October 2010 - 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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