4 overlapped potential and density for unique potential 5 overlapped potential and density for unique potential 6 overlapped potential and density for unique potential 7 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 4 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 5 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 6 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 7 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... Rmax 7.0000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table nfound nheap nheapx nsc r 1000 469 469 3 5.2890 2000 730 730 3 5.7147 3000 907 907 3 5.9455 4000 1040 1040 3 6.1157 5000 1177 1177 3 6.2616 6000 1319 1319 3 6.3835 7000 1412 1413 3 6.4825 8000 1443 1444 3 6.5749 9000 1469 1473 3 6.6585 10000 1432 1474 3 6.7377 11000 1367 1474 3 6.8062 12000 1202 1474 3 6.8680 13000 870 1474 3 6.9289 14000 251 1474 3 6.9856 . . . . . .. . This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored. However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting. Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message. Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention. ************************************ I have attached both *original.cif file* (with all 8 atomic species and fractional occupancy) and *modified.cif file* (Cr replaced by Al and all site occupancy set to 1) with this mail for your perusal. I hope some experts in the mailing list would suggest me some solutions. Many more thanks in advance for your valuable time and suggestions.... Best regards, Rana

1 0

debye function
by Kleber Daum Machado 24 Aug '10

24 Aug '10

Hi, I'd like to know the explicit mathematical expressions that are represented by the functions debye(temp,thetad) and eins(temp,thetae). Are they given in some documentation file or article? Thank you very much Kleber

3 3

Re: [Ifeffit] updating ifeffit manually
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Matt, Thanks for the information. I could not get the runner.exe to work. So installed the updates directly as you suggested. It works perfectly. Aranwela These were the steps I have followed. Updating Ifeffit manually (if, somehow, it does not update automatically) 1. Check the latest update installed (typically in C:\Program Files\Ifeffit\config\iff_xxx). In my case it was iff_009.2. Then check the current available update level from the cars webpage: http://cars9.uchicago.edu/~ifeffit/updates/current.datAt present it is at 013. 3. Download the missing updates from http://cars9.uchicago.edu/~ifeffit/updates/iff_XXX.zip Remember you need to change XXX to the appropriate file # (to 010 for an example). ( I had to download iff_010, iff_011, iff_012 and iff_013 and saved them on to the desktop). 4. These are zipped files. Need to unzip those into the C:\Program Files\Ifeffit folder. But one has to do this in sequence (it is said). ( In my case I unzipped 010 first then 011, next 012 and 013 after that. Unzipping is easy in windows 7. Just right click on the zipped folder and select ‘extract all’ then browse to the Ifeffit folder (In my case C:\Program Files\Ifeffit). It will prompt you to choose between two or three options. (In all cases I chose ‘copy and replace’ or just ‘replace’. That’a all. Everything should work perfectly. Date: Mon, 16 Aug 2010 14:06:47 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7 Message-ID: <AANLkTinvBiq0ES9TLN2Air38tWw4VgCroOSJbsCSNU7X(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Aranwela, Thanks for the report. I do think this is a permissions problem. That's not to say it's not a real problem, just that it should be solvable. I just tested this by resetting the "update level" in config/current.dat, and forcing the updater to run. It worked fine to download and install the update. That was on a Mac running Windows 7 (64 bit) as a virtual machine. The account I used does have full Administrator control. The process running the updater definitely needs to be be able to write to C:\Program Files\Ifeffit (or wherever you installed to). Would you be willing to try to download the update zip file (say, iff_013.zip) and unzip it into your installation directory, as described at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater and let us know what does and doesn't work? I'm sure that others would find your report helpful. Cheers, --Matt

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Updating Ifeffit manually
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Matt, Thanks for the information. I could not get the runner.exe to work. So installed the updates directly as you suggested. It works perfectly. Aranwela These were the steps I have followed. Updating Ifeffit manually (if, somehow, it does not update automatically) 1. Check the latest update installed (typically in C:\Program Files\Ifeffit\config\iff_xxx). In my case it was iff_009. 2. Then check the current available update level from the cars webpage: http://cars9.uchicago.edu/~ifeffit/updates/current.dat At present it is at 013. 3. Download the missing updates from http://cars9.uchicago.edu/~ifeffit/updates/iff_XXX.zip Remember you need to change XXX to the appropriate file # (to 010 for an example). ( I had to download iff_010, iff_011, iff_012 and iff_013 and saved them on to the desktop). 4. These are zipped files. Need to unzip those into the C:\Program Files\Ifeffit folder. But one has to do this in sequence (it is said). ( In my case I unzipped 010 first then 011, next 012 and 013 after that. Unzipping is easy in windows 7. Just right click on the zipped folder and select ‘extract all’ then browse to the Ifeffit folder (In my case C:\Program Files\Ifeffit). It will prompt you to choose between two or three options. (In all cases I chose ‘copy and replace’ or just ‘replace’. That’a all. Everything should work perfectly. Date: Mon, 16 Aug 2010 14:06:47 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7 Message-ID: <AANLkTinvBiq0ES9TLN2Air38tWw4VgCroOSJbsCSNU7X(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Aranwela, Thanks for the report. I do think this is a permissions problem. That's not to say it's not a real problem, just that it should be solvable. I just tested this by resetting the "update level" in config/current.dat, and forcing the updater to run. It worked fine to download and install the update. That was on a Mac running Windows 7 (64 bit) as a virtual machine. The account I used does have full Administrator control. The process running the updater definitely needs to be be able to write to C:\Program Files\Ifeffit (or wherever you installed to). Would you be willing to try to download the update zip file (say, iff_013.zip) and unzip it into your installation directory, as described at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater and let us know what does and doesn't work? I'm sure that others would find your report helpful. Cheers, --Matt

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Re: [Ifeffit] IFEFFIT update (windows7)
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Todd, Thanks for the information. But I have already tried that. Doesn't work for me. But since it has worked for you I guess the problem is still in my computer. Unfortunately I do not know what it is. So, I am going to download and install updates directly as Matt has suggested. Thanks. Aranwela Date: Tue, 17 Aug 2010 08:52:28 -0600 From: "Monson, Todd" <tmonson(a)sandia.gov> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] updating Athena in Win 7 Message-ID: <AC050BA7EAC9A34E9A05BC31C3AA2E8B186774E38A(a)ES02SNLNT.srn.sandia.gov> Content-Type: text/plain; charset="us-ascii" Aranwela, It sounds like you're having the same problem that I was having. You need to change the permissions in the Ifeffit folder under program files. There is a good discussion of this that worked for me under Vol. 90, Issue 5 of the Ifeffit digest. This is a copy of the portion of that conversion that you need: "Right click on the IFEFFIT folder in Program Files and select Properties. Select the Security tab and then click the Edit button. For all of the group or user names listed make sure Allow is marked for all permissions (Checking Full Control should select all of the permissions in the list below it). Hit the Apply button and then the OK button. Then try opening Athena again and see if it successfully runs through the update process. " Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Help with cif file
by Kleper Rocha 18 Aug '10

18 Aug '10

3 2

updating Athena in Win 7
by Monson, Todd 17 Aug '10

17 Aug '10

Aranwela, It sounds like you're having the same problem that I was having. You need to change the permissions in the Ifeffit folder under program files. There is a good discussion of this that worked for me under Vol. 90, Issue 5 of the Ifeffit digest. This is a copy of the portion of that conversion that you need: "Right click on the IFEFFIT folder in Program Files and select Properties. Select the Security tab and then click the Edit button. For all of the group or user names listed make sure Allow is marked for all permissions (Checking Full Control should select all of the permissions in the list below it). Hit the Apply button and then the OK button. Then try opening Athena again and see if it successfully runs through the update process. " Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Help with cif file
by Kleper Rocha 17 Aug '10

17 Aug '10

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Re: [Ifeffit] PYTHON scripting on MacOS & XP (Joel Brugger)
by Brugger, Joel (SAM) 17 Aug '10

17 Aug '10

Hi Matt, Thanks for the update. We had trouble getting the XP version to work. We're running Win XP under parallels on the Mac. Ifeffit (1.2.11), python (2.5) and the wrapper installed successfully. The ifeffit.py shell (in the python/scripts directory) does not recognise any python commands. And opening python in the ifeffit directory - it does not recognise ifeffit in the "import ifeffit" command. What are we doing wrong? Thanks, Joel & Barbara

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incorporating feff 8 into Artemis
by Jatinkumar Rana 17 Aug '10

17 Aug '10

Dear All, Recently, I have decided to upgrade to Feff8.20. We have got Feff820a.exe file. I would like to know if there is any specific procedure to replace older Feff6 with this Feff820a.exe in artemis ? Thank you very much in advance !!! Best regards, Rana

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problem with the current Ifeffit installer for windows
by Bruce Ravel 16 Aug '10

16 Aug '10

Hi all, Last week, I discovered a problem that might affect some of you. The current Windows installer package, ifeffit-1.2.11.exe, has a problem to do with how the ifeffit library was compiled. Fortunately, this problem was subsequently fixed. If you have installed the updates that have come out since ifeffit-1.2.11.exe was released, then you are fine. If, however, you have installed the installer *without* installing the updates, then your version of Artemis will be performing its fits slightly incorrectly. To find out if your installation is affected, start Artemis and select "About Ifeffit" from the Help menu. * If the version number for Ifeffit displayed in the echo area at the bottom of the Artemis window says "1.2.11" then you need to update. * If the version number says "1.2.11c" then you are fully updated and will not suffer from this problem. If you need to update but are, for some reason, unable to do so by the normal channel, there are instructions for updating by hand at this wiki page: http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater If you are using the incorrect version of the Ifeffit library, your fits will still be reasonable, but the best fit values of your parameters and all statistical parameters will be calculated differently from the normal version of Ifeffit. In my limited experience, best fit values tend not to different outside of their error bars, but they are different. The reason I noticed this problem is because here at Brookhaven, our internet access goes through a proxy server. If you are not configured to have the runner go through the proxy server, then it will be unable to find and download the updates. The solution I found for my colleague's computer was to set the http_proxy variable in C:\Program Files\Ifeffit\config\updater.ini to the address and port of the local proxy. I will work on making a new installer next week when I return from an experiment at the APS. For those affected by this long-standing but recently-discovered problem, I apologize. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7
by hemantha aranwela 16 Aug '10

16 Aug '10

Message: 4 Date: Thu, 12 Aug 2010 12:47:50 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: "Beauchemin, Suzanne" <Suzanne.Beauchemin(a)nrcan-rncan.gc.ca> Subject: [Ifeffit] Fwd: Windows 7? Message-ID: <201008121247.50747.bravel(a)bnl.gov> Content-Type: Text/Plain; charset="iso-8859-1" Hi all, This afternoon I was asked the following: > They are talking here to move us all from XP to Window 7... I checked on > your website and Athena is compatible with XP, Windows 2000, Windows > 95/98/ME but there is no mention of Window 7. Is it also adapted for > Window 7? Not having used Windows 7 myself, I don't have a lot to say. I know that everything worked OK with Vista, so I presume that the same is true of 7. Would anyone else like to comment to Suzanne on this issue? Thanks, B Hi Suzanne and Bruce, It works fine with Windows 7. But the updating is the problem. Runner.exe doesn't work properly. The window (runner) opens and download the files but does not install. Initially I thought it is due to the security settings and changed those. Still, no improvement. Thanks. Aranwela

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Haha
by Scott Calvin 15 Aug '10

15 Aug '10

Hi all, For a little comic relief, I just came across this graph: http://www.usablemarkets.com/wp-content/uploads/2010/06/fed-rate-3.jpg I have never seen a graph unrelated to XAFS looks more like (noisy) XAFS data... --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] updating Athena in Windows 7
by Monson, Todd 14 Aug '10

14 Aug '10

My difficulty in updating Athena was indeed a permissions problem. After following Laurent's suggestions, I was able to edit and save the updater.ini file as well as successfully download and install the updates to Athena while starting up the program. Thanks for all the help! Todd ---------------------------------------------------------------------- Message: 1 Date: Wed, 11 Aug 2010 07:13:23 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] updating Athena in Windows 7 (Matt Newville) Message-ID: <AANLkTin3bADHAyZX8g2jRZ5WvcJvKOhPF1mGS0qFMwCF(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Todd, That sounds like a permissions problem to me. Some account needs to be able to write to that file.... If updating the updater.ini file is not working, and Laurent's suggestions don't let you edit that file, you could also try downloading and installing the update zip files by hand. This is a bit more work (compared to editing updater.ini!), but the description at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater guides you through it. Hope that helps, --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 90, Issue 6 **************************************

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PYTHON scripting on MacOS & XP
by Brugger, Joel (SAM) 14 Aug '10

14 Aug '10

We used python scripting in 2005 (Win XP). However trying to get back into it we ran into trouble: - We're now using MacOS X, but could not find a python wrapper in the current iXAFS or IFEFFIT installs; is python scripting supported on the mac at all? - We then tried to get back to the PC version, only to discover that the wrapper also seems to be absent from the latest install. Can you please help us to get going again with python scripting? If this option is not supported anymore, can you recommend an alternative? Thanks, Joel & Barbara

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two measurements of the same compound in different beam-lines
by María Elena Montero Cabrera 13 Aug '10

13 Aug '10

Hi all! I have performed two independent XAFS measurements of Cr K-edge of the same Fe-Cr sample at two different beam-lines at SSRL. I have obtained the Fe-K edge data only once. The quality of data are different in each measurement. However, I cannot average spectra from different Cr-K measurements, and I don't know if I could take somehow advantage from having almost twice the information for the Cr- K adge, or I have to use only the better quality data and discard the other. What do you advice? If I can use both measurements, how can I do the fitting in Artemis? Thank you very much and all take care -- María Elena Dra. María Elena Montero Cabrera Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

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S K-edge of CdS(ZnOOH) Thin Films
by Kevin McPeak 13 Aug '10

13 Aug '10

Hi all, On Aug 22nd I will acquiring S K-edge XANES spectra (at APS 9-BM) of CdS(ZnOOH) thin films that I have grown in my lab. The films are grown in such a way that their composition and thickness vary as a function of position. View the following pdfs for details on thickness and composition: http://dunx1.irt.drexel.edu/~kmm333/cdzns/figure1.pdf http://dunx1.irt.drexel.edu/~kmm333/cdzns/figure3.pdf The idea is to take scans at various position along the middle of the substrate and observe how the different amounts of oxygen affect the Sulfur species present. Foreseeable issues are: 1). The CdS(ZnOOH) films are deposited on FTO (250 nm F:SnO2 film deposited on 2 mm of soda lime glass). There is 0.2 wt% SO3 (0.05 at% S) in the glass according to the manufacturer. We will run a scan on the bare FTO before starting work on CdS(ZnOOH), hopefully the SO3 in the glass is below the detection level. 2). If the SO3 in the glass is an issue I also have a sample where the CdS(ZnOOH) film is deposited on <100> Silicon. In earlier work I tried using this sample at the Cd and Zn K-edge at the APS 10-BM (to reduce scatter from the glass) but I ended up getting Bragg peaks in the spectra. Outside of spinning the substrate (not really an option here) do you have any suggestions for avoiding the Si Bragg peaks? I read one paper where they discussed deglitching but I am not sure how well that would go over with reviewers. Furthermore, grazing-incidence is not an option at 9-BM. All of the measurements above either have been (Cd and Zn) or will be (S) acquired in fluorescence. I am meeting with the beamline scientist to discuss this next Thursday but I figured it was a good idea to get input from the list as well. Any advice is most appreciated. Regards, Kevin McPeak kmm333(a)drexel.edu 312.371.5477 -- PhD Candidate Chemical Engineering Drexel University

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Fwd: Windows 7?
by Bruce Ravel 12 Aug '10

12 Aug '10

Hi all, This afternoon I was asked the following: > They are talking here to move us all from XP to Window 7... I checked on > your website and Athena is compatible with XP, Windows 2000, Windows > 95/98/ME but there is no mention of Window 7. Is it also adapted for > Window 7? Not having used Windows 7 myself, I don't have a lot to say. I know that everything worked OK with Vista, so I presume that the same is true of 7. Would anyone else like to comment to Suzanne on this issue? Thanks, B ------------------------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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amplitude values too high (>>100%)
by Edgar Macias 11 Aug '10

11 Aug '10

Hello, I am looking for some help on trying to understand what is wrong with our data. We are very impressed with the high values of amplitude (up to 390.24) that we got working with Artemis and we know are wrong. Hope somebody could help us and take a look into these files, we will appreciate it. Thank you in advance!

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Re: [Ifeffit] updating Athena in Windows 7 (Matt Newville)
by Monson, Todd 11 Aug '10

11 Aug '10

Matt, I tried resetting the timestamp to 0 under: Ifeffit\config\updater.ini. However, I could not save the changed updater.ini file. I verified that I have administrator privileges on my computer. Could something else be preventing me from updating the updater.ini file and in turn updating Athena? Todd Date: Wed, 28 Jul 2010 07:37:52 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] updating Athena in Windows 7 Message-ID: <AANLkTinxBX3aCXUGdN5XZCajMuK5gWCyftb9N-6YvpVz(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Todd, On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd <tmonson(a)sandia.gov> wrote: > On Saturday, while starting up Athena, I was informed that there was > an update to Athena available.? I tried installing the update but > failed.? I am afraid this is due to some user permission issue in > windows 7.? How can I try to reinstall the update and ensure that it works? You can change the file current.dat in C:\Program Files\Ifeffit\config. It probably reads 013 right now, and you could change that to 012 or even lower. That will cause an update the next time ifeffit looks for updates, which only happens when one of the programs starts and if the time in Ifeffit\config\updater.ini is past. To force a check for updates the next time ifeffit runs, change updater.ini to read timestamp = 0 In general, I believe this should work for Windows 7 (I have access to two Windows 7 64-bit machines, and all seems to be working on them, though I admit to not stressing them too much). So, as you say, I would also guess that the trouble you had was "only" permission issues. But, please let us know how it goes, Sorry for the trouble, --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 89, Issue 19 ***************************************

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How to analyze this data
by Elsa E. Sileo 10 Aug '10

10 Aug '10

I have some measurements at the As edge of As(V) adsorbed onto pure goethite (alfa-FeOOH), Mn partially substituted Goethite (alfa-Mn,Fe.OOH), Al substituted goethite (alfa-Al,FeOOH) and Mn and Al goethite (alfa-Al,Mn,FeOOH) The EXAFS signals change from one spectrum to another. I have refined the distances As-Fe on pure goethite, but when I try to refine Mn-FeOOH or Al,FeOOH, the analysis gets more difficult because As forms different complexes with Al and Fe. Unfortunately for me is almost impossible to have the pure phases alfa-MnOOH or alfa-AlOOH, and measured the As adsorbed. How can I analyze the spectra and have some knowledge about the As-surface complexes formed? Thanks, Elsa Dra. Elsa E. Sileo Solidos Inorganicos INQUIMAE - Dto. Qca. Inorganica, Analitica y Qca. Fisica; FCEN, UBA Int. Güiraldes 2160, Pabellón 2, Piso 3, Ciudad Universitaria - C1428EHA CABA - Argentina Tel: (54 11) 4576 3380 ext. 113 Fax: (54 11) 4576 3341 e-mail: sileo(a)qi.fcen.uba.ar

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Re: [Ifeffit] Physical meaning of POLARIZATION card 0 0 1
by Joshua Kas 06 Aug '10

06 Aug '10

Does this POL card > setting mean that the electric vector is along the z/c axis of the > crystal axis? Not quite. FEFF doesn't really know about crystal symmetry. The coordinates in the POLARIZATION card are the same as those in the feff.inp file under the ATOMS card. If the c axis of the crystal happens to be along the z direction, then POLARIZATION 0 0 1 sets the electric field vector along the c axis. You will have to look at the coordinates in the feff.inp to figure out which direction the c axis is. I may be wrong, but I think atoms/webatoms puts the c-axis in the z direction by default. Cheers, Josh Kas > I did read the Feff manual and the POL card but I am > still confused how to relate these to the crystal structure and > orientation. > > Thank you all in advance, > > -- > Chris Patridge > PhD. Candidate > Dept. of Chemistry > SUNY University at Buffalo > Buffalo, NY 14260 > Contact: 315-529-0501 > >

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Physical meaning of POLARIZATION card 0 0 1
by Chris Patridge 06 Aug '10

06 Aug '10

Hello everyone, I am working on modeling HfO2 using L3 Hf edge data. Using the default Feff input generated in Artemis, there is some significant mismatch between the data and theory so I augmented the Feff file by adding the POLARIZATION card setting the values of x y z to (0 0 1). Summing the theoretical paths in this calculation looked much closer and fitting the theory gives the results pasted in the text file. Does this POL card setting mean that the electric vector is along the z/c axis of the crystal axis? I did read the Feff manual and the POL card but I am still confused how to relate these to the crystal structure and orientation. Thank you all in advance, -- Chris Patridge PhD. Candidate Dept. of Chemistry SUNY University at Buffalo Buffalo, NY 14260 Contact: 315-529-0501

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Stoichiometry from EXAFS data
by Peter Zalden 02 Aug '10

02 Aug '10

Dear Feff users, lately, we measured a sample containing Sb and Te at EXAFS beamline CEMO, Hasylab and are wondering whether one can determine the stoichiometry from the height of the different K edges´ steps, if one normalizes the values on the edge steps of the elements (cf. http://physics.nist.gov/PhysRefData/XrayMassCoef/tab3.html) The absorption gases and the specimen were not changed for the different K edges. Of course, I have already tried doing so and from statistical reproducibility and from the resulting values compared to the expected ones I would estimate an error of this method of about 1%. A source of error that I could imagine originates from the different beam position at different energies combined with a slight inhomogenity in the pressed sample powder. Now my question is: Are there any other sources of error that I should take into accout? Is there any reference on this method from a more experienced user that I could cite? Kind regards, Peter --- Dipl.-Phys. Peter Zalden I. Physikalisches Institut IA, RWTH Aachen, 52056 Aachen EMAIL: zalden(a)physik.rwth-aachen.de

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Large Amplitude Values
by Gavin Garside 31 Jul '10

31 Jul '10

Fellow X-Ray Absorption Enthusiasts, I have recently compiled a model that gives excellent visual fits in R, q, and k space for bond spacing in a BCC structure. This model gives bond spacings that make sense, and are very close to what would be expected from this set. The R factors are very low, and the enot values correspond quite well to the edge. However, our amplitude values are much larger than typically expected. They come in at the range of 1.8 up to 5.0, but only on a few data sets. On all the rest the amplitude values are 0.4 to 1.0. Could this increase in amplitude be attributed to the fact that we ran florescence measurements instead of transmission, and have a weaker signal coming to the detector? What else could be causing this in only one data set? All samples used in this model have the same structure. Thanks in advance to any replies, your help and time is appreciated. Gavin gavin_garside(a)yahoo.com

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Large Amplitude Values
by Gavin Garside 30 Jul '10

30 Jul '10

Group, I have recently compiled a model that gives excellent visual fits in R, q, and k space. This model also bond spacings that make sense, and are very close to what would be expected from this set. The R factors are very low, and the enot values correspond quite well to the edge. However, our amplitude values are much larger than typically expected. They come in at the range of 1.8 up to 5.0, but only on a few data sets. On all the rest the amplitude values are 0.4 to 1.0. Could this increase in amplitude be attributed to the fact that we ran florescence measurements instead of transmission? What else could be causing this in only one data set, where they all have the same structure. Thanks in advance to any replies, your help and time is appreciated. Gavin gavin_garside(a)yahoo.com

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Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of absorbing atoms"
by Jatinkumar Rana 29 Jul '10

29 Jul '10

Dear Matt, Dear Scott, Thank you very much for the detailed explanation on Delta E0 and S02. Now, things are becoming more clear to me. Best regards, Rana On 28.07.2010 19:00, 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: Case of "nonequivalent multiple atomic sites of absorbing > atoms" (Matt Newville) > 2. Re: Case of "nonequivalent multiple atomic sites of absorbing > atoms" (Scott Calvin) > 3. Re: updating Athena in Windows 7 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 28 Jul 2010 06:46:24 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of > absorbing atoms" > Message-ID: > <AANLkTikm-ufMHua8Tpoq3ja7Xr0Bc+XxFPWfSh75RZgO(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Rana, > > Delta E0 is a shift in the Energy origin of k, that is where k=0. For > the experimental data, this was chosen empirically (and so somewhat > arbitrarily) from the measured data. For the FEFF calculation, it was > chosen at the calculated absorption threshold (lowest available > electronic level), but is known to not be perfect at this, especially > in Feff6. > > Though E0 is meant to be the absorption threshold, it is more > important that the FEFF calculation and measured data agree. Because > of this, Delta E0 is best left as an adjustable parameter in the > analysis. > > It is generally found that a single Delta E0 parameter is needed *per > measured data set and per FEFF calculation*, because measured data can > be shifted in energy and because each calculation can have a different > definition of E0. It is possible to read the FEFF outputs and try to > figure out how different these energies are and so set (not allow to > float) the different E0 values. I believe this can work well, but it > is not automated, and so not often used. In addition, usually one > uses a different Delta E0 for each data set, but well-aligned data > that re-use a FEFF calculation (say, data taken on the same system at > different external conditions) can often get by with sharing a single > Delta E0 parameter. > > S02 is meant to express the incomplete overlap of the "passive > electrons" in the absorbing atom. Removing the deep core electron can > allow the other (L, M, N, O) electrons to relax slightly from their > ground state. That relaxation reduces the overlap of the "initial" > and "final" states of the transition that gives rise to XAFS, and so > reduces the full effect. FEFF6 does not do a very good job of > estimating this effect. > > In practice, S02 can also mask other "amplitude issues", some > theoretical (the inelastic losses that fold into the mean-free-path > are not perfect) and some experimental (it is easier to mis-measure > the amplitude than the phase of an oscillation). For XAFS, these > experimental problems all tend to spoil the amplitude of the > meaurement more than the phase: pin-holes in the sample, slight > misalignment of the sample, over-absorption for fluorescence > measurements, energy bandwidth of the incident beam and harmonic > content of the incident beam. > > The rule of thumb is that it is OK to use the same S02 for all samples > of a particular absorbing atom. Many would add "measured at the same > beamline" to that rule, so that effects of energy bandwidth and > harmonic content are compensated. > > Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Wed, 28 Jul 2010 08:05:23 -0400 > From: Scott Calvin<SCalvin(a)slc.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Case of "nonequivalent multiple atomic sites of > absorbing atoms" > Message-ID:<8295E519-0FC0-4D2C-8C33-944E9BF0F53D(a)slc.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Rana, > > Currently, S02 is usually described as being due to the relaxation of > the other electrons in an atom when a core electron is removed, > resulting in incomplete overlap of initial and final states. This > appears to be a fairly good description, as careful experiments show > good agreement with theoretical calculations based on this idea. > > Note, however, that there could be some other contributors to S02. A > photon could, in addition to exciting the core electron at the edge, > also excite a valence electron. > > There's a small thread on the transferability of S02 here: > > http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg01626.html > > E0 is a tricky concept, in my opinion: it is the energy origin in the > EXAFS equation. Perhaps a theorist can give me a pithy physical > interpretation of what happens at that energy, but I don't know there > needs to be anything; at k near 0, the path expansion is not > convergent, so I'm not sure we should expect anything special to > happen exactly at 0. In other words, it's not exactly the Fermi level > or any other special energy. > > E0 is dependent on oxidation state; it can shift by an electron volt > or two when oxidation states vary. > > Note that oxidation state is a simplistic measure of what's happening > with the electron distribution in a material. Suppose fluorine is > substituted for iodine in some material. Formally, the oxidation state > of the atom they are bonded to is not changed by the substitution. But > in reality, the electron distribution is different, and a small E0 > shift would not be surprising. > > I think the bottom line, then, is this: > > S02 is completely transferable for the same element at multiple > absorbing sites. > > Delta E0 is transferable with some caution for the same element at > multiple absorbing sites if the oxidation state is the same. > > One other note: there's no rule that when trying constraints, you have > to start unconstrained and add constraints to see the effect on the > fit. With complicated systems like yours, it often pays to start with > unrealistically simple constrains (not only E0's and S02's the same, > but also sigma2's), and see if you're on the right track. Then look at > the effect of relaxing constraints. > > --Scott Calvin > Sarah Lawrence College > > > > On Jul 28, 2010, at 4:00 AM, Jatinkumar Rana wrote: > > >> Dear Users, >> >> Since long, i was trying to understand the physical meaning of term >> "Delta E0" and "S02" in EXAFS equation. I have little bit of idea >> about both of them. for example, S02 is element specific and it is >> transferable between samples (if we consider same absorbing atom). >> >> However, I am not able to realize their importance in terms of their >> "physical meaning" as far as interaction of photoelectron is >> concerned. Therefore, it is difficult for me to understand their >> influence on EXAFS. >> >> I am dealing with a case of "nonequivalent multiple atomic sites of >> absorbing atoms". It is quite obvious that in such kind of case no. >> of variables are more than no. of independent points and there is a >> need to constrain the parameters to solve such problems. >> >> I have following questions : >> >> How do i understand "Delta E0" and "S02" theoretically (in terms of >> photoelectron interaction) ? >> >> Can i constrain "Delta E0" for all absorbing atomic site as same ? >> (my assumption : all absorbing atoms are at same oxidation level) >> >> your comments and suggestions would be highly appreciated... >> >> Best regards, >> Rana >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> > > > ------------------------------ > > Message: 3 > Date: Wed, 28 Jul 2010 07:37:52 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] updating Athena in Windows 7 > Message-ID: > <AANLkTinxBX3aCXUGdN5XZCajMuK5gWCyftb9N-6YvpVz(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Todd, > > On Mon, Jul 26, 2010 at 3:39 PM, Monson, Todd<tmonson(a)sandia.gov> wrote: > >> On Saturday, while starting up Athena, I was informed that there was an >> update to Athena available.? I tried installing the update but failed.? I am >> afraid this is due to some user permission issue in windows 7.? How can I >> try to reinstall the update and ensure that it works? >> > You can change the file current.dat in C:\Program > Files\Ifeffit\config. It probably reads > > 013 > > right now, and you could change that to 012 or even lower. That will > cause an update the next time ifeffit looks for updates, which only > happens when one of the programs starts and if the time in > Ifeffit\config\updater.ini is past. To force a check for updates the > next time ifeffit runs, change updater.ini to read > > timestamp = 0 > > In general, I believe this should work for Windows 7 (I have access to > two Windows 7 64-bit machines, and all seems to be working on them, > though I admit to not stressing them too much). So, as you say, I > would also guess that the trouble you had was "only" permission > issues. But, please let us know how it goes, > > Sorry for the trouble, > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 89, Issue 19 > *************************************** > > >

