Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
Hello Shelly and Scott, Thank you both again for your suggestions. It seems that after making the MS path more linear in my cif file, the FEFF calculation increased the amplitude value of the path and dramatically increased the sigma^2 value in the fit. Strangely, the fit values for the distances remain pretty much the same and the statistical figures of merit have improved, but the sigma^2 values are now much more reasonable (about twice as large, but I have a more triangular than linear model, so you're right Scott, your explanation does not work for my case). I guess the increased amplitude made a difference? Hello Abhijeet, I used a rudimentary geometrical way to get my bond angles. For a 3 atom triangle M-O-A, the effective MS path length (R_MOA) is twice the sum of the individual bond distances. So if you have the R_MOA, R_MO, and R_MA distances from your fits, you can use R_MOA - R_MO - R_MA to get the O-A bond length. And with the 3 sides of the triangle, you can use the geometrical Cosine Rule to get any of the 3 bond angles. This is just geometry so I don't know what the error propagation for this would be. Thanks again everyone! han sen On Oct 7, 2010, at 6:36 AM, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: More than 256 paths on Mac OS 10.5? (Scott Calvin) 2. Re: sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Han Sen Soo) 3. Re: sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Scott Calvin) 4. Multiple scattering paths in fitting (Abhijeet Gaur) 5. schemes for delr and sigma2 for multiple scattering paths (Jatinkumar Rana) 6. Re: Multiple scattering paths in fitting (Frenkel, Anatoly) -- Message: 1 Date: Wed, 6 Oct 2010 10:01:27 -0700 From: Scott Calvin dr.scott.cal...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] More than 256 paths on Mac OS 10.5? Message-ID: 6dd333d2-f58c-4e55-ab0d-430483ef9...@gmail.edu Content-Type: text/plain; charset=US-ASCII; format=flowed 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. -- Message: 2 Date: Wed, 6 Oct 2010 10:36:25 -0700 From: Han Sen Soo hs...@lbl.gov To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 Message-ID: bc995ec7-578e-4256-9d62-de5e73831...@lbl.gov Content-Type: text/plain; charset=us-ascii 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-requ...@millenia.cars.aps.anl.gov wrote
Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
Not at all unusual, Han Sen. If you think about the EXAFS equation, you'll see that sigma^2 and amplitude primarily affect the amplitude of the signal, while distances affect the position of the peak in the Fourier transform (or equivalently, the spacing of peaks in chi(k)). So sigma^2 and amplitude can trade off without affecting distance- based aspects of the fit much. That's why I suggested you try forcing the sigma^2 to a reasonable value to see what happened to your fit. Sometimes none of the aspects of the fit you're interested in depend strongly on the sigma^2 of low- amplitude paths--particularly if what you're interest in is distances or information that is in part derived from distances, like phase identification. In those cases, the anomalous sigma^2 can be a yellow flag (think about what might be causing it and decide if it's a problem to your scientific case) rather than a red flag (drop everything and resolve the problem before proceeding). Also, note from the EXAFS equation that sigma^2 is weighted by k^2, and amplitude is not. If fits using different k-weights result in significantly different values of sigma^2, that can be a clue that the issue is actually one of amplitude, as in your case. At any rate, I'm glad you solved your issue in such a satisfying way! --Scott Calvin Sarah Lawrence College On Oct 7, 2010, at 11:22 AM, Han Sen Soo wrote: Hello Shelly and Scott, Thank you both again for your suggestions. It seems that after making the MS path more linear in my cif file, the FEFF calculation increased the amplitude value of the path and dramatically increased the sigma^2 value in the fit. Strangely, the fit values for the distances remain pretty much the same and the statistical figures of merit have improved, but the sigma^2 values are now much more reasonable (about twice as large, but I have a more triangular than linear model, so you're right Scott, your explanation does not work for my case). I guess the increased amplitude made a difference? Hello Abhijeet, I used a rudimentary geometrical way to get my bond angles. For a 3 atom triangle M-O-A, the effective MS path length (R_MOA) is twice the sum of the individual bond distances. So if you have the R_MOA, R_MO, and R_MA distances from your fits, you can use R_MOA - R_MO - R_MA to get the O-A bond length. And with the 3 sides of the triangle, you can use the geometrical Cosine Rule to get any of the 3 bond angles. This is just geometry so I don't know what the error propagation for this would be. Thanks again everyone! han sen ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] sigma^2 values for multiple scattering paths
Hi Han Sen: I agree that the small sigma2 values for the MS paths is suspect. The data is saying that it wants more amplitude from these paths than is physically possible. One way to increase the amplitude of the paths is to make the scattering angle closer to 180deg for a linear path. It is a bit tedious to edit the feffit input file to get that to run, but can be done with a bit of geometry. This will not work for a triangle MS path. In that case I would look for additional contribution from other MS or SS paths at the same distance. Another way to force sigma2 to be larger would be to use a Debye or Einstein Model to model both the SS and MS path. That will make sigma2 for both of them at least reasonable. Although the fit will not be as perfect. HTH, Shelly On Wed, Oct 6, 2010 at 12:26 AM, Han Sen Soo hs...@lbl.gov wrote: 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] sigma^2 values for multiple scattering paths
