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

Re: [Ifeffit] Asymmetric error bars in IFeffit
by Scott Calvin 24 Oct '10

24 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 24 Oct '10

24 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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