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

Asymmetric error bars in IFeffit
by Scott Calvin 25 Oct '10

25 Oct '10

Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber- scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Scott Calvin 25 Oct '10

25 Oct '10

I don't think it's at all strange, Anatoly, and I think Matthew's solution is the right one--it seems obvious in retrospect that the parameter that Ifeffit should evaluate is 1/R, but apparently it wasn't obvious to me on Friday. :) As for obtaining N instead of R, the beauty of both of our algorithms is that they don't depend on finding N; they depend on finding the ratio of N's for different shells. Finding N accurately is notoriously challenging: you need some way of getting S02, you need to have the normalization right, and you're sunk if there are data quality issues like an inhomogeneous sample, uncorrected self-absorption, or significant beam harmonics. But finding the ratio of N for two or more different shells doesn't depend so strongly on any of those things. Since my method implicitly involves multiple ratios of coordination numbers, it is not so clear how to invert it. In any case, I expect Matthew's solution to work, and will pursue it further on Monday. --Scott Calvin Sarah Lawrence College On Oct 24, 2010, at 5:59 PM, Frenkel, Anatoly wrote: > Scott, > It is a strange result. Suppose you fit a bulk metal foil and vary > the 1nn coordination number. You will not get 12 +/- 1000. You will > get about 12 +/- 0.3 depending on the data quality and the k range, > and on the amplitude factor you fix constant. Then, suppose you take > your formula for a particle radius from your JAP article and > propagate this uncertainty to get the radius uncertainty. That would > give you a huge error because you are in the flat region of the N(R) > function and R does bit affect N. > The meaning of your large error bar is, I think, that you are in > such a large limit of sizes that they cannot be inverted to get N > and thus the errors cannot be propagated to find Delta R. > Why don't you try to obtain N instead of R? You will get much > smaller error bars and you can find the lower R limit from your N(R) > equation (by plugging in N - deltaN you will find R - delta R). > > The right limit is infinity as you pointed out. > > Anatoly > > ________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Fri Oct 22 16:23:08 2010 > Subject: [Ifeffit] Asymmetric error bars in IFeffit > > Hi all, > > I'm puzzling over an issue with my latest analysis, and it seemed > like the sort of thing where this mailing list might have some good > ideas. > > First, a little background on the analysis. It is a simultaneous fit > to four samples, made of various combinations of three phases. > Mossbauer has established which samples include which phases. One of > the phases itself has two crystallographically inequivalent > absorbing sites. The result is that the fit includes 12 Feff > calculations, four data sets, and 1000 paths. Remarkably, everything > works quite well, yielding a satisfying and informative fit. > Depending on the details, the fit takes about 90 minutes to run. > Kudos to Ifeffit and Horae for making such a thing possible! > > Several of the parameters that the fit finds are "characteristic > crystallite radii" for the individual phases. In my published fits, > I often include a factor that accounts for the fact that a phase is > nanoscale in a crude way: it assumes the phase is present as spheres > of uniform radius and applies a suppression factor to the > coordination numbers of the paths as a function of that radius and > of the absorber-scatterer distance. Even though this model is rarely > strictly correct in terms of morphology and size dispersion, it > gives a first-order approximation to the effect of the reduced > coordination numbers found in nanoscale materials. Some people, > notably Anatoly Frenkel, have published models which deal with this > effect much more realistically. But those techniques also require > more fitted variables and work best with fairly well-behaved > samples. I tend to work with "messy" chemical samples of free > nanoparticles where the assumption of sphericity isn't terrible, and > the size dispersion is difficult to model accurately. > > At any rate, the project I'm currently working on includes a fitted > characteristic radius of the type I've described for each of the > phases in each of the samples. And again, it seems to work pretty > well, yielding values that are plausible and largely stable. > > That's the background information. Now for my question: > > The effect of the characteristic radius on the spectrum is a > strongly nonlinear function of that radius. For example, the > difference between the EXAFS spectra of 100 nm and 1000 nm single > crystals due to the coordination number effect is completely > negligible. The difference between 1 nm and 10 nm crystals, however, > is huge. > > So for very small crystallites, IFeffit reports perfectly reasonable > error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat > larger crystallites, however, it tends to report values like 10 +/- > 500 nm. I understand why it does that: it's evaluating how much the > parameter would have to change by to have a given impact on the chi > square of the fit. And it turns out that once you get to about 10 > nm, the size could go arbitrarily higher than that and not change > the spectrum much at all. But it couldn't go that much lower without > affecting the spectrum. So what IFeffit means is something like "the > best fit value is 10 nm, and it is probable that the value is at > least 4 nm." But it's operating under the assumption that the > dependence of chi-square on the parameter is parabolic, so it comes > up with a compromise between a 6 nm error bar on the low side and an > infinitely large error bar on the high side. Compromising with > infinity, however, rarely yields sensible results. > > Thus my question is if anyone can think of a way to extract some > sense of these asymmetric error bars from IFeffit. Here are > possibilities I've considered: > > --Fit something like the log of the characteristic radius, rather > than the radius itself. That creates an asymmetric error bar for the > radius, but the asymmetry the new error bar possesses has no > relationship to the uncertainty it "should" possess. This seems to > me like it's just a way of sweeping the problem under the rug and is > potentially misleading. > > --Rerun the fits setting the variable in question to different > values to probe how far up or down it can go and have the same > effect on the fit. But since I've got nine of these factors, and > each fit takes more than an hour, the computer time required seems > prohibitive! > > --Somehow parameterize the guessed variable so that it does tend to > have symmetric error bars, and then calculate the characteristic > radius and its error bars from that. But it's not at all clear what > that parameterization would be. > > --Ask the IFeffit mailing list for ideas! > > Thanks! > > --Scott Calvin > Sarah Lawrence College > <ATT00001..txt>