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updating Athena in Windows 7
by Monson, Todd 28 Jul '10

28 Jul '10

On Saturday, while starting up Athena, I was informed that there was an update to Athena available. I tried installing the update but failed. I am afraid this is due to some user permission issue in windows 7. How can I try to reinstall the update and ensure that it works? Thanks, Todd Todd Monson Sandia National Labs Nanomaterials Sciences P.O. Box 5800, MS 1415 Albuquerque, NM 87185-1415 (505) 845-2129 Fax: (505) 844-5470

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Case of "nonequivalent multiple atomic sites of absorbing atoms"
by Jatinkumar Rana 28 Jul '10

28 Jul '10

Dear Users, Since long, i was trying to understand the physical meaning of term "Delta E0" and "S02" in EXAFS equation. I have little bit of idea about both of them. for example, S02 is element specific and it is transferable between samples (if we consider same absorbing atom). However, I am not able to realize their importance in terms of their "physical meaning" as far as interaction of photoelectron is concerned. Therefore, it is difficult for me to understand their influence on EXAFS. I am dealing with a case of "nonequivalent multiple atomic sites of absorbing atoms". It is quite obvious that in such kind of case no. of variables are more than no. of independent points and there is a need to constrain the parameters to solve such problems. I have following questions : How do i understand "Delta E0" and "S02" theoretically (in terms of photoelectron interaction) ? Can i constrain "Delta E0" for all absorbing atomic site as same ? (my assumption : all absorbing atoms are at same oxidation level) your comments and suggestions would be highly appreciated... Best regards, Rana

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Re: [Ifeffit] Ifeffit Digest, Vol 89, Issue 17
by Jatinkumar Rana 28 Jul '10

28 Jul '10

Hello Darek, Thank you so much for your reply. Yes, i can rely on model, we have performed reitveld refinement to get the crystallographic data. To my knowledge, there should not be any other phases. Your suggestion is quite right. Somehow, i have to constrain my parameters (to reduce the no. of parameters) and try to fit it. However, I would like to ask you following questions. I am confused about the term "Delta E0" what is the theoretical meaning of that in terms of photoelectron interactions ? If you have multiple atomic sites of absorbing atom, should "Delta E0" be same for all of them (assuming all absorbing atoms are at same oxidizing state) ? I am looking forward to your comments.. Best regards, Rana On 27.07.2010 19:00, 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. updating Athena in Windows 7 (Monson, Todd) > 2. ODP: Ifeffit Digest, Vol 88, Issue 12 (Zajac, Dariusz A.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 26 Jul 2010 14:39:00 -0600 > From: "Monson, Todd"<tmonson(a)sandia.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] updating Athena in Windows 7 > Message-ID: > <AC050BA7EAC9A34E9A05BC31C3AA2E8B183C0D11B5(a)ES02SNLNT.srn.sandia.gov> > Content-Type: text/plain; charset="us-ascii" > > On Saturday, while starting up Athena, I was informed that there was an update to Athena available. I tried installing the update but failed. I am afraid this is due to some user permission issue in windows 7. How can I try to reinstall the update and ensure that it works? > Thanks, > Todd > > Todd Monson > Sandia National Labs > Nanomaterials Sciences > P.O. Box 5800, MS 1415 > Albuquerque, NM 87185-1415 > (505) 845-2129 > Fax: (505) 844-5470 > >

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Re: [Ifeffit] Ifeffit Digest, Vol 88, Issue 12
by Jatinkumar Rana 27 Jul '10

27 Jul '10

Dear Darek, Sorry for the late response. To fit the "first shell" the No.of independent points and No.of variables which i use are as follows: I use deltaK=11, deltaR = 1.1 so No.of independent points are 8 and No.of variables are 4 (i.e. N, e0, delr, and ss2) I set s02=0.9. Best regards, Rana On 14.06.2010 19:00, 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. XAFS fitting with multiple atomic sites of absorbing atom > (Jatinkumar Rana) > 2. ODP: XAFS fitting with multiple atomic sites of absorbing > atom (Zajac, Dariusz A.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 14 Jun 2010 12:00:27 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: Ifeffit users<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XAFS fitting with multiple atomic sites of > absorbing atom > Message-ID:<4C15FDBB.1050203(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear users, > > I have measured XAFS spectra on Mn and Fe edge on my material. The > material contains 3 different atomic positions for Mn and 4 different > atomic positions for Fe. > > Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn > atomic position one-by-one (i.e. first take one Fe/Mn position, > calculate Feff paths, consider certain paths to fit specific R-range, > then take another Fe/Mn position and do the same) but the fit was not > good visually and in terms of goodness of fit parameters. > > Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all > Fe/Mn atomic position together i.e. I separately calulated Feff paths > for each Fe/Mn atomic position and summed up related paths from each > Feff calculation for fitting a specific R-range. (The assumption being, > the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution > from all Fe/Mn atomic position in crystal structure). > > Anybody in the group could comment about my approach to fit such problem ? > > Is there any specific strategy to fit such problem ? > > I would be thankful if you could suggest some literature available on > such problems. > > Thanks in advance. > > Best regards, > Rana > > > ------------------------------ > > Message: 2 > Date: Mon, 14 Jun 2010 13:34:18 +0200 > From: "Zajac, Dariusz A."<dariusz.zajac(a)desy.de> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] ODP: XAFS fitting with multiple atomic sites of > absorbing atom > Message-ID: > <35E004AD6290A7438FCA34BBF325F41601206741(a)ADXV2.win.desy.de> > Content-Type: text/plain; charset="iso-8859-2" > > > Dear Rana, > could you specify how many independent data points and variables you have and you use for fitting? > thnx > darek > > -----Wiadomo?? oryginalna----- > Od: ifeffit-bounces(a)millenia.cars.aps.anl.gov w imieniu Jatinkumar Rana > Wys?ano: Pn 2010-06-14 12:00 > Do: Ifeffit users > Temat: [Ifeffit] XAFS fitting with multiple atomic sites of absorbing atom > > Dear users, > > I have measured XAFS spectra on Mn and Fe edge on my material. The > material contains 3 different atomic positions for Mn and 4 different > atomic positions for Fe. > > Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn > atomic position one-by-one (i.e. first take one Fe/Mn position, > calculate Feff paths, consider certain paths to fit specific R-range, > then take another Fe/Mn position and do the same) but the fit was not > good visually and in terms of goodness of fit parameters. > > Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all > Fe/Mn atomic position together i.e. I separately calulated Feff paths > for each Fe/Mn atomic position and summed up related paths from each > Feff calculation for fitting a specific R-range. (The assumption being, > the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution > from all Fe/Mn atomic position in crystal structure). > > Anybody in the group could comment about my approach to fit such problem ? > > Is there any specific strategy to fit such problem ? > > I would be thankful if you could suggest some literature available on > such problems. > > Thanks in advance. > > Best regards, > Rana > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 88, Issue 12 > *************************************** > > >

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Re: [Ifeffit] ATHENA: \\\"you have not used any memory yet\\\"
by Claire Gervais 23 Jul '10

23 Jul '10

Hello, You are right, this is exactly by googling that I have found that I was not alone to have this problem! I did change the fonts to have all windows entirely visible, but it did not improve. Still stuck with no OK in view. Indeed, it seems that the application waits for me. I am in Gnome, but I don't think it's the point, otherwise it would work under Windows in Virtualbox, no...? I am not an expert in GUI however. Claire ------------------------------------- > > Claire, > > Please use the mailing list. That way, others can find solutions to problems > by doing a google search. > > Is your problem related to question 13 at > http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions > > Are you a KDE user? The "everything is grey" could be a kwin visual cue that > the application is waiting for input that you cannot find because the column > selection dialog is off the bottom of the screen. > > B ------------------------------------

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Ei component
by Abhijeet Gaur 17 Jul '10

17 Jul '10

Hi all My question is about Ei component taken for the problem of poor energy resolution. How it can be calculated using measured energy resolution ? How Ei can be calculated using a known sample, such as a foil for which we have comparable spectra on a beamline with better energy resolution ? With regards Abhijeet Gaur Vikram University Ujjain, India

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Re: [Ifeffit] Neg SS
by Abhijeet Gaur 16 Jul '10

16 Jul '10

Hi Thanks for the quick response. As per the data collection range is concerned, we have limitation of 300eV above the edge. I think I had done data processing in Athena right. I know that the peak at position less than 1 Angs can not be real but I am unable to remove it by data processing in Athena. As per the model is concerned I am attaching herewith feff calculation result and the XRD results for different bondlengths of the sample. By comparing them it seems that model is right. On the other hand poor energy resolution is also one of the reasons for this kind of results. I had alraedy read about this Ei component earlier in papers, but I am unable to follow the procedure like how to calculate it using a known standard. From where I can get literature related to this? It will be really helpfull. With regards Abhijeet Gaur

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Re: [Ifeffit] ATHENA: \"you have not used any memory yet\"
by Bruce Ravel 14 Jul '10

14 Jul '10

On Wednesday, July 14, 2010 10:45:45 am you wrote: > Thank you for answering me. > > What I mean with stalled it that the cursor is "running" when it is on the > main Athena window, everything is gray and no file appears on the right (in > the group list). > > And, I do not see any OK button in the "data columns" window... I know that > my laptop has a small screen, but I have checked at the whole window > (moving around with ALT F7) and there is really no OK button. GUI > problem...? > > I will try on another 64bit system and will let you know. > Claire, Please use the mailing list. That way, others can find solutions to problems by doing a google search. Is your problem related to question 13 at http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions Are you a KDE user? The "everything is grey" could be a kwin visual cue that the application is waiting for input that you cannot find because the column selection dialog is off the bottom of the screen. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Negative ss problem
by Abhijeet Gaur 14 Jul '10

14 Jul '10

Hi all, I read the discussion on negative Debye waller factor. As per the discussion the negative value of this factor shows that the model has shortcomings, so it should be corrected. I am also getting the same problem while fitting one of my samples. It is a Cu complex whose EXAFS data is taken at Dispersive EXAFS beamline at RRCAT, Indore, India. In the complex the nearest neighbours of Copper atom are Nitrogen and Oxygen. I am getting a very good fit upto 3rd shell but the problem is that all ss parameters are coming negative. I checked the model it seem correct. Also I am getting a peak below 1 Angs which is also getting fitted but I am not able to get that whether it is a real or due to some noise. I am attaching herewith the results of data analysis and fitting. Thanks in advance With regards Abhijeet Gaur Vikram University Ujjain, INDIA

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Re: [Ifeffit] Negative ss problem
by Chris Patridge 14 Jul '10

14 Jul '10

Hello, It seems to me that you have some more problems than just ss values. The data collection range seems a little short just ~300 eV past the edge. Amp is quite high and delr is very large. I am an expert by no means but I might suggest that you have the wrong model. The model is trying to compensate for high R space magnitude by making amp above 1 and ss negative. Have you considered your data processing in Athena? Did you use the default settings? I would guess Cu-O bonds might be too short for the presets in Athena. How did you check your model? Buena salud, Chris Patridge On Jul 14, 2010, at 2:59 AM, Abhijeet Gaur <abhijeetgaur9(a)gmail.com> wrote: > Hi all, > I read the discussion on negative Debye waller factor. As > per the discussion the negative value of this factor shows that the > model has shortcomings, so it should be corrected. > I am also getting the same problem while fitting one of my > samples. It is a Cu complex whose EXAFS data is taken at Dispersive > EXAFS beamline at RRCAT, Indore, India. > In the complex the nearest neighbours of Copper atom are > Nitrogen and Oxygen. > I am getting a very good fit upto 3rd shell but the problem > is that all ss parameters are coming negative. I checked the model > it seem correct. > Also I am getting a peak below 1 Angs which is also getting > fitted but I am not able to get that whether it is a real or due to > some noise. > I am attaching herewith the results of data analysis and > fitting. > Thanks in advance > With regards > Abhijeet Gaur > Vikram University > Ujjain, INDIA > <Cu complex fitting results.doc> > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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ATHENA: "you have not used any memory yet"
by Claire Gervais 13 Jul '10

13 Jul '10

Hello, I have recently installed ATHENA on my laptop (Lenovo X200) and runs into trouble when I try to open a file: The "data column" window opens well, and the plot is there but then I am stalled. At the bottom of the main window is written: "you have not used any memory yet" I know that a previous thread was written on it ([Ifeffit] A problem with Athena from 2008) but it seems to remain an open issue... Here is my configuration: OS: Ubuntu Jaunty AMD64 Athena version: 0.8.059 Ifeffit version: 1.2.11d I have also tried with a previous Athena version, and on WindowsXP via Virtualbox. The problem remains. My data file is according to ATHENA standard (i.e. # for comments followed by columns). If you have any idea, I would be delighted to read it! Thanks, Claire ---------------------------------------------------------------------- Claire Gervais PhD Chemistry & Material Sciences, Visiting scientist Smithsonian Museum Conservation Institute Museum Support Center 4210 Silver Hill Road Suitland, Maryland 20746 USA Web: http://www.claire-et-net.ch ---------------------------------------------------------------------

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Vanadium center fitting issues
by Christopher Allen 10 Jul '10

10 Jul '10

Hi, I wanted to get some advice on a vanadium centered material I’ve been trying to fit for quite a while w/ repeated failure. Based on XRD and electrochemistry I’m pretty confident in the material/model, and I have the input file for the material. The first shell out to 2.2 angstroms in R space is a distorted VO6 w/ bond lengths ranging from 1.6 to 2.2 angstroms, similar to the V2O5 which has been discussed on the mailing list recently (July 7th). The last two peaks from 2.2 to 3.3 angstroms presumably include 4 V-P and 1 more V-O single scattering paths. (the best fit I could get on the 4V-P/1V-O used only the first of these two peaks.) With regards to the first shell fitting, is it appropriate to be grouping the V-O bonds in terms of 1 short, 4 medium, and 1 long bond distance to cut down on variables? I noticed in the V2O5 previously discussed, that he used one ss and delr term for all 6 V-O paths, but I guess that just means making some assumptions that any variations in ss and delr are isotropic throughout. Is that correct? I’ve had real issues w/ those peaks representing V-P/V-O from 2-3.3 angstroms so I wonder if it’s unreasonable to try and extract this information based on the k space or if possible thats not what I have there. Could it be that I need to account for the two inequivalent V centers? (In that case, wouldn’t the number of variables be doubled?) Thanks for any comments, Chris -- Chris Allen Northeastern University Center for Renewable Energy Technology 317 Egan Research Center 360 Huntington Ave. Boston, MA 02115 617-373-5630

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3 Year XAFS Postdoc Position at The University of Manchester
by Sven L.M. Schroeder 08 Jul '10

08 Jul '10

Dear colleagues Robert Dryfe and I have been awarded funding for a postdoctoral XAFS position, for a 3 year appointment to study metal nanoparticle deposition and growth at liquid-liquid interfaces: http://www.jobs.ac.uk/job/ABI341/research-associate/ This NSF- and EPSRC-supported project will make use of facilities at DIAMOND and the APS, in close collaboration with Mark Schlossman from University of Illinois at Chicago, who will lead on interfacial diffraction and X-ray reflectivity measurements on the same systems. More information about the project is available here: http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/H047786/1 Applications or informal enquiries can be directed to myself or Robert Dryfe. Best wishes Sven -- Dr Sven L.M. Schroeder (mailto:s.schroeder@manchester.ac.uk) Head of Research / Reader School of Chemical Engineering and Analytical Science (CEAS) The University of Manchester, Manchester M13 9PL, United Kingdom http://www.ceas.manchester.ac.uk http://www.slmslab.info Also at: School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom Tel +44 (161) 306 4502 Fax +44 (161) 306 8867 Office: Room C57 (Jackson's Mill) DISCLAIMER The views expressed within this message are those of the sender, not those of The University of Manchester or one of its Departments. While all emails and attachments are scanned for viruses before sending, we cannot accept any responsibility for viruses, so please scan all emails and attachments. This email is intended for the addressee only. If you are not the intended recipient, please notify the sender and delete this email immediately. END OF MESSAGE

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background fitting functions in Artemis
by Chris Patridge 07 Jul '10

07 Jul '10

Hello all, If a background is difficult to remove due to short paths lengths, can a background fitting be used in the Artemis fit? I have a large data range giving near two times the ind points even when including the background function. After fitting the data, it gave a number of correlations some of which are negative. The parameters give reasonable values and uncertainties and I feel confident about the model. I know the fit is not great but can I use this as the starting point or is the background just giving me a large fudge factor? Thank you, Chris Patridge

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Clarification needed on the structured 2nn peak
by Varadarajan Sridharan 07 Jul '10

07 Jul '10

Greetings to all I am a beginner to EXAFS. Recently I had carried out Cd K-edge EXAFS measurements on Cd1-xCaxO solid solution. The end members CdO and CaO belong to same crystal structure Fm-3m. I had analysed the spectrum with Atthena and fitted with Arthemis. I am attaching the Athena project file (***.prj) and that of Arthemis project file (***.apr) for your reference. Athena: As per the crystal structure of CdO, the first nearest neighbour is at 2.345 A corresponding to Cd-O1 inter atomic distance and 2nn distance is 3.3.16 A corresponding to Cd-Cd1 inter atomic distance. Though I am able get the first peak in chi(R) plot at expected position, I am having some problems for the second peak. The second peak has features; main one and a shoulder. The main peak itself appears at lower R compared to expected one. Intensity of the shoulder increases with Ca substitution at the expense of main peak itself. Can any one comment on this? My predicament: If I associate, based on the structure of second peak, bimodal distribution for the Cd-Cd1 interatomic distance, the difference of 0.4 A is 11%. This value gives me an uneasy feeling. Is it possible to accommodate this difference within the setting of F m-3m? OR It is due the multi scattering is the problem? Arthemis: For CdO: The k^3 weighted chi fitting, I agree is far from satisfaction. Std of delR is a bothering point. I had included 20 paths. Even for the CdO with F m-3m, the calculated second peak has a shoulder at lower R. I could see a small contribution from path 4. But I am not sure if that is all. How to float the individual GDS parameter for each and every path? What can be done to improve the fitting? Thanking you all in advance Varadarajan Sridharan ---------------------------------- Condensed matter Physics Division Materials Science division Indira Gandhi Centre for Atomic Research Kalpakkam 603 102 India

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Re: [Ifeffit] Ifeffit Digest, Vol 89, Issue 3
by Varadarajan Sridharan 07 Jul '10

07 Jul '10

Dear Matt, I agree to your point. AS of now I am not attempting to fit the Ca substituted system for two reasons 1.I am specifically looking for the "cause" for the structure in the second peak. The structure is present in the calculated CdO Chi(R) plot itself. 2. Apart from that when I tried to put in Ca in the ATOM, Ca is not at all appearing in the list after running ATOM. Can you help me out in this matter as well. Thanking you ---- Varadarajan Sridharan On Tue, Jul 6, 2010 at 10:30 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: Clarification needed on the structured 2nn peak > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 6 Jul 2010 07:52:16 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Clarification needed on the structured 2nn peak > Message-ID: > <AANLkTinjUxHwVBBkCBiONWnNNptLnpSKpI9mnri3HbBv(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Varadarian, > > I didn't look at your attachments, but have you considered that there > might be some Cd-Ca in the second shell? I didn't see what value of > x you had in Cd(1-x)CaxO, but if the oxides form a solid solution one > might naively expect the second shell to have (1-x) Cd and x Ca > coordination. Ca and Cd scatter photoelectrons differently enough > to be distinguishable in the EXAFS. It might be that there is extra > disorder too, say if the typical Cd-Ca distance was different from the > typical Cd-Cd distance. > > Cheers, > > --Matt > > On Tue, Jul 6, 2010 at 7:29 AM, Varadarajan Sridharan > <varadu.sridh(a)gmail.com> wrote: > > Greetings to all > > > > ?? I am a beginner to EXAFS. > > > > ? Recently I had carried out Cd K-edge EXAFS? measurements on Cd1-xCaxO > > solid solution. The end members CdO and CaO belong to same crystal > structure > > Fm-3m. > > > > ?? I had analysed the spectrum with Atthena and fitted with Arthemis. I > am > > attaching the Athena project file (***.prj) and that of Arthemis project > > file (***.apr) for your reference. > > > > Athena: > > > > ?? As per the crystal structure of CdO, the first nearest neighbour is at > > 2.345 A corresponding to Cd-O1 inter atomic distance and 2nn distance is > > 3.3.16 A corresponding to Cd-Cd1 inter atomic distance. Though I am able > get > > the first peak in chi(R) plot at expected position, I am having some > > problems for the second peak. The second peak has features; main one and > a > > shoulder. The main peak itself appears at lower R compared to expected > one. > > Intensity of the shoulder increases with Ca substitution at the expense > of > > main peak itself. > > > > ??????????? Can any one comment on this? > > > > ???? My predicament: If I associate, based on the structure of second > peak, > > bimodal distribution for the Cd-Cd1 interatomic distance, the difference > of > > 0.4 A is 11%. This value gives me an uneasy feeling. Is it possible to > > accommodate this difference within the setting of F m-3m? > > > > ????????????????????????????????? OR > > > > ???????????????????????????????? It is due the multi scattering is the > > problem? > > > > Arthemis: > > > > For CdO: ?The k^3 weighted chi fitting, I agree is far from satisfaction. > > Std of delR is a bothering point. I had included 20 paths. Even for the > CdO > > with F m-3m, the calculated second peak has a shoulder at lower R. I > could > > see a small contribution from path 4. But I am not sure if that is all. > > > > How to float the individual GDS parameter for each and every path? What > can > > be done to improve the fitting? > > > > Thanking you all in advance > > > > Varadarajan Sridharan > > > > ---------------------------------- > > > > Condensed matter Physics Division > > > > Materials Science division > > > > Indira Gandhi Centre for Atomic Research > > > > Kalpakkam 603 102 > > > > India > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 89, Issue 3 > ************************************** >

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XAFS Postdoc position at HASYLAB
by Welter, Edmund 01 Jul '10

01 Jul '10

Dear colleagues, at the Hamburger Synchrotron Strahlungslabor (HASYLAB) a postdoc position in the XAFS business is available. For more information please follow: http://www.desy.de/v2/docs/1275482643-e.pdf The main tasks of the successful applicant will be the operation of the X1 XAFS-beamline, to take care of our industrial XAFS users and last but not least DESY is strongly encouraging postdocs to work in their own field of science. If you have questions about this mail or the available position please do not reply to the mailing list, but contact me directly instead. Best regards, Edmund Welter

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can sigma square ever be less than zero?
by Chris Patridge 29 Jun '10

29 Jun '10

Hello all, I am working on W L3 edge data. W is acting as a substitution dopant in vanadium dioxide at rather low concentration. In a past mailing conversation discussing Feff6 overestimation of E0 for heavier elements it was mentioned that the E0 could be past the rising edge due to the white line from W data. Well using this comment I aligned data using the theory method well explained by Shelly Kelly SnO2 example. Literature suggests W approximates WO2 cubic structure locally instead of the VO2 unit structure. Then fitting the first oxygen coordination shell paths which are well isolated from the other paths, it gives reasonable values for amplitude and enot of 0.77 (0.17) and -1.14 (3.06) respectively. delr is -0.067 (0.028) and then ss comes out to -0.00036 (0.00414). Can ss be negative if the uncertainty brings it above 0? Thank you all, Chris Patridge PhD Candidate Department of Chemistry NSC 405 SUNY Buffalo 315-529-0501

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Postdoctoral position open
by Mukerjee, Sanjeev 28 Jun '10

28 Jun '10

Dear Members, I have an opening for a postdoctoral position in my research group and center starting in August of 2010. The position will be for two years with renewal option at the end of the first. Qualification for this position is a recent Ph.D in physics or chemistry in the field related to synchrotron spectroscopy. Most important would be to have good experience conducting in situ x-ray absorption studies including EXAFS data analysis. We will train the person on other more specific aspects of the spectroscopy as conducted by the research group. Proficiency in basic electrochemistry including classical methods are a must. Please apply with resume and one or two key publications to me personally as soon as possible. We promise a very vibrant research environment and opportunity to develop a portfolio for future career options such as academic positions. This includes training in proposal writing and teaching graduate level courses. In addition this position carries competitive salary and benefits. Sincerely Sanjeev Mukerjee (Professor) Department of Chemistry and Chemical Biology Director of the Northeastern University Center for Renewable Energy Technology (NUCRET) Northeastern University, 360 Huntington Avenue, Boston, MA 02115 Phone (617) 373 2382 Fax (617) 373 8949 URL: www.northeastern.edu/nucret www.northeastern.edu/leap

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Help with artemis!
by JESUS ISAAC AGUIRRE QUIROZ 24 Jun '10

24 Jun '10

Hi everyone, i'm using a macbook with mac OSX. I'm trying to open some files in artemis (just starting) I can open the Cu010k file from the examples folder but when i try to open the respective atoms file (a friend of mine was able to open these files with no problems on windows xp) but artemis shows a message saying "artemis trapped one or more errors! Error message dumped to screen" and nothing happens. I tried to build up the atoms file starting with a blank page and introducing all respective values but it still shows the same error. I'm thinking i may have an old version or I may have missed something about the installation because i had some problems with athena and now i'm working with artemis and i can't even get started. Thanks for your help and advice... _________________________________________________________________ Enciende tu hotness con Hotmail www.hotmailhotness.com.mx

