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

Linux command line ff2chi yields no output
by Francisco Garcia 12 May '11

12 May '11

Dear users, I was able to install iffefit on linux. From the command line I run: feff6 feff.inp This worked fine and several feffnnnn.dat files were generated. Then, I wrote an input script, tmp.iff (shortened list of paths here), for ifeffit as follows: # tmp.iff path(1, file=feff0001.dat, s02 = 0.9, sigma2 = 0 .001) path(2, file=feff0002.dat, s02 = 0.9, sigma2 = 0 .001) path(3, file=feff0003.dat, s02 = 0.9, sigma2 = 0 .001) path(4, file=feff0004.dat, s02 = 0.9, sigma2 = 0 .001) path(5, file=feff0005.dat, s02 = 0.9, sigma2 = 0 .001) path(6, file=feff0006.dat, s02 = 0.9, sigma2 = 0 .001) path(7, file=feff0007.dat, s02 = 0.9, sigma2 = 0 .001) path(8, file=feff0008.dat, s02 = 0.9, sigma2 = 0 .001) path(9, file=feff0009.dat, s02 = 0.9, sigma2 = 0 .001) path(10, file=feff0010.dat, s02 = 0.9, sigma2 = 0 .001) path(11, file=feff0011.dat, s02 = 0.9, sigma2 = 0 .001) ff2chi(1-11, group=mycalc) fftf(mycalc.chi, kmin=1, kmax=15, dk=0.5, kweight=2.0, kwindow='hanning') # My aim here is to sum the paths to generate chi(k). Now if I run the following command: ifeffit -x tmp.iff the following output is printed on the screen: reading feff0101.dat reading feff0102.dat reading feff0103.dat reading feff0104.dat reading feff0105.dat reading feff0106.dat reading feff0107.dat reading feff0108.dat reading feff0109.dat reading feff0001.dat reading feff0002.dat reading feff0003.dat reading feff0004.dat reading feff0005.dat reading feff0006.dat reading feff0007.dat reading feff0008.dat reading feff0009.dat reading feff0010.dat reading feff0011.dat It appears that the feffnnnn.dat files were read successfully. However, no mycalc.chi output was produced by ff2chi() [and therefore no mycalc.chir_* output was produced by fftf()]. I don't know if my approach is missing an important step or my entire procedure is nonsensical. Thanks a lot!

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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 10 May '11

10 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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Re: [Ifeffit] EXAFS on multi phase systems
by Rana, Jatinkumar Kantilal 06 May '11

06 May '11

Hi Scott, Hi Bruce, Thanks a lot for directing me to the available literatures. It will be of great help. With best regards, Jatin ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Thursday, May 05, 2011 7:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 99, Issue 1 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. EXAFS on multi phase systems (Jatinkumar Rana) 2. Re: EXAFS on multi phase systems (Scott Calvin) 3. Re: EXAFS on multi phase systems (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 05 May 2011 09:26:02 +0200 From: Jatinkumar Rana <jatinkumar.rana(a)helmholtz-berlin.de> To: Ifeffit users <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] EXAFS on multi phase systems Message-ID: <4DC2510A.7030907(a)helmholtz-berlin.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Dear ifeffit users, I was wondering if one could apply EXAFS to multi-phase systems (e.g. two phase systems) where both phases could be crystallographically different but contain same absorbing atom. Can anyone suggest any literature which dealt with such a problem ?? With best regards, Jatinkumar Rana Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Institut f?r angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583 ------------------------------ Message: 2 Date: Thu, 5 May 2011 07:46:33 -0700 From: Scott Calvin <dr.scott.calvin(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: Scott Calvin <scalvin(a)slc.edu> Subject: Re: [Ifeffit] EXAFS on multi phase systems Message-ID: <43612A83-383E-46DC-8182-4986C8C66FA1(a)gmail.edu> Content-Type: text/plain; charset="windows-1252"; Format="flowed"; DelSp="yes" Hi Jatinkumar, It's fairly common to do so. With linear combination analysis or principle component analysis, it's necessarily the case. But it's also done with modelling using FEFF. I personally have published many papers of this type. One early paper of mine that does this is: ?X-ray absorption spectroscopy of highly-cycled Li/CPE/FeS2 cells,? E. Strauss, S. Calvin, H. Mehta,* D. Golodnitksy, S. G. Greenbaum, M. L. denBoer, V. Dusheiko, and E. Peled, Solid State Ionics 164, 51 (2003). --Scott Calvin Sarah Lawrence College On May 5, 2011, at 12:26 AM, Jatinkumar Rana wrote: > Dear ifeffit users, > > I was wondering if one could apply EXAFS to multi-phase systems (e.g. > two phase systems) where both phases could be crystallographically > different but contain same absorbing atom. > > Can anyone suggest any literature which dealt with such a problem ?? > > With best regards, > > Jatinkumar Rana