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Frenkel, Anatoly 25 Oct '10

25 Oct '10

Scott, It is a strange result. Suppose you fit a bulk metal foil and vary the 1nn coordination number. You will not get 12 +/- 1000. You will get about 12 +/- 0.3 depending on the data quality and the k range, and on the amplitude factor you fix constant. Then, suppose you take your formula for a particle radius from your JAP article and propagate this uncertainty to get the radius uncertainty. That would give you a huge error because you are in the flat region of the N(R) function and R does bit affect N. The meaning of your large error bar is, I think, that you are in such a large limit of sizes that they cannot be inverted to get N and thus the errors cannot be propagated to find Delta R. Why don't you try to obtain N instead of R? You will get much smaller error bars and you can find the lower R limit from your N(R) equation (by plugging in N - deltaN you will find R - delta R). The right limit is infinity as you pointed out. Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Frenkel, Anatoly 23 Oct '10

23 Oct '10

Matthew, if you relied on FEFF as one part of the complex calculation, where the other part was the experimentally extracted one, you could've as well done everything with just FEFF. Why didn't you? A. ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 18:01:17 2010 Subject: Re: [Ifeffit] Asymmetric error bars in IFeffit Another reason, from my point of view, is that FEFF wasn't accurate enough to use on its own without references. Also, it still can be argued that the process of data reduction and filtering produces distortions which aren't captured by using FEFF alone. Further, if one is comparing very similar systems, e.g. bulk and nano of the same stuff, then with the exception of multiple scattering, the one system should be an ideal reference for the other. A trick I used to do: Suppose, for instance, that I wanted to fit a shell of Zn surrounded by Si (not an actual case). There's no Si-rich zinc silicide to use as a reference, but it's not too hard to make theta-CuAl2, a compound in which all Cu atoms are surrounded by Al in the first shell (this was done). From this, amp and phase functions could be extracted which refer to Cu looking at Al (Cu->Al). Next, to transform this into the desired Zn->Si, I would do FEFF calculations on identical structures with the atoms changed around and take: A(Zn->Si, semi-empirical) = A(Cu->Al, expt)*[A(Zn->Si, FEFF)/A(Cu->Al, FEFF)] phi(Zn->Si, semi-empirical) = phi(Cu->Al, expt)+[Phi(Zn->Si, FEFF)-phi(Cu->Al, FEFF)] with A, phi being amplitude and phase for a given shell, and appropriate account being taken of the distance differences involved. This makes sense if you consider A~ = A*exp(i*phi) to be one of the factors in a complex chi~ such that chi = Im(chi~), and you're essentially making a correction to ln(A~). Yes, this was low-rent and subject to errors, but it seemed to make sense provided one didn't try to take it too far, for instance trying to change Al for Au or an oxide for a metal. Brings back memories, not all of them fond :-) mam ----- Original Message ----- From: Frenkel, Anatoly <mailto:frenkel@bnl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Friday, October 22, 2010 2:38 PM Subject: Re: [Ifeffit] Asymmetric error bars in IFeffit On a related subject, now I understand why we use the concept of chemical transferability of amplitudes and phases by recycling the same FEFF path for different systems. The true reason is historic: back then it took one hour for one FEFF calculation.... Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Frenkel, Anatoly 22 Oct '10