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Sodium uranate fit problem
by Andy Connelly 23 Jun '10

23 Jun '10

Hello all, I've been following this mailing list for ages and have learnt a lot, thank you. Now I have a problem and am hoping someone can help. I have some really nice sodium uranate (Na2U2O7) data from the NSLS (X23A2) that I collected (embarrassingly) a couple of years ago. I have been trying to fit it and have never managed to get a satisfactory fit even to the first shell. >From the literature there should be 2 uranyl oxygens and 6 equatorial oxygens. If I fit these paths I get an amp (S02) value of 0.32 and negative sigma squared values (ss). I have tried to add paths from the second shell to reduce this amp value but no success. I do not believe that this value is real but I cannot find any problem in the background or in the fit. I have found similar problems for lithium uranate and some glass samples, all of which should have similar uranium coordinations. I can bring ss into a more sensible value but amp is always very low. I have tried several different .cif files for different uranate or uranyl systems and they all give roughly the same result. I have found similar problems with some data I collected at Daresbury on a different Na2U2O7 sample so I do not think it is the sample or the beamline. Does anyone have any thoughts why this might be so? Any help or suggestions would be most appreciated. Thank you all in advance, Best regards Andy Connelly

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distinct crystal positions for the absorber atom
by Chris Patridge 22 Jun '10

22 Jun '10

Hello everyone, I am working on fitting the first shell of a double layer vanadium oxide material. The data is V K edge data with 3 scans merged. There is two positions for vanadium in the unit structure with equal occupancy. I started modeling using equal weighting between the 2 feff calculations for each unique vanadium. Setting amp*0.5 seems straight forward. The first shell consists of oxygen coordinated and the next shell is dominated by the vanadium of the adjacent edge sharing polyhedra. Feff0 appears to give a better fit by itself with lower uncertainties than using both model in concert or Feff1 by itself. Can this problem lie in the fact that the bond lengths are quite short (1.6 A) for V-O and discerning the background and signal causes an error? I feel reasonably confident in the crystallography. I pasted the fit results below and included bmps and artemis file there. If there is something suspect please let me know or if you have a suggestion. Thank you all in advance, Christopher Patridge PhD Candidate SUNY University at Buffalo Dept of Chemistry 315-529-0501 Independent points = 7.691406250 Number of variables = 4.000000000 Chi-square = 2503.896487489 Reduced Chi-square = 678.304233648 R-factor = 0.029837426 Measurement uncertainty (k) = 0.000474272 Measurement uncertainty (R) = 0.000888467 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 0.8044660 +/- 0.1118000 (1.0000) enot = -1.9212800 +/- 1.8083430 (0.0000) ssO = 0.0001680 +/- 0.0018760 (0.0030) alpha = 0.0011620 +/- 0.0078840 (0.0000)

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XAFS fitting with multiple atomic sites of absorbing atom
by Jatinkumar Rana 14 Jun '10

14 Jun '10

Dear users, I have measured XAFS spectra on Mn and Fe edge on my material. The material contains 3 different atomic positions for Mn and 4 different atomic positions for Fe. Initially, I tried fitting Fe-edge/Mn-edge spectra using indiviual Fe/Mn atomic position one-by-one (i.e. first take one Fe/Mn position, calculate Feff paths, consider certain paths to fit specific R-range, then take another Fe/Mn position and do the same) but the fit was not good visually and in terms of goodness of fit parameters. Then, i tried fitting Fe-edge/Mn-edge spectra, taking into account all Fe/Mn atomic position together i.e. I separately calulated Feff paths for each Fe/Mn atomic position and summed up related paths from each Feff calculation for fitting a specific R-range. (The assumption being, the experimental Fe-edge/Mn-edge XAFS spectra has varying contribution from all Fe/Mn atomic position in crystal structure). Anybody in the group could comment about my approach to fit such problem ? Is there any specific strategy to fit such problem ? I would be thankful if you could suggest some literature available on such problems. Thanks in advance. Best regards, Rana

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Re: [Ifeffit] Large Enot values
by Paul Bingham 13 Jun '10

13 Jun '10

Thanks Shelly. I have tried doing as you suggest, shifting manually the value of E0 by +10 eV in Athena before fitting in Artemis. Thankfully the delta E of the new fit is close to zero which I think means that the theory and the data do agree, i.e. I am fitting the first shell with the correct atom type. I am still a little unclear as to why such a large energy shift might arise and will look into this further. Any tips or suggestions would again be very welcome and I would very much appreciate it if you can send me a copy of your book chapter which you mentioned. Best Regards Paul. -- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473 Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > 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: Large Enot values (shelly Kelly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Jun 2010 09:18:33 -0500 > From: "shelly Kelly" <dr.sdkelly(a)gmail.com> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Large Enot values > Message-ID: <4c1245c4.9d90d80a.567d.3528(a)mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Hi  paul: > > Have you tried to shift eo in athena by 10 ev? If you have and the fit still > gives a large deltaE then the theory and the data do not agree.  DeltaE > changes the spectra most strongly at low k, so another thing to try is to > increase kmin in the ft.  > > You can also use the theory to help remove the background in athena.  If > you have tried all these and it doesn't work.  I'd try a different > theory.  Either a different se oxide or a different atom type. > > Of course my book chapter goes over how to do these thing. I'll send you a > copy if you ask.  I've also posted example athena projects > on xafs.org. > > Good luck. > > > > -- Sent from my Palm Pr? > On Jun 8, 2010 5:55 PM, Paul Bingham <p.a.bingham(a)sheffield.ac.uk> > wrote: > > Thanks Bruce, > > > > I agree that the Se-O bond lengths are short but in SeO2, and Na2SeO3 as > Se4+ > > "standards" there are Se-O bond lengths average around 1.7A. For example when > I > > run feff on the SeO2 cif file it gives 1 Se-O bond at 1.623A and 2 at > 1.793A, > > averaging at roughly 1.7A. > > > > I'm confident that the XANES I have for this sample show that the Se is > pretty > > much all present as Se4+ and I think the first shell is very likely to > consist > > of oxygens. > > > > I also tried another shell from the same feff as included in the data I > sent, > > using O1_1 instead of O2_1 and the fit including Delr still points to an > > average Se-O bond length of about 1.7A with an Enot of around 10. > > > > I will try fitting with feffs based on different cif files with some > different > > Se-O bond lengths, but if you have any other suggestions I'd be grateful. > > > > Thanks very much for your advice - it's appreciated. > > > > Regards > > > > Paul. > > -- > > Dr. Paul Bingham > > Postdoctoral Research Associate > > Immobilisation Science Laboratory > > Dept. of Engineering Materials > > University of Sheffield > > Mappin Street > > Sheffield > > S1 3JD > > UK > > > > Email: p.a.bingham(a)sheffield.ac.uk > > Direct Line: (0114) 2225473 > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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Re: [Ifeffit] Large Enot values
by Paul Bingham 11 Jun '10

11 Jun '10

Thanks Bruce, I agree that the Se-O bond lengths are short but in SeO2, and Na2SeO3 as Se4+ "standards" there are Se-O bond lengths average around 1.7A. For example when I run feff on the SeO2 cif file it gives 1 Se-O bond at 1.623A and 2 at 1.793A, averaging at roughly 1.7A. I'm confident that the XANES I have for this sample show that the Se is pretty much all present as Se4+ and I think the first shell is very likely to consist of oxygens. I also tried another shell from the same feff as included in the data I sent, using O1_1 instead of O2_1 and the fit including Delr still points to an average Se-O bond length of about 1.7A with an Enot of around 10. I will try fitting with feffs based on different cif files with some different Se-O bond lengths, but if you have any other suggestions I'd be grateful. Thanks very much for your advice - it's appreciated. Regards Paul. -- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

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Scott Calvin PhD Thesis
by María Elena Montero Cabrera 10 Jun '10

10 Jun '10

Hello to all! Would you tell me, please, how to obtain Scott Calvin PhD Thesis, or, at least, his e-mail? I am reading a paper whose reference 30th is that document, and I have already spent 3 hours navigating by university libraries without any success. Thank you very much for any help, regards -- María Elena Dra. María Elena Montero Cabrera Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

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NACSSC - two more days for oral presentation abstracts
by Carlo Segre 09 Jun '10

09 Jun '10

Hello All: The deadline for oral presentations abstracts for the 1st North American Core Shell Spectroscopy Conference is just 2 days away! The conference will feature a symposium in honor of Ed Stern and is an ideal place for graduate students and postdocs to present their results. Please see the conference web page and the attached announcement. http://www.dxcicdd.com/cssc We urge you to consider attending the conference and submitting an abstract. Carlo Segre & Daniel Haskel

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C and N NEXAFS normalization
by Peter Nico 08 Jun '10

08 Jun '10

Hello All, I am looking for thoughts and opinions regarding the best way to approach post-edge fitting and normalization of C and N NEXAFS data. I know soft x-rays aren't exactly the focus of the list, but it is still the best access to a lot of people with a lot of XAS knowledge, and I would be very interested in your opinions. Obviously, linear or quad curve fitting followed by normalization is standard and well accepted for hard x-ray spectra. However, as far as I can tell there is no such accepted norm of C and N NEXAFS treatment. I have seen that some groups use a single point normalization, e.g. 310 for the case of C, and simply divide through the entire spectrum with this value. Other groups take the min and max value of the spectrum and map it onto a 0 to 1 scale. Neither of these approaches seems satisfactory to me for data with obvious backgrounds like those attached. While these data are not perfect, it seems like they should definitely be useable. My thought is why not do a 'standard' hard x-ray type normalization like that shown with an e0 set to the theoretical ionization potential for C or N. I understand that this has problems with the potential of including tailing sigma* transitions or first EXAFS oscillations in the background region because it doesn't extend far enough beyond the edge. However, it seems to me an approach like this must be 'less-wrong' than the more simplistic methods mentioned above and capable of yielding useful data. Thoughts, comments, jeers? --Peter

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Large Enot values
by Paul Bingham 08 Jun '10

08 Jun '10

Hi, I have been struggling with a tricky problem and cannot resolve it - hopefully someone out there can help! I have collected fluorescence XANES and EXAFS at the Se K-edge and I'm currently trying to fit the EXAFS (see attached files). The XANES agrees very well with a number of my standards and shows that the vast majority, if not all, of the Se is present in this material (an amorphous oxide-based system) as Se4+. I have tried to fit the EXAFS using a single Se-O path from a range of cif files (the simplest being SeO2). Other ions than O present incorrect bond lengths and I am convinced the first shell is oxygen. I can obtain a decent fit in terms of most parameters, as long as I disregard the consistently high value of Enot. Guidelines indicate that Enot should be less than about 5(ish), but I consistently get values of 10-12 when I try to fit my spectra, of which one is present in the attached files. I have checked my background subtraction and tried as many different options, changes and tweaks that I know or can find suggested (too many to list here) but I cannot obtain a fit with Enot below about 10 and so I ask my colleagues out there who are more experienced than I with EXAFS - can anyone shed any light on (a) the potential cause/s and (b) any potential solution/s? Thanks in advance for your time. Best Regards Paul Bingham -- Dr. Paul Bingham Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

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Re: [Ifeffit] Ifeffit Digest, Vol 88, Issue 4
by Jatinkumar Rana 08 Jun '10

08 Jun '10

Dear Dominik, Thank you so very much for your detailed explanation about the effects of particle size on XAFS spectra. Warm wishes, Rana On 07.06.2010 19:00, 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. particle size effects on XAFS spectra (Jatinkumar Rana) > 2. Re: particle size effects on XAFS spectra (Dominik Samuelis) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 07 Jun 2010 14:49:33 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: Ifeffit users<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] particle size effects on XAFS spectra > Message-ID:<4C0CEADD.8040600(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Users, > > I am working with the EXAFS technique for the characterization of my > powder sample. I must admit that i am very much new to the technique and > its analysis. I have read many tutorials on preparing sample for XAFS > measurement (both transmission and fluoroscence). However, i am dealing > with the powder having particle size much more smaller than one > absorption length. > > I would like to know will it create any destructive effect on my XAFS > spectra ?? > > Many thanks in advance... > > Warm wishes, > Rana > > > ------------------------------ > > Message: 2 > Date: Mon, 07 Jun 2010 15:21:14 +0200 > From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] particle size effects on XAFS spectra > Message-ID:<4C0CF24A.10407(a)fkf.mpg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Rana, > > yes, it will have effects on your XAFS spectra, but not really > destructive. EXAFS only really vanishes if you have isolated atoms. As > long as your particles still have several hundred atoms with some > coordination shell-like ordering, EXAFS oscillations will show up. > > However, the amplitude of the XAFS signals will be smaller than in bulk > material, due to the lower average coordination number of the central > atoms. If you e.g. have 5 nm particles (some 2000 atoms), already almost > half of the atoms (~800) is sitting on the particle surface and > therefore has a reduced coordination number. > > There's a wealth of information in literature where people actually use > this effect for determining the particle size from XAFS. > > Another thing to keep in mind is that often it's not really clear how > the surfaces of a particle looks like chemically - there might be > adsorbates, or even passivation layers. If you're e.g. doing EXAFS on > untreated 5nm Si particles, you can't really expect to see anything > close to bulk Si, because the top layer might be SiO2 > > Best regards, > Dominik > > > > On 07.06.2010 14:49, Jatinkumar Rana wrote: > >> Dear Users, >> >> I am working with the EXAFS technique for the characterization of my >> powder sample. I must admit that i am very much new to the technique and >> its analysis. I have read many tutorials on preparing sample for XAFS >> measurement (both transmission and fluoroscence). However, i am dealing >> with the powder having particle size much more smaller than one >> absorption length. >> >> I would like to know will it create any destructive effect on my XAFS >> spectra ?? >> >> Many thanks in advance... >> >> Warm wishes, >> Rana >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > >

1 0

particle size effects on XAFS spectra
by Jatinkumar Rana 07 Jun '10

07 Jun '10

Dear Users, I am working with the EXAFS technique for the characterization of my powder sample. I must admit that i am very much new to the technique and its analysis. I have read many tutorials on preparing sample for XAFS measurement (both transmission and fluoroscence). However, i am dealing with the powder having particle size much more smaller than one absorption length. I would like to know will it create any destructive effect on my XAFS spectra ?? Many thanks in advance... Warm wishes, Rana

2 1

1st North American Core Shell Spectroscopy Conference
by Carlo Segre 04 Jun '10

04 Jun '10

Hello All: Please share this announcement with anyone whom you feel might be interested. I am positive that I am not getting this out to the entire core shell spectroscopy community. The abstract deadline has been extended until June 1 for oral presentations. ---- Conference Announcement ---- 1st North American Core Shell Spectroscopy Conference to be held jointly with the 59th Denver X-ray Conference 2-6 August 2010 Ι Denver Marriott Tech Center Hotel, Denver, CO <https://resweb.passkey.com/Resweb.do?mode=welcome_ei_new&eventID=1454471> The first North American Core Shell Spectroscopy Conference will be held jointly with the 59th Denver X-Ray Conference, 2-6 August 2010. The conference will feature poster sessions as well as oral presentations and students, in particular are encouraged to participate with oral presentation submissions. All topics relating to core shell spectroscopy are welcome, including: · X-ray Absorption Spectroscopy · X-ray Fluorescence Spectroscopy / Fluorescence Mapping · Resonant Inelastic X-ray Scattering / X-ray Raman Scattering · X-ray Magnetic Circular Dichroism The conference will feature a special session and dinner in honor of Ed Stern. The list of invited speakers for this special session includes Dr. Mali Balasubramanian, Argonne National Laboratory Prof. Jerry Seidler, University of Washington Prof. Anatoly Frenkel, Yeshiva University Dr. Ken Kemner, Argonne National Laboratory Prof. John Rehr, University of Washington Prof. Michael Paesler, North Carolina State University The other invited speakers are: Dr. Corwin Booth, Lawrence Berkeley National Laboratory Prof. James Penner-Hahn, University of Michigan Prof. Daryl Crozier - Simon Fraser University Prof. Bruce Bunker - University of Notre Dame Prof. Trevor Tyson - New Jersey Institute of Technology Dr. Joshua Kas - University of Washington Dr. Simon Bare - UOP LLC Participants will be able to attend Denver X-Ray Conference Sessions being held in adjacent rooms. Details of the oral presentation sessions will be posted on the DXC web site <http://www.dxcicdd.com/default.htm> as they are available. Students are able to register for a reduced cost, are eligible for special student room rates <http://www.dxcicdd.com/10/details.htm#studentrooms>, and may apply for funding <http://www.dxcicdd.com/10/files/2010-DXC-Student-Travel-Grant-application.p…> to attend the conference. Abstract submissions for oral presentations will be open until June 1 and can be made on the Denver X-Ray Conference web site by selecting the "Submit Abstract for the Joint Meeting with the North American Core Shell Spectroscopy Conference" link on the left side of the page (the 8th button down) or directly at the abstract submission page <http://www.dxcicdd.com/cssc/cssc_abstract.asp>. For more information, visit http://www.dxcicdd.com or contact: Denise Flaherty, Conference Coordinator flaherty(a)icdd.com<mailto:flaherty@icdd.com> ICDD 12 Campus Boulevard Newtown Square, PA 19073 -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

2 2

plots from athena
by Saugata Datta 01 Jun '10

01 Jun '10

Hello, if you can help me with this question: I am trying to plot directly from athena via powerpoint for a publication/manuscript quality plot., I read a message posted that " "If you want to adjust things like fonts and line sizes on the plot for publication, then you have the option to save the plot as a metafile from the PGPlot window and import it into PowerPoint. Then convert the metafile into a drawing object with the "ungroup" feature. From this point you can change fonts, line shapes, colors, etc. to get the plot how you want it to look for publication. You can then re-save that slide as a picture (gif, tiff, metafile, etc) to be imported into the manuscript. This can get time intensive, but it's an alternative if all you want to do is adjust fonts and line colors/sizes. One caveat though, don't change the data! You can easily and unknowingly change the data if you're not careful (performing an action on one part of the drawing object without realizing another is highlighted for example) so always compare the final product to the original to make sure it's the same"... But I cannot find where the PGPlot window is., if you can kindly help. Say I want to plot six standards plotted /stacked one on top of the other in one figure, with correct seuqnce of legend? Can I do this without exporting to excel??? Thanks again... Saugata _________________________________________________________________ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID2…

2 1

Exporting derivative data
by Paul Bingham 31 May '10

31 May '10

Hi, I wonder if you can help: I'm using Athena to process some XANES data and wish to export the derivative data so that I can use a package such as Excel to prepare the data for publication. However, the derivative data that is presented visually in the graphics window is a much cleaner, smoother data set than the one I get when I export it in either deriv Mu(E) or deriv Norm(E). I tried the smoothing option in Data-Smooth mu(E) with 3 iterations and again with 10 iterations on the interpolative smoothing. Both gave far noisier data than the data shown in the Graphics window. Please can you tell me how to get exported derivative data that will be (more or less) the same as that shown in the graphics window? Basically I' hoping for WYSIWYG if that's possible? Any thoughts or suggestions would be very welcome and thanks for your time. -- Dr. Paul Bingham Postdoctoral Research Associate Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

4 3

the use of constraints
by Kellie Aldi 28 May '10

28 May '10

Hi, I have a question on the use of constraints and restraints in EXAFS data fitting. I am using SixPack to build a model for the EXAFS of some synthetic layered transition metal (TM) oxides with relatively large amounts of layer vacancies. I am refining the occupancy of the layer TM site, from which I can determine the amount of layer vacancies. I want to include a parameter in this model that refines the number of these vacancies that are capped by interlayer TM (something that can happen in these structures), but I am having difficulty in deciding a responsible way to define the parameters of this variable. I am modifying the intensity of the interlayer TM scattering paths with a parameter fcap = (1-focc)*percap where focc is the refined occupancy of the layer TM site, and percap is the percentage of vacancies, "1-focc", that are capped by interlayer TM. However, just letting percap float, the value goes greater that 1... which, as a percentage, does not make much sense physically in my model. So I want to keep the value of this between 0 and 1. I have tried what was suggested on the IFEFFIT frequently asked questions page regarding constraints and restraints. I don't feel comfortable simply using a constraint and forcing the value to be between 0 and 1 using the suggested min/max idiom. I like better the idea of penalizing a fit when percap is outside of a defined range and thus "encouraging" the fit to settle percap somewhere inside this range. But in trying to use the restraint idea, including the fix suggested by Matt Newville for only penalizing the fit outside of the min/max range, percap still goes slightly above 1 (about 1.02) and in my results I get a value for the "penalty" that I am unsure how to interpret. Can this value be used to understand why the restraint still allows the value of percap to be outside of the defined "ideal" range? I am trying to understand how the restraint that Matt Newville defined in the link in the restraints/constraints FAQ works, but I am relatively new to EXAFS modeling and thus shaky on my skills at defining these parameters and knowing how certain math functions can be used. Are there any other help sections or guides that might address the use of such restraints? Or any suggestions on how to re-define this restraint? I would greatly appreciate any suggestions/input! Thanks, Kellie Aldi

3 2

athena an widows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Inst. f. Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) - Campus Süd Engesserstrasse 18 76131 Karlsruhe email: matthias.bauer(a)kit.edu phone: +49 721 608 4320

1 0

athena an windows 7
by Matthias Bauer 28 May '10

28 May '10

Dear all, i have a problem with running athena on windows 7. I can open the program, but when I try to open a file, just by clicking "open" the interfaces closes and only the graph window remains open. Does anyone encounter the same problem or even has a solution? Many thanks, matthias Dr. Matthias Bauer Karlsruhe Institute of Technologie - Campus Süd Inst. für Technische Chemie und Polymerchemie Engesserstrasse 18 76128 Karlsruhe email: matthias.bauer(a)kit.edu phone: 0049 721 608 4320

1 0

fitting
by mohamed sobhy 26 May '10

26 May '10

----- Forwarded Message ---- From: mohamed sobhy <bakhshwan1981(a)yahoo.com> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Thu, May 20, 2010 4:14:18 PM Subject: [Ifeffit] fitting Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So how can I get the right coordination number? How to improve the fitting of second shell? thanks _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

1 0

co-ordination number for given shell
by Jatinkumar Rana 25 May '10

25 May '10

Dear Ifeffit users, I am working on EXAFS analysis of a mineral Arrojadite. It has very very complicated crystal structure. I have measured EXAFS in fluoresence mode on Mn and Fe edge. The mineral contains Mn and Fe as divalent cations distributed over 7 different atomic positions e.g. 3 different Mn atomic position (Mn1, Mn2 and Mn3) and 4 different Fe position (Fe4, Fe5, Fe6, Fe7). My question is : How do i know that How many paths should i take into consideration to fit 1st shell, 2nd shell and 3rd shell.. ?? I have rough idea that the first shell is octahedral Oxygen ions. I tried fitting first shell taking into account first 6 Oxygen paths and it gave reasonably good fit to first shell. But the confusion is how to consider paths for 2nd Shell, 3rd shell....etc. Your feedback is highly appreciated. P.S. I have attached artemis file (both Fe and Mn edge) with this mail for your reference. Best regards, Jatin

1 0

Re: [Ifeffit] calibrating and aligning samples for LCF
by Monson, Todd 24 May '10