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Re: [Ifeffit] EXAFS on multi phase systems
by Scott Calvin 05 May '11

05 May '11

Hi Jatinkumar, It's fairly common to do so. With linear combination analysis or principle component analysis, it's necessarily the case. But it's also done with modelling using FEFF. I personally have published many papers of this type. One early paper of mine that does this is: “X-ray absorption spectroscopy of highly-cycled Li/CPE/FeS2 cells,” E. Strauss, S. Calvin, H. Mehta,* D. Golodnitksy, S. G. Greenbaum, M. L. denBoer, V. Dusheiko, and E. Peled, Solid State Ionics 164, 51 (2003). --Scott Calvin Sarah Lawrence College On May 5, 2011, at 12:26 AM, Jatinkumar Rana wrote: > Dear ifeffit users, > > I was wondering if one could apply EXAFS to multi-phase systems (e.g. > two phase systems) where both phases could be crystallographically > different but contain same absorbing atom. > > Can anyone suggest any literature which dealt with such a problem ?? > > With best regards, > > Jatinkumar Rana

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EXAFS on multi phase systems
by Jatinkumar Rana 05 May '11

05 May '11

Dear ifeffit users, I was wondering if one could apply EXAFS to multi-phase systems (e.g. two phase systems) where both phases could be crystallographically different but contain same absorbing atom. Can anyone suggest any literature which dealt with such a problem ?? With best regards, Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

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Bug in Athena merge preferences?
by Scott Calvin 28 Apr '11

28 Apr '11

Hi Bruce (and Ifeffiteers), I'm not positive this is a bug--maybe I'm just misunderstanding how the features are supposed to work. (It wouldn't be the first time!) In Athena 0.8.061 on a Mac running OS 10.5.8, I tried the following (I tried it in more than one project, to make sure it's not an intermittent bug): --Under Edit Preferences/Merge/Merge_Weight, choose "n" and apply to future sessions --Close Athena and reopen --Open a project --Mark two data sets. --Change the "importance" of one of them. --Under the merge menu, choose "weight by importance." --Under the merge menu, "merge marked data in chi(k)" The result for me is that the merged file ignores the importance I've assigned. I've also tried it in mu(E), with the same result. It seems that perhaps the "n" value in the preferences overrides the "weight by importance" option in the menu? If so, that's not the way I expect preferences and menu options to interact. Trying it with applying the "n" only to the current session also has an interesting behavior, although not necessarily the "wrong" one: it seems to just change the radio button in the menu. Also, if I change the radio button in the menu directly, the option under Preferences changes to match. For the current session, I can understand the argument that this is a reasonable behavior. But it is likely to cause confusion if a user changes it in the menu and then tries to use the preferences to check what the future sessions value is set to--if they haven't previously changed the preferences directly during the session, they might naturally assume that the value there is the value for future sessions, but in reality it just represents the most recent menu choice they made, and could be different in a future session. My suggested fix to both issues: the preferences should control what value the radio button takes on when Athena is first opened, and changes to the preferences should cause an immediate change to the status of the radio button. Subsequent changes to the radio button should not change the value under the preferences. And the behavior of the merge function should always reflect the current value of the radio button. --Scott Calvin Sarah Lawrence College

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GAANN Fellowships
by Carlo Segre 27 Apr '11

27 Apr '11

Dear All: Illinois Institute of Technology still has some GAANN Fellowships available in Physics and specifically for students interested in synchrotron radiation research. More information is available at http://www.iit.edu/research/undergraduate_research/news/gaan_award.shtml Note that the deadlines are not in force at this time, we will still accept applications. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org

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Re. Cofigurationally averaged EXAFS from MD
by Marcus Karolewski 22 Apr '11

