Re: [Ifeffit] large Eo's and neg. D-W factors
Scott, Thanks for the clues! The restraints seem to be working to get the DW factors positive. I'm still battling Ifeffit reversing the paths, but things are getting slowly better. Rich Hi Rich, I know you posted this a while ago, so you may have gotten other answers, but I don't see them in my overflowing inbox. :) Years ago, I did some work with V2O3, and it was a very stubborn system to get a good fit on. Other people I knew who were working on the system have also had some trouble. This and other evidence led to some people publishing speculations on local distortions that get averaged out in XRD but show up in EXAFS. I also recall people talking about similar difficulties with other vanadium oxide systems. (Sorry; I don't have those references handy anymore, but searches should locate them). As far as the second issue you mention, with Ifeffit reversing the position of two atoms of the same species, it does happen some times. Why not? A V-O path is basically a V-O path to FEFF; it doesn't know that one's a single bond and one's a double bond. But since moving a path by more than about 0.1 Angstrom in Ifeffit starts to reduce the accuracy of the FEFF calculation, it's something you do want to try to prevent. One way to do that is with restraints; it shouldn't take much incentive for Ifeffit to refrain from switching the paths. --Scott Calvin Sarah Lawrence College At 05:02 PM 4/18/2007, you wrote: Greetings! I have inherited a vanadium EXAFS data set (due to a group member graduating - lucky dog!) that is giving me major fits. I am getting consistent numbers with all my fits which visually look fantastic, that is until I look at the numbers...one Debye-Waller factor is negative (a V-O path) and the Eo's are large, the V-Cl path is on the order of -20 eV, the V=O path is on the order of 17 eV, and the V-O path falling at -11 eV. ARe there any tricks outside of restraints or constraints that I can attempt to get more realistic values? (I understand that a large Eo can be realistic, but a negative Debye-Waller factor doesn't make sense.) I can restrain the V-O Debye-Waller factor and get a positive value, but then the V=O D-W factor is negative. If I restrain both D-W factors, the fit falls apart, suggesting something else is wrong that I just can't find. Another issue I'm having involves something in Artemis that's confusing me. Sometimes after a fit, the Artemis Pallet shows the V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6 Angstroms, completely reversed to the FEFF model. I have seen this when I separated the chlorides as well (I attempted to model the Cl at different distances as reported by Deguns, et. al. (attached) due to the immediate environment around the V in our sample being similar to the one they report in scheme 1-(I), p5008). Attached is a text file that shows an Artemis Pallet output illustrating what I'm trying to describe for the V=O and V-O paths. The Artemis project that generated the output is also attached. ___ 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] large Eo's and neg. D-W factors
My observation (not rigorously tested though): the longer it takes to get a good fit, the more suspicious are the results! Anatoly -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Richard Mayes Sent: Wednesday, May 02, 2007 8:56 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] large Eo's and neg. D-W factors Scott, Thanks for the clues! The restraints seem to be working to get the DW factors positive. I'm still battling Ifeffit reversing the paths, but things are getting slowly better. Rich Hi Rich, I know you posted this a while ago, so you may have gotten other answers, but I don't see them in my overflowing inbox. :) Years ago, I did some work with V2O3, and it was a very stubborn system to get a good fit on. Other people I knew who were working on the system have also had some trouble. This and other evidence led to some people publishing speculations on local distortions that get averaged out in XRD but show up in EXAFS. I also recall people talking about similar difficulties with other vanadium oxide systems. (Sorry; I don't have those references handy anymore, but searches should locate them). As far as the second issue you mention, with Ifeffit reversing the position of two atoms of the same species, it does happen some times. Why not? A V-O path is basically a V-O path to FEFF; it doesn't know that one's a single bond and one's a double bond. But since moving a path by more than about 0.1 Angstrom in Ifeffit starts to reduce the accuracy of the FEFF calculation, it's something you do want to try to prevent. One way to do that is with restraints; it shouldn't