24 May '10

I have XAFS data from several Fe nanoparticle samples as well as some Fe and Fe oxide standards collected during two different months. I would like to fit the Fe nanoparticle data using LCF and the Fe & Fe oxide standards. Data collected from Fe foil during the two months have been calibrated in energy. What is the best way to calibrate or align the other nanoparticle samples and standards collected during both of these sessions prior to doing LCF? Thanks, Todd -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Saturday, May 22, 2010 11:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 87, Issue 28 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. XANES and DOS calculations (Joanna Czapla) ---------------------------------------------------------------------- Message: 1 Date: Sat, 22 May 2010 17:21:41 +0200 From: Joanna Czapla <czapla.asia(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] XANES and DOS calculations Message-ID: <AANLkTimVJVPZoDKuU0NW8GEr9wdrrOI7OyfaAeOxSzMN(a)mail.gmail.com> Content-Type: text/plain; charset=windows-1252 Dear Feff Users, first of all I must admit that I am a total beginner and probably there are some things which I don?t understand very well. I need to make XANES and DOS calculations for K-edge of sulfur and then compare them with experiment. I use feff 8.4. First, I started from inorganic compounds such as CdS. I generated feff.inp file in ATOMS and first run feff with default values (generated by ATOMS). The fit wasn?t perfect so I started to change parameters-FMS and SCF but there was so significant improvement. I can only add that others fit are even worse. My question is which parameter I should change or which card should I add to make XANES calculations better? Maybe you can recommend any paper? The second question is about DOS calculations. I took the pDOS functions for each atom, set Fermi level from ldosNN files, but the main peaks are below this level and I don?t have any correspondence with XANES spectrum. For other compounds I have the same problem. Should I add any extra shift? I will be grateful for your advice. Regards Joanna Czapla I add the original feff.inp file generated by ATOMS: * This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE name: CdS (greenockite) (cubic zinc sulfide structure) TITLE formula: CdS TITLE sites: Cd1,S1 TITLE refer1: wyckoff 1,III,110 TITLE refer2: TITLE schoen: TITLE notes1: cubic zinc sulfide structure * S K edge energy = 2472.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 5.54240 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 8.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 16 S 2 2 0.001 1 48 Cd 3 3 4 2 16 S 2 2 4 ATOMS * this list contains 87 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 0 -1.45450 1.45450 1.45450 1 Cd1 2.51927 1 1.45450 -1.45450 1.45450 1 Cd1 2.51927 2 1.45450 1.45450 -1.45450 1 Cd1 2.51927 3 -1.45450 -1.45450 -1.45450 1 Cd1 2.51927 4 2.90900 2.90900 0.00000 2 S1 4.11395 5 -2.90900 2.90900 0.00000 2 S1 4.11395 6 2.90900 -2.90900 0.00000 2 S1 4.11395 7 -2.90900 -2.90900 0.00000 2 S1 4.11395 8 2.90900 0.00000 2.90900 2 S1 4.11395 9 -2.90900 0.00000 2.90900 2 S1 4.11395 10 0.00000 2.90900 2.90900 2 S1 4.11395 11 0.00000 -2.90900 2.90900 2 S1 4.11395 12 2.90900 0.00000 -2.90900 2 S1 4.11395 13 -2.90900 0.00000 -2.90900 2 S1 4.11395 14 0.00000 2.90900 -2.90900 2 S1 4.11395 15 0.00000 -2.90900 -2.90900 2 S1 4.11395 16 4.36350 1.45450 1.45450 1 Cd1 4.82403 17 1.45450 4.36350 1.45450 1 Cd1 4.82403 18 -4.36350 -1.45450 1.45450 1 Cd1 4.82403 19 -1.45450 -4.36350 1.45450 1 Cd1 4.82403 20 1.45450 1.45450 4.36350 1 Cd1 4.82403 21 -1.45450 -1.45450 4.36350 1 Cd1 4.82403 22 -4.36350 1.45450 -1.45450 1 Cd1 4.82403 23 -1.45450 4.36350 -1.45450 1 Cd1 4.82403 24 4.36350 -1.45450 -1.45450 1 Cd1 4.82403 25 1.45450 -4.36350 -1.45450 1 Cd1 4.82403 26 -1.45450 1.45450 -4.36350 1 Cd1 4.82403 27 1.45450 -1.45450 -4.36350 1 Cd1 4.82403 28 5.81800 0.00000 0.00000 2 S1 5.81800 29 -5.81800 0.00000 0.00000 2 S1 5.81800 30 0.00000 5.81800 0.00000 2 S1 5.81800 31 0.00000 -5.81800 0.00000 2 S1 5.81800 32 0.00000 0.00000 5.81800 2 S1 5.81800 33 0.00000 0.00000 -5.81800 2 S1 5.81800 34 -4.36350 4.36350 1.45450 1 Cd1 6.34002 35 4.36350 -4.36350 1.45450 1 Cd1 6.34002 36 -4.36350 1.45450 4.36350 1 Cd1 6.34002 37 -1.45450 4.36350 4.36350 1 Cd1 6.34002 38 4.36350 -1.45450 4.36350 1 Cd1 6.34002 39 1.45450 -4.36350 4.36350 1 Cd1 6.34002 40 4.36350 4.36350 -1.45450 1 Cd1 6.34002 41 -4.36350 -4.36350 -1.45450 1 Cd1 6.34002 42 4.36350 1.45450 -4.36350 1 Cd1 6.34002 43 1.45450 4.36350 -4.36350 1 Cd1 6.34002 44 -4.36350 -1.45450 -4.36350 1 Cd1 6.34002 45 -1.45450 -4.36350 -4.36350 1 Cd1 6.34002 46 5.81800 2.90900 2.90900 2 S1 7.12557 47 -5.81800 2.90900 2.90900 2 S1 7.12557 48 2.90900 5.81800 2.90900 2 S1 7.12557 49 -2.90900 5.81800 2.90900 2 S1 7.12557 50 5.81800 -2.90900 2.90900 2 S1 7.12557 51 -5.81800 -2.90900 2.90900 2 S1 7.12557 52 2.90900 -5.81800 2.90900 2 S1 7.12557 53 -2.90900 -5.81800 2.90900 2 S1 7.12557 54 2.90900 2.90900 5.81800 2 S1 7.12557 55 -2.90900 2.90900 5.81800 2 S1 7.12557 56 2.90900 -2.90900 5.81800 2 S1 7.12557 57 -2.90900 -2.90900 5.81800 2 S1 7.12557 58 5.81800 2.90900 -2.90900 2 S1 7.12557 59 -5.81800 2.90900 -2.90900 2 S1 7.12557 60 2.90900 5.81800 -2.90900 2 S1 7.12557 61 -2.90900 5.81800 -2.90900 2 S1 7.12557 62 5.81800 -2.90900 -2.90900 2 S1 7.12557 63 -5.81800 -2.90900 -2.90900 2 S1 7.12557 64 2.90900 -5.81800 -2.90900 2 S1 7.12557 65 -2.90900 -5.81800 -2.90900 2 S1 7.12557 66 2.90900 2.90900 -5.81800 2 S1 7.12557 67 -2.90900 2.90900 -5.81800 2 S1 7.12557 68 2.90900 -2.90900 -5.81800 2 S1 7.12557 69 -2.90900 -2.90900 -5.81800 2 S1 7.12557 70 -7.27250 1.45450 1.45450 1 Cd1 7.55780 71 -1.45450 7.27250 1.45450 1 Cd1 7.55780 72 7.27250 -1.45450 1.45450 1 Cd1 7.55780 73 1.45450 -7.27250 1.45450 1 Cd1 7.55780 74 4.36350 4.36350 4.36350 1 Cd1 7.55780 75 -4.36350 -4.36350 4.36350 1 Cd1 7.55780 76 -1.45450 1.45450 7.27250 1 Cd1 7.55780 77 1.45450 -1.45450 7.27250 1 Cd1 7.55780 78 7.27250 1.45450 -1.45450 1 Cd1 7.55780 79 1.45450 7.27250 -1.45450 1 Cd1 7.55780 80 -7.27250 -1.45450 -1.45450 1 Cd1 7.55780 81 -1.45450 -7.27250 -1.45450 1 Cd1 7.55780 82 -4.36350 4.36350 -4.36350 1 Cd1 7.55780 83 4.36350 -4.36350 -4.36350 1 Cd1 7.55780 84 1.45450 1.45450 -7.27250 1 Cd1 7.55780 85 -1.45450 -1.45450 -7.27250 1 Cd1 7.55780 86 END 2010/5/21 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. fitting (mohamed sobhy) > ? 2. update error in Windows 7 (pkraal(a)geo.uu.nl) ? 3. Re: update > error in Windows 7 (Laurent Menard) ? 4. Re: update error in Windows 7 > (Bryan Gauntt) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 May 2010 14:14:18 -0700 (PDT) > From: mohamed sobhy <bakhshwan1981(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] fitting > Message-ID: <725080.73390.qm(a)web50302.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear all thanks for your help and explanation about the background I > fitted my data after removing the background and in the attached file > I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. > So how can I get the right coordination number? > How to improve the fitting of second shell? > thanks > > > > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/201005 > 20/4d94da82/attachment.html> > > ------------------------------ > > Message: 2 > Date: Fri, 21 May 2010 12:09:24 +0200 > From: pkraal(a)geo.uu.nl > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] update error in Windows 7 > Message-ID: > ? ? ? ?<3ded096a7acb18ecc34d49196967ce21.squirrel(a)webmail.geo.uu.nl> > Content-Type: text/plain;charset=iso-8859-1 > > Dear sir or madam, > > I am using IFEFFIT on a Windows 7 system. When the runner informs that > updates are available, I select to download and install them. Then, > the first package is downloaded, but during expanding and installation > of this package the update basically stops and the runner gives an > error associated with access to bin/athena.exe. Windows 7 (like Vista > pretty easily stressed when you try to change software) does not > inform me that a program is trying to change the system or whatever, > so I don't know what to do. Is there anybody out there with similar > problems and maybe, even better, a solution? > > Regards and many thanks, > > Peter Kraal. > > > > ------------------------------ > > Message: 3 > Date: Fri, 21 May 2010 09:23:38 -0400 > From: "Laurent Menard" <menard(a)email.unc.edu> > To: "'XAFS Analysis using Ifeffit'" > ? ? ? ?<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] update error in Windows 7 > Message-ID: <01cb01caf8e8$d2cc0e90$78642bb0$(a)unc.edu> > Content-Type: text/plain; ? ? ? charset="US-ASCII" > > Peter, > > You need to make sure you have permission in Windows to write to the > IFEFFIT folder. ?If I remember correctly all you have to do is right > click on the IFEFFIT folder, select Properties. ?Go to the Security > Tab and then select the Edit button. ?Make sure that under Users all > of the "allow" boxes are checked then click OK. ?IFEFFIT should > install the updates the next time it checks for updates. > > Regards, > Laurent > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > pkraal(a)geo.uu.nl > Sent: Friday, May 21, 2010 6:09 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] update error in Windows 7 > > Dear sir or madam, > > I am using IFEFFIT on a Windows 7 system. When the runner informs that > updates are available, I select to download and install them. Then, > the first package is downloaded, but during expanding and installation > of this package the update basically stops and the runner gives an > error associated with access to bin/athena.exe. Windows 7 (like Vista > pretty easily stressed when you try to change software) does not > inform me that a program is trying to change the system or whatever, > so I don't know what to do. Is there anybody out there with similar > problems and maybe, even better, a solution? > > Regards and many thanks, > > Peter Kraal. > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > ------------------------------ > > Message: 4 > Date: Fri, 21 May 2010 09:26:01 -0400 > From: Bryan Gauntt <bdg160(a)psu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] update error in Windows 7 > Message-ID: > ? ? ? ?<AANLkTikFXm8cspcd65cHnFcT7R9MN78Gf8gjwBAY6oWB(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Peter, > I found that setting both Artemis and Athena to run in compatibility > mode (XP Service Pack 3) did the trick for me. ?You can do this by > locating the executables in the start menu and right clicking them. > Select "properties" and then the "compatibility" tab. Under > "compatibility mode" select the box next to "Run this program in > compatibility mode," and then select Windows XP (Service Pack 3) from > the drop-down list. > > Best of luck, > Bryan Gauntt > > On Fri, May 21, 2010 at 6:09 AM, ?<pkraal(a)geo.uu.nl> wrote: >> Dear sir or madam, >> >> I am using IFEFFIT on a Windows 7 system. When the runner informs >> that updates are available, I select to download and install them. >> Then, the first package is downloaded, but during expanding and >> installation of this package the update basically stops and the >> runner gives an error associated with access to bin/athena.exe. >> Windows 7 (like Vista pretty easily stressed when you try to change >> software) does not inform me that a program is trying to change the >> system or whatever, so I don't know what to do. Is there anybody out >> there with similar problems and maybe, even better, a solution? >> >> Regards and many thanks, >> >> Peter Kraal. >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > > -- > Bryan D. Gauntt > > PhD Candidate > Department of Materials Science and Engineering > 274 Materials Research Lab > Penn State University > (814) 574-2751 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 87, Issue 27 > *************************************** > ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 87, Issue 28 ***************************************

2 1

XANES and DOS calculations
by Joanna Czapla 22 May '10

22 May '10

Dear Feff Users, first of all I must admit that I am a total beginner and probably there are some things which I don’t understand very well. I need to make XANES and DOS calculations for K-edge of sulfur and then compare them with experiment. I use feff 8.4. First, I started from inorganic compounds such as CdS. I generated feff.inp file in ATOMS and first run feff with default values (generated by ATOMS). The fit wasn’t perfect so I started to change parameters-FMS and SCF but there was so significant improvement. I can only add that others fit are even worse. My question is which parameter I should change or which card should I add to make XANES calculations better? Maybe you can recommend any paper? The second question is about DOS calculations. I took the pDOS functions for each atom, set Fermi level from ldosNN files, but the main peaks are below this level and I don’t have any correspondence with XANES spectrum. For other compounds I have the same problem. Should I add any extra shift? I will be grateful for your advice. Regards Joanna Czapla I add the original feff.inp file generated by ATOMS: * This feff8 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE name: CdS (greenockite) (cubic zinc sulfide structure) TITLE formula: CdS TITLE sites: Cd1,S1 TITLE refer1: wyckoff 1,III,110 TITLE refer2: TITLE schoen: TITLE notes1: cubic zinc sulfide structure * S K edge energy = 2472.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 5.54240 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 8.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 16 S 2 2 0.001 1 48 Cd 3 3 4 2 16 S 2 2 4 ATOMS * this list contains 87 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 S1 0.00000 0 -1.45450 1.45450 1.45450 1 Cd1 2.51927 1 1.45450 -1.45450 1.45450 1 Cd1 2.51927 2 1.45450 1.45450 -1.45450 1 Cd1 2.51927 3 -1.45450 -1.45450 -1.45450 1 Cd1 2.51927 4 2.90900 2.90900 0.00000 2 S1 4.11395 5 -2.90900 2.90900 0.00000 2 S1 4.11395 6 2.90900 -2.90900 0.00000 2 S1 4.11395 7 -2.90900 -2.90900 0.00000 2 S1 4.11395 8 2.90900 0.00000 2.90900 2 S1 4.11395 9 -2.90900 0.00000 2.90900 2 S1 4.11395 10 0.00000 2.90900 2.90900 2 S1 4.11395 11 0.00000 -2.90900 2.90900 2 S1 4.11395 12 2.90900 0.00000 -2.90900 2 S1 4.11395 13 -2.90900 0.00000 -2.90900 2 S1 4.11395 14 0.00000 2.90900 -2.90900 2 S1 4.11395 15 0.00000 -2.90900 -2.90900 2 S1 4.11395 16 4.36350 1.45450 1.45450 1 Cd1 4.82403 17 1.45450 4.36350 1.45450 1 Cd1 4.82403 18 -4.36350 -1.45450 1.45450 1 Cd1 4.82403 19 -1.45450 -4.36350 1.45450 1 Cd1 4.82403 20 1.45450 1.45450 4.36350 1 Cd1 4.82403 21 -1.45450 -1.45450 4.36350 1 Cd1 4.82403 22 -4.36350 1.45450 -1.45450 1 Cd1 4.82403 23 -1.45450 4.36350 -1.45450 1 Cd1 4.82403 24 4.36350 -1.45450 -1.45450 1 Cd1 4.82403 25 1.45450 -4.36350 -1.45450 1 Cd1 4.82403 26 -1.45450 1.45450 -4.36350 1 Cd1 4.82403 27 1.45450 -1.45450 -4.36350 1 Cd1 4.82403 28 5.81800 0.00000 0.00000 2 S1 5.81800 29 -5.81800 0.00000 0.00000 2 S1 5.81800 30 0.00000 5.81800 0.00000 2 S1 5.81800 31 0.00000 -5.81800 0.00000 2 S1 5.81800 32 0.00000 0.00000 5.81800 2 S1 5.81800 33 0.00000 0.00000 -5.81800 2 S1 5.81800 34 -4.36350 4.36350 1.45450 1 Cd1 6.34002 35 4.36350 -4.36350 1.45450 1 Cd1 6.34002 36 -4.36350 1.45450 4.36350 1 Cd1 6.34002 37 -1.45450 4.36350 4.36350 1 Cd1 6.34002 38 4.36350 -1.45450 4.36350 1 Cd1 6.34002 39 1.45450 -4.36350 4.36350 1 Cd1 6.34002 40 4.36350 4.36350 -1.45450 1 Cd1 6.34002 41 -4.36350 -4.36350 -1.45450 1 Cd1 6.34002 42 4.36350 1.45450 -4.36350 1 Cd1 6.34002 43 1.45450 4.36350 -4.36350 1 Cd1 6.34002 44 -4.36350 -1.45450 -4.36350 1 Cd1 6.34002 45 -1.45450 -4.36350 -4.36350 1 Cd1 6.34002 46 5.81800 2.90900 2.90900 2 S1 7.12557 47 -5.81800 2.90900 2.90900 2 S1 7.12557 48 2.90900 5.81800 2.90900 2 S1 7.12557 49 -2.90900 5.81800 2.90900 2 S1 7.12557 50 5.81800 -2.90900 2.90900 2 S1 7.12557 51 -5.81800 -2.90900 2.90900 2 S1 7.12557 52 2.90900 -5.81800 2.90900 2 S1 7.12557 53 -2.90900 -5.81800 2.90900 2 S1 7.12557 54 2.90900 2.90900 5.81800 2 S1 7.12557 55 -2.90900 2.90900 5.81800 2 S1 7.12557 56 2.90900 -2.90900 5.81800 2 S1 7.12557 57 -2.90900 -2.90900 5.81800 2 S1 7.12557 58 5.81800 2.90900 -2.90900 2 S1 7.12557 59 -5.81800 2.90900 -2.90900 2 S1 7.12557 60 2.90900 5.81800 -2.90900 2 S1 7.12557 61 -2.90900 5.81800 -2.90900 2 S1 7.12557 62 5.81800 -2.90900 -2.90900 2 S1 7.12557 63 -5.81800 -2.90900 -2.90900 2 S1 7.12557 64 2.90900 -5.81800 -2.90900 2 S1 7.12557 65 -2.90900 -5.81800 -2.90900 2 S1 7.12557 66 2.90900 2.90900 -5.81800 2 S1 7.12557 67 -2.90900 2.90900 -5.81800 2 S1 7.12557 68 2.90900 -2.90900 -5.81800 2 S1 7.12557 69 -2.90900 -2.90900 -5.81800 2 S1 7.12557 70 -7.27250 1.45450 1.45450 1 Cd1 7.55780 71 -1.45450 7.27250 1.45450 1 Cd1 7.55780 72 7.27250 -1.45450 1.45450 1 Cd1 7.55780 73 1.45450 -7.27250 1.45450 1 Cd1 7.55780 74 4.36350 4.36350 4.36350 1 Cd1 7.55780 75 -4.36350 -4.36350 4.36350 1 Cd1 7.55780 76 -1.45450 1.45450 7.27250 1 Cd1 7.55780 77 1.45450 -1.45450 7.27250 1 Cd1 7.55780 78 7.27250 1.45450 -1.45450 1 Cd1 7.55780 79 1.45450 7.27250 -1.45450 1 Cd1 7.55780 80 -7.27250 -1.45450 -1.45450 1 Cd1 7.55780 81 -1.45450 -7.27250 -1.45450 1 Cd1 7.55780 82 -4.36350 4.36350 -4.36350 1 Cd1 7.55780 83 4.36350 -4.36350 -4.36350 1 Cd1 7.55780 84 1.45450 1.45450 -7.27250 1 Cd1 7.55780 85 -1.45450 -1.45450 -7.27250 1 Cd1 7.55780 86 END 2010/5/21 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. fitting (mohamed sobhy) > 2. update error in Windows 7 (pkraal(a)geo.uu.nl) > 3. Re: update error in Windows 7 (Laurent Menard) > 4. Re: update error in Windows 7 (Bryan Gauntt) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 20 May 2010 14:14:18 -0700 (PDT) > From: mohamed sobhy <bakhshwan1981(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] fitting > Message-ID: <725080.73390.qm(a)web50302.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Dear all thanks for your help and explanation about the background > I > fitted my data after removing the background and in the attached file I > got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. > So how can I get the right coordination number? > How to improve the fitting of second shell? > thanks > > > >

1 0

update error in Windows 7
by pkraal＠geo.uu.nl 21 May '10

21 May '10

Dear sir or madam, I am using IFEFFIT on a Windows 7 system. When the runner informs that updates are available, I select to download and install them. Then, the first package is downloaded, but during expanding and installation of this package the update basically stops and the runner gives an error associated with access to bin/athena.exe. Windows 7 (like Vista pretty easily stressed when you try to change software) does not inform me that a program is trying to change the system or whatever, so I don't know what to do. Is there anybody out there with similar problems and maybe, even better, a solution? Regards and many thanks, Peter Kraal.

3 2

fitting
by mohamed sobhy 20 May '10

20 May '10

Dear all thanks for your help and explanation about the background I fitted my data after removing the background and in the attached file I got this fitting, although all the values are good but I think the coordination number should be less than 8 (for the first shell) due to irradiation. So how can I get the right coordination number? How to improve the fitting of second shell? thanks

1 0

question about E0
by Janeth Lozano 20 May '10

20 May '10

Hi everybody, My question is about the E0, i am making fits where the E0 final is some high, around 8eV, i tried to change the feff calculation with the card EXCHANGE to lower the E0 but it did not work, after the fit i obtained the same E0 around 8 eV, what can i do to improve the E0 around 5 eV, any suggestion? Distance and sigmas are reasonable but my E0 not at all Thanks Janeth Lozano PhD Student mlozano(a)mda.cinvestav.mx

4 3

small screens and my software
by Bruce Ravel 17 May '10

17 May '10

Hi all, Today I received a very common question. An Athena user had just purchased a new laptop and Athena did not display properly on the small screen. When reading in a file, the "OK" button on the column selection dialog was off the bottom of the screen. This question comes up with enough regularity that I wrote a FAQ entry about how to work around this problem. See question 14 at http://cars9.uchicago.edu/ifeffit/FAQ/HoraeQuestions Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

2 2

Sample Charging
by Pralay K. Santra 15 May '10

15 May '10

Hi, I am performing EXAFS experiments on semiconductor nanoparticles. As these samples are highly insulating, they will be charged under the X-ray radiation. Does this charging effect the EXAFS signal (transmission as well as the fluorescence)? If yes, how can one can remove this charging effect? Will it be good enough to mix the sample with graphite and perform the EXAFS? With regards, Pralay. -- Research Student Prof D. D. Sarma's Group (http://sscu.iisc.ernet.in/DDSarma) Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore 560 012 INDIA Ph No: +91 80 2293 2336 (Extn: 2052) Fax No: +91 80 2360 1310 Mob No: +91 9845123219

1 0

Re: [Ifeffit] Differences between fluorescence and transmission of the same sample
by Ditty Dixon 14 May '10

14 May '10

---------- Forwarded message ---------- From: Ditty Dixon <ditty.dixon(a)gmail.com> Date: Fri, May 14, 2010 at 4:35 PM Subject: Re: Ifeffit Digest, Vol 87, Issue 18 To: ifeffit(a)millenia.cars.aps.anl.gov Hello Carlo, Thank you so much. We already tried with other catalyst like RuSe and CoSe. What was more exiting for me was the similarity between the data for anode pellet, cathode removed, and fluo data(attachment). Actually we want to generate exact conditions in a Direct Methanol fuel cell (methanol crossover and starvation), so we still like to keep both pt system there. Thank you once again, Ditty On Fri, May 14, 2010 at 3:09 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: fitting (Iztok Ar?on) > 2. Re: Differences between fluorescence and transmission of the > same sample (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 May 2010 08:59:20 +0200 > From: Iztok Ar?on <iztok.arcon(a)ung.si> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] fitting > Message-ID: <4BECF4C8.2090302(a)ung.si> > Content-Type: text/plain; charset="iso-8859-2"; Format="flowed" > > Dear Mohamed, > > There is an example of CeO2 EXAFS analysis, taking into account > background problems, > in the following paper: > *J. Pade?nik Gomil?ek, I. Kozjek-?kofic, N. Bukovec, A. Kodre > */X-ray absorption study of CeO2 and Ce/V mixed oxide thin films > obtained by sol-gel deposition. /* > *Thin solid films, vol. 446, issue 1, (2004) 117-123. > regards > Iztok Arcon > > mohamed sobhy wrote: > > > Dear all > > I am trying to use artemis to do fitting to CeO2. But really I cant > > get the right way to do that. > > During the fitting, I am using amp as set and change in N degeneracy > > of the path. attached is the best fit i got but it still not good and > > the chi-square is 41.109065479 > > so can you suggest me what to do > > > > thanks > > > > Mohamed > > > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > -- > Iztok Arcon > University of Nova Gorica > Vipavska 13, POB 301 > 5001 Nova Gorica, Slovenia > > tel: +386 5 331 5227 > fax: +386 5 331 5240 > e-mail: iztok.arcon(a)ung.si > http://www.ung.si/~arcon <http://www.ung.si/%7Earcon> > http://www.ung.si/~arcon/xas <http://www.ung.si/%7Earcon/xas> > >

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 18
by Ditty Dixon 14 May '10

14 May '10

Hello Carlo, Thank you so much. We already tried with other catalyst like RuSe and CoSe. What was more exiting for me was the similarity between the data for anode pellet, cathode removed, and fluo data(attachment). Actually we want to generate exact conditions in a Direct Methanol fuel cell (methanol crossover and starvation), so we still like to keep both pt system there. Thank you once again, Ditty On Fri, May 14, 2010 at 3:09 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: fitting (Iztok Ar?on) > 2. Re: Differences between fluorescence and transmission of the > same sample (Carlo Segre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 May 2010 08:59:20 +0200 > From: Iztok Ar?on <iztok.arcon(a)ung.si> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] fitting > Message-ID: <4BECF4C8.2090302(a)ung.si> > Content-Type: text/plain; charset="iso-8859-2"; Format="flowed" > > Dear Mohamed, > > There is an example of CeO2 EXAFS analysis, taking into account > background problems, > in the following paper: > *J. Pade?nik Gomil?ek, I. Kozjek-?kofic, N. Bukovec, A. Kodre > */X-ray absorption study of CeO2 and Ce/V mixed oxide thin films > obtained by sol-gel deposition. /* > *Thin solid films, vol. 446, issue 1, (2004) 117-123. > regards > Iztok Arcon > > mohamed sobhy wrote: > > > Dear all > > I am trying to use artemis to do fitting to CeO2. But really I cant > > get the right way to do that. > > During the fitting, I am using amp as set and change in N degeneracy > > of the path. attached is the best fit i got but it still not good and > > the chi-square is 41.109065479 > > so can you suggest me what to do > > > > thanks > > > > Mohamed > > > > > >------------------------------------------------------------------------ > > > >_______________________________________________ > >Ifeffit mailing list > >Ifeffit(a)millenia.cars.aps.anl.gov > >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > -- > Iztok Arcon > University of Nova Gorica > Vipavska 13, POB 301 > 5001 Nova Gorica, Slovenia > > tel: +386 5 331 5227 > fax: +386 5 331 5240 > e-mail: iztok.arcon(a)ung.si > http://www.ung.si/~arcon <http://www.ung.si/%7Earcon> > http://www.ung.si/~arcon/xas <http://www.ung.si/%7Earcon/xas> > >

1 0

Differences between fluorescence and transmission of the same sample
by Ditty Dixon 14 May '10

14 May '10

Hello ifeffit users, I am working in the area of In-situ XAS analysis of Fuel cell catalyst. The heart of the fuel cell, MEA(membrane electrode assembly) consist of nafion membrane and the catalyst sprayed on both sides which act as Cathode and Anode(the whole max thickness 1mm). I have a system where Platinum is a common metal catalyst for both anode and cathode, with anode made of alloy of Pt and Ru(nano) ,and Cathode pure Pt(both 2mg/cm2 metal loading). An In-situ transmission XAS measurements on such a system gives no information as the transmission signal will contain both Pt signal from anode and cathode and two different process taking place oxidation and reduction. So we deal with the situation by removing the catalyst from one side. But when we did our measurements in fluorescence(without removing any catalyst) we got two different signals when we turned the cell 180 degree. If the anode was facing the fluo detector we got characteristic signal for Pt/Ru alloy(dampening in FT) and when cathode was facing, that of pure Pt. Is this a solution to separate the signals from anode and cathode without removing any catalyst?. I have attached the file for the fluorescence measurements for my MEA. Thanks in Advance, Ditty On Wed, May 5, 2010 at 5:43 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: Differences between fluorescence and transmission of the > same sample (Bruce Ravel) > 2. Re: Ifeffit Digest, Vol 87, Issue 4 (Bruce Ravel) > 3. Differences between fluorescence and transmission of the same > sample (Andrew Campos) > 4. Re: Differences between fluorescence and transmission of the > same sample (Ditty Dixon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 May 2010 10:30:18 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Differences between fluorescence and > transmission of the same sample > Message-ID: <201005051030.18579.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > Andrew, > > I suspect that you are seeing what Grant refers to in his tutorials as > "leakage". That is, your transmission data appears to my eye to be > what happens when you have a wide spread in sample thickness under the > beam, ranging from gaps to very thick particles. > > If you go to > > http://gbxafs.iit.edu/training/tutorials.html > > And follow the link to the "Sample preparation" presentation, the > effect of leakage is shown on slide 16. > > On the following slide, Grant points out that this thickness effect > always reduces amplitudes. That is the case above the edge for your > data. And if you normalize data distorted in that way, you end up > with an artificially enhanced pre-edge peak, again as in your data. > > My US$0.02, > B > > > On Wednesday 05 May 2010 09:55:16 am Andrew Campos wrote: > > Hi everyone, > > > > My lab mates are running in-situ H2 reduction of Cobalt/SiO2 catalysts > > using the Co K-edge and are obtaining differences between the > > fluorescence and transmission signals. The in-situ cell does have > > quite a bit of sample thickness (2-3 mm approx) and I was wondering if > > the fluorescence signal only has a penetration depth of a few > > micrometers. If this is the case that would explain it where the side > > that is further away from the heating element is more oxidized than > > the rest of the sample. > > > > Has anyone run into this problem before? We're using the basic > > furnace/cryostat unit (in-situ cell manufactured by the exafsco) and a > > 13 element fluorescence detector (germanium diode). > > > > I appreciate any insight into the issue, I have attached a > > fluorescence and transmission spectrum collected at the same time > > where the transmission and fluorescence are in the .prj file. > > > > Thanks so much! > > Andrew > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 2 > Date: Wed, 5 May 2010 10:39:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4 > Message-ID: <201005051039.14501.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Wednesday 05 May 2010 07:56:47 am baran yildirim wrote: > > My problem is similar; I am trying to simulate a doped crystal > > (different than chp 10 in Atemis doc, this time impurity atom is > > subjected to XAS) and the host is similar to inverse-spinel type: > > include both tetrahedral and octahedral sites in its structure. The > > dopant may settle in tetrahedral or octahedral sites. > > Indeed. Similar enough that you also should read the paper by Scott > Calvin that I suggested to Maria Elena. > > > 1- I managed to simulate the doped structure as changing the FEFF inp > > file manually (first I run Atoms as if impurity ions settle in all > > sites and then keep it in 0 potential and change the 1st potential > > with the original atom) and did it for both sites, thus i have 2 batch > > of paths and then fit it. It seems it works (Question: Do you think > > what i am doing is logical? or any other suggestion? ) > > I think that's a good approach. > > Question 15 at > > http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling > > gives a bit more information. The link to the page authored by Scott > is quite useful. > > > > 2- But problems do not end :) Another problem is impurity ion may > > take different valences: it can be trivalent or divalent. In FEFF 9.0 > > i found kinda solution using ION command, it doesnt do what i > > exactly want but i can get some idea on what happens if the charge > > distribution changes. But unfortunately, i cant try it in ARTEMIS > > since i can not install FEFF 9.0 in ARTEMIS. As far as i understood > > the program structure is changed completely. But I didnt give up :)I > > generated the chi file in FEFF 9.0 and load it in ARTEMIS and continue > > to analyze but the results are not promising. (Question: Is there any > > way to run it together? and any suggestion in changing the valance? ) > > Artemis does not support Feff9 at this time. > > I actually have not played around with Feff9 yet, myself, so I won't > be able to help with the rest. Perhaps one of the Seattlites can help > .... > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 3 > Date: Wed, 5 May 2010 11:24:16 -0400 > From: Andrew Campos <acampo2(a)tigers.lsu.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Differences between fluorescence and transmission > of the same sample > Message-ID: > <z2md94177571005050824k8abda3a0n708eaada202fdc6e(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dr. Ravel, > > Thanks so much for the link and the advice! I appreciate it greatly. I > will advise my lab mates as such and may have to only use the > fluorescence data if that is indeed the case. > > I also included the file where the lower temperature is included and > you might come to the same conclusion. The samples that I ran were > pre-sieved, and the ones included in the .prj file aren't so that > should be pursued prior to running the experiment. If they crush the > particle and sieve the sample, I think that we can be more certain > that this is not the case. This was very helpful! > > Andrew >

2 1

fitting
by mohamed sobhy 14 May '10

14 May '10

Dear all I am trying to use artemis to do fitting to CeO2. But really I cant get the right way to do that. During the fitting, I am using amp as set and change in N degeneracy of the path. attached is the best fit i got but it still not good and the chi-square is 41.109065479 so can you suggest me what to do thanks Mohamed

7 7

Debye model on Artemis
by Kleber Daum Machado 12 May '10

12 May '10

Hi Matt, Concerning the third cumulant, my problem is to use a particular model for it. Some articles (Frenkel and Rehr, PRB 48 (1993) 585; Araujo et al, PRB 74 (2006) 184102) show how to use the Einstein model on Artemis, since these articles show the expressions that should be defined for sigma^2(T) and C3(T) for this model in Artemis (eqs. 11 and 18 of Frenkel and eqs. 2 and 3 of Araujo). In fact, I have already tested them on my analysis, using the eins function for sigma^2 and defining the C3(T) expression given in those articles in Artemis. I'd like to test Debye model too, and my problem is to use Debye model for sigma^2(T) and C3(T). For sigma^2(T) Artemis has the debye function already predefined. I'd like to use/write an expression for C3(T) considering Debye model, but I didn't find anything about such expression on the literature. Kleber

3 2

Debye model on artemis
by Kleber Daum Machado 11 May '10

11 May '10

I'd like to use the third cumulant option in Artemis, but considering the Debye model. Artemis has a Debye function for the second cumulant (Debye-Waller factor) but not to the third. How could this be done in Artemis? Kleber

3 2

values of f(k),δ(k) and λ(k)
by Neetu parsai 11 May '10

11 May '10

Hello, Can some one give me the values of theoretically calculated functions f(k),δ(k) and λ(k), that can be used in EXAFS equation to calculate structural parameters. If these values are given in FEFF, how can I get those. I require it to use in EXAFS equaiton using some another computer program. Thanks Mrs.Neetu Parsai Head Department of Engg.Physics Sanghvi Innovative Academy Indore. Residence: 130 Hemu colony, New G.D.C.Road, Indore-452015(M.P.) India.