22 Apr '11

> From: Francisco Garcia <garcia.ff.000(a)gmail.com> > I want to compute the ?average EXAFS spectra? using 500 snapshots of > atomic coordinates from my MD simulations. Dear Francisco and others, I am still exploring this area myself, but as suggested by Matt Newville, the best approach probably is to search through the MD configuration file for each absorber atom, generate its feff.inp file (based on a neighbour list), then execute FEFF and add the resulting chi(k) to an accumulator. I have a Windows program that will do this for a system with up to 3 atom types (e.g. O, Zn, H only) for both FEFF 7 and 8. It is easy to use, but does not recognize bonds that cross periodic boundaries. It is thus necessary to specify a central region of interest that is representative of the "bulk" of the system. This could be a problem if you have used a small MD simulation cell. Typically 10,000 absorbers require about 1 day of execution time, so doing 500 snapshots should be fairly easy. This is not the end of the fitting problem, unfortunately. Before making a comparison of the "synthetic" XAFS spectrum with experimental data, you need to fit E0 and S02. FEFF cannot necessarily calculate these accurately, but they have no bearing on the accuracy of your MD structural model. I feel that the E0 and S02 fits are best done using experimental standards. Attempting to fit them without knowledge of structure (e.g. by alignment-type operations between experimental and MD data) produces only approximate values - such fits also attempt to compensate, inappropriately, for any MD-related errors. After adjusting the MD-XAFS spectra for E0 and S02, you will likely find that the R-space peaks differ significantly from the experimental values in terms of position, height and width. Assuming your snapshots are representative of the canonical distribution, these remaining differences reflect the limitations of the potential. The structural sensitivity of XAFS is such that even quite small differences between potentials (e.g. cut-off distance) can produce visibly significant results. There are at least 2 ways to compare the experimental and (adjusted) MD XAFS spectra. (a) Visible or least-squares comparison of the spectra (in the R range of interest). (b) Direct extraction of cumulants from the MD data (by statistical analysis of atoms in the same region used to generate the XAFS), which are then used (with the inclusion of global scaling factors for dR and C2) to fit/reconstruct the experimental spectrum in Artemis (good MD data should produce not only good fits, but also scale factors near 1.0). Please contact me directly if you are interested to discuss further, or in using the code. I have glossed over some minor details (e.g. input data format, FEFF versions, chik.dat quirks, how to extract cumulants). Regards, Marcus Karolewski Message: 2 Date: Mon, 11 Apr 2011 13:18:04 -0700 From: Francisco Garcia <garcia.ff.000(a)gmail.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS from MD simulations Message-ID: <BANLkTinqbsgn6_JL_iVTcL1dfN39g1_Pig(a)mail.gmail.com> Content-Type: text/plain; charset=windows-1252 Dear users, I want to compute the ?average EXAFS spectra? usin 500 snapshots of atomic coordinates from my MD simulations. The idea is to compute the EXAFS spectra for each snapshot and then average the spectra over all snapshots (the so-called "MD EXAFS" approach). I know how to use Artemis to generate the EXAFS spectrum of a single snapshot. However, generating the EXAFS data for each of the 500 snapshots individually will be too time consuming and messy (this is essentially a book-keeping approach). I was wondering if there is a time-saving strategy/script for computing the average EXAFS instead of the snapshot-by-snapshot approach. For example, is it possible to include the coordinates of all the snapshots in a single feff.inp file and feed it to Artemis? Or if I have the feff.inp file for each snapshot, is it possible to write a script for Artemis that will compute each EXAFS spectra individually and dump them in a specified directory? Thank you very much.

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Re: [Ifeffit] Peak fitting to XANES data
by Bruce Ravel 21 Apr '11

21 Apr '11

Hi Zhixi, I am responding to your question on the Ifeffit mailing list (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) which is the appropriate venue for questions about the software. I encourage you to join the mailing list and use it for future questions about XAS or the use of our software. As for your questions, there are at least two options. The button labeled "Write a log file" actually exports a column data file with the results of the fit in the header and columsn of data containing the data, the fit, and each of the lineshapes. This file can be imported easily into Origin or most any other plotting program. The header also provides the parameters and formulas of the lineshapes, so you can easily replicate the fitted functions. The other option is that the tab labeled has the parameter values from the fit, so you can use those to replicate the line shapes. HTH, B On Thursday, April 21, 2011 11:04:10 am you wrote: > Good morning, > > Thank you for your attention. I use the peak fitting to some XANES data > using an arc-tangent and a Lorentzian. I got the fitting results and > analytical line shapes at Graphics Window #1, i.e. fit, step, peak 1. I > want to obtain the data of these lines, but I did not find the method. I > have no idea about this problem because I have to use the data in Origin > soft. > > Thank you for your help. > > Sincerely, > > Zhixi Zhao > Institute of Applied Ecology -- 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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Fwd: atoms.inp Mn3O4
by Bruce Ravel 20 Apr '11