22 Oct '10

On a related subject, now I understand why we use the concept of chemical transferability of amplitudes and phases by recycling the same FEFF path for different systems. The true reason is historic: back then it took one hour for one FEFF calculation.... Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College

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Zn foil data
by Jonathan L Keating 21 Oct '10

21 Oct '10

Dear All Firstly, lots of thanks to the contributors of the mailing list for providing such a great platform to discuss and help with exafs analysis. I have a request and wonder if anybody may have some Zn XAS foil data with data extending beyond 13 inverse Angstroms in k-space? Many Thanks Jon

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Re: [Ifeffit] calibration/aligment...2 (Scott Calvin)
by ornella smila castro 15 Oct '10

15 Oct '10

Dear Scott, this is exactly why I was confused about alignment, since I want to see that shift!! Thank you so much for your precious help. it is very clear now.. With best wishes, Ornella > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 92, Issue 13 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Thu, 14 Oct 2010 17:54:36 -0500 > > 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: calibration/aligment...2 (Scott Calvin) > 2. Re: MPSE (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Oct 2010 11:37:43 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] calibration/aligment...2 > Message-ID: <04C38483-D6F6-4F2D-B206-AFFB25B30429(a)gmail.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Thanks, Ornella, that clarifies what you're doing. > > My recommendation is to look closely at the 6 reference spectra and > see if there appears to be a systematic energy shift between them. For > example, each spectrum might be shifted by about 0.3 eV from the > spectrum before it. Or the first two spectra might appear aligned, but > then the third through sixth are shifted by 1.5 eV. In either of those > cases, you should align them. In my second example, I might throw out > the second spectrum as an additional precaution (if the shift occurred > "all at once," it might have occurred during the scan before which it > appears). In either case, it doesn't really matter which scan you > choose to align to (and calibrate, if you have a way of doing that). > > If, on the other hand, the 6 reference spectra appear to basically > overplot except for random noise, I would not try to align them further. > > I would treat the 6 spectra for the electrolysed solution similarly-- > align them to each other if there is a systematic energy shift. > > What you should not do, in my opinion, is to align the electrolysed > scans to the reference scans. You actually expect there to be a > chemical shift between the two sets of data, and aligning one to the > other would remove that! > > --Scott Calvin > Sarah Lawrence College > > On Oct 14, 2010, at 11:00 AM, ornella smila castro wrote: > > > Hi Matt and Scott, > > > > First, thank you so much for replying to my questions. > > I realised that I should have been a bit more accurate on the type > > of experiments I am doing. > > To start with, I am doing electrochemistry combined with EXAFS. I am > > using an integrated electrolysis/EXAFS cell. Our experiments are as > > follow: in the case of this experiment in particular, we have a > > solution of ruthenium-based compound that we flow through a channel > > through which the beam passes and that we call "reference". we > > record let's say 6 spectra in a row (we use a flow in order to avoid > > beam damage on our sample).we didn't do any reference spectra (if > > you mean running a scan of a Ru foil before starting the actual > > experiment). then, we make up a new solution but this time we > > electrolysed the solution (by applying a potential) in order to get > > the cationic produced species. (the obtained spectra will therefore > > be a mixture of the neutral and the cationic species). and we record > > as well a set of 6 spectra. > > Here is what I did and what I was wondering if it was the right > > thing to do: I have considered the first spectra of the first set of > > scans as the reference for calibration/alignment. is it ok? > > Thus, I am wondering if when I process the second set of data > > (electrolysed solution), which spectra I should take as a starting > > point for calibrating/aligning my second series of scans: the one I > > used for the first serie or the first of the second set of scans? > > > > I hope this is clear... > > > > Thanks again for your help, > > Ornella > >

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Re: [Ifeffit] MPSE
by Joshua Kas 14 Oct '10

14 Oct '10

Hi Mehmet, The documentation in feff9 for MPSE is (obviously) not very good. What you will need, to start, is a calculation of the bulk loss function L(E) = -Im[1/epsilon(E)] for your material. I can discuss the details with you over email if you like. Cheers, Josh Kas joshua.j.kas(a)gmail.com > Dear all, > > > > i want to run FEFF with the many pole self energy MPSE. In the > documentation > to FEFF9 is written that I have to use the formula detailed in > 'EpsInvFormula.ps' to calculate the optical constants. > > Where can I get this file? > > > > Many thanks > > > > Mehmet from University Duisburg-Essen in Germany > > > >