2 1

Re: [Ifeffit] atoms.inp files
by csr019＠latech.edu 10 May '10

10 May '10

Yes I am new to EXAFS, so no offense taken. Thanks for the link on how to do it. ~Corisma ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

1 0

asking for model compound data
by María Elena Montero Cabrera 10 May '10

10 May '10

Hello to all! I have looked to Matt Newville's data for model compounds, and I have not found those for gamma-Fe2O3, so called maghemite. Carlo Segre has provided me those from Litle Library, I thank very much his kindness. He has suggested me to obtain this way newer data. Would any of you provide me that, please? Thanking in advance -- María Elena Dra. María Elena Montero Cabrera Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

1 0

Re: [Ifeffit] atoms.inp files
by csr019＠latech.edu 10 May '10

10 May '10

Thanks for responding Mohamed. I previously had looked at the website that you mentioned (http://cars9.uchicago.edu/~newville/adb/search.html) but did not see either files (TiAl or TiAl3) on there. Do you or anyone else know of another place I can look? ~Corisma Robinson ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

3 2

Fwd: All that old figures
by Eugenio Otal 10 May '10

10 May '10

Hi, when I was writing my thesis I get bored to see the old figures of photoelectrons scattering in the classical books (*Konigsberger *, etc). So I decided to make them again. Hope it is useful. Regards ,euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Dr. Eugenio H. Otal Solid State Chemistry and Catalysis Laboratory, Empa - Swiss Federal Laboratories for Materials Science and Technology, Ueberlandstrasse 129, CH-8600 Duebendorf, Switzerland, Tel +41 44 823 41 31, Fax +41 44 823 40 19, eugenio.otal(a)empa.ch, www.empa.ch/abt131, 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -

1 0

atoms.inp files
by csr019＠latech.edu 07 May '10

07 May '10

Hello, Does anyone have an atoms.inp file prepared or know where I can find one for: 1) TiAl and 2) TiAl3 Thanks!! ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

2 1

energy resolution
by M Ceolin 05 May '10

05 May '10

Hi all. I would like to know if anyone knows an experimental method to determine the energy resolution in the XANES region of a XAS spectrum. I do not explored the previous entries in the list so I beg you pardon if it was already discussed. Thank you for the information. Marcelo **************************************************************** Prof. Dr. Marcelo Ceolin Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas UNLP-CONICET Diagonal 113 y 64 Casilla de Correo 16 (sucursal 4) (B1906ZAA) La Plata Argentina Tel: +54-221-4257291 or 4257430 (int:156) Fax: +54-221-4254642 e-mail: mceolin(a)inifta.unlp.edu.ar or mrceolin(a)yahoo.com.ar WEB: http://www.inifta.unlp.edu.ar/investig/ceolin.htm ****************************************************************

5 4

Differences between fluorescence and transmission of the same sample
by Andrew Campos 05 May '10

05 May '10

Dr. Ravel, Thanks so much for the link and the advice! I appreciate it greatly. I will advise my lab mates as such and may have to only use the fluorescence data if that is indeed the case. I also included the file where the lower temperature is included and you might come to the same conclusion. The samples that I ran were pre-sieved, and the ones included in the .prj file aren't so that should be pursued prior to running the experiment. If they crush the particle and sieve the sample, I think that we can be more certain that this is not the case. This was very helpful! Andrew

4 4

Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 6
by Andrew Campos 05 May '10

05 May '10

Dr. Dixon, Thanks for your input! As you can see I'm really not completely sure what the problem is, and the fact that you're getting something similar with your in situ fuel cell experiments is encouraging. I will try and see what is the best course of action from this and from Dr. Ravel's advise as well! Thanks for all the help! Andrew

1 0

Re: [Ifeffit] Differences between fluorescence and transmission of the same sample
by Ditty Dixon 05 May '10

05 May '10

Hello Andrew, We have similar situation in our fuel cell in-situ measurements, our membrane electrode assembly having a thickness approx 1mm is usually coated with Pt/C on one side(Cathode), and PtRu/C(alloy) on the other side(anode). We usually get a pronounced signal of the sample facing the fluorescence detector. For eg in our case if the Anode is facing the fluorescence detector we get a lower white line and a splitting in the FT which is characteristic of the Pt/Ru alloy nanoparticles and the transmission signal is completely different. Best Wishes, Ditty On Wed, May 5, 2010 at 3:55 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: Ifeffit Digest, Vol 87, Issue 4 (baran yildirim) > 2. Differences between fluorescence and transmission of the same > sample (Andrew Campos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 May 2010 14:56:47 +0300 > From: baran yildirim <yildirimbaran(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4 > Message-ID: <C5C497A1-0207-4F6E-9167-3840543BC7E9(a)gmail.com> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Dear IFEFFIT researchers, > > My problem is similar; I am trying to simulate a doped crystal > (different than chp 10 in Atemis doc, this time impurity atom is > subjected to XAS) and the host is similar to inverse-spinel type: > include both tetrahedral and octahedral sites in its structure. The > dopant may settle in tetrahedral or octahedral sites. > 1- I managed to simulate the doped structure as changing the FEFF inp > file manually (first I run Atoms as if impurity ions settle in all > sites and then keep it in 0 potential and change the 1st potential > with the original atom) and did it for both sites, thus i have 2 batch > of paths and then fit it. It seems it works (Question: Do you think > what i am doing is logical? or any other suggestion? ) > 2- But problems do not end :) Another problem is impurity ion may > take different valences: it can be trivalent or divalent. In FEFF 9.0 > i found kinda solution using ION command, it doesnt do what i > exactly want but i can get some idea on what happens if the charge > distribution changes. But unfortunately, i cant try it in ARTEMIS > since i can not install FEFF 9.0 in ARTEMIS. As far as i understood > the program structure is changed completely. But I didnt give up :)I > generated the chi file in FEFF 9.0 and load it in ARTEMIS and continue > to analyze but the results are not promising. (Question: Is there any > way to run it together? and any suggestion in changing the valance? ) > 3-Final problem "The concentration of the dopant in the structure". I > tried to change the occupancy, there is no option in "feff inp" but > just SO2 parameter, i changed the SO2 parameters as suggested in > previous mail, although I can not guess the SO2 parameter changing > with the occupancy. The results are not satisfactory, initial trial > with just one octa & one tetra configuration seems more logical. Again > i didnt give up; I generated another crude solution: there are 30 > sites in unit cell and %10 concentration means doping in 3 sites, so > i generated 2 octa 1 tetra batch of paths(and vice versa) and tried to > merge&fit it. But still no success and then i gave up !! (Question: > Any help?? ) > 4- Extra problem regarding FEFF 9.0. I change the paths dat file > manually and unclick the paths box and give arbitrary feff inp file. I > thought it has a modular structure and all modules read the previous > file as an input, so whatever i give as a feff inp the final graph is > the result of paths.dat is my assumption right? > > > Thanks in advance for your help > Regards, > baran > > > On May 4, 2010, at 8:00 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: fitting simultaneously two different K-edges (Matt Newville) > > 2. S02 parameter (Enzo Liotti) > > 3. Re: S02 parameter (Bruce Ravel) > > 4. expected network outage to millenia.cars.aps.anl.gov > > (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 3 May 2010 20:47:02 -0500 > > From: Matt Newville <newville(a)cars.uchicago.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] fitting simultaneously two different K-edges > > Message-ID: > > <p2tb8522e3d1005031847g176e6685k2c078e39a247135b(a)mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Dear Maria, > > > > If you haven't already done so, I would suggest that you begin by > > separately fitting the data for each edge on each sample. This will > > give you a good understanding of the local structure around each metal > > ion. Once you have this intimacy with the structural models, you > > will be able to tell what might be constrained between the two > > different metal atoms. Once you get to that point, getting the > > software to combine the fits will not seem very hard ;). > > > > > > --Matt > > > > > > 2010/5/1 Mar?a Elena Montero Cabrera <elena.montero(a)cimav.edu.mx>: > >> Dear friends, Sam Webb, Bruce Ravel or any other, > >> > >> I have XAFS measurements, performed at SSRL at room temperature, of > >> three > >> compounds. All compounds have multielemental character and I have K- > >> edge > >> XAFS of two elements in each compound. It is desirable to make > >> IFEFFIT > >> fitting of both edges simultaneously. In all cases random solution of > >> competing elements is assumed, but there are ferroelectricity, > >> superconductivity or magnetic behaviors that are desirable to be > >> explained. > >> In each case, XAFS would confirm or reject the random character of > >> the > >> solution. I am not such an expert for resolving by myself how to fit > >> together two edges using Artemis software. I'll present each case > >> in the > >> following: > >> > >> 1. rutheno-cuprate (Ru1-xNbx)Sr2Eu1.4 Ce0.6Cu2O10+? compounds > >> series was > >> studied in both Ru and Nb K-edges. Changes in interatomic distances > >> that > >> could be obtained by EXAFS would tell something about oxygen > >> octahedra > >> around Ru and Nb. > >> > >> 2. g-Fe1-xCrxO3 maghemite for x=0.25, 0.5 and 0.75 was investigated > >> by XAFS > >> in both Fe and Cr K-edges. Possible distortion of oxygen octahedra > >> around > >> both Fe(III) and Cr(III) cations would tell something about not > >> confirmed > >> ferroelectricity. > >> > >> 3. LaFeNiTiO3 has been confirmed to display magnetic behavior and was > >> studied by its Fe and Ti K-edges. Interatomic distances that could be > >> obtained by EXAFS are interesting for checking possible preferential > >> occupation of sites by Fe or Ti atoms. > >> > >> Would any of you, please, suggest how to use Artemis or Sixpack for > >> solving > >> these problems? > >> > >> Sincerely yours > >> > >> -- > >> Mar?a Elena > >> > >> Dra. Mar?a Elena Montero Cabrera > >> Departamento de Medio Ambiente y Energ?a > >> Centro de Investigaci?n en Materiales Avanzados (CIMAV) > >> Miguel de Cervantes 120, Compl. Ind. Chihuahua > >> Chihuahua CP 31109, Chih. M?xico > >> Tel (614) 4391123 > >> > >> _______________________________________________ > >> Ifeffit mailing list > >> Ifeffit(a)millenia.cars.aps.anl.gov > >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 4 May 2010 12:09:33 +0100 > > From: Enzo Liotti <E.Liotti(a)lboro.ac.uk> > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] S02 parameter > > Message-ID: > > < > 225D20E4A8281F4E9DCFE465D9B75D0B102BCF75D3(a)STAFFMBX-1.lunet.lboro.ac.uk > > > > > > > Content-Type: text/plain; charset="us-ascii" > > > > Hello, > > > > I'm trying to use EXAFS to study the intermetallics present in a > > complex Al alloy. > > The three main phases present in the alloy are Al3Ti, Al13Cr2 and > > Al13Fe4. The first is tetragonal and the other two are monoclinic. > > > > To create the theoretical model in Artemis I inserted in Atoms the > > crystallographic informations available in literature and I run it > > and FEFF. Since in the monoclinic structure the absorbing atom > > occupies more than one position I created as many FEFF calculations > > as the number of positions of the Absorbing atom changing every time > > the core atom in the Atoms page. > > > > My question now regards the S02 parameter (path amplitude), how do I > > model it when I've got more than one FEFF calculation for a single > > compound? and how do I do when I have more than one compound with > > more than one FEFF calculation each ones (for example if I have a > > mixture of two similar intermetallics like Al3Ti and Al11Ti5 )? > > > > > > Best regards > > > > Enzo > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 4 May 2010 09:09:31 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] S02 parameter > > Message-ID: <201005040909.31674.bravel(a)bnl.gov> > > Content-Type: Text/Plain; charset="iso-8859-1" > > > > On Tuesday 04 May 2010 07:09:33 am Enzo Liotti wrote: > >> Hello, > >> > >> I'm trying to use EXAFS to study the intermetallics present in a > >> complex Al > >> alloy. The three main phases present in the alloy are Al3Ti, > >> Al13Cr2 and > >> Al13Fe4. The first is tetragonal and the other two are monoclinic. > >> > >> To create the theoretical model in Artemis I inserted in Atoms the > >> crystallographic informations available in literature and I run it > >> and > >> FEFF. Since in the monoclinic structure the absorbing atom occupies > >> more > >> than one position I created as many FEFF calculations as the number > >> of > >> positions of the Absorbing atom changing every time the core atom > >> in the > >> Atoms page. > >> > >> My question now regards the S02 parameter (path amplitude), how do > >> I model > >> it when I've got more than one FEFF calculation for a single > >> compound? and > >> how do I do when I have more than one compound with more than one > >> FEFF > >> calculation each ones (for example if I have a mixture of two similar > >> intermetallics like Al3Ti and Al11Ti5 )? > > > > > > As a purely practical matter (without any consideration of physics or > > of how the theory works), there are two options. You either make them > > all the same or you don't make them all the same. > > > > That's not a very profound answer, I admit, but if you start to > > scratch the surface, you'll eventually find a way to think about this > > sort of question. > > > > In purely statistical terms, you are asking whether or not to add more > > parameters. In this case, as in every case, that is a simple enough > > thing to test. Try making a fit with all S02 parameters the same, > > then try making a fit with two or more being different. If the fit is > > improved in the sense of the reduced chi-square being significantly > > smaller, then you may have improved the quality of the fit. Another > > way to state this question is: "Do the data support the evaluation of > > more than one such parameter?" A question of the "do the data support > > support" variety is always easy to answer -- you just try it and see. > > > > Of course, these are not arbitrary parameters -- they have specific > > meaning. In the case of S02, this parameter is a measure of the > > non-unity overlap of the electronic states of the absorbing atom > > before and after the creation of the core-hole. That is, it is > > somehow a measure of the relaxation of the electrons in the presence > > of the core hole. As such, we expect S02 to be a number around, but > > smaller than, 1. > > > > However, there are a lot of things that effect the amplitude in an > > EXAFS analysis. Problems with the sample, with the linearity of the > > detectors, with the processing of the data, or even with the theory > > can all contribute to the evaluation of the EXAFS amplitude. All > > those effects are difficult or impossible to distinguish from the > > physical S02 in a statistical sense. Thus, your measure of S02 in > > EXAFS analysis includes the effect of relaxation in the presence of a > > core-hole, but it also includes all those others issues that may or > > may not exist in your data. > > > > For many years, the concept of "chemical transferability" has been > > currency in the EXAFS community. That is, we presume that for > > properly created and measured samples of the same absorber and edge, > > the S02 value for one such sample can be used in teh analysis of > > another. Stated another way, S02 is a property of the species of the > > absorber. Some years ago, Frank Bridges and his group published such > > a survey. Recent work from John Rehr's group has elaborated on this, > > demonstrating that S02 is, in the strictest sense, neither > > transferable nor constant in energy. However, these effects are small > > such that chemical transferability remains a useful and defensible > > practice in many EXAFS analyses. > > > > So, back to your question -- how do you deal with S02 in a mixed > > compound or in a compound with multiple crystallographic sites? Or, > > more generally, how do you deal with S02 when you have to run Feff > > more than once to perform a single fit? > > > > Well ... you either make them all the same or you don't make them all > > the same. > > > > Regardless of how you proceed, you need to verify that your choice is > > statistically defensible. More importantly, if you introduce more > > than one such parameter, you need to be able justify that decision in > > terms of the physics or chemistry. In the case of a mixed compound, > > you need to be able to explain why the amplitudes for the species in > > the mixture should be different. If you have no such physical or > > chemical explanation, then you have to ask yourself if the parameter > > you added was not just a "fudge factor" that made the fit better > > numerically without adding meaning to your results. > > > > Fortunately, Artemis makes it relatively easy to tie parameter values > > together and to allow them to float separately. (Pro tip: Use def > > parameters.) > > > > As a general practice, I would start with a single S02 and see how the > > fit goes. If it goes well, I might declare victory and move on. If > > it goes poorly, I might consider introducing other S02 parameters, > > taking care that I can defend the choice statistically and physically. > > > > HTH, > > B > > > > > > -- > > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > > Building 535A > > Upton NY, 11973 > > > > My homepage: http://xafs.org/BruceRavel > > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > > > > ------------------------------ > > > > Message: 4 > > Date: Tue, 4 May 2010 10:17:35 -0500 > > From: Matt Newville <newville(a)cars.uchicago.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] expected network outage to > > millenia.cars.aps.anl.gov > > Message-ID: > > <o2lb8522e3d1005040817nfe57bac2m5f1955ed35fc3356(a)mail.gmail.com> > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hi Folks, > > > > The APS networking people will be doing some hardware work next week > > which means that millenia.cars.aps.anl.gov will be inaccessible to the > > outside world May 10,11,12, and 17. Because of this, xafs.org, the > > Ifeffit wiki, and this mailing list will all appear to be down on > > these days. > > > > --Matt > > > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 87, Issue 4 > > ************************************** > > > > ------------------------------ > > Message: 2 > Date: Wed, 5 May 2010 09:55:16 -0400 > From: Andrew Campos <acampo2(a)tigers.lsu.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Differences between fluorescence and transmission > of the same sample > Message-ID: > <x2gd94177571005050655teffb1ea9xea56a0fdf31ba585(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi everyone, > > My lab mates are running in-situ H2 reduction of Cobalt/SiO2 catalysts > using the Co K-edge and are obtaining differences between the > fluorescence and transmission signals. The in-situ cell does have > quite a bit of sample thickness (2-3 mm approx) and I was wondering if > the fluorescence signal only has a penetration depth of a few > micrometers. If this is the case that would explain it where the side > that is further away from the heating element is more oxidized than > the rest of the sample. > > Has anyone run into this problem before? We're using the basic > furnace/cryostat unit (in-situ cell manufactured by the exafsco) and a > 13 element fluorescence detector (germanium diode). > > I appreciate any insight into the issue, I have attached a > fluorescence and transmission spectrum collected at the same time > where the transmission and fluorescence are in the .prj file. > > Thanks so much! > Andrew >

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Re: [Ifeffit] Ifeffit Digest, Vol 87, Issue 4
by baran yildirim 05 May '10

05 May '10

Dear IFEFFIT researchers, My problem is similar; I am trying to simulate a doped crystal (different than chp 10 in Atemis doc, this time impurity atom is subjected to XAS) and the host is similar to inverse-spinel type: include both tetrahedral and octahedral sites in its structure. The dopant may settle in tetrahedral or octahedral sites. 1- I managed to simulate the doped structure as changing the FEFF inp file manually (first I run Atoms as if impurity ions settle in all sites and then keep it in 0 potential and change the 1st potential with the original atom) and did it for both sites, thus i have 2 batch of paths and then fit it. It seems it works (Question: Do you think what i am doing is logical? or any other suggestion? ) 2- But problems do not end :) Another problem is impurity ion may take different valences: it can be trivalent or divalent. In FEFF 9.0 i found kinda solution using ION command, it doesnt do what i exactly want but i can get some idea on what happens if the charge distribution changes. But unfortunately, i cant try it in ARTEMIS since i can not install FEFF 9.0 in ARTEMIS. As far as i understood the program structure is changed completely. But I didnt give up :)I generated the chi file in FEFF 9.0 and load it in ARTEMIS and continue to analyze but the results are not promising. (Question: Is there any way to run it together? and any suggestion in changing the valance? ) 3-Final problem "The concentration of the dopant in the structure". I tried to change the occupancy, there is no option in "feff inp" but just SO2 parameter, i changed the SO2 parameters as suggested in previous mail, although I can not guess the SO2 parameter changing with the occupancy. The results are not satisfactory, initial trial with just one octa & one tetra configuration seems more logical. Again i didnt give up; I generated another crude solution: there are 30 sites in unit cell and %10 concentration means doping in 3 sites, so i generated 2 octa 1 tetra batch of paths(and vice versa) and tried to merge&fit it. But still no success and then i gave up !! (Question: Any help?? ) 4- Extra problem regarding FEFF 9.0. I change the paths dat file manually and unclick the paths box and give arbitrary feff inp file. I thought it has a modular structure and all modules read the previous file as an input, so whatever i give as a feff inp the final graph is the result of paths.dat is my assumption right? Thanks in advance for your help Regards, baran On May 4, 2010, at 8:00 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: fitting simultaneously two different K-edges (Matt Newville) > 2. S02 parameter (Enzo Liotti) > 3. Re: S02 parameter (Bruce Ravel) > 4. expected network outage to millenia.cars.aps.anl.gov > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 May 2010 20:47:02 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] fitting simultaneously two different K-edges > Message-ID: > <p2tb8522e3d1005031847g176e6685k2c078e39a247135b(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Maria, > > If you haven't already done so, I would suggest that you begin by > separately fitting the data for each edge on each sample. This will > give you a good understanding of the local structure around each metal > ion. Once you have this intimacy with the structural models, you > will be able to tell what might be constrained between the two > different metal atoms. Once you get to that point, getting the > software to combine the fits will not seem very hard ;). > > > --Matt > > > 2010/5/1 Mar?a Elena Montero Cabrera <elena.montero(a)cimav.edu.mx>: >> Dear friends, Sam Webb, Bruce Ravel or any other, >> >> I have XAFS measurements, performed at SSRL at room temperature, of >> three >> compounds. All compounds have multielemental character and I have K- >> edge >> XAFS of two elements in each compound. It is desirable to make >> IFEFFIT >> fitting of both edges simultaneously. In all cases random solution of >> competing elements is assumed, but there are ferroelectricity, >> superconductivity or magnetic behaviors that are desirable to be >> explained. >> In each case, XAFS would confirm or reject the random character of >> the >> solution. I am not such an expert for resolving by myself how to fit >> together two edges using Artemis software. I'll present each case >> in the >> following: >> >> 1. rutheno-cuprate (Ru1-xNbx)Sr2Eu1.4 Ce0.6Cu2O10+? compounds >> series was >> studied in both Ru and Nb K-edges. Changes in interatomic distances >> that >> could be obtained by EXAFS would tell something about oxygen >> octahedra >> around Ru and Nb. >> >> 2. g-Fe1-xCrxO3 maghemite for x=0.25, 0.5 and 0.75 was investigated >> by XAFS >> in both Fe and Cr K-edges. Possible distortion of oxygen octahedra >> around >> both Fe(III) and Cr(III) cations would tell something about not >> confirmed >> ferroelectricity. >> >> 3. LaFeNiTiO3 has been confirmed to display magnetic behavior and was >> studied by its Fe and Ti K-edges. Interatomic distances that could be >> obtained by EXAFS are interesting for checking possible preferential >> occupation of sites by Fe or Ti atoms. >> >> Would any of you, please, suggest how to use Artemis or Sixpack for >> solving >> these problems? >> >> Sincerely yours >> >> -- >> Mar?a Elena >> >> Dra. Mar?a Elena Montero Cabrera >> Departamento de Medio Ambiente y Energ?a >> Centro de Investigaci?n en Materiales Avanzados (CIMAV) >> Miguel de Cervantes 120, Compl. Ind. Chihuahua >> Chihuahua CP 31109, Chih. M?xico >> Tel (614) 4391123 >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> > > > ------------------------------ > > Message: 2 > Date: Tue, 4 May 2010 12:09:33 +0100 > From: Enzo Liotti <E.Liotti(a)lboro.ac.uk> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] S02 parameter > Message-ID: > <225D20E4A8281F4E9DCFE465D9B75D0B102BCF75D3(a)STAFFMBX-1.lunet.lboro.ac.uk > > > > Content-Type: text/plain; charset="us-ascii" > > Hello, > > I'm trying to use EXAFS to study the intermetallics present in a > complex Al alloy. > The three main phases present in the alloy are Al3Ti, Al13Cr2 and > Al13Fe4. The first is tetragonal and the other two are monoclinic. > > To create the theoretical model in Artemis I inserted in Atoms the > crystallographic informations available in literature and I run it > and FEFF. Since in the monoclinic structure the absorbing atom > occupies more than one position I created as many FEFF calculations > as the number of positions of the Absorbing atom changing every time > the core atom in the Atoms page. > > My question now regards the S02 parameter (path amplitude), how do I > model it when I've got more than one FEFF calculation for a single > compound? and how do I do when I have more than one compound with > more than one FEFF calculation each ones (for example if I have a > mixture of two similar intermetallics like Al3Ti and Al11Ti5 )? > > > Best regards > > Enzo > > ------------------------------ > > Message: 3 > Date: Tue, 4 May 2010 09:09:31 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] S02 parameter > Message-ID: <201005040909.31674.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Tuesday 04 May 2010 07:09:33 am Enzo Liotti wrote: >> Hello, >> >> I'm trying to use EXAFS to study the intermetallics present in a >> complex Al >> alloy. The three main phases present in the alloy are Al3Ti, >> Al13Cr2 and >> Al13Fe4. The first is tetragonal and the other two are monoclinic. >> >> To create the theoretical model in Artemis I inserted in Atoms the >> crystallographic informations available in literature and I run it >> and >> FEFF. Since in the monoclinic structure the absorbing atom occupies >> more >> than one position I created as many FEFF calculations as the number >> of >> positions of the Absorbing atom changing every time the core atom >> in the >> Atoms page. >> >> My question now regards the S02 parameter (path amplitude), how do >> I model >> it when I've got more than one FEFF calculation for a single >> compound? and >> how do I do when I have more than one compound with more than one >> FEFF >> calculation each ones (for example if I have a mixture of two similar >> intermetallics like Al3Ti and Al11Ti5 )? > > > As a purely practical matter (without any consideration of physics or > of how the theory works), there are two options. You either make them > all the same or you don't make them all the same. > > That's not a very profound answer, I admit, but if you start to > scratch the surface, you'll eventually find a way to think about this > sort of question. > > In purely statistical terms, you are asking whether or not to add more > parameters. In this case, as in every case, that is a simple enough > thing to test. Try making a fit with all S02 parameters the same, > then try making a fit with two or more being different. If the fit is > improved in the sense of the reduced chi-square being significantly > smaller, then you may have improved the quality of the fit. Another > way to state this question is: "Do the data support the evaluation of > more than one such parameter?" A question of the "do the data support > support" variety is always easy to answer -- you just try it and see. > > Of course, these are not arbitrary parameters -- they have specific > meaning. In the case of S02, this parameter is a measure of the > non-unity overlap of the electronic states of the absorbing atom > before and after the creation of the core-hole. That is, it is > somehow a measure of the relaxation of the electrons in the presence > of the core hole. As such, we expect S02 to be a number around, but > smaller than, 1. > > However, there are a lot of things that effect the amplitude in an > EXAFS analysis. Problems with the sample, with the linearity of the > detectors, with the processing of the data, or even with the theory > can all contribute to the evaluation of the EXAFS amplitude. All > those effects are difficult or impossible to distinguish from the > physical S02 in a statistical sense. Thus, your measure of S02 in > EXAFS analysis includes the effect of relaxation in the presence of a > core-hole, but it also includes all those others issues that may or > may not exist in your data. > > For many years, the concept of "chemical transferability" has been > currency in the EXAFS community. That is, we presume that for > properly created and measured samples of the same absorber and edge, > the S02 value for one such sample can be used in teh analysis of > another. Stated another way, S02 is a property of the species of the > absorber. Some years ago, Frank Bridges and his group published such > a survey. Recent work from John Rehr's group has elaborated on this, > demonstrating that S02 is, in the strictest sense, neither > transferable nor constant in energy. However, these effects are small > such that chemical transferability remains a useful and defensible > practice in many EXAFS analyses. > > So, back to your question -- how do you deal with S02 in a mixed > compound or in a compound with multiple crystallographic sites? Or, > more generally, how do you deal with S02 when you have to run Feff > more than once to perform a single fit? > > Well ... you either make them all the same or you don't make them all > the same. > > Regardless of how you proceed, you need to verify that your choice is > statistically defensible. More importantly, if you introduce more > than one such parameter, you need to be able justify that decision in > terms of the physics or chemistry. In the case of a mixed compound, > you need to be able to explain why the amplitudes for the species in > the mixture should be different. If you have no such physical or > chemical explanation, then you have to ask yourself if the parameter > you added was not just a "fudge factor" that made the fit better > numerically without adding meaning to your results. > > Fortunately, Artemis makes it relatively easy to tie parameter values > together and to allow them to float separately. (Pro tip: Use def > parameters.) > > As a general practice, I would start with a single S02 and see how the > fit goes. If it goes well, I might declare victory and move on. If > it goes poorly, I might consider introducing other S02 parameters, > taking care that I can defend the choice statistically and physically. > > HTH, > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > > > ------------------------------ > > Message: 4 > Date: Tue, 4 May 2010 10:17:35 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] expected network outage to > millenia.cars.aps.anl.gov > Message-ID: > <o2lb8522e3d1005040817nfe57bac2m5f1955ed35fc3356(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Folks, > > The APS networking people will be doing some hardware work next week > which means that millenia.cars.aps.anl.gov will be inaccessible to the > outside world May 10,11,12, and 17. Because of this, xafs.org, the > Ifeffit wiki, and this mailing list will all appear to be down on > these days. > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 87, Issue 4 > **************************************

