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

Re: [Ifeffit] EXAFS
by Scott Calvin 11 May '11

11 May '11

Hi Francisco, I'll take a shot at some of these questions--I'm sure others will chime in as well. On May 11, 2011, at 2:34 PM, Francisco Garcia wrote: > Dear all, > > I tried computing K-edge chi(k) for a solvated metal ion. For each > snapshot, I simply carved out a cluster of radius 6 Ang around the > metal. > > 1. if I set RMAX to say 5.5 in feff.inp, the chi(k) plot looks totally > different from the case where the RMAX line is commented out > (particularly k>10). I thought RMAX is the largest metal-H or metal-O > separation but I think I am wrong > RMAX is the longest half-path length to include in chi(k). For direct scattering paths, it is therefore the most distant scattering pair that is allowed to contribute. So your understanding of the meaning is essentially correct. In FEFF7, the documentation says it defaults to 2.2 times the nearest neighbor if it is not included. So commenting out RMAX does not mean to include all paths! That could be responsible for a considerable difference in chi(k). > 2. I dont quite understand why the number of paths increases > (sometimes by a factor of 3) when I set RMAX as opposed to the case > where I comment it out. See above. If your nearest neighbor is at, say, 1.8 angstroms, then commenting out RMAX is equivalent to setting it to 3.96 angstroms. That's much less than 5.5, and explains the smaller number of paths. > > 3. From time to time I get warnings indicating that a water O-H > distance is too short: > > WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. > atoms 5 7 > 5 0.14400 2.09700 1.16300 > 7 0.77400 2.67400 1.00800 > > I tried setting FOLP to 0.8 for H but the warnings persist. Don't worry about it. This FEFF warning doesn't really expect hydrogens, and so sometimes gives a warning for atoms that would be close if they were anything bigger, but are OK if one is a hydrogen. Looking at the coordinates it specifies in your example, the two atoms are about 1 angstrom apart--OK if one is a proton. > > 4. On what criteria are sigma2 and s02 chosen? They are not usually > reported in published theoretical papers and I was wondering if they > are arbitrary. FEFF is not usually used for EXAFS on its own. Most people use a fitting program, such as Ifeffit, to optimize the values of S02 and sigma2 to provide the best fit. (Although S02 in particular is often fit for a known material, and then that value used.) When used in that way, FEFF should be run with S02 = 1 and sigma2 = 0 to avoid confusion. > > 5. Finally, is the chi(k) dependent of which version of FEFF is being > used. I am asking this because the peak height of my FEFF6 chi(k) is > slightly lower than that of published results using FEFF8. > Yes, they are slightly different. For EXAFS, they probably aren't different enough to affect the answers to your scientific questions much, though. --Scott Calvin Sarah Lawrence College

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EXAFS
by Francisco Garcia 11 May '11

11 May '11

Dear all, I tried computing K-edge chi(k) for a solvated metal ion. For each snapshot, I simply carved out a cluster of radius 6 Ang around the metal. 1. if I set RMAX to say 5.5 in feff.inp, the chi(k) plot looks totally different from the case where the RMAX line is commented out (particularly k>10). I thought RMAX is the largest metal-H or metal-O separation but I think I am wrong 2. I dont quite understand why the number of paths increases (sometimes by a factor of 3) when I set RMAX as opposed to the case where I comment it out. 3. From time to time I get warnings indicating that a water O-H distance is too short: WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 5 7 5 0.14400 2.09700 1.16300 7 0.77400 2.67400 1.00800 I tried setting FOLP to 0.8 for H but the warnings persist. 4. On what criteria are sigma2 and s02 chosen? They are not usually reported in published theoretical papers and I was wondering if they are arbitrary. 5. Finally, is the chi(k) dependent of which version of FEFF is being used. I am asking this because the peak height of my FEFF6 chi(k) is slightly lower than that of published results using FEFF8. Thanks

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Re: [Ifeffit] Question about transform windows and statistical parameters
by Scott Calvin 11 May '11