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Re: [Ifeffit] calibration/aligment...2
by Scott Calvin 14 Oct '10

14 Oct '10

Thanks, Ornella, that clarifies what you're doing. My recommendation is to look closely at the 6 reference spectra and see if there appears to be a systematic energy shift between them. For example, each spectrum might be shifted by about 0.3 eV from the spectrum before it. Or the first two spectra might appear aligned, but then the third through sixth are shifted by 1.5 eV. In either of those cases, you should align them. In my second example, I might throw out the second spectrum as an additional precaution (if the shift occurred "all at once," it might have occurred during the scan before which it appears). In either case, it doesn't really matter which scan you choose to align to (and calibrate, if you have a way of doing that). If, on the other hand, the 6 reference spectra appear to basically overplot except for random noise, I would not try to align them further. I would treat the 6 spectra for the electrolysed solution similarly-- align them to each other if there is a systematic energy shift. What you should not do, in my opinion, is to align the electrolysed scans to the reference scans. You actually expect there to be a chemical shift between the two sets of data, and aligning one to the other would remove that! --Scott Calvin Sarah Lawrence College On Oct 14, 2010, at 11:00 AM, ornella smila castro wrote: > Hi Matt and Scott, > > First, thank you so much for replying to my questions. > I realised that I should have been a bit more accurate on the type > of experiments I am doing. > To start with, I am doing electrochemistry combined with EXAFS. I am > using an integrated electrolysis/EXAFS cell. Our experiments are as > follow: in the case of this experiment in particular, we have a > solution of ruthenium-based compound that we flow through a channel > through which the beam passes and that we call "reference". we > record let's say 6 spectra in a row (we use a flow in order to avoid > beam damage on our sample).we didn't do any reference spectra (if > you mean running a scan of a Ru foil before starting the actual > experiment). then, we make up a new solution but this time we > electrolysed the solution (by applying a potential) in order to get > the cationic produced species. (the obtained spectra will therefore > be a mixture of the neutral and the cationic species). and we record > as well a set of 6 spectra. > Here is what I did and what I was wondering if it was the right > thing to do: I have considered the first spectra of the first set of > scans as the reference for calibration/alignment. is it ok? > Thus, I am wondering if when I process the second set of data > (electrolysed solution), which spectra I should take as a starting > point for calibrating/aligning my second series of scans: the one I > used for the first serie or the first of the second set of scans? > > I hope this is clear... > > Thanks again for your help, > Ornella

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Re: [Ifeffit] calibration/aligment...2
by ornella smila castro 14 Oct '10

14 Oct '10

Hi Matt and Scott, First, thank you so much for replying to my questions. I realised that I should have been a bit more accurate on the type of experiments I am doing. To start with, I am doing electrochemistry combined with EXAFS. I am using an integrated electrolysis/EXAFS cell. Our experiments are as follow: in the case of this experiment in particular, we have a solution of ruthenium-based compound that we flow through a channel through which the beam passes and that we call "reference". we record let's say 6 spectra in a row (we use a flow in order to avoid beam damage on our sample).we didn't do any reference spectra (if you mean running a scan of a Ru foil before starting the actual experiment). then, we make up a new solution but this time we electrolysed the solution (by applying a potential) in order to get the cationic produced species. (the obtained spectra will therefore be a mixture of the neutral and the cationic species). and we record as well a set of 6 spectra. Here is what I did and what I was wondering if it was the right thing to do: I have considered the first spectra of the first set of scans as the reference for calibration/alignment. is it ok? Thus, I am wondering if when I process the second set of data (electrolysed solution), which spectra I should take as a starting point for calibrating/aligning my second series of scans: the one I used for the first serie or the first of the second set of scans? I hope this is clear... Thanks again for your help, Ornella > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 92, Issue 11 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Thu, 14 Oct 2010 12:00:01 -0500 > > 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. MPSE (Mehmet Kaya) > 2. calibration/alignment (ornella smila castro) > 3. Re: calibration/alignment (Scott Calvin) > 4. Re: calibration/alignment (Matt Newville) > 5. Re: calibration/alignment (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Oct 2010 12:23:06 +0200 > From: "Mehmet Kaya" <mehmet.kaya(a)uni-due.de> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] MPSE > Message-ID: <000401cb6ac0$a110d0d0$e3327270$@kaya@uni-due.de> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > > > i want to run FEFF with the many pole self energy MPSE. In the documentation > to FEFF9 is written that I have to use the formula detailed in > 'EpsInvFormula.ps' to calculate the optical constants. > > Where can I get this file? > > > > Many thanks > > > > Mehmet from University Duisburg-Essen in Germany > > > >