2 1

Differences between fluorescence and transmission of the same sample
by Andrew Campos 05 May '10

05 May '10

Hi everyone, My lab mates are running in-situ H2 reduction of Cobalt/SiO2 catalysts using the Co K-edge and are obtaining differences between the fluorescence and transmission signals. The in-situ cell does have quite a bit of sample thickness (2-3 mm approx) and I was wondering if the fluorescence signal only has a penetration depth of a few micrometers. If this is the case that would explain it where the side that is further away from the heating element is more oxidized than the rest of the sample. Has anyone run into this problem before? We're using the basic furnace/cryostat unit (in-situ cell manufactured by the exafsco) and a 13 element fluorescence detector (germanium diode). I appreciate any insight into the issue, I have attached a fluorescence and transmission spectrum collected at the same time where the transmission and fluorescence are in the .prj file. Thanks so much! Andrew

2 1

expected network outage to millenia.cars.aps.anl.gov
by Matt Newville 04 May '10

04 May '10

Hi Folks, The APS networking people will be doing some hardware work next week which means that millenia.cars.aps.anl.gov will be inaccessible to the outside world May 10,11,12, and 17. Because of this, xafs.org, the Ifeffit wiki, and this mailing list will all appear to be down on these days. --Matt

1 0

S02 parameter
by Enzo Liotti 04 May '10

04 May '10

Hello, I'm trying to use EXAFS to study the intermetallics present in a complex Al alloy. The three main phases present in the alloy are Al3Ti, Al13Cr2 and Al13Fe4. The first is tetragonal and the other two are monoclinic. To create the theoretical model in Artemis I inserted in Atoms the crystallographic informations available in literature and I run it and FEFF. Since in the monoclinic structure the absorbing atom occupies more than one position I created as many FEFF calculations as the number of positions of the Absorbing atom changing every time the core atom in the Atoms page. My question now regards the S02 parameter (path amplitude), how do I model it when I've got more than one FEFF calculation for a single compound? and how do I do when I have more than one compound with more than one FEFF calculation each ones (for example if I have a mixture of two similar intermetallics like Al3Ti and Al11Ti5 )? Best regards Enzo

2 1

fitting simultaneously two different K-edges
by María Elena Montero Cabrera 04 May '10

04 May '10

Dear friends, Sam Webb, Bruce Ravel or any other, I have XAFS measurements, performed at SSRL at room temperature, of three compounds. All compounds have multielemental character and I have K-edge XAFS of two elements in each compound. It is desirable to make IFEFFIT fitting of both edges simultaneously. In all cases random solution of competing elements is assumed, but there are ferroelectricity, superconductivity or magnetic behaviors that are desirable to be explained. In each case, XAFS would confirm or reject the random character of the solution. I am not such an expert for resolving by myself how to fit together two edges using Artemis software. I'll present each case in the following: 1. rutheno-cuprate (Ru1-xNbx)Sr2Eu1.4 Ce0.6Cu2O10+δ compounds series was studied in both Ru and Nb K-edges. Changes in interatomic distances that could be obtained by EXAFS would tell something about oxygen octahedra around Ru and Nb. 2. g-Fe1-xCrxO3 maghemite for x=0.25, 0.5 and 0.75 was investigated by XAFS in both Fe and Cr K-edges. Possible distortion of oxygen octahedra around both Fe(III) and Cr(III) cations would tell something about not confirmed ferroelectricity. 3. LaFeNiTiO3 has been confirmed to display magnetic behavior and was studied by its Fe and Ti K-edges. Interatomic distances that could be obtained by EXAFS are interesting for checking possible preferential occupation of sites by Fe or Ti atoms. Would any of you, please, suggest how to use Artemis or Sixpack for solving these problems? Sincerely yours -- María Elena Dra. María Elena Montero Cabrera Departamento de Medio Ambiente y Energía Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

3 2

Unreasonable Fits on one of my computers in Artemis (Mac)
by Stefan Mangold 02 May '10

02 May '10

Dear List, I have produced a fit with 2 structure, which went reasonable well. So I saved the Artemis file on the first maschine (a MacPro with 20 Gb Ram). Made with "Artemis 0.8.011 using darwin, perl 5.008009, Tk 804.028, and Ifeffit 1.2.10". Switched to a MacBookPro at home and copied the Artemis-file over (Same version Artemis 0.8.011 using darwin, perl 5.008009, Tk 804.028, and Ifeffit 1.2.10) and got a completely different result. Did I anything unreasonable by just copying the file over an think to proceed? Did I missed anything? Since the experiment is rather small (1.2 Mb) it should not be a memory issue? Thanks for any help or advice? Regards Stefan Mangold

2 1

Re: [Ifeffit] SixPack PCA (Andrew)
by fred.mosselmans＠diamond.ac.uk 01 May '10

01 May '10

-----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 30 April 2010 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 86, Issue 15 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..." Hi I am even less of an expert but think Andrew has misread the Beauchemin paper as you want a low Spoil. They say <3 is good and more than 6 rotten. Cheers Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

1 0

SixPack PCA
by Andrew 29 Apr '10

29 Apr '10

Nagappan, I'm by no means a statistical expert. There are some rules of thumbs in the literature regarding what Spoil value to believe in or not. Some resources that you can look up: 1. Beauchemin, S.; Hesterberg, D.; Beauchemin, M., Soil Sci Soc Am J 2002, 66 (1), 83-91. (( in the above work they included standards which had SPOIL values greater than 6, so they would have rejected a standard with a value lower than 6)) 2. Malinowski, E. R., Factor Analysis in Chemistry. Wiley: New York, 2002; p 432. I might be wrong on this but when these programs use the formulas for calculating F-values and SPOIL values, they assume that all points are independent. One question that comes up sometimes is "How many independent points are there in a XANES spectrum?" In EXAFS many people use the Nyquist criterion. And what I'm getting at is you have to be cautious in using a rule of thumb for the XANES analysis. If there are other techniques you can use to help you identify what is in your sample try those as well. The manual on Athena also points out that the number of independent points collected in a XANES spectrum is difficult to determine. Without additional information: the quality of the data collected (the signal-to-noise), what edge you collected your spectra, are you fitting standards that you collected in the same set of runs as your samples, I think it's difficult for anyone to go into further depth. Please look up the above two references, this should at least give you a better idea. Hope this helps! Andrew Campos

1 0

SixPack PCA
by Nagappan Ramaswamy 29 Apr '10

29 Apr '10

Hello, In the Target Transform step of PCA analysis using the SixPack program, I am trying to understand the significance of the parameter called SPOIL? Can this parameter can be used as a measure of merit of the target? If so, what range is acceptable. Also what does it mean if SPOIL value is zero? Thanks Nagappan

1 0

SixPack PCA
by Nagappan Ramaswamy 29 Apr '10

29 Apr '10

Hello, In the Target Transform step of PCA analysis using the SixPack program, I am trying to understand the significance of the parameter called SPOIL? Can this parameter can be used as a measure of merit of the target? If so, what range is acceptable. Also what does it mean if SPOIL value is zero? Thanks Nagappan

1 0

Deadline extended - North American Core Shell Spectroscopy Conference
by Carlo Segre 27 Apr '10

27 Apr '10

Hello All: Please share this announcement with anyone whom you feel might be interested. I am positive that I am not getting this out to the entire core shell spectroscopy community. Note hat the abstract deadline has been extended until May 15 for oral presentations. The Ed Stern Symposium will feature the following invited speakers: Dr. Mali Balasubramanian, Argonne National Laboratory Prof. Jerry Seidler, University of Washington Prof. Anatoly Frenkel, Yeshiva University Dr. Ken Kemner, Argonne National Laboratory Prof. John Rehr, University of Washington Prof. Michael Paesler, North Carolina State University other invited speakers will include Dr. Corwin Booth, Lawrence Berkeley National Laboratory Prof. James Penner-Hahn, University of Michigan and more to come... ---- Conference Announcement ---- 1st North American Core Shell Spectroscopy Conference to be held jointly with the 59th Denver X-ray Conference 2-6 August 2010 Ι Denver Marriott Tech Center Hotel, Denver, CO <https://resweb.passkey.com/Resweb.do?mode=welcome_ei_new&eventID=1454471> The first North American Core Shell Spectroscopy Conference will be held jointly with the 59th Denver X-Ray Conference, 2-6 August 2010. The conference will feature poster sessions as well as oral presentations and students, in particular are encouraged to participate with oral presentation submissions. All topics relating to core shell spectroscopy are welcome, including: · X-ray Absorption Spectroscopy · X-ray Fluorescence Spectroscopy / Fluorescence Mapping · Resonant Inelastic X-ray Scattering / X-ray Raman Scattering · X-ray Magnetic Circular Dichroism The conference will feature a special session and dinner in honor of Ed Stern. The list of invited speakers for this special session includes Dr. Mali Balasubramanian, Argonne National Laboratory Prof. Jerry Seidler, University of Washington Prof. Anatoly Frenkel, Yeshiva University Dr. Ken Kemner, Argonne National Laboratory Prof. John Rehr, University of Washington Prof. Michael Paesler, North Carolina State University Participants will be able to attend Denver X-Ray Conference Sessions being held in adjacent rooms. Details of the oral presentation sessions will be posted on the DXC web site <http://www.dxcicdd.com/default.htm> as they are available. Students are able to register for a reduced cost, are eligible for special student room rates <http://www.dxcicdd.com/10/details.htm#studentrooms>, and may apply for funding <http://www.dxcicdd.com/10/files/2010-DXC-Student-Travel-Grant-application.p…> to attend the conference. Abstract submissions for oral presentations will be open until May 15 and can be made on the Denver X-Ray Conference web site by selecting the "Submit Abstract for the Joint Meeting with the North American Core Shell Spectroscopy Conference" link on the left side of the page (the 8th button down) or directly at the abstract submission page <http://www.dxcicdd.com/cssc/cssc_abstract.asp>. For more information, visit http://www.dxcicdd.com or contact: Denise Flaherty, Conference Coordinator flaherty(a)icdd.com<mailto:flaherty@icdd.com> ICDD 12 Campus Boulevard Newtown Square, PA 19073 -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org ---------- Forwarded message ---------- Date: Thu, 15 Apr 2010 08:36:48 -0500 (CDT) From: Carlo Segre <segre(a)iit.edu> To: ingrid.pickering(a)usask.ca Subject: Invitation to speak at the North American Core Shell Spectroscopy Conference Dear Prof. Pickering: The first "North American Core Shell Spectroscopy" conference will take place this year concomitantly with the Denver X-ray conference August 2-6, 2010. We are organizing this conference to provide an opportunity for researchers in North America to gather and present their research in years when there is no International XAFS Conference. One of the major goals is to have a high degree of participation from students and postdoctoral scientists in both the oral and poster sessions. On behalf of the organizing committee, I would like to invite you to give a talk at one of our sessions. Since we are leaving the logistical organization of this conference to the ICDD Conference Staff, we can offer the same reduced registration fee that is provided to the Denver X-ray Conference invited speakers. The plans for the conference include a symposium in honor of Ed Stern on Tuesday, August 3, a poster session and a series of oral sessions running concurrently with the Denver X-ray Conference sessions. We hope that you can accept this invitation, and look forward to seeing you in Denver. Sincerely yours, Carlo Segre, for The Organizing committee. -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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fitting
by mohamed sobhy 23 Apr '10

23 Apr '10

Dear all I am trying to fit some data of coordination number 8, but I always find the fitting of the first shell give the coordination number only about 0.5. I do not know what is wrong. Do I need to fit first and second and third shells altogether, and if that is right how Can I do that?? Thanks

2 1

APS/IIT Summer XAFS School
by Matt Newville 18 Apr '10

18 Apr '10

Hi Folks, The APS/IIT Summer XAFS School (July 12-16, 2010) is now accepting applications. Flyer attached. --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 86, Issue 9
by hmx＠helmholtz-berlin.de 17 Apr '10

17 Apr '10

Dear Dave, Thank you so much for your reply. I hope someone in the mailing list knows the solution to this problem. I am looking forward for further suggestions from mailing list. Thank you very much. Best regards, Jatin > 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. EXAFS related querry (Jatinkumar Rana) > 2. Re: Data file for Arrojadite with screenshots (Barton, David (DG)) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 15 Apr 2010 15:02:08 +0200 > From: Jatinkumar Rana <jatinkumar.rana(a)helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] EXAFS related querry > Message-ID: <4BC70E50.4090208(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Bruce, > > I am trying to fit EXAFS data for Arrojadite (a naturally occuring > phosphate mineral) measured on Fe-edge. > > When i load crystallogrphic file in to FEFF, i get Degeneracy (N) for > all path as 1 or 2. I know from the crystal structure of Arrojadite that > it is not true. > > Kindly help me in solving this problem. > > Best regards, > Jatin > > > ------------------------------ > > Message: 2 > Date: Fri, 16 Apr 2010 10:18:11 -0400 > From: "Barton, David (DG)" <DGBarton(a)dow.com> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Data file for Arrojadite with screenshots > Message-ID: > <517848624ACEC544A60E405637427377066D0CA0(a)USMDLMDOWX025.dow.com> > Content-Type: text/plain; charset="us-ascii" > > Jatin, > > This is an issue with the challenge of dealing with occupancy factors of > less than one in ATOMS. When you plot this crystal structure in a > visualization program you quickly notice there are overlapping atoms > with different identities. Of course this is why they put in occupancy > factors into the crystal structure file. For example, if you look at > the last two lines or your crystal file: > O 0.13830 0.00130 0.23150 O27 0.500 > F 0.13830 0.00130 0.23150 F 0.500 > > you will notice that the O and F have exactly the same coordinates and > 50% occupancy. The big question is how to deal with this complexity > and build an appropriate model. There have been several discussions in > the past on this mailing list that you should read. I am definitely not > an expert in this type of analysis so I can provide no additional help, > but some others may chime in. > > Dave Barton > > > ________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of > Jatinkumar Rana > Sent: Friday, April 16, 2010 3:45 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data file for Arrojadite with screenshots > > > Dear Bruce, > > Thank you very much for your reply. > > I used structural file from ICSD database > (http://icsd.ill.eu/icsd/index.php?action=Details&id[]=50276) I have > attached the same file with this mail also. > > The following screenshot shows the core atom (Fe) i selected to > get scattering paths. > > > > > The following screenshot shows the actual problem : The > Degeneracy (Deg : N) is 1 or 2 for all the paths which is not true from > the structure. > > > > > > > Many more thanks in advance. > > Best regards, > Jatin > > On 15.04.2010 19:00, 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: Emission spectra of Cobalt (Timna-Josua Kuehn) > (Timna-Josua Kuehn) > 2. EXAFS related querry (Jatinkumar Rana) > 3. Re: EXAFS related querry (Bruce Ravel) > > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 14 Apr 2010 22:07:06 +0200 > From: "Timna-Josua Kuehn" <timjoku(a)uni-bonn.de> > <mailto:timjoku@uni-bonn.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Emission spectra of Cobalt > (Timna-Josua Kuehn) > Message-ID: <201004142207.06319.timjoku(a)uni-bonn.de> > <mailto:201004142207.06319.timjoku@uni-bonn.de> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Joshua, > > thanks for this explanation of the XES command. I was > not aware of it. > However, I can not find the data file of the XES > simulation yet, although no > error is reportet! There is some file called > "xsect.dat", where something > about "em" is written, but there are no XES spectra in > it. Does one have to > process this file's data or even some more files? > > Regards > > Timna-Josua Kuehn > > > > > Date: Mon, 12 Apr 2010 11:19:17 -0700 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > <mailto:joshua.j.kas@gmail.com> > > Hi Timna, > The energy arguments for the XES in FEFF84 are > energies of the valence > electron relative to vacuum, so emin should be a > negative number. > Try > XES -20 0 0.3 > This should capture at least some of the XES. > You can play with emin to get > the range right. Note that the number of energy > points in FEFF84 is fixed, > and if you specify a small energy step (the > third parameter) you will not > achieve the full range that you specify. > Cheers, > Josh Kas > > > > > Date: Mon, 12 Apr 2010 12:47:11 +0200 > From: "Timna-Josua Kuehn" > <timjoku(a)uni-bonn.de> <mailto:timjoku@uni-bonn.de> > > Dear all, > > I am trying to simulate Cobalt Kbeta > emission spectra. Actually I just > exchanged the XANES card with XES, as is > explained and set emin = 7700 eV > and > emax = 7800 eV with estep = 100 to > calculate the whole Co Kbeta line at > 7649.43 eV. > But I do not find a file that contains > the emission data. I am thankful > for each helpful advice. > > Best regards > > Timna > > > > Timna-Josua Kuehn (PhD student) > Synchrotron Radiation Group > Institute of Physics > University of Bonn > Germany > > > > > ------------------------------ > > Message: 2 > Date: Thu, 15 Apr 2010 15:07:18 +0200 > From: Jatinkumar Rana > <jatinkumar.rana(a)helmholtz-berlin.de> > <mailto:jatinkumar.rana@helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] EXAFS related querry > Message-ID: <4BC70F86.6020808(a)helmholtz-berlin.de> > <mailto:4BC70F86.6020808@helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; > format=flowed > > Dear Bruce, > > I am trying to fit EXAFS data for Arrojadite (a > naturally occuring > phosphate mineral) measured on Fe-edge. > > When i load crystallogrphic file in to FEFF, i get > Degeneracy (N) for > all path as 1 or 2. I know from the crystal structure of > Arrojadite that > it is not true. > > Kindly help me in solving this problem. > > Best regards, > Jatin > > > > ------------------------------ > > Message: 3 > Date: Thu, 15 Apr 2010 10:01:09 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > <mailto:bravel@bnl.gov> > To: XAFS Analysis using Ifeffit > <ifeffit(a)millenia.cars.aps.anl.gov> > <mailto:ifeffit@millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] EXAFS related querry > Message-ID: <201004151001.09115.bravel(a)bnl.gov> > <mailto:201004151001.09115.bravel@bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Thursday 15 April 2010 09:07:18 am Jatinkumar Rana > wrote: > > > Dear Bruce, > > I am trying to fit EXAFS data for Arrojadite (a > naturally occuring > phosphate mineral) measured on Fe-edge. > > When i load crystallogrphic file in to FEFF, i > get Degeneracy (N) for > all path as 1 or 2. I know from the crystal > structure of Arrojadite that > it is not true. > > Kindly help me in solving this problem. > > Best regards, > Jatin > > > As I say here: > > > http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest > > "Remember that if you do not provide enough information > to reproduce the > problem on my own computer, there will be little I can > do to help you. As I > explain on that page, you should send along a project > file, a data file, a > screenshot -- something that helps to explain your > problem." > > In this case, you would be much more likely to get a > useful response from > someone on the mailing list were you to include the > crystal data you are > working from. > > B > > > > >

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Data file for Arrojadite with screenshots
by Jatinkumar Rana 16 Apr '10

16 Apr '10

Dear Bruce, Thank you very much for your reply. I used structural file from ICSD database (http://icsd.ill.eu/icsd/index.php?action=Details&id[]=50276) I have attached the same file with this mail also. The following screenshot shows the core atom (Fe) i selected to get scattering paths. The following screenshot shows the actual problem : The Degeneracy (Deg : N) is 1 or 2 for all the paths which is not true from the structure. Many more thanks in advance. Best regards, Jatin On 15.04.2010 19:00, 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: Emission spectra of Cobalt (Timna-Josua Kuehn) > (Timna-Josua Kuehn) > 2. EXAFS related querry (Jatinkumar Rana) > 3. Re: EXAFS related querry (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 14 Apr 2010 22:07:06 +0200 > From: "Timna-Josua Kuehn"<timjoku(a)uni-bonn.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Emission spectra of Cobalt (Timna-Josua Kuehn) > Message-ID:<201004142207.06319.timjoku(a)uni-bonn.de> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Joshua, > > thanks for this explanation of the XES command. I was not aware of it. > However, I can not find the data file of the XES simulation yet, although no > error is reportet! There is some file called "xsect.dat", where something > about "em" is written, but there are no XES spectra in it. Does one have to > process this file's data or even some more files? > > Regards > > Timna-Josua Kuehn > > > >> Date: Mon, 12 Apr 2010 11:19:17 -0700 >> From: Joshua Kas<joshua.j.kas(a)gmail.com> >> >> Hi Timna, >> The energy arguments for the XES in FEFF84 are energies of the valence >> electron relative to vacuum, so emin should be a negative number. >> Try >> XES -20 0 0.3 >> This should capture at least some of the XES. You can play with emin to get >> the range right. Note that the number of energy points in FEFF84 is fixed, >> and if you specify a small energy step (the third parameter) you will not >> achieve the full range that you specify. >> Cheers, >> Josh Kas >> >> >> >>> Date: Mon, 12 Apr 2010 12:47:11 +0200 >>> From: "Timna-Josua Kuehn"<timjoku(a)uni-bonn.de> >>> >>> Dear all, >>> >>> I am trying to simulate Cobalt Kbeta emission spectra. Actually I just >>> exchanged the XANES card with XES, as is explained and set emin = 7700 eV >>> and >>> emax = 7800 eV with estep = 100 to calculate the whole Co Kbeta line at >>> 7649.43 eV. >>> But I do not find a file that contains the emission data. I am thankful >>> for each helpful advice. >>> >>> Best regards >>> >>> Timna >>> >>> >>> >>> Timna-Josua Kuehn (PhD student) >>> Synchrotron Radiation Group >>> Institute of Physics >>> University of Bonn >>> Germany >>> > > > ------------------------------ > > Message: 2 > Date: Thu, 15 Apr 2010 15:07:18 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] EXAFS related querry > Message-ID:<4BC70F86.6020808(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Bruce, > > I am trying to fit EXAFS data for Arrojadite (a naturally occuring > phosphate mineral) measured on Fe-edge. > > When i load crystallogrphic file in to FEFF, i get Degeneracy (N) for > all path as 1 or 2. I know from the crystal structure of Arrojadite that > it is not true. > > Kindly help me in solving this problem. > > Best regards, > Jatin > > > > ------------------------------ > > Message: 3 > Date: Thu, 15 Apr 2010 10:01:09 -0400 > From: Bruce Ravel<bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] EXAFS related querry > Message-ID:<201004151001.09115.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Thursday 15 April 2010 09:07:18 am Jatinkumar Rana wrote: > >> Dear Bruce, >> >> I am trying to fit EXAFS data for Arrojadite (a naturally occuring >> phosphate mineral) measured on Fe-edge. >> >> When i load crystallogrphic file in to FEFF, i get Degeneracy (N) for >> all path as 1 or 2. I know from the crystal structure of Arrojadite that >> it is not true. >> >> Kindly help me in solving this problem. >> >> Best regards, >> Jatin >> > As I say here: > > http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest > > "Remember that if you do not provide enough information to reproduce the > problem on my own computer, there will be little I can do to help you. As I > explain on that page, you should send along a project file, a data file, a > screenshot -- something that helps to explain your problem." > > In this case, you would be much more likely to get a useful response from > someone on the mailing list were you to include the crystal data you are > working from. > > B > >

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Re: [Ifeffit] Emission spectra of Cobalt
by Joshua Kas 15 Apr '10

