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

schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 07 Oct '10

07 Oct '10

Dear all, It is reasonable to assign a constant fraction by which unit cell expands at a given temperature of XAFS measuremnt and so the variation in the path lengths for every single scattering paths could be assigned as delr = alpha * Reff. Similarly, one can assign sigma2 value for each single scattering path depending on both type of scatterer and its distance from the absorbing atom. Now coming to multiple scattering paths, Sigma2 for multiple scattering paths can be constrained based on the sigma2 of related single scattering paths and a definite path-geometry-dependent scheme (Triangle, collinear, reversed etc.) could be applied. Is there any such scheme for delr of multiple scattering paths ? or we can simply assume that all paths (single scattering and multiple scattering) undergo uniform expansion by a factor alpha. Thank you so much in advance for your valuable time... With best regards, Jatin Rana

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
by Scott Calvin 06 Oct '10

06 Oct '10

On Oct 6, 2010, at 10:41 AM, Han Sen Soo wrote: > Hello Scott, > Just to make sure I understand what you mean, are you saying that in > your 3 atom system, the S1 and S2 atoms have relatively fixed > locations but A may have large vibrational amplitudes in the A-S1 > and A-S2 directions? So the round-trip 3 atom MS path has a small > sigma^2 value since the variation in the A-S1-S2-A path is dictated > by the more or less fixed S1 and S2 end-points (with minimal > perpendicular contribution), whereas the 2 individual SS paths have > large sigma^2 value due to the large A-S vibrations? > Yes--you explained it far better than I did. :) --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
by Han Sen Soo 06 Oct '10

06 Oct '10

Hello Scott, Just to make sure I understand what you mean, are you saying that in your 3 atom system, the S1 and S2 atoms have relatively fixed locations but A may have large vibrational amplitudes in the A-S1 and A-S2 directions? So the round-trip 3 atom MS path has a small sigma^2 value since the variation in the A-S1-S2-A path is dictated by the more or less fixed S1 and S2 end-points (with minimal perpendicular contribution), whereas the 2 individual SS paths have large sigma^2 value due to the large A-S vibrations? I tried setting the sigma^2 value to a reasonable number for the MS path and it appears to increase the R factor slightly and tries to maximize the floating degeneracy I set (with a restrain to be physically reasonable based on my model). It does not look as good but at least it seems more plausible. I will try out Shelly's suggestions to see if they work too. I guess what I wanted to find out is whether the model I included is telling me that something is terribly wrong. Thank you all again for your responses! han sen On Oct 6, 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: sigma^2 values for multiple scattering paths (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 6 Oct 2010 09:39:49 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: "Dr.Scott.Calvin(a)gmail.com" <Dr.Scott.Calvin(a)gmail.com> > Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths > Message-ID: <AB39966C-893D-4947-BED2-A26FC6534315(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > 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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 92, Issue 4 > **************************************

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Re: [Ifeffit] More than 256 paths on Mac OS 10.5?
by Scott Calvin 06 Oct '10

06 Oct '10

Thanks, Matt! --Scott Calvin Sarah Lawrence College On Oct 6, 2010, at 9:08 AM, Matt Newville wrote: > Hi Scott, > > > The attached zip file has dynamic libraries (and static program > ifeffit) built with 1024 paths and feff files. It contains the files > > lib/libifeffit.dylib > lib/libifeffit.so > bin/ifeffit > > The zip file should be unzipped under > /Applications/iXAFS.app/Contents/Resources/local/ > to overwrite the above files. You should be able to open the iXAFS > Shell and type > > cd /Applications/iXAFS.app/Contents/Resources/local/ > unzip ~/Downloads/iXAFS_1024paths.zip > athena > > > Athena and Artemis will automatically use the new dynamic library. >

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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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