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Re: [Ifeffit] calibration/alignment
by Scott Calvin 14 Oct '10

14 Oct '10

On Oct 14, 2010, at 7:39 AM, Matt Newville wrote: > If you're just getting started, I would say to not worry about energy > alignment until it becomes an obvious problem. A cautionary tale (with details made up, since I don't remember them!) from when I was just starting out as to what constitutes an "obvious problem": I collected five transmission EXAFS scans on the same sample. The scans were on top of each other when I looked at the graph, so I merged them...and proceeded to get somewhat screwy fits. The problem? I only looked at the graph across the whole spectra--say, 1500 eV. It turns out there was about a 0.7 eV shift between each scan and the next one, for a total of roughly 3 eV . That was small enough so as to be invisible when looked at on that scale. When I looked at just the XANES, though, the shift did become "obvious." I aligned the spectra and merged them, and suddenly the problems in the fit went away! Since then, I've seen the same thing happen with students to whom I am teaching the technique. On the other hand, there's no magic "blessing" given by the process of alignment. Suppose I have ten scans of very noisy data, and no reference. If I used the auto-align procedure in Athena, it sometimes shifts a scan 0.3 eV one way, sometimes 0.2 eV the other way, with no apparent rhyme or reason. Looking at the graphs, even zoomed in, just shows a bunch of noisy data roughly on top of each other. In that case, there's no reason to believe there are actual shifts between scans, and I would NOT align them prior to merging. Finally, beamline scientists usually have a very good idea whether their line is prone to drifts. Ask them! --Scott Calvin Sarah Lawrence College

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calibration/alignment
by ornella smila castro 14 Oct '10

14 Oct '10

Hi everyone, I am trying to do some data processing with Athena but I am already stuck at the first step. The thing is: I read the worked example section of the "Athena's user guide" and on the example on the iron foil, it is mentioned to calibrate the data at the right energy (until here evrything is fine) but then it is said to align the data. Can anyone explain to me what does "alignment" exactly means, and what is the aim of "aligning the data". The data that I have collected were through a channel through which a solution flow (~200 microliters/hr) so I am not convinced that alignment makes sense. Many thanks, Ornel

2 1

Re: [Ifeffit] calibration/alignment
by Scott Calvin 14 Oct '10

14 Oct '10

Hi Ornel, Alignment is used to compensate for monochromators that do not maintain stable energy calibration between scans. In conventional measurements, you'll generally have several scans that are supposed to be of the same sample under identical conditions, and those scans may need to be aligned with each other. That is not the case for a time series, which is what I think you are saying you have. So in a time series, how do you compensate for any energy drift of the monochromator? If you are recording a simultaneous reference spectrum, you can align the reference spectra to each other. (Athena automatically will shift the sample spectra by the same amount that the reference spectra are shifted.) If you have a time series but don't have a simultaneous reference spectra, it becomes tougher. If you collected a reference spectrum before and after the time series, you could try to interpolate any shift that's seen, although that's dicey; shifts sometimes occur in jumps. But if there's no shift, you're probably OK! If you have a time series and no reference at all, or a reference only before the series, you're out of luck. You're relying then on the assumption of energy stability, which on some beamlines might be OK...but it is best to confirm that by at least measuring a reference before and after. --Scott Calvin Sarah Lawrence College On Oct 14, 2010, at 2:46 AM, ornella smila castro wrote: > Hi everyone, > > I am trying to do some data processing with Athena but I am already > stuck at the first step. The thing is: I read the worked example > section of the "Athena's user guide" and on the example on the iron > foil, it is mentioned to calibrate the data at the right energy > (until here evrything is fine) but then it is said to align the > data. Can anyone explain to me what does "alignment" exactly means, > and what is the aim of "aligning the data". The data that I have > collected were through a channel through which a solution flow (~200 > microliters/hr) so I am not convinced that alignment makes sense. > > Many thanks, > Ornel > <ATT00001..txt>

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MPSE
by Mehmet Kaya 13 Oct '10

13 Oct '10

Dear all, i want to run FEFF with the many pole self energy MPSE. In the documentation to FEFF9 is written that I have to use the formula detailed in 'EpsInvFormula.ps' to calculate the optical constants. Where can I get this file? Many thanks Mehmet from University Duisburg-Essen in Germany