15 Apr '10

Hi Timna, The energy arguments for the XES in FEFF84 are energies of the valence electron relative to vacuum, so emin should be a negative number. Try XES -20 0 0.3 This should capture at least some of the XES. You can play with emin to get the range right. Note that the number of energy points in FEFF84 is fixed, and if you specify a small energy step (the third parameter) you will not achieve the full range that you specify. Cheers, Josh Kas On Mon, Apr 12, 2010 at 10:00 AM, <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. Emission spectra of Cobalt (Timna-Josua Kuehn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Apr 2010 12:47:11 +0200 > From: "Timna-Josua Kuehn" <timjoku(a)uni-bonn.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Emission spectra of Cobalt > Message-ID: <201004121247.12223.timjoku(a)uni-bonn.de> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > I am trying to simulate Cobalt Kbeta emission spectra. Actually I just > exchanged the XANES card with XES, as is explained and set emin = 7700 eV > and > emax = 7800 eV with estep = 100 to calculate the whole Co Kbeta line at > 7649.43 eV. > But I do not find a file that contains the emission data. I thankful for > each > helpful advice. > > Best regards > > Timna > > > > Timna-Josua Kuehn (PhD student) > Synchrotron Radiation Group > Institute of Physics > University of Bonn > Germany > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 86, Issue 5 > ************************************** >

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2nd Announcement - North American Core Shell Spectroscopy Conference
by Carlo Segre 15 Apr '10

15 Apr '10

There are still two more weeks for abstract submission to the 1st North American Core Shell Spectroscopy Conference to be held jointly with the 59th Denver X-ray Conference 2-6 August 2010 Ι Denver Marriott Tech Center Hotel, Denver, CO <https://resweb.passkey.com/Resweb.do?mode=welcome_ei_new&eventID=1454471> The first North American Core Shell Spectroscopy Conference will be held jointly with the 59th Denver X-Ray Conference, 2-6 August 2010. The conference will feature poster sessions as well as oral presentations and students, in particular are encouraged to participate with oral presentation submissions. All topics relating to core shell spectroscopy are welcome, including: · X-ray Absorption Spectroscopy · X-ray Fluorescence Spectroscopy / Fluorescence Mapping · Resonant Inelastic X-ray Scattering / X-ray Raman Scattering · X-ray Magnetic Circular Dichroism The conference will feature a special session and dinner in honor of Ed Stern. The list of invited speakers for this special session includes Dr. Mali Balasubramanian, Argonne National Laboratory Prof. Jerry Seidler, University of Washington Prof. Anatoly Frenkel, Yeshiva University Dr. Ken Kemner, Argonne National Laboratory A complete list will be posted on the Denver X-ray Conference Site as soon as it is known. Participants will be able to attend Denver X-Ray Conference Sessions being held in adjacent rooms. Details of the oral presentation sessions will be posted on the DXC web site <http://www.dxcicdd.com/default.htm> as they are available. Students are able to register for a reduced cost, are eligible for special student room rates <http://www.dxcicdd.com/10/details.htm#studentrooms>, and may apply for funding <http://www.dxcicdd.com/10/files/2010-DXC-Student-Travel-Grant-application.p…> to attend the conference. Abstract submissions for oral presentations will be open until April 30 and can be made on the Denver X-Ray Conference web site by selecting the "Submit Abstract for the Joint Meeting with the North American Core Shell Spectroscopy Conference" link on the left side of the page (the 8th button down) or directly at the abstract submission page <http://www.dxcicdd.com/cssc/cssc_abstract.asp>. For more information, visit http://www.dxcicdd.com or contact: Denise Flaherty, Conference Coordinator flaherty(a)icdd.com<mailto:flaherty@icdd.com> ICDD 12 Campus Boulevard Newtown Square, PA 19073 -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org ---------- Forwarded message ---------- Date: Thu, 15 Apr 2010 08:36:48 -0500 (CDT) From: Carlo Segre <segre(a)iit.edu> To: ingrid.pickering(a)usask.ca Subject: Invitation to speak at the North American Core Shell Spectroscopy Conference Dear Prof. Pickering: The first "North American Core Shell Spectroscopy" conference will take place this year concomitantly with the Denver X-ray conference August 2-6, 2010. We are organizing this conference to provide an opportunity for researchers in North America to gather and present their research in years when there is no International XAFS Conference. One of the major goals is to have a high degree of participation from students and postdoctoral scientists in both the oral and poster sessions. On behalf of the organizing committee, I would like to invite you to give a talk at one of our sessions. Since we are leaving the logistical organization of this conference to the ICDD Conference Staff, we can offer the same reduced registration fee that is provided to the Denver X-ray Conference invited speakers. The plans for the conference include a symposium in honor of Ed Stern on Tuesday, August 3, a poster session and a series of oral sessions running concurrently with the Denver X-ray Conference sessions. We hope that you can accept this invitation, and look forward to seeing you in Denver. Sincerely yours, Carlo Segre, for The Organizing committee. -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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EXAFS related querry
by Jatinkumar Rana 15 Apr '10

15 Apr '10

Dear Bruce, I am trying to fit EXAFS data for Arrojadite (a naturally occuring phosphate mineral) measured on Fe-edge. When i load crystallogrphic file in to FEFF, i get Degeneracy (N) for all path as 1 or 2. I know from the crystal structure of Arrojadite that it is not true. Kindly help me in solving this problem. Best regards, Jatin

2 1

EXAFS related querry
by Jatinkumar Rana 15 Apr '10

15 Apr '10

Dear Bruce, I am trying to fit EXAFS data for Arrojadite (a naturally occuring phosphate mineral) measured on Fe-edge. When i load crystallogrphic file in to FEFF, i get Degeneracy (N) for all path as 1 or 2. I know from the crystal structure of Arrojadite that it is not true. Kindly help me in solving this problem. Best regards, Jatin

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Re: [Ifeffit] Emission spectra of Cobalt (Timna-Josua Kuehn)
by Timna-Josua Kuehn 14 Apr '10

14 Apr '10

Hi Joshua, thanks for this explanation of the XES command. I was not aware of it. However, I can not find the data file of the XES simulation yet, although no error is reportet! There is some file called "xsect.dat", where something about "em" is written, but there are no XES spectra in it. Does one have to process this file's data or even some more files? Regards Timna-Josua Kuehn > Date: Mon, 12 Apr 2010 11:19:17 -0700 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > > Hi Timna, > The energy arguments for the XES in FEFF84 are energies of the valence > electron relative to vacuum, so emin should be a negative number. > Try > XES -20 0 0.3 > This should capture at least some of the XES. You can play with emin to get > the range right. Note that the number of energy points in FEFF84 is fixed, > and if you specify a small energy step (the third parameter) you will not > achieve the full range that you specify. > Cheers, > Josh Kas > > > > Date: Mon, 12 Apr 2010 12:47:11 +0200 > > From: "Timna-Josua Kuehn" <timjoku(a)uni-bonn.de> > > > > Dear all, > > > > I am trying to simulate Cobalt Kbeta emission spectra. Actually I just > > exchanged the XANES card with XES, as is explained and set emin = 7700 eV > > and > > emax = 7800 eV with estep = 100 to calculate the whole Co Kbeta line at > > 7649.43 eV. > > But I do not find a file that contains the emission data. I am thankful > > for each helpful advice. > > > > Best regards > > > > Timna > > > > > > > > Timna-Josua Kuehn (PhD student) > > Synchrotron Radiation Group > > Institute of Physics > > University of Bonn > > Germany

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Emission spectra of Cobalt
by Timna-Josua Kuehn 12 Apr '10

12 Apr '10

Dear all, I am trying to simulate Cobalt Kbeta emission spectra. Actually I just exchanged the XANES card with XES, as is explained and set emin = 7700 eV and emax = 7800 eV with estep = 100 to calculate the whole Co Kbeta line at 7649.43 eV. But I do not find a file that contains the emission data. I thankful for each helpful advice. Best regards Timna Timna-Josua Kuehn (PhD student) Synchrotron Radiation Group Institute of Physics University of Bonn Germany

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Cr(III) adsorbed to or coprecipitated with iron oxides
by Luxton.Todd＠epamail.epa.gov 08 Apr '10

08 Apr '10

I am trying to track down spectra of Cr(III) adsorbed to or coprecipitated with iron oxides. Any data would be great. Thanks Todd Luxton PhD. Post Doctoral Research Soil Scientist U.S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Ave. Cincinnati, OH 45224-7879 Luxton.Todd(a)epa.gov Office: (513) 569-7210 Fax: (513) 569-7879

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raw xmu data of fe foil
by Neetu parsai 07 Apr '10

07 Apr '10

Hi, Can anyone give me raw xmu data of fe foil at room temperature that I need for some data analysis. Thanks Mrs.Neetu Parsai Head Department of Engg.Physics Sanghvi Innovative Academy Indore. Residence: 130 Hemu colony, New G.D.C.Road, Indore-452015(M.P.) India.

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No background subtraction in some cases?
by Alexander Riskin 02 Apr '10

02 Apr '10

Dear all, Recently we've measured samples at the DUBBLE Beamline at ESRF for iron and molybdenum (K-edge). After measuring, the DUBBLE software generates a .dat file which must then be translated to other files (depending on the fact whether transmission or fluorescence is measured) using some script in linux. When we try to import some of these transformed files (for transmission measured) into Athena however, the program fails to subtract a background from mu(E), therefore no k and R-space plots are available (see project files MoPEL002 and MoPEL004, the original dat.sample files are included in the zip files). Other files however, work fine (both transmission and fluorescence measured ones). After analyzing the structure of the .dat files, it was discovered which columns are the Io an It data and the correct ln(Io/It) could be manually generated. This manual procedure yields data sets identical to the ones in the dat.sample files, we named them dat.good files. When importing these files into Athena, the background subtraction works fine. It is the exact same data however... Although the problem can be bypassed by processing the data manually, the fact that Athena processes some files correctly and others not seems very strange to us since they all come from the same beamline. We thought it would be interesting to let you all know. Thanks for your time and for making such wonderful software, Alexander Riskin -- Alexander Riskin Universiteit Hasselt IMO - Inorganic and Physical Chemistry Agoralaan – Building D BE-3590 Diepenbeek / Belgium tel. +32.(0)11.26.83.94 fax. +32.(0)11.26.83.23 email: alexander.riskin(a)uhasselt.be

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Fwd: about athena
by Bruce Ravel 30 Mar '10

30 Mar '10

Hi all, Could one of you Mac folks advise Delphine on this issue? B ---------- Forwarded Message ---------- Subject: about athena Date: Tuesday 30 March 2010 From: Delphine Cabaret <delphine.cabaret(a)impmc.jussieu.fr> To: bravel(a)bnl.gov Dear Bruce, How do you do since Camerino ? I would like to install Athena on my Macintosh (MacOS X.6.1). Unfortunately the installation fails from the files copids from the sourceforge. Do you have a version of the program that runs on MaxOS 10.6 ? Thanks for your answer. Best regards delphine -- Delphine Cabaret Maitre de Conferences Université Pierre et Marie Curie (Paris 6) ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ------------------------------------------------------- -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Measurements Group, Beamlines X23A2, X24A, U7A Building 535A, Room M7 Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Call for Papers - 1st North American Core Shell Spectroscopy Conference
by Carlo Segre 29 Mar '10

29 Mar '10

Call for Papers 1st North American Core Shell Spectroscopy Conference to be held jointly with the 59th Denver X-ray Conference 2-6 August 2010 Denver Marriott Tech Center Hotel, Denver, Colorado, U.S.A. The first North American Core Shell Spectroscopy Conference will be held jointly with the 59th Denver X-Ray Conference, 2-6 August 2010. The conference will feature poster sessions as well as oral presentations and students are particularly encouraged to participate with oral presentation submissions. All topics relating to core shell spectroscopy are welcome, including * X-ray Absorption Spectroscopy * X-ray Fluorescence Spectroscopy / Fluorescence Mapping * Resonant Inelastic X-ray Scattering / X-ray Raman Scattering * X-ray Magnetic Circular Dichroism The conference will feature a special session and dinner in honor of Ed Stern. The list of invited speakers for this special session will be posted on the Denver X-ray Conference web site as it is finalized. Participants will be able to attend Denver X-Ray Conference Sessions being held in adjacent rooms. Details of the oral presentation sessions will be posted on the DXC web site as they are available. http://www.dxcicdd.com/default.htm Students will be able to register for a reduced cost, be eligible for special student room rates, and apply for funding to attend the conference. Abstract submissions for oral presentations will be open until April 30 and can be made on the Denver X-Ray Conference web site by selecting the "Submit Abstract for the Joint Meeting with the North American Core Shell Spectroscopy Conference" link on the left side of the page (the 8th button down) or directly at the abstract submission page http://www.dxcicdd.com/cssc/cssc_abstract.asp Visit www.dxcicdd.com<http://www.dxcicdd.com/> or more information or contact: Denise Flaherty, Conference Coordinator ICDD 12 Campus Boulevard Newtown Square, PA 19073 P: 610-325-9814 F: 610-325-9823 E: flaherty(a)icdd.com<mailto:flaherty@icdd.com> WWW.DXCICDD.COM<http://WWW.DXCICDD.COM>

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Re: [Ifeffit] Measuring particle size of metal oxide
by Scott Calvin 28 Mar '10

28 Mar '10

Hi Bill, Sorry for my slow response; I've been swamped. And ironically, the fact that I'm very interested in your topic and wanted to give a good reply slowed me from getting to it! I'm also going to repost your question and my response to the IFEFFIT mailing list, as I think it's of general interest. I think you're missing a key idea concerning this procedure. Both my method and Anatoly Frenkel's method for finding particle size rely on comparing the effective coordination for different paths. I am skeptical of EXAFS determinations of particle size using only one path, as coordination number is hard to tease out from other effects that suppress amplitude (sample quality, disorder, vacancies...). But the relative coordination number of different shells is more reliable. So you should be using more than one path, each with its own r (the absorber-scatterer distance), in order to refine a single value for R, the crystallite radius. If you're using Artemis, this is simple enough to do, as each path has a reff value (which is r in the formula you give), and you can define a guessed parameter R. (To do this right, you need to make sure that the r for multiple-scattering paths is the distance from the absorber to the furthest scatterer, not the half-path length. That means putting the value in "by hand" for those paths, rather than using reff.) (If you want a really quick and dirty method, collect a reference for a bulk standard and for your sample, and multiply the FT of the bulk spectrum by the formula, adjusting R until you get a good match. The quick and dirty method doesn't handle multiple-scattering correctly, and has the usual problem of the fact that even for direct-scattering paths the peaks of the FT are shifted from actual absorber-scatterer distances. But it is model-free, which can be nice in some cases.) By the way, the formula you've cited is derived for spherical particles. If they're kinda sorta spherical, it will still give a decent approximation and fit. But if the particles are needle-shaped or flat plates, then it doesn't work well. You either have to derive another formula, or look at Anatoly's papers, which have addressed a number of common morphologies. So far, everything I've said applies to metals, and you asked about oxides. While most of this also applies to oxides, it's important to realize that the nearest-neighbor oxide paths are not suppressed at all; i.e. the formula doesn't apply until the first metal-metal path (but does apply to metal-oxide paths further out). This is because the surface of such particles is generally comprised of oxygen atoms, and the first scattering shell is thus fully populated no matter how small the particles are. --Scott Calvin Sarah Lawrence College On Mar 8, 2010, at 1:45 PM, bill.schwartz(a)yale.edu wrote: > Hi Scott, > > We met a couple of times at the EXAFS last two EXAFS workshops at > BNL, for relative beginners like me. > > I am attempting to determine the particle size of PdO particles > supported on Alumina (3% PdO/Al2O3). > > I am wondering if I can collect EXAFS data and use the formula in > your 2003 Journal of Applied Physics paper(*) to estimate PdO > particle size: > > N_nano = [1-3/4(r/R)+1/16(r/R)^3]N_bulk > > Here is a little more background: > > PdO particles on metal oxide supports are generally smaller and more > dispersed in comparison to Pd metal on the same support. Also, if > PdO is reduced and then re-oxidized at varying temperatures, the re- > oxidized PdO particle size varies with temperature, with higher > oxidation temperatures resulting in smaller PdO particle size. > > I have prepared a series of samples of 3% PdO/Al2O3, where the PdO > has been been reduced and then re-oxideized at various temperatures, > and I would like to use EXAFS to determine the coordination number > of my various samples. > > A major difference in my planned experiment compared to what you > described in your paper is that you examined nickel metal, while I > am looking at a metal oxide. > > So my current questions are: > > 1) Is the above formula reasonable for determining bulk particle > radius (R) of metal oxides? > > 2) If yes, then what is r, since scattering distance between Pd - > Pd and Pd - O are different? Is it reasonable to average the > distances? > > 3) Can N(nano) be determined by averaging the coordination numbers > for the Pd-Pd and Pd-O paths? > > Any guidance you can provide will be greatly appreciated. > > Sincerely, > > Bill > > (*) Determination of crystallite size in a magnetic nanocomposite > using extended x-ray absorption fine structure > > > > >

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Anharmonic correction (Aaron Slowey)
by grant bunker 26 Mar '10

26 Mar '10

Aaron - There are a couple of things you should watch out for when fitting cumulants. First, you should make sure in the fitting process that the third cumulant C3 doesn't get much more than twice C2^(3/2) (i.e. 2 sigma^3) - values much larger than that are probably unphysical, even if they happen to give you a better fit. Second, the cumulant expansion loses its utility if it doesn't converge quickly enough. It's essentially an expansion in terms of order k*sigma, and if that approaches 1 the higher order cumulants may be large enough that convergence is questionable. If you are lucky and the effective distribution is Gaussian, or most of the variance is due to Gaussian broadening of a skewed distribution, it may converge OK, but that shouldn't be assumed a priori. Grant Bunker http://gbxafs.iit.edu

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Anharmonic correction (Aaron Slowey)
by grant bunker 26 Mar '10

26 Mar '10

When fitting the third cumulant, you should watch out for a couple of things. First, you should make sure in the fitting process that the third cumulant C3 doesn't get much more than twice C2^(3/2) (i.e. 2 sigma^3) - values much larger than that are probably unphysical, even if they happen to give you a better fit. Second, the cumulant expansion loses its utility if it doesn't converge quickly enough. It's essentially an expansion in terms of order k*sigma, and if that approaches 1 the higher order cumulants may be large enough that convergence is questionable. If you are lucky and the effective distribution is Gaussian, or most of the variance is due to Gaussian broadening of a skewed distribution, it may converge OK, but that shouldn't be assumed a priori. Grant Bunker On Mar 26, 2010, at 1:41 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. Anharmonic correction (Aaron Slowey) > 2. Re: Anharmonic correction (Scott Calvin) > 3. Re: Anharmonic correction (Frenkel, Anatoly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 26 Mar 2010 10:13:56 -0700 > From: Aaron Slowey <aslowey(a)usgs.gov> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Anharmonic correction > Message-ID: <9683660E-9ED8-4DBB-8E26-88586073B0F8(a)usgs.gov> > Content-Type: text/plain; charset="us-ascii" > > Dear XAFS community: > > I am fitting Hg L3-edge EXAFS of what I think are mercury sulfide nanoparticles. I fit Fourier filtered 1st shell Hg-to-Sulfur pair correlations for 5 spectra and obtain interatomic distances (r) that are 0.2 angstroms shorter than a cubic HgS(s) (i.e., metacinnabar) and Hg-to-S coordination numbers (N) that range from 2.6 to 3.0 (compared to N = 4 for metacinnabar). Delta_E0 values are less than a few eV, so I think the r's are not 'incorrect' as far as these preliminary fits are based on harmonic atomic vibrations/Gaussian pair-distribution functions. > > What intrigues me most about these data is that the fitted N's are consistent with the average 1st-shell Hg-S coordinations of 1 to 2 nm HgS clusters obtained by isotropically truncating the metacinnabar crystal lattice. In one case, I can also fit first-nearest Hg neighbors in the first shell, and this N is also consistent with a 1 nm HgS cluster. > > My objective is to scrutinize the tentative conclusion that the mercury sulfides in the samples consist of 1 to 2 nm subunits (within a larger aggregate, as determined by DLS). For instance, while the fitted N's are consistent with nanoclusters, the assumption of a metacinnabar lattice to estimate N of nanoclusters is undermined by the shorter interatomic distances fitted to the data. This got me reading the work of Manceau and Combes from the late 1980s and Frenkel et al. (2001) J. Phys. Chem. B. In Frenkel's paper (p. 12691), they describe that they used a "third cumulant" to account for anharmonic corrections, but I'm not sure how exactly this is implemented. > > It is something that you request in a feff.inp file, or is it a path parameter for IFEFFIT to include in its calculations? > > I am using Artemis on Mac OS X 10.6 (thanks to iXAFS 2.1.1 beta!!) to execute FEFF 7 calculations and fit my data. I noticed parameters called "3rd" and "4th" in the path dialog; is "3rd" the same parameter as, for example, the sigma_sub_i_superscript_(3) term in eqn (2) of Frenkel et al. (2001)? > > Thanks for reading this lengthy note... > > Aaron > > Branch of Regional Research, Water Resources > U.S. Geological Survey > Office (650) 329-5474 > Lab (650) 329-4069 > Fax (650) 329-4463 > 345 Middlefield Road, Mail Stop 466 > Menlo Park, California 94025 > http://profile.usgs.gov/aslowey > >

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Anharmonic correction
by Aaron Slowey 26 Mar '10

26 Mar '10

Dear XAFS community: I am fitting Hg L3-edge EXAFS of what I think are mercury sulfide nanoparticles. I fit Fourier filtered 1st shell Hg-to-Sulfur pair correlations for 5 spectra and obtain interatomic distances (r) that are 0.2 angstroms shorter than a cubic HgS(s) (i.e., metacinnabar) and Hg-to-S coordination numbers (N) that range from 2.6 to 3.0 (compared to N = 4 for metacinnabar). Delta_E0 values are less than a few eV, so I think the r's are not 'incorrect' as far as these preliminary fits are based on harmonic atomic vibrations/Gaussian pair-distribution functions. What intrigues me most about these data is that the fitted N's are consistent with the average 1st-shell Hg-S coordinations of 1 to 2 nm HgS clusters obtained by isotropically truncating the metacinnabar crystal lattice. In one case, I can also fit first-nearest Hg neighbors in the first shell, and this N is also consistent with a 1 nm HgS cluster. My objective is to scrutinize the tentative conclusion that the mercury sulfides in the samples consist of 1 to 2 nm subunits (within a larger aggregate, as determined by DLS). For instance, while the fitted N's are consistent with nanoclusters, the assumption of a metacinnabar lattice to estimate N of nanoclusters is undermined by the shorter interatomic distances fitted to the data. This got me reading the work of Manceau and Combes from the late 1980s and Frenkel et al. (2001) J. Phys. Chem. B. In Frenkel's paper (p. 12691), they describe that they used a "third cumulant" to account for anharmonic corrections, but I'm not sure how exactly this is implemented. It is something that you request in a feff.inp file, or is it a path parameter for IFEFFIT to include in its calculations? I am using Artemis on Mac OS X 10.6 (thanks to iXAFS 2.1.1 beta!!) to execute FEFF 7 calculations and fit my data. I noticed parameters called "3rd" and "4th" in the path dialog; is "3rd" the same parameter as, for example, the sigma_sub_i_superscript_(3) term in eqn (2) of Frenkel et al. (2001)? Thanks for reading this lengthy note... Aaron Branch of Regional Research, Water Resources U.S. Geological Survey Office (650) 329-5474 Lab (650) 329-4069 Fax (650) 329-4463 345 Middlefield Road, Mail Stop 466 Menlo Park, California 94025 http://profile.usgs.gov/aslowey

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Fwd: A problem Using FEFF8
by Bruce Ravel 25 Mar '10

25 Mar '10

Hi all, I am forwarding this email I received about a problem runninng Feff8. Does anyone have any advice for this fellow? B ---------- Forwarded Message ---------- Subject: A problem Using FEFF8 Date: Tuesday 23 March 2010 From: 裘南 <qiun(a)ihep.ac.cn> To: bravel(a)anl.gov Dear Mr. Bruce, My name is QIU Nan, I am a student from Institute of High Energy Physics, Chinese Academy of Science. I encountered a preblem When I calculated O K edge of cerium oxide(CeO2) using FEFF8. FEFF found bad counts: Occupation number in getorb is 4.000 , then FEFF repeated pteration again and again. The attached files are feff.inp I used and log1.dat that FEFF generated. Would you so kind to help me to finish this calculation? Best Wishes! QIU Nan 2010-03-24 ------------------------------------------------------- -- Bruce Ravel ----------------------------------- bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Measurements Group, Beamlines X23A2, X24A, U7A Building 535A, Room M7 Brookhaven National Laboratory Upton NY, 11973, USA My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] A problem Using FEFF8
by Joshua Kas 25 Mar '10

25 Mar '10

Hi Qui Nan, There are several other parameters to the SCF card that may help. Try the following, * SCF rscf lscf niter ca nmix SCF 8.0 0 30 0.05 0 ca is the convergence factor in the Broyden algorithm. A lower value of ca will stabilize the SCF, but cause slower convergence. nmix is the number of iterations using the mixing algorithm before starting the Broyden algorithm. I have found that this is usually where the bad counts problem occurs, which is why I set it to 0. If this still doesn't work, try other values for the ca and nmix parameters. I have found that changing the ca and nmix parameters will usually (not always) fix the problem. Please email the list again if you continue to have problems. Cheers, Josh Kas > Dear Mr. Bruce, > My name is QIU Nan, I am a student from Institute of High Energy > Physics, Chinese Academy of Science. > I encountered a preblem When I calculated O K edge of cerium oxide(CeO2) > using FEFF8. FEFF found bad counts: Occupation number in getorb is 4.000 > , then FEFF repeated pteration again and again. The attached files are > feff.inp I used and log1.dat that FEFF generated. Would you so kind to help > me to finish this calculation? > Best Wishes! > QIU Nan > 2010-03-24 > > > > > ------------------------------------------------------- > -- > Bruce Ravel ----------------------------------- bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Measurements Group, Beamlines X23A2, X24A, U7A > > Building 535A, Room M7 > Brookhaven National Laboratory > Upton NY, 11973, USA > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ >

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Is Athena NFS safe?
by David Ehle 23 Mar '10

23 Mar '10

Bruce, Is Athena NFS safe? i.e. If you have a user logged in on two different computers using a single NFS mounted home directory, are there any potential problems or conflicts when running Athena on both computers? Thanks! David.

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Logicused in Artemis to do the error minimization
by Pralay K Santra 08 Mar '10

08 Mar '10

Dear All, After the final fitting in Artemis, we get the (i) total error; (ii) the final value of the parameters; (iii) the error in the parameters as well as (iv) the dependencies among the parameters. What is kind of logic used in Artemis to calculate these values? Is it Genetic optimization procedure used in this process? Can anyone help me by giving some references. I was going through the old posts and found two posts. One is this one: http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling and the other one mentioned in the same. I am sorry to ask for some help which is not directly related to the XAFS. Thanks in advance. With regards, Pralay. --- Research Student. Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore 560012 INDIA

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iXAFS for Snow Leopard, aka 2.1 beta 1
by Ken McIvor 02 Mar '10

02 Mar '10

GOOD NEWS, EVERYONE ------------------- iXAFS 2.1 Beta 1 is now available for download: http://mrcat.iit.edu/ixafs/iXAFS%202.1.1%20b1.dmg It is a universal binary supporting Leopard and Snow Leopard. NO TIGER? --------- I don't know how to get one build to run on all three versions of OS X. I'd rather drop Tiger than further delay the beta. I FOUND A BUG ------------- Thanks for helping with the beta! Please email me directly instead of posting to the Ifeffit mailing list. OLD VERSIONS, EWW ----------------- I'm afraid so. The next release will update the bundled copies of Ifeffit and Horae. DIDN'T YOU SAY MARCH 1ST? ------------------------- Yes, I'm sorry for the delay. WHEN'S THE 2.2 RELEASE? ----------------------- Q2 2010. ;-)

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Re: [Ifeffit] kind of solve the problem (can't save files)
by Michael Gaultois 27 Feb '10

27 Feb '10

Good afternoon Jaziel! If it involves security, permissions, protection and all that jazz, try right clicking on the executable (the Athena program) and then selecting "Run as Administrator." See if it works. Sometimes if it involves permissions issue this can be the case. Can you provide any further details about these libraries you speak of? Specific error messages are very helpful in helping diagnose the problem. If it's on a shared computer, the system administrator might have frozen the operating system drive *(i.e.* they don't want people changing anything, so they prevent you from writing things to the C:), which might explain why you can save to external devices. Warm regards, Mike -- Michael Gaultois 165 - 110 Science Place Department of Chemistry University of Saskatchewan Saskatoon, SK S7N 5C9 Canada Tel: (306) 966-8422 Fax: (306) 966-4730 "La patience est amère, mais son fruit est doux." Phaedrus "We are like butterflies who flutter for a day and think it's forever." Carl Sagan > Message: 1 > Date: Fri, 26 Feb 2010 17:32:06 -0700 > From: Jaziel Soto <jaziel7somu(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] kind of solve the porblem... > Message-ID: > <d733687f1002261632n27063659o4daf76f61e9e682d(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi everyone (again), I kind of solve the problem. I can't save in C: but it > lets me save in external devices. I got some help and this person said the > problem might be something about security of vista and 7, something about > libraries (I don't know that much) the program uses that security doesn't > let me save on C: If someone has had a seemed problem have an idea of how > to > solve please comment... >

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kind of solve the porblem...
by Jaziel Soto 27 Feb '10

27 Feb '10

Hi everyone (again), I kind of solve the problem. I can't save in C: but it lets me save in external devices. I got some help and this person said the problem might be something about security of vista and 7, something about libraries (I don't know that much) the program uses that security doesn't let me save on C: If someone has had a seemed problem have an idea of how to solve please comment...