11 May '11

Hi Brandon, I don't find this terribly surprising. First, a little background which you may or may not know: Reduced chi-square is a statistical parameter which requires a knowledge of the uncertainty of the measurement to compute. In theory, therefore, it "knows" that a "good" fit to noisy data will not be as close in an absolute sense as a "good" fit to high-quality data. The problem, however, is that it's difficult to know what is the proper quantity to use for the uncertainty of the measurement in EXAFS analysis. One could use the standard deviation of subsequent scans, but that is only sensitive to random scan-to-scan error. Something like, say, a monochromator glitch is quite reproducible, and yet most of us would consider it to be part of the measurement error. So the default behavior of Ifeffit is to look at the Fourier transform between 15 and 25 angstroms, and figure that any amplitude there is due to error of some kind, and not signal. It then makes the assumption that the same amount of error is present in the range being fit (i.e. the error is "white"), and from there computes the reduced chi-square. This is in some sense a dubious procedure, but the real problem is that we don't have a good method for estimating the measurement uncertainty, so we have to do something. As long as we are comparing fits to exactly the same data, on the same k-range, with the same k-weight, with the same windows, then changes in reduced chi-square are worth looking at. If all you've done is change a constraint or change the R-range being fit, for instance, a lower reduced chi-square is a good sign (use the Hamilton test if you want to be rigorous about it.) But change the k-range, or the k-weight, or the window, or the data, and Ifeffit's estimate of the uncertainty can change wildly, causing a correspondingly wild change in reduced chi-square. After all, one glitch toward the end of the k-range you are thinking can introduce a lot of high-R amplitude in to the Fourier transform, and different windows would treat it very differently. But single-point glitches often don't have much effect on the results of your fit, precisely because they do affect the high-R part of the Fourier transform much more than low-R part. Ifeffit's default behavior can be overridden, if you so choose. The parameter "epsilon" (available on the Data panel of Artemis) overrides Ifeffit's usual estimate for uncertainty. So in your case, I suggest putting a number--any number--in for epsilon, and then comparing fits using the two windows. Probably you will find that the reduced chi- squares become much more similar to each other. Incidentally, while in this case the default behavior of Ifeffit is merely distracting, there is a circumstance where it can be a more substantial problem: mutliple data-set fits (e.g. on multiple edges of the same sample). If Ifeffit finds uncertainties for the different data sets that are quite different from each other because, for instance, of the presence of a glitch in one, it will in effect weight the data very differently when doing a fit. In multiple-data set fits, therefore, it is often advisable to come up with your own scheme for setting epsilons (perhaps inversely proportional to the edge jump of the set, or something like that), to avoid wonky weightings. --Scott Calvin Sarah Lawrence College On May 11, 2011, at 12:47 PM, Brandon Reese wrote: > Hello everybody, > > I am working on fitting some EXAFS of amorphous materials and have > noticed an odd (in my mind) behavior when changing transform > windows. I settled on a fit using all three k-weights and the > Hanning transform window obtaining statistical parameters of > R=0.0018 and chi_R=361. I decided to change the transform window to > a Kaiser-Bessel to see what would happen. The refined parameters > came out more or less the same, well within the error bars, with the > Hanning windows having slightly smaller error bars. But my > statistical parameters changed significantly to R=0.0022 and > chi_R=89.354. It seems that this large change may be related to why > we can't use the chi_R parameter to compare fits over different k- > ranges, but I am not sure about that. Have other people seen this? > I would guess it means that when looking for trends in different > data sets, it is more important to be consistent, rather than which > specific window type is used. > > Thanks, > Brandon > <ATT00001..txt>

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What does FEFF stand for?
by Francisco Garcia 10 May '11

10 May '11

Dear all, I wish to ask a somewhat novice question: What does the acronym FEFF stand for? Thank you.