1 0

Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 12 Oct '10

12 Oct '10

Hi Matt, Thank you very much. I have gone through the chapter in your Tutorial and things are more convincing now. With best regards, Jatin Rana HZB Berlin On 09.10.2010 19:00, 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: schemes for delr and sigma2 for multiple scattering paths > (Matt Newville) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Jatinkumar Rana) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 8 Oct 2010 13:13:23 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID: > <AANLkTimBJbC9EqyUs31kiHuU9F+fHSVv+ib5oXBKq5Kb(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Jatin, > > I tried to answer both of these question in chapter 3 of > http://xafs.org/Tutorials?action=AttachFile&do=view&target=Newville_xas_fun… > > Does the explanation there help? If not, do you have any suggestions > for making it clearer? > > The basic physics is that an absorbed x-ray creates a photo-electron > which will scatter from its neighbors. A portion of the scattered > portion (so, a small amount) of that photo-electron will return to the > absorbing atom. But Pauli's exclusion principle tells us that if an > electron is at the absorbing atom, and has the same energy (and other > quantum numbers) as the outgoing photo-electron, the outgoing > photo-electron cannot be created in the first place. Thus, the > scattering of the photo-electron from the neighbors affects whether > the photo-electron can be created, and so whether the x-ray will be > absorbed. > > The effect can be either destructive or constructive, as with nearly > any wave-like phenomenon. It does seem a bit circular that the > photo-electron scattering affects the existence of the photo-electron, > but quantum mechanics leads to many much stranger behaviors. > > --Matt > > > ------------------------------ > > Message: 2 > Date: Sat, 09 Oct 2010 09:41:12 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID:<4CB01C98.4020103(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello Chris, Bruce, > > Thank you so very much for your detailed explanations. > > With best regards, > Jatin Rana > HZB Berlin > > > > > > On 08.10.2010 19:00, 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: schemes for delr and sigma2 for multiple scattering paths >> (Chris Patridge) >> 2. Re: schemes for delr and sigma2 for multiple scattering paths >> (Bruce Ravel) >> 3. Re: schemes for delr and sigma2 for multiple scattering paths >> (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 8 Oct 2010 10:09:34 -0400 >> From: Chris Patridge<patridge(a)buffalo.edu> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple >> scattering paths >> Message-ID:<68FC92BB-B842-48F2-8596-7675D168EB16(a)buffalo.edu> >> Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes >> >> Hello Jatin, >> >> I don't confess expertise but i think the absorption coeff. relates to >> the overlap between the initial and final wavefunction. Therefore the >> interference between outgoing and backscattering modulates the final >> wavefunction which manifests as the exafs fluctuations past the edge >> which in turn changes the It signal so we can use the difference >> between Io and It to measure exafs data. Any additional comments are >> welcomed if I am mistaken as I said I am not an expert. >> >> Buena salud, >> >> Chris Patridge >> >> >> On Oct 8, 2010, at 9:30 AM, Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de >> > wrote: >> >> >> >>> Hi Scott, >>> >>> Nice to see you back-in-action from holidays. Thank you very much >>> for your suggestions. >>> >>> Since last few days i was trying to visualize the physical process >>> going on inside an absorbing atom when we measure EXAFS, i met few >>> really basic questions, which of course, could be due to lack of my >>> understandings. Therefore, I tried to go through literatures and >>> EXAFS books but i am not satisfied. >>> >>> Therefore, i decided to put them to mailing list >>> >>> My first question is : >>> >>> In EXAFS, the oscillations are due to the intereference between the >>> outgoing photo electron from absorbing atom and incoming >>> backscattered photoelectron from the scatterer. Depending upon, how >>> much they are out of phase w.r.t each other we get oscillations in >>> EXAFS curve. These oscillations are nothing but the variation in the >>> absobtion coefficient of sample as the energy of incident photon is >>> varied. >>> >>> I wonder, how, the intereference between the photo electrons is >>> related to absorbtion coefficient of sample ?? >>> >>> because, It = I0 * exp (-ut) >>> >>> My second question is : >>> >>> While measuring EXAFS at beamline, we only measure the intial >>> intensity (Io) and the transmitted intenstiy from sample (It). In >>> other words, we only measure the number of photons before and after >>> the sample and variation in abs.coeffi.(u) is related to variation >>> in It. >>> >>> How interference between photoelectrons will be reflected as >>> variation in abs.coeffi. (u) of sample while we never measure photo >>> electrons in EXAFS?? >>> >>> We only measure Io and It. >>> >>> Also, whether the intereference between photo electrons is >>> constructive or destructive, the incident photon will lose its >>> energy once it knocks an electron from say K-shell of absorbing atom >>> and hence photon is said to have absorbed. >>> >>> I will be really thankful to you for your valuable explanation. >>> >>> With Best regards, >>> Jatin Rana >>> HZB, Berlin >>> >>> >>> >>> >>> >>> On 07.10.2010 19:00, 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: Multiple scattering paths in fitting (Frenkel, Anatoly) >>>> 2. Re: schemes for delr and sigma2 for multiple scattering >>>> paths >>>> (Scott Calvin) >>>> >>>> >>>> --- >>>> ------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Thu, 7 Oct 2010 09:38:26 -0400 >>>> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >>>> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >>>> Subject: Re: [Ifeffit] Multiple scattering paths in fitting >>>> Message-ID: >>>> <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> For relationships between sigma2 for MS and SS paths, some are >>>> listed in the Appendix to this article: >>>> >>>> P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). >>>> >>>> Anatoly >>>> >>>> >>>> >>>>