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Help, can't save anything on athena
by Jaziel Soto 25 Feb '10

25 Feb '10

Hi everyone, i'm using athena 0.8.061 and iffefit 1.2.11c installed on 32 bits widows 7. In a laptop toshiba (if it helps). My problem is that i can't save anything i work. I've tried everything that comes to my mind and i still cant save. I just hear a noise (advice) and nothing happens. I had vista, and i thought installing windows 7 might solve the problem but it didn't, so i'm asking for help now.

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Atomic concentration
by Bruce Ravel 25 Feb '10

25 Feb '10

> Dear Bruce, > I have a question about ATOMS application. I would like to get input file > of stoichiometric SrBi2Ta2O9 (SBT) and off-stoichiometric > Sr0.8Bi2.2Ta2O9(offstoich-SBT) with space group of A2 > 1am. How can I get the right crystal coordinations by changing the atomic > concentrations; i.e. decreasing Sr to Sr0.8 and increasing Bi2 to Bi2.2 in > off-stoichiometric Sr0.8Bi2.2Ta2O9 ? > Best Regards > > -- > O. Murat OZKENDIR I have forwarded this to the Ifeffit mailing list, which is the right place for questions like this. Here's some info about the mailing list as well as some hints on how to get more information about XAFS: http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest You question seems a little unclear and open-ended. Question 15 at http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling might help. Perhaps someone else on the list has some advice for you. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] ifeffit OS X 10.6
by Matt Newville 24 Feb '10

24 Feb '10

Hi Thorsten, Thorsten Bartels-Rausch <thorsten.bartels-rausch(a)psi.ch> wrote: > Hi Matt > > thanks for the ifeffit software package that we also use here at the Swiss Light Source (PSI SLS). May > I kindly ask, if you have a binary version of the package that runs under Os X 10.6 Snow Leopard (64 bit)? > Or should I follow the instruction to compile the package from source? Would you know if that works on > Snow Leopard. > > Thanks for any help. Seems as if I upgraded too fast. > best, thorsten Sorry, I don't know much about the status of binary packages for OS X other that what's listed on the download page. I wouldn't be surprised if Jeff Terry or Paul Fons had made a 64-bit version, but I don't know for sure. I'm sending this to the mailing list in case they or someone else knows more. Building from source on a Mac is not too painful if you have experience building software on Unix systems. --Matt

3 3

standard values
by Neetu parsai 21 Feb '10

21 Feb '10

Hi all, I am searching for the values of mean free path and Debye waller factor of transition metals. Is there any citation available on these values? I want to understand how these are calculated. Mrs.Neetu Parsai Head Department of Engg.Physics Sanghvi Innovative Academy Indore. Residence: 130 Hemu colony, New G.D.C.Road, Indore-452015(M.P.) India.

2 1

[OT] Ifeffit mailing-list available also on Gmane
by Mauro Rovezzi 20 Feb '10

20 Feb '10

Dear all, A short off-topic message to inform you that I have subscribed (in accord with Matt) the Ifeffit mailing-list to the http://gmane.org archive. This will permit to follow this (traffic-growing) discussion forum also via a newsreader or RSS feeds. Below a copy of the subscription. MR Begin forwarded message: Newsgroups: gmane.discuss.subscribe Subject: Re: subscribe ifeffit(a)millenia.cars.aps.anl.gov The following message is a courtesy copy of an article that has been posted to gmane.discuss.subscribe as well. * mauro.rovezzi (at) esrf.eu [2010-02-06 16:21]: > #gmane.science.physics.ifeffit ifeffit(a)millenia.cars.aps.anl.gov > Discussion of Ifeffit, Athena, Artemis, and SixPack, as well as > related X-ray Absorption Fine Structure (XAFS) analysis programs. > mailman dummy encode=encrypt > spam=ignore > lang=eng > url=http://cars9.uchicago.edu/ifeffit/ Subscription messages for the requested mailing lists have been sent. The resulting groups will be created when the first message arrives from the mailing lists. Wolfgang -- Gmane -- Mail To News And Back Again: http://gmane.org

2 1

How to evaluate the fitted result by LCF?
by 康明亮 18 Feb '10

18 Feb '10

Dear, I want to consult how to evaluate the fitted result by LCF. R-factor within what range is reasonable and allowable? Attached are the fitted results, athena-SSRF.prj extention and .gif picture.Why there is still a large deviation for sample K (excluded FeSeO3 from this sample)? Thanks a lot! Best wishes Mingliang

1 0

Athena Freezing Desktop
by David Ehle 17 Feb '10

17 Feb '10

Bruce, Sorry for the accusatory subject line - I can't prove Athena is the culprit but I figured that others with the same problem would be searching for similar terms. Running Athena from the current debian package for Lenny (2:1.2.11d-1) we have been seeing desktop freezes after some hard to characterize period of use. The time period seems to usually be a few hours, and there is a belief that it is connected to having more than a few raw data files open in Athena. Users have previously seen Athena crash/freeze when they have "too many" files open, or Athena open for "too long" but I haven't been able to get any firm numbers. The concern is that while previously when Athena crashed or froze, only Athena was effected. Now it seems that the whole desktop becomes non-responsive. The reason I'm suggesting there is a link between Athena and the Desktop (XFCE4) problem is that if you connect to the system via SSH and kill Athena, the Desktop becomes unfrozen and the user can continue with what they are doing. We have seen this occur on both beamlines, with different users and different data sets so I doubt it is data specific, but can send your some sample files if that will be useful. In one case I was able to collect an error message from the .xsession-errors file of a user who was experiencing the problem: ** (xfwm4:21854): WARNING **: Unmanaged net_wm_state (window 0x3800008) X Error: BadWindow (invalid Window parameter) 3 Major opcode: 7 Minor opcode: 0 Resource id: 0x329 kbuildsycoca running... Reusing existing ksycoca kbuildsycoca running... Reusing existing ksycoca kbuildsycoca running... Reusing existing ksycoca Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 3891. Use of uninitialized value in concatenation (.) or string at /usr/bin/athena line 4700. I'm afraid I don't know if the lines before the lines that explicitly mention athena are related, or if these messages have anything to do with the desktop freezing problem - I think I have the seen the freeze without the errors. Please advise if we can provide you with other information to make figuring out easier. When this problem occurs at 3AM it really upsets our users (which tends to upset the staff when they get called about it...) so we have started running a second system just for Athena. Can you make any suggestions on the minimum vs optimal hardware for Athena? For tracking many (30+) raw data files to see how a run is progressing, can you suggest minimum RAM, CPU power, # of Cores? Thanks!! Please CC ehle(a)iit.edu with any responses as I'm not an active subscriber to this list. David Ehle MRCAT -IIT

4 9

Is possible to shift the spectra in athena?
by 康明亮 16 Feb '10

16 Feb '10

Dear, I want to consult if is possible to shift a spectra in athena? As shown in the attached file athena.prj, I want to include red-(Se) to do LCF. But I forgot to measure the red-Se(0) spectra, only grey-Se(0) was measured. However, according to the literature, these two references have the same energy position only with different amplitude at the white line peak. Since the white line peak would shift if the same sample was measured at different facility, thus I need to do horizontal translate the spectra of red-Se(0) which measured at another facility. is it possible to do this in athena? Thanks! Best regards Mingliang

2 1

Bruce ayuda, problemas con athena
by Jaziel Soto 14 Feb '10

14 Feb '10

Me encuentro usando el athena 0.8.061 y el ifeffit 1.2.11c instalado en windows vista de 32 bits. Tengo puesta la compatibilidad de windows xp service pack 2, ejecutándolo con privilegios de administrador y después de haber trabajado algo, cuando quiero grabar los .prj no pasa nada. Entonces lo que trabajo no tiene sentido por que no lo puedo guardar.

7 9

Lanthanides convergence
by Eugenio Otal 09 Feb '10

09 Feb '10

Hi, I am performing some simulations for Er2O3 and found that the best agreement with experimental data are found when I use UNFREEZEF card. With this card I find some coditions I cannot acchieve convergence, I atach the inp and output files. At the end of the output fila I find: Electronic configuration iph il N_el 0 0 1.601 0 1 1.494 0 2 10.380 Found bad counts. Occupation number in getorb is 1.000 Will repeat this iteration 0 3 0.656 1 0 0.371 1 1 6.451 1 2 1.822 1 3 9.026 2 0 1.985 2 1 5.571 2 2 0.000 2 3 0.000 Core-valence separation WARNING: fatal error in subroutine corval. Try to reduce ca1 in SCF card. If does not help, SEND bug report to AUTHORS CORVAL-1 I tried to change the ca en SCF card and no good results. Thanks in advance, euG

1 0

Iffeit oin snow leopard
by Jose Mustre 05 Feb '10

05 Feb '10

Hi Jeff, I would like to try the beta version of iXAFS for Snow Leopard. We have here in Cinvestav-Merida sevral MAC Pros's with Snow Leoprad, and we have been relying on iFeffit for our ddata analaysis. So I would appreciate very much to have this version. Thanks very much, Jose Jose Mustre Departamento de Fisica Aplicada Cinvesatv-Merida 999 942-9435 mustre(a)mda.cinvestav.mx

1 0

consultation
by 康明亮 04 Feb '10

04 Feb '10

Dear, I want to to ask a question about using Linear Combination Fitting in Athena. I normalized all the references(measured in transmission mode) and samples (fuorescence mode) with Athena, and then wish to use LCF to quantify each unique component in the samples. But I noted that the normalized samples spectra had lower height at the white line peak than any references(shown pic-1.emf in annex), thus the fitted spectra were also higher than the original sample spectra (shown pic-2 and -3.emf in annex). I do not know why? I also attached all the original data(before normalization). Wish to obtain guidance from you. Thanks! Best wishes Mingliang

5 7

about energy error in XANES
by mzhu＠udel.edu 30 Jan '10

30 Jan '10

Dear All, My XANES data were collected with Si(111) monochromator with a step size of 0.5 ev. I want to determine the energy position of the white line (the maximum absorbance) after internal energy calibration. I am wondering how to determine its error. Is it -0.5 ~ +0.5 ev, due to the step size(0.5ev) for data collection? Does it depend on the monochromator? Thanks. Best wishes, Mengqiang ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html

1 0

ATHENA on Ubuntu
by Andi Idhil 27 Jan '10

27 Jan '10

Dear All, I ve installed ifeffit on my ubuntu desktop. I try to load it and apparently faster than in my windows desktop. The problem is, when i have selected the EXAFS data file in athena data column, i could not find the OK button in the lower left part of the window so i could not continue to work. Does anybody have solution for this ? Thank you very much Andi Villigen

2 2

consultation
by 康明亮 27 Jan '10

27 Jan '10

Dear Bruce, I want to sonsult a question about using Linear Combination fitting. I normalized all the standards (measured in transmission mode) and samples (fuorescence mode) with Athena, and then wish to use LCF to quantify each unique component in the samples. But I noted that the normalized samples spectra are lower than any references, thus the fit results are also high than the original spectra. I do not know why? Wish to obtain guidance from you. Thanks! In addition, I wish to use Artemis to do some fitting for XAFS data(processed by Athena firstly). It is my first time to perform such work, is there an helpful manual avaible online for freshman? Thanks! Best wishes Mingliang

2 1

Re: [Ifeffit] iXAFS for OS X 10.6
by フォンスポール 27 Jan '10

27 Jan '10

Hi Jeff, (A somewhat belated) happy new year. I was at the APS recently and it so happened that Bruce was using sector 20 right before me. I was curious about the version of ixafs for snow leopard and if there was any way that I might be of some help to you (Bruce mentioned your surgery). I also noticed your note (just now) on the ifeffit list about wanting to run a beta. I would be glad to help out in this regard (I have been postponing the upgrade to snow leopard up to this point as ixafs is a must have for me. Thanks for your efforts. Sincerely, Paul

2 1

Re: [Ifeffit] SIXPack How to plot the data
by Abhijeet Gaur 27 Jan '10

27 Jan '10

"Vijay, I have used SixPack sometimes. The programming is a little less forgiving than Athena and Artemis for inputting of data. What I would try if I were you is first importing your data into Athena. I've only used this program for PCA and LCF so I don't know if this will work for the other types of analysis but this is what I do to get my data working. 1) Import the data into Athena (which requires that you specify your mu0, muE) 2) Click on the checkbox for the individual file that you want to make "ready" for SixPack 3) Go to file -> saved marked group to file as -> mu(E) .. (( if you want to export it as normalized that is fine but make sure you do your background subtraction, I still save it as a .mu in that case anyhow but I just choose norm(E) instead of mu(E) )) 4) Then Athena prompts you with "marked".. What you need to do is to save it as a .mu file ((or .chi if you're doing EXAFS analysis, but I have not done that so you're going to have to figure out how to do that if that's what you're needing it for)).. So an example file name is one.mu.. (don't put numbers in your file name, the compiler doesn't like it, i.e. cu2ostd.mu is a bad file name) 5) I prefer to remove the header files from the .mu file itself (the stuff with the '#' symbol), I forget if this upsets the SixPack program. Please see below for what type of file output that I have been able to use. Then in the end you should have two columns, instead of the three that you had in your mail that you sent to the list. If you want me to send you an example file, just e-mail me. Example output of a file that I exported from Athena to imported into SixPack: 7068.0174 -0.18245200 7068.9274 -0.18305700 7070.0074 -0.18422800 7070.9874 -0.18216700 7071.9974 -0.18503600 7072.8774 -0.18276100 7074.0574 -0.18661000 7075.1174 -0.18699300 7076.0174 -0.18723800 7076.9074 -0.18667400 7077.9074 -0.18584000 7079.0474 -0.19024300 I hope this helps! Andrew Campos" Hi all, Thanks a lot Andrews, the procedure you describes definitely works in all the cases of SIXPack except in case of SAMView. I had asked the same question to Sam webb sir and I am lucky that I got a response from him too. The response is: "Hi Abhijeet - The file attached got added as text to the message, so I copied it and pasted it into a notepad document. Make sure there is not a blank line at the end of the data. I've attached my file. When you load, it'll come up with the generic reader. Choose column 1 as E, column 2 as I0 and column 3 as I1. Make sure that you have "1" line selected as the offset (to ignore the header). It should read correctly and then make sure you plot MuT, not MuF. Worked simply for me. Also make sure you are doing this in the viewer and not in another module. The SamView module imports all data, and writes a 2 column ascii. The other use a plain, 2 column ascii format. Hope that helps. Sam" The file sent by Sam webb sir is attached. Thus, now I am able to understand how to plot the data in SAMView as well as other analysis sections. Thanks to mailing list members. with regards Abhijeet Gaur

1 0

How to calculate F-value for XANES PCA results
by Andrew 27 Jan '10

27 Jan '10

Hi everyone, I was looking through the literature on how to handle PC analysis data and saw that there are several different methods you can use for determining how many components there are in the series of scans. Included in SixPack are the indicator function, scree test, and the ability to quickly do the reduced eigenvalue ratios. I've been digging through the literature as to how to calculate the F-values. The closest to an answer that I got was: "The above-mentioned reduction of the body of experimental data, that is, the decision of what components correspond to the noise and what are the principal components, is now made on the basis of an F test of the variance associated with eigenvalue k and the summed variance associated with noise eigenvalues (k+1, ..., c). The null hypothesis is that a given factor k is a member of the pool of noise factors. The probability that an F value would be higher than the current value is given by %SL (percentage of significance level). Thus, the kth factor is accepted as a principal component if %SL is lower than some test level." (Garcia 1995). We ran the PCA on the reduction of iron while scanning at increased temperatures. I checked the foil standard but did not see any shift in the max at 7112, we scanned at 0.5 eV intervals (2 eV resolution at the beam). I thought I understood what that statement was saying but I'm almost certain I'm doing something wrong. I have attached the .xlsx file that I was working on and hope someone can point me to the right direction. The file includes the components of the PCA and some of the variances that I was calculating. If there is a paper that someone shows an actual calculation of this in the supplemental materials that would have been exactly what I was looking for! Thanks for the help! Andrew Campos Fernandez-Garcia, M., C. Marquez Alvarez, and G.L. Haller, The Journal of Physical Chemistry, 1995, 99(33), 12565-12569.

4 3

Re: [Ifeffit] SIXPack : How to plot data file
by Andrew 25 Jan '10

25 Jan '10

Vijay, I have used SixPack sometimes. The programming is a little less forgiving than Athena and Artemis for inputting of data. What I would try if I were you is first importing your data into Athena. I've only used this program for PCA and LCF so I don't know if this will work for the other types of analysis but this is what I do to get my data working. 1) Import the data into Athena (which requires that you specify your mu0, muE) 2) Click on the checkbox for the individual file that you want to make "ready" for SixPack 3) Go to file -> saved marked group to file as -> mu(E) .. (( if you want to export it as normalized that is fine but make sure you do your background subtraction, I still save it as a .mu in that case anyhow but I just choose norm(E) instead of mu(E) )) 4) Then Athena prompts you with "marked".. What you need to do is to save it as a .mu file ((or .chi if you're doing EXAFS analysis, but I have not done that so you're going to have to figure out how to do that if that's what you're needing it for)).. So an example file name is one.mu.. (don't put numbers in your file name, the compiler doesn't like it, i.e. cu2ostd.mu is a bad file name) 5) I prefer to remove the header files from the .mu file itself (the stuff with the '#' symbol), I forget if this upsets the SixPack program. Please see below for what type of file output that I have been able to use. Then in the end you should have two columns, instead of the three that you had in your mail that you sent to the list. If you want me to send you an example file, just e-mail me. Example output of a file that I exported from Athena to imported into SixPack: 7068.0174 -0.18245200 7068.9274 -0.18305700 7070.0074 -0.18422800 7070.9874 -0.18216700 7071.9974 -0.18503600 7072.8774 -0.18276100 7074.0574 -0.18661000 7075.1174 -0.18699300 7076.0174 -0.18723800 7076.9074 -0.18667400 7077.9074 -0.18584000 7079.0474 -0.19024300 I hope this helps! Andrew Campos

1 0

Re: [Ifeffit] SIXPack : How to plot data file
by Abhijeet Gaur 25 Jan '10

25 Jan '10

Hi all, As I already said I am not able to find any column of mu(E) in the column assingment, so I am not able to plot it. But, when I opened the E, I0, It format file the SIXPack is giving the following error Error: 1 IndexError Exception in Tk callback Function: <method generic.pressedabutton of generic instance at 01054EE4> (type: <type 'instance method'>) Args: (<Tkinter.Event instance at 010B23FC>,) Event type: ButtonPress (type num: 4) Traceback (innermost last): File "Pmw.pyc", line 1772, in __call__ None File "xasinput.pyc", line 1413, in pressedabutton None File "xasinput.pyc", line 1432, in readgenericdata None IndexError: string index out of range ================================================ Event contents: char: ?? delta: 1 height: 0 keycode: 1 keysym: ?? keysym_num: 1 num: 1 send_event: 0 serial: 9011 state: 0 time: 3310421 type: 4 widget: .20405404.16206244.16205940.12263724.16545596.17214596.17274484.17277060.17279988 width: 0 x: 23 x_root: 176 y: 13 y_root: 404 Error: 2 TypeError Exception in Tk callback Function: <method Main.loaddatafile of Main instance at 00D5ACCC> (type: <type 'instance method'>) Args: () Traceback (innermost last): File "Pmw.pyc", line 1772, in __call__ None File "spsamview.pyc", line 366, in loaddatafile None File "spsamview.pyc", line 423, in selectfile None File "spsamview.pyc", line 511, in rescaleplot None File "spsamview.pyc", line 567, in makeplot None TypeError: unsupported operand type(s) for / I am not able to understand these errors. I am attaching the data file ( Cu foil data) that I am trying to open in SIXPack. With thanks Vijay Hinge

1 0

Request for ZrB2 structure file
by ashfaq ahmad 25 Jan '10

25 Jan '10

Dear Can any one send me structure/Atom file of ZrB2 compound. Mine is not working properly. Ashfaq _________________________________________________________________ Windows Live Hotmail: Your friends can get your Facebook updates, right from Hotmail®. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

1 0

Re: [Ifeffit] SIXPack : How to load data file
by Carlo Segre 24 Jan '10

24 Jan '10

Please take a look at Matt newville's response on the mailing list. You ned to provide more specifics for us to be able to help. For example, attach the data file you are having problems with and provide all error messages that appear. C.S. On Sun, 24 Jan 2010, Rashmi Shrivastava wrote: > Hello Sir, > Sorry for replying late. > I am running SIXPack on Windows-XP version. I had already opened these data > file in Athena and had done analysis on them. But when I try to open these > data files in SIXPack, column assingment is required. First I tried to open > the E, mu(E) format text file, SIXPack asks for column assingment, but there > is no column for mu(E). Then I tried E, I0, It data format and I checked the > respected column, but still not able to plot the data. Each time it is > giving some error in data plotting like background error, plotting error. > The data is loading but I am not able to plot it. > > With thanks > Vijay Hinge > Research Scholar > Ujjain (India) > On Fri, Jan 22, 2010 at 7:50 PM, Carlo Segre <segre(a)iit.edu> wrote: > >> >> Hi Rashmi: >> >> What platform are you running on? >> >> Carlo >> >> >> On Fri, 22 Jan 2010, Rashmi Shrivastava wrote: >> >> Hi all, >>> I am doing some data analysis of XANES as well as EXAFS data using >>> data analysis software SIXPack. I am not able to load any data file. I >>> used >>> E and mu(E) data format file. Also I try to open E, I0, It data format >>> file >>> but still not able to open or plot any data. I also tried to open the >>> example data given with the programm, but got the same result. I had gone >>> through the SIXPack Documentation, but not able to get how to load a data >>> file. If someone can please guide me, I will be very thankful. >>> >>> with regards >>> Vijay Hinge >>> School of Studies in Physics >>> Vikram University, Ujjain (INDIA) >>> >>> >> -- >> Carlo U. Segre -- Professor of Physics >> Associate Dean for Graduate Admissions, Graduate College >> Illinois Institute of Technology >> Voice: 312.567.3498 Fax: 312.567.3494 >> segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org >> > -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 83, Issue 22
by Abhijeet Gaur 23 Jan '10

23 Jan '10

Dear Rashmi, Vijay, Abhijeet, ...., Can you please ask this question more precisely? Asking for "guidance" is a bit too vague to expect a helpful answer. > I am doing some data analysis of XANES as well as EXAFS data using > data analysis software SIXPack. I am not able to load any data file. This is confusing. How would you be able to use SIXPack if you are not able to load any data file? Is the program not responding at all? Does it crash when trying to load particular files?? I have no idea. Again, please ask a specific question (for example: why can I not open the attached data file with SIXPack?), and give as much relevant information as you can: what operating system are you using, what you did (File->Open: did a dialog box open??), what SIXPack "does" (any error messages, for example), Can Athena open the file, and so on. We're not there to see what you are (and are not) doing. Please remember that you are sending this request for help to hundreds of people hoping that one of them will be kind enough to volunteer to answer. Being polite is wise, but being clear and to the point is also important. Cheers, --Matt Hello Sir, Thanks for your suggestions. Actually sometimes we are not able to frame the question correctly, which is also one of the reason of not getting a response. To be specific, I had already opened these data file in Athena and had done analysis on them. But when I try to open these data files in SIXPack, column assingment is required. First I tried to open the E, mu(E) format text file, SIXPack asks for column assingment, but there is no column for mu(E). Then I tried E, I0, It data format and I checked the respected column, but still not able to plot the data. Each time it is giving some error in data plotting like background error, plotting error. The data is loading but I am not able to plot it. I think now I had made myself clear for getting some response. With thanks Vijay Hinge

2 1

Re: [Ifeffit] Fiiting Result
by Abhijeet Gaur 23 Jan '10

23 Jan '10

Hi Abhijeet, Sorry, I guess Cu2O is coordinated by 2 oxygen atoms and 12 cu atoms. If the cluster of atoms that you give to FEFF doesn't match the structure of the sample then the fit will not work. But I think that your structure isn't obviously wrong. Cheers, Shelly Hi Madam Thanks for youe response. Actually, I had tried the fitting by taking the data of Cu2O from the database, but still there are same problem like low SO2, negative SS2, high energy shift delE. If you can please suggest me a paper in which the fitting results of Cu2O and CuO are published, I can compare my results with the published results. I just want to make it clear that where I am going wrong. Also, I am sorry to all members of mailing list for asking the same problem again and again. With thanks Abhijeet Gaur

1 0

Re: [Ifeffit] Problem opening up project files
by Lisa Van Loon 22 Jan '10

22 Jan '10

Hi Bruce, Thanks for looking into this and determining what the problem was. Now that I know the cause, I can avoid the "unpleasantness" associated with not being able to reopen a project in the future. My officemate thanks you :) Lisa

1 0

SIXPack : How to load data file
by Rashmi Shrivastava 22 Jan '10

22 Jan '10

Hi all, I am doing some data analysis of XANES as well as EXAFS data using data analysis software SIXPack. I am not able to load any data file. I used E and mu(E) data format file. Also I try to open E, I0, It data format file but still not able to open or plot any data. I also tried to open the example data given with the programm, but got the same result. I had gone through the SIXPack Documentation, but not able to get how to load a data file. If someone can please guide me, I will be very thankful. with regards Vijay Hinge School of Studies in Physics Vikram University, Ujjain (INDIA)

2 1

Fwd: ZrB2 structure file
by Bruce Ravel 22 Jan '10

22 Jan '10

Please note that the address for this mailing list is ifeffit(a)millenia.cars.aps.anl.gov The ifeffit-owner address should not be used for normal traffic. Mail sent to that address does NOT get posted to the mailing list. Please make sure that your address book contains the correct information. That said, hopefully someone can help Ashfaq with his problem. B ---------- Forwarded Message ---------- Subject: ZrB2 structure file Date: Friday 22 January 2010 From: ashfaq ahmad <ashfaq48(a)hotmail.com> To: ifeffit-owner(a)millenia.cars.aps.anl.gov Dear Can any one send me structure/Atom file of ZrB2 compound. Mine is not working properly. Ashfaq -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

1 0

SIXPack: How to load a data file
by Abhijeet Gaur 22 Jan '10

22 Jan '10

Hi all, I am doing some data analysis of XANES as well as EXAFS data using data analysis software SIXPack. I am not able to load any data file to get the spectra plotted. I used E and mu(E) data format file. Also I try to open E, I0, It data format file but still not able to open or plot any data. I also tried to open the example data given with the programm, but got the same result. I had gone through the SIXPack Documentation, but not able to get how to load a data file. If someone can please guide me, I will be very thankful. with regards Vijay Hinge School of Studies in Physics Vikram University, Ujjain (INDIA)

1 0