- 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