1 0

Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 09 Oct '10

09 Oct '10

Hello Chris, Bruce, Thank you so very much for your detailed explanations. With best regards, Jatin Rana HZB Berlin On 08.10.2010 19:00, 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: schemes for delr and sigma2 for multiple scattering paths > (Chris Patridge) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Bruce Ravel) > 3. Re: schemes for delr and sigma2 for multiple scattering paths > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 8 Oct 2010 10:09:34 -0400 > From: Chris Patridge<patridge(a)buffalo.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID:<68FC92BB-B842-48F2-8596-7675D168EB16(a)buffalo.edu> > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > Hello Jatin, > > I don't confess expertise but i think the absorption coeff. relates to > the overlap between the initial and final wavefunction. Therefore the > interference between outgoing and backscattering modulates the final > wavefunction which manifests as the exafs fluctuations past the edge > which in turn changes the It signal so we can use the difference > between Io and It to measure exafs data. Any additional comments are > welcomed if I am mistaken as I said I am not an expert. > > Buena salud, > > Chris Patridge > > > On Oct 8, 2010, at 9:30 AM, Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de > > wrote: > > >> Hi Scott, >> >> Nice to see you back-in-action from holidays. Thank you very much >> for your suggestions. >> >> Since last few days i was trying to visualize the physical process >> going on inside an absorbing atom when we measure EXAFS, i met few >> really basic questions, which of course, could be due to lack of my >> understandings. Therefore, I tried to go through literatures and >> EXAFS books but i am not satisfied. >> >> Therefore, i decided to put them to mailing list >> >> My first question is : >> >> In EXAFS, the oscillations are due to the intereference between the >> outgoing photo electron from absorbing atom and incoming >> backscattered photoelectron from the scatterer. Depending upon, how >> much they are out of phase w.r.t each other we get oscillations in >> EXAFS curve. These oscillations are nothing but the variation in the >> absobtion coefficient of sample as the energy of incident photon is >> varied. >> >> I wonder, how, the intereference between the photo electrons is >> related to absorbtion coefficient of sample ?? >> >> because, It = I0 * exp (-ut) >> >> My second question is : >> >> While measuring EXAFS at beamline, we only measure the intial >> intensity (Io) and the transmitted intenstiy from sample (It). In >> other words, we only measure the number of photons before and after >> the sample and variation in abs.coeffi.(u) is related to variation >> in It. >> >> How interference between photoelectrons will be reflected as >> variation in abs.coeffi. (u) of sample while we never measure photo >> electrons in EXAFS?? >> >> We only measure Io and It. >> >> Also, whether the intereference between photo electrons is >> constructive or destructive, the incident photon will lose its >> energy once it knocks an electron from say K-shell of absorbing atom >> and hence photon is said to have absorbed. >> >> I will be really thankful to you for your valuable explanation. >> >> With Best regards, >> Jatin Rana >> HZB, Berlin >> >> >> >> >> >> On 07.10.2010 19:00, 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: Multiple scattering paths in fitting (Frenkel, Anatoly) >>> 2. Re: schemes for delr and sigma2 for multiple scattering >>> paths >>> (Scott Calvin) >>> >>> >>> --- >>> ------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Thu, 7 Oct 2010 09:38:26 -0400 >>> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >>> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] Multiple scattering paths in fitting >>> Message-ID: >>> <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> For relationships between sigma2 for MS and SS paths, some are >>> listed in the Appendix to this article: >>> >>> P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). >>> >>> Anatoly >>> >>> >>> >>>