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Re: [Ifeffit] What does FEFF stand for?
by Scott Calvin 10 May '11

10 May '11

I looked into this a bit further, Bruce, and I'd tentatively say the curved-wave corrections do turn out to be the source of the "eff": The earliest use of f_eff I can find is from a 1986 Phys. Rev. B article entitled "Spherical-wave effects in photoelectron diffraction," by Sagurton et al. (John Rehr is also in the author list). It says "an approximaton for including SW [spherical wave] corrections suggested recently by Rehr, Albers, and Natoli has been incorporated in some of our calculations...the net limiting result is a calculation procedure in which an effective scattering factor f_eff,j(r,theta_j) which depends on r takes the place of the usual PW [plane wave] f_j(theta_j)." In addition, was FEFF3 a multiple-scattering code? The comments in its header and the 1991 JACS article on it mention only single-scattering. It would make an extraordinary amount of sense that the "eff" would refer to FEFF's ability to handle multiple-scattering paths, but I don't think that's the actual historical origin of the terminology. And as for Anatoly's suggestion, I'll, uh, leave that one be for the moment. --Scott Calvin Sarah Lawrence College On May 10, 2011, at 12:17 PM, Bruce Ravel wrote: > On Tuesday, May 10, 2011 03:03:23 pm Scott Calvin wrote: >> My understanding, although I could be wrong is that the "effective" >> part came from an improvement of the theory to account for curved- >> wave >> effects. In other words, early theories approximated the >> photoelectron >> as a plane wave, but of course it spreads out radially from the >> absorbing atom. That change necessitated tweaking the definitions of >> the factors, so it became the "effective" f. > > I think you are mistaken. My memory of the etymology has to do with > the formalism dating back to Feff5 for computing MS paths. > > For a purely single scattering theory, you have an F and a phi > (without the subscript eff). That is, you can simply compute the > scatting function for the one scatterer and be done with it. > > Feff's path expansion introduced two clever things to the EXAFS > business. One is that it provided a formalism for computing a single > function that takes into account the angle-dependent scattering > functions of all atoms in an arbitrary-geometry multiple scattering > path. This allows one to treat a MS path with the familiar SS EXAFS > equation only by replacing F and phi with F_eff and phi_eff. That > innovation is central to how Ifeffit works. > > The second clever thing is that it's really fast. That's not such a > big deal today, but back in the mid-90s, when a Feff run could take > several minutes, a faster algorithm was very welcome indeed. > > B > >

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Re: [Ifeffit] What does FEFF stand for?
by Scott Calvin 10 May '11

10 May '11

Right, Chris. There is a factor in the EXAFS equation, f(k). In different parts of the literature, f(k) sometimes has different meanings, but within the context of FEFF it refers to the effect of the potential of the scattering atom on both the scattering amplitude (the real part) and phase (the imaginary part). Thus, it stands for "f effective." My understanding, although I could be wrong is that the "effective" part came from an improvement of the theory to account for curved-wave effects. In other words, early theories approximated the photoelectron as a plane wave, but of course it spreads out radially from the absorbing atom. That change necessitated tweaking the definitions of the factors, so it became the "effective" f. --Scott Calvin Sarah Lawrence College On May 10, 2011, at 11:53 AM, Christopher Patridge wrote: > On 5/10/2011 2:49 PM, Francisco Garcia wrote: > > Dear all, > > I wish to ask a somewhat novice question: What does the acronym FEFF > stand for? > > Thank you. > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov<mailto:Ifeffit@millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > I am pretty sure it stand for the calculated Effective Scattering > factor F(eff)ective. > > buena salud, > > Chris Patridge > > > <ATT00001..txt>

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atoms possible bugs
by George Sterbinsky 10 May '11

10 May '11

Hello, I want to make everyone aware of some bugs that I think I have found in atoms, and pose some questions regarding the bugs, to anyone who may have seen them before. I have attached two atoms input files, generated using the Artemis atoms interface. The file A2n_atoms.inp is for a monoclinic structure in the A 2/n setting. On running atoms, one will find that there are six Ga atoms within a 4 A radius from the central Ga atom. If one reduces the the cluster size from 8 A in the .inp file to 6 A, one finds that now there are only two Ga atoms within 4 A of the central Ga atom. So it appears that atoms does not necessarily include all atoms within the cluster radius. The leads me to the question: how big should I make the cluster if I want to include all atoms within 6 A? An input file for the same structure converted to the C 2/c setting is also attached. When running atoms in the Artemis interface, the message "The axis lengths and angles specified are not appropriate for the given space group" is returned. Although, it appears that a Feff.inp file is still generated. It also appears to not have the same cluster size dependence as the A2/n structure. So can I trust this feff.inp file even though I received an error message? It seems to me that the answer would be yes, atoms did the calculations correctly and the error message being generated is just a bug, but I'm not certain about this. Thank you, George

