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 (Shelly Kelly/Bruce Ravel); Re: Ifeffit Digest, Vol 92, Issue 2
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-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: 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 + (GMT) From: Elsa Sileo e_si...@yahoo.es To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 92, Issue 1 Message-ID: 532560.26796...@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-requ...@millenia.cars.aps.anl.gov ifeffit-requ...@millenia.cars.aps.anl.gov escribi?: De: ifeffit-requ...@millenia.cars.aps.anl.gov ifeffit-requ...@millenia.cars.aps.anl.gov Asunto: Ifeffit Digest, Vol 92, Issue 1 Para: ifeffit@millenia.cars.aps.anl.gov Fecha: s?bado, 2 de octubre, 2010 14:00 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. 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 + (GMT) From: Elsa Sileo e_si...@yahoo.es To: ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] Incorrect distances obtaines from Scorodite CIF ??? file Message-ID: 957578.81901...@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 ? ? ? ? -- next part -- An HTML attachment was scrubbed... URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101001/09162041/attachment.html -- next part -- A non-text attachment was scrubbed... Name: SCORODIT.CIF Type: application/octet-stream Size: 2671 bytes Desc: not available URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20101001/09162041/attachment-0001.obj -- Message: 2 Date: Fri, 1 Oct 2010 15:39:16 -0500 From: Shelly Kelly dr.sdke...@gmail.com To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Incorrect distances obtaines from Scorodite CIF ??? file Message-ID: ??? aanlktinissmlx8ge6vm4lrdvk9x=n-qsnme4u8k+m...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi Elsa: If you open the scorodit.cif file you will find that the space group is P c a b. When you read the file into Artemis the space group gets scrambled up.? If you fix the space group on the atoms page, it will work. Shelly On Fri, Oct 1, 2010 at 12:06 PM, Elsa Sileo e_si...@yahoo.es wrote: 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 ___ 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
[Ifeffit] sigma^2 values for multiple scattering paths
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] Help with Artemis fit
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 unphysical fit.pdf Description: Adobe PDF document ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