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 08 Oct '10

08 Oct '10

Hi Scott, Nice to see you back-in-action from holidays. Thank you very much for your suggestions. Since last few days i was trying to visualize the physical process going on inside an absorbing atom when we measure EXAFS, i met few really basic questions, which of course, could be due to lack of my understandings. Therefore, I tried to go through literatures and EXAFS books but i am not satisfied. Therefore, i decided to put them to mailing list My first question is : In EXAFS, the oscillations are due to the intereference between the outgoing photo electron from absorbing atom and incoming backscattered photoelectron from the scatterer. Depending upon, how much they are out of phase w.r.t each other we get oscillations in EXAFS curve. These oscillations are nothing but the variation in the absobtion coefficient of sample as the energy of incident photon is varied. I wonder, how, the intereference between the photo electrons is related to absorbtion coefficient of sample ?? because, It = I0 * exp (-ut) My second question is : While measuring EXAFS at beamline, we only measure the intial intensity (Io) and the transmitted intenstiy from sample (It). In other words, we only measure the number of photons before and after the sample and variation in abs.coeffi.(u) is related to variation in It. How interference between photoelectrons will be reflected as variation in abs.coeffi. (u) of sample while we never measure photo electrons in EXAFS?? We only measure Io and It. Also, whether the intereference between photo electrons is constructive or destructive, the incident photon will lose its energy once it knocks an electron from say K-shell of absorbing atom and hence photon is said to have absorbed. I will be really thankful to you for your valuable explanation. With Best regards, Jatin Rana HZB, Berlin On 07.10.2010 19:00, 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: Multiple scattering paths in fitting (Frenkel, Anatoly) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Oct 2010 09:38:26 -0400 > From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Multiple scattering paths in fitting > Message-ID: > <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > For relationships between sigma2 for MS and SS paths, some are listed in the Appendix to this article: > > P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). > > Anatoly > > > >

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
by Scott Calvin 07 Oct '10

07 Oct '10

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

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
by Han Sen Soo 07 Oct '10

07 Oct '10

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-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: 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.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] More than 256 paths on Mac OS 10.5? > Message-ID: <6DD333D2-F58C-4E55-AB0D-430483EF97F4(a)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 <hssoo(a)lbl.gov> > To: ifeffit(a)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-DE5E73831893(a)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-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 >> ************************************** > > > > > ------------------------------ > > Message: 3 > Date: Wed, 6 Oct 2010 10:51:59 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)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: <CBC93BEC-49EA-40CB-B700-4CD1E421D1A5(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > 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 > > > > ------------------------------ > > Message: 4 > Date: Thu, 7 Oct 2010 12:51:01 +0530 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Multiple scattering paths in fitting > Message-ID: > <AANLkTim8q3nucice-cVa-F2jpqCR=abDbkKk=AJj2X87(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I just read the discussion on "sigma^2 values for multiple > scattering paths ". One thing is clear that inclusion of multiple scattering > path may increase the quality of fit. I have also some questions related to > MS paths. > 1. What else information can be obtained from multiple scattering paths? > 2. What values of delr should be relevant for MS paths. > 3. How can we determine the bond-angles from multiple-sacttering paths using > Artemis fitting method. > > With thanks > Abhijeet Gaur > School of Studies in Physics > Vikram University, Ujjain. >

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Scott Calvin 07 Oct '10

07 Oct '10

Jatin, IF the uniform expansion model is valid for single scattering paths, then it is for multiple scattering paths as well. For some materials, particularly those with cubic space groups, that's got a good chance of being a useful model. Others tends to distort with changes in temperature, doping, etc., and it may not work as well. But even in those cases, if you've decided how to constrain the delr for single- scattering paths, you'll do reasonably well by using some kind of appropriate average of the delr's for related single-scattering paths. --Scott Calvin Sarah Lawrence College On Oct 7, 2010, at 3:05 AM, Jatinkumar Rana wrote: > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Multiple scattering paths in fitting
by Abhijeet Gaur 07 Oct '10

07 Oct '10

Hi all, I just read the discussion on "sigma^2 values for multiple scattering paths ". One thing is clear that inclusion of multiple scattering path may increase the quality of fit. I have also some questions related to MS paths. 1. What else information can be obtained from multiple scattering paths? 2. What values of delr should be relevant for MS paths. 3. How can we determine the bond-angles from multiple-sacttering paths using Artemis fitting method. With thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain.

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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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