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Re: [Ifeffit] Athena (Question about LC fitting)
by Bruce Ravel 10 May '11

10 May '11

Belay, I am CCing my response to the Ifeffit Mailing List, which is the appropriate venue for questions about the use fo the software. I encourage you to subscribe to and use the mailing list. On Tuesday, May 10, 2011 08:50:10 am you wrote: > Dear Dr. Ravel, > I am doing my PhD in title with identication of Fe-phases in cement > hydrates. I am using Athena for LC fitting. I use EXAFS spectra for the > fittings. My question is before LC fitting of EXAFS spectra , do I need to > calibrate the energy? I have normlized and alligned the spectra very well. > The problem is data calibration, when I calibrate the spectra, the energy > shifts and it destroys the fitting. Can you please give a clue why this > happens or do I make a mistake on the procedure? Thanks so much for your > cooperation. Alignment puts a group of spectra on the same relative energy scale. It is often necessary to do an explicit alignment when working at a beamline with an unstable and unencoded monochromator, as might be found at some older beamlines. Calibration intends to put a single spectrum on the correct absolute energy scale. That is, if you know what point in a spectrum represents a particular absolute energy, then calibration does as I said. LCF requires that the ensemble of data and standards all be aligned -- i.e. put on the same relative energy axis. Once that is done, you can proceed with LCF analysis. LCF does not require that the data be calibrated, only that they be aligned. That is, LCF requires that all the data+standards be on the same relative energy axis, but does not require that that energy axis be calibrated. The reason that is so is because LCF fitting is an abstract, numerical function that treats one data set (the "data") as a linear combination of two or more other data sets (the "standards"). No part of that mathematical process requires knowledge of the species of the absorber atom. Indeed, LCF does not require that the x-axis represent energy, only that it be the same for all data+standards. That said, the interpretation of your data might be easier to consider and easier to present in publcation if your data is calibrated. For instance, the Xray Data Booklet tells us that copper metal has an edge at 8979 eV. Calibration is the process of transforming your data such that its edge does, in fact, happen at 8979 eV. In Athena, using the calibration dialog both does an energy shift and sets the E0 value to 8979. If you want to calibrate your data as well as aligning your data, I find it less confusing to do the calibration first. I believe that the procedures can be commutative, but calibrating after aligning is confusing to me and more prone to error for me. Someone else might give you different advice. Finally, remember that calibration requires actual knowledge (as opposed to some assumption) about what point in a spectrum represents a particular absolute energy value. While you might reasonably assign the first big peak in the first derivative of copper metal to 8979 eV, you cannot correctly assign the first big peak in the first derivative of copper oxide to 8979 eV due to the upwards shift in threshold energy in the oxide. HTH, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Re: [Ifeffit] Linux command line ff2chi yields no output
by Francisco Garcia 09 May '11

09 May '11

Dear users, I posted a question on feff6 not yielding the any *.chi output. I was using the feff6 binary in ifeffit. However, I complied the feff6lite f77 code and run it and I got the chi.dat output file--which is exactly what I need. So kindly disregard my previous question. Thank you.

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ifeffit-first derivative fits
by Ganga Hettiarachchi 07 May '11

07 May '11

Bruce, Problem is that when we do the fit in derivative and, save the results, something other than first derivative is written to the file. Have you ever looked at the saved/written file of a first derivative fit? Thanks, Ganga -------------------- Ganga M. Hettiarachchi, Ph.D. Assistant Professor of Soil and Environmental Chemistry Department of Agronomy 2107 Throckmorton Plant Sciences Center Kansas State University Manhattan, KS 66506 USA 785-532-7209 (office) 785-532-6094 (FAX)

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