take much incentive for Ifeffit to refrain from switching the paths. --Scott Calvin Sarah Lawrence College At 05:02 PM 4/18/2007, you wrote: Greetings! I have inherited a vanadium EXAFS data set (due to a group member graduating - lucky dog!) that is giving me major fits. I am getting consistent numbers with all my fits which visually look fantastic, that is until I look at the numbers...one Debye-Waller factor is negative (a V-O path) and the Eo's are large, the V-Cl path is on the order of -20 eV, the V=O path is on the order of 17 eV, and the V-O path falling at -11 eV. ARe there any tricks outside of restraints or constraints that I can attempt to get more realistic values? (I understand that a large Eo can be realistic, but a negative Debye-Waller factor doesn't make sense.) I can restrain the V-O Debye-Waller factor and get a positive value, but then the V=O D-W factor is negative. If I restrain both D-W factors, the fit falls apart, suggesting something else is wrong that I just can't find. Another issue I'm having involves something in Artemis that's confusing me. Sometimes after a fit, the Artemis Pallet shows the V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6 Angstroms, completely reversed to the FEFF model. I have seen this when I separated the chlorides as well (I attempted to model the Cl at different distances as reported by Deguns, et. al. (attached) due to the immediate environment around the V in our sample being similar to the one they report in scheme 1-(I), p5008). Attached is a text file that shows an Artemis Pallet output illustrating what I'm trying to describe for the V=O and V-O paths. The Artemis project that generated the output is also attached. ___ 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 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] large Eo's and neg. D-W factors
Hi Rich, I know you posted this a while ago, so you may have gotten other answers, but I don't see them in my overflowing inbox. :) Years ago, I did some work with V2O3, and it was a very stubborn system to get a good fit on. Other people I knew who were working on the system have also had some trouble. This and other evidence led to some people publishing speculations on local distortions that get averaged out in XRD but show up in EXAFS. I also recall people talking about similar difficulties with other vanadium oxide systems. (Sorry; I don't have those references handy anymore, but searches should locate them). As far as the second issue you mention, with Ifeffit reversing the position of two atoms of the same species, it does happen some times. Why not? A V-O path is basically a V-O path to FEFF; it doesn't know that one's a single bond and one's a double bond. But since moving a path by more than about 0.1 Angstrom in Ifeffit starts to reduce the accuracy of the FEFF calculation, it's something you do want to try to prevent. One way to do that is with restraints; it shouldn't take much incentive for Ifeffit to refrain from switching the paths. --Scott Calvin Sarah Lawrence College At 05:02 PM 4/18/2007, you wrote: Greetings! I have inherited a vanadium EXAFS data set (due to a group member graduating - lucky dog!) that is giving me major fits. I am getting consistent numbers with all my fits which visually look fantastic, that is until I look at the numbers...one Debye-Waller factor is negative (a V-O path) and the Eo's are large, the V-Cl path is on the order of -20 eV, the V=O path is on the order of 17 eV, and the V-O path falling at -11 eV. ARe there any tricks outside of restraints or constraints that I can attempt to get more realistic values? (I understand that a large Eo can be realistic, but a negative Debye-Waller factor doesn't make sense.) I can restrain the V-O Debye-Waller factor and get a positive value, but then the V=O D-W factor is negative. If I restrain both D-W factors, the fit falls apart, suggesting something else is wrong that I just can't find. Another issue I'm having involves something in Artemis that's confusing me. Sometimes after a fit, the Artemis Pallet shows the V=O feature as the one at 1.8 Angstroms and the V-O feature at 1.6 Angstroms, completely reversed to the FEFF model. I have seen this when I separated the chlorides as well (I attempted to model the Cl at different distances as reported by Deguns, et. al. (attached) due to the immediate environment around the V in our sample being similar to the one they report in scheme 1-(I), p5008). Attached is a text file that shows an Artemis Pallet output illustrating what I'm trying to describe for the V=O and V-O paths. The Artemis project that generated the output is also attached. ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