On Wednesday 06 October 2010 01:26:55 am Han Sen Soo wrote: 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 Han Sen, It is always useful to remember the physical meanings of the parameters use in the EXAFS equation. sigma^2 is a mean square variation in the distance between the absorber and a scatterer. Suppose we have this configuration: X--O--Y that is, absorber X, scatterer Y and a colinear O atom in between. The path length for the path X-Y-X is the same as for X-O-Y-X and for X-O-Y-O-X. If we just consider thermal motion of the atoms along that axis, then the mean square variation in paths lengths for those three paths must also me the same. That's neither deep nor complicated -- its just geometry. The argument in the last paragraph neglected the prospect of the O atom experiencing thermal motion perpendicular to that axis. That effect means that sigma^2(X-O-Y-O-X) sigma^2(X-O-Y-X) sigma^2(X-Y-X) A common approximation made in data analysis is that this perpendiular effect is small compared to the uncertainties in sigma^2 and so those three sigma^2 values are constrained to be the same. In no case can I understand a physical explanation for the the MS sigma^2 being smaller than for the SS. That said, you have a fit and a result. When you float the MS sigma^2 it comes out smaller. I would suggest that is telling you something about the fitting problem rather than something about the physics of the atomic configuration. A smaller sigma^2 means that the contribution from those paths is being enhanced. That might be due to a correlation with an amplitude parameter. It might be due to a data quality problem. It might be due to a mistake in the implementation of your fitting model. This sort of thing happens all the time. I frequently analyze data and come up with a curious, unphysical result like this. It hasn't yet meant that I have discovered some wonderous new physics. Very occassionally, it means that I have uncovered a shortcoming in Feff, but that is exceedingly rare. Usually it means that I have a problem with my data or I have made a mistake filling in all the boxes in Artemis. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] sigma^2 values for multiple scattering paths (Shelly Kelly/Bruce Ravel); Re: Ifeffit Digest, Vol 92, Issue 2
-- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101001/57efe1e3/attachment-0001.htm -- ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 92, Issue 1 ** t -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101005/e01e3861/attachment-0001.htm -- Message: 2 Date: Tue, 5 Oct 2010 22:26:55 -0700 From: Han Sen Soo hs...@lbl.gov To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] sigma^2 values for multiple scattering paths Message-ID: c2181cec-4451-47db-b5d4-1926c3212...@lbl.gov Content-Type: text/plain; charset=us-ascii 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 -- Message: 3 Date: Tue, 5 Oct 2010 17:28:02 -0700 From: Scott Calvin dr.scott.cal...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] More than 256 paths on Mac OS 10.5? Message-ID: e766085e-4695-44cd-a548-9b2b62da7...@gmail.edu Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes 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 -- Message: 4 Date: Wed, 6 Oct 2010 09:02:21 -0500 From: Shelly Kelly dr.sdke...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths Message-ID: aanlktimtgeazknmeydzopnkihh0cax5gitjryxbyc...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Han Sen: I agree that the small sigma2 values for the MS paths is suspect. The data is saying that it wants more amplitude from these paths than is physically possible. One way to increase the amplitude of the paths is to make the scattering angle closer to 180deg for a linear path. It is a bit tedious to edit the feffit input file to get that to run, but can be done with a bit of geometry. This will not work for a triangle MS path. In that case I would look for additional contribution from other MS or SS paths at the same distance. Another way to force sigma2 to be larger would be to use a Debye or Einstein Model to model both the SS and MS path. That will make sigma2 for both of them at least reasonable. Although the fit will not be as perfect. HTH, Shelly On Wed, Oct 6, 2010 at 12:26 AM, Han Sen Soo hs...@lbl.gov wrote: 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Message: 5 Date: Wed, 6 Oct 2010 10:02:24 -0400 From: Bruce Ravel bra...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths Message-ID: 201010061002.24587.bra...@bnl.gov Content-Type: Text/Plain; charset=iso-8859-1 On Wednesday 06 October 2010 01:26:55 am Han Sen Soo wrote: 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
Re: [Ifeffit] sigma^2 values for multiple scattering paths
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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
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-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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.cal...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Cc: dr.scott.cal...@gmail.com dr.scott.cal...@gmail.com Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths Message-ID: ab39966c-893d-4947-bed2-a26fc6534...@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 92, Issue 4 ** ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