20 Apr '11

Angelika, As you can see, I am responding to this email via the Ifeffit mailing list, which is the appropriate venue for questions about the software. It seems as though you took the crystal data from Matt's Atoms.inp database. It was not our intention to vouch for all the data you find there. Caveat lector, and all that. That particular file was something I converted from a public database from American Mineralogist. The citation for those data are included in the atoms.inp file. There are several CIF files for Mn3O4 available from http://www.crystallography.net/. I'm afraid that I am not clear what is wrong with the feff.inp file you attached. It looks like a plausible structure to me, although I am not particularly familiar with what Mn3O4 should look like. Perhaps someone else on the list is familiar with this material and can help Angelika better than I can .... Regards, B ---------- Forwarded Message ---------- Subject: atoms.inp Mn3O4 Date: Wednesday, April 20, 2011, 12:33:37 pm From: "Frau Dr. A. Chasse" <angelika.chasse(a)physik.uni-halle.de> To: bravel(a)bnl.gov Dear prof. Ravel, I have used atoms.f to produce a file for calculations af O K-edge XAS of Mn3O4 with the attached input file. I my opinion the constructed structure is not correct. I have also tried the file with shift, but no improvement. Look for the first two Mn atoms! If you look in feff.inp, you do not see the tetraeder of Mn atoms around O, which we should see in the spinel-like structure. May be you can help me. With best regards, Angelika Chasse -- , PD Dr. Angelika Chasse Martin-Luther-Universität Halle-Wittenberg Naturwissenschaftliche Fakultät II Institut für Physik D-06099 Halle (Saale) Telefon: +49 (0)345 55 25436 Telefax: +49 (0)345 55 25446 Email : angelika.chasse(a)physik.uni-halle.de ----------------------------------------- -- 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/ title name: Mn3O4 hausmannite title formula: Mn3O4 title sites: Mn1--2,O1 title refer1: Baron V, Gutzmer J, Rundlof H, Tellgren R title refer2: American Mineralogist 83 (1998) 786-793 title schoen: D_4h^19 space I 41/a m d a = 5.7691 b = 5.7691 c = 9.4605 rmax = 6.00 core = O1 atom Mn 0.00000 0.75000 0.12500 Mn1 Mn 0.00000 0.00000 0.50000 Mn2 O 0.00000 0.47230 0.25920 O1 ------ * This feff.inp file generated by ATOMS, version 2.50 * ATOMS written by and copyright (c) Bruce Ravel, 1992-1999 * Space group "I 41/A M D" may be referenced to a different origin. * If the atom list seems incorrect, put this line in your input file * shift 0 0.25 -0.125 * and run atoms again.- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 22991.6 cm^-1, delta mu = 22978.8 cm^-1 * specific gravity = 4.827, cluster contains 77 atoms. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * mcmaster corrections: 0.00766 ang^2 and 0.365E-04 ang^4 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: Mn3O4 hausmannite TITLE formula: Mn3O4 TITLE sites: Mn1--2,O1 TITLE refer1: Baron V, Gutzmer J, Rundlof H, Tellgren R TITLE refer2: American Mineralogist 83 (1998) 786-793 TITLE schoen: D_4h^19 EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 4.25031 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 0 0 0 EXAFS RPATH 8.50062 * kmax [ delta_k delta_e ] *XANES 4.0 0.07 0.5 * r_fms [ l_fms ] *FMS 4.25031 0 * *RPATH 0.10000 * emin emax resolution *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 8 O -1 -1 0 1 25 Mn -1 -1 3 2 8 O -1 -1 4 ATOMS 0.00000 0.00000 0.00000 0 O1 0.00000 1.44228 -1.28247 -0.08704 1 Mn2 1.93196 -1.44228 -1.28247 -0.08704 1 Mn2 1.93196 0.00000 1.60208 -1.26960 1 Mn1 2.04415 0.00000 0.15980 2.27809 1 Mn2 2.28369 0.00000 -2.56494 0.00000 2 O1 2.56494 -1.28247 -1.28247 2.19105 2 O1 2.84432 1.28247 -1.28247 2.19105 2 O1 2.84432 2.88455 0.00000 -0.17407 2 O1 2.88980 -2.88455 0.00000 -0.17407 2 O1 2.88980 1.28247 1.60208 2.36512 2 O1 3.13133 -1.60208 -1.28247 -2.36513 2 O1 3.13133 1.60208 -1.28247 -2.36513 2 O1 3.13133 -1.28247 1.60208 2.36512 2 O1 3.13133 0.00000 3.20416 0.00000 2 O1 3.20416 1.60208 1.60208 -2.53920 2 O1 3.40306 -1.60208 1.60208 -2.53920 2 O1 3.40306 2.88455 1.60208 1.09553 1 Mn1 3.47670 -2.88455 1.60208 1.09553 1 Mn1 3.47670 0.00000 -2.72475 2.27809 1 Mn2 3.55161 2.88455 0.15980 -2.45216 1 Mn2 3.78936 -2.88455 0.15980 -2.45216 1 Mn2 3.78936 0.00000 3.04435 2.27809 1 Mn2 3.80234 0.00000 -1.28247 -3.63472 1 Mn1 3.85434 2.88455 -2.56494 -0.17407 2 O1 3.86392 -2.88455 -2.56494 -0.17407 2 O1 3.86392 -2.88455 3.20416 -0.17407 2 O1 4.31481 2.88455 3.20416 -0.17407 2 O1 4.31481 0.00000 -4.16702 -1.26960 1 Mn1 4.35614 -4.32683 -1.28247 -0.08704 1 Mn2 4.51373 4.32683 -1.28247 -0.08704 1 Mn2 4.51373 0.00000 0.31961 4.55618 2 O1 4.56737 -2.88455 -2.72475 -2.45216 1 Mn2 4.66454 2.88455 -2.72475 -2.45216 1 Mn2 4.66454 2.88455 -1.28247 3.46065 1 Mn1 4.68417 -2.88455 -1.28247 3.46065 1 Mn1 4.68417 -1.44228 4.48663 -0.08704 1 Mn2 4.71355 1.44228 4.48663 -0.08704 1 Mn2 4.71355 -2.88455 3.04435 -2.45216 1 Mn2 4.85817 2.88455 3.04435 -2.45216 1 Mn2 4.85817 0.00000 0.31961 -4.90432 2 O1 4.91473 -4.16702 -1.28247 -2.36513 2 O1 4.96010 1.28247 -4.16702 2.36512 2 O1 4.96010 4.16702 -1.28247 -2.36513 2 O1 4.96010 -1.28247 -4.16702 2.36512 2 O1 4.96010 -1.44228 1.60208 4.64321 1 Mn2 5.11920 1.44228 1.60208 4.64321 1 Mn2 5.11920 -4.16702 1.60208 -2.53920 2 O1 5.13598 4.16702 1.60208 -2.53920 2 O1 5.13598 -1.60208 -4.16702 -2.53920 2 O1 5.13598 1.60208 -4.16702 -2.53920 2 O1 5.13598 1.28247 4.48663 2.19105 2 O1 5.15512 -4.48663 -1.28247 2.19105 2 O1 5.15512 4.48663 -1.28247 2.19105 2 O1 5.15512 -1.28247 4.48663 2.19105 2 O1 5.15512 -2.88455 -4.16702 1.09553 1 Mn1 5.18506 2.88455 -4.16702 1.09553 1 Mn1 5.18506 1.44228 1.60208 -4.81729 1 Mn2 5.27760 -1.44228 1.60208 -4.81729 1 Mn2 5.27760 4.48663 1.60208 2.36512 2 O1 5.31886 -1.60208 4.48663 -2.36513 2 O1 5.31886 1.60208 4.48663 -2.36513 2 O1 5.31886 -4.48663 1.60208 2.36512 2 O1 5.31886 0.00000 -2.88455 4.55618 2 O1 5.39253 0.00000 2.88455 4.55618 2 O1 5.39253 -2.88455 0.31961 4.73025 2 O1 5.54960 -2.88455 0.31961 -4.73025 2 O1 5.54960 2.88455 0.31961 -4.73025 2 O1 5.54960 2.88455 0.31961 4.73025 2 O1 5.54960 0.00000 -2.88455 -4.90432 2 O1 5.68973 0.00000 2.88455 -4.90432 2 O1 5.68973 5.76910 0.00000 0.00000 2 O1 5.76910 0.00000 -5.76910 0.00000 2 O1 5.76910 0.00000 5.76910 0.00000 2 O1 5.76910 -5.76910 0.00000 0.00000 2 O1 5.76910 0.00000 4.48663 -3.63472 1 Mn1 5.77417 0.00000 -1.28247 5.82578 1 Mn1 5.96527 END

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Looking for reviewers for another chapter
by Scott Calvin 19 Apr '11

19 Apr '11

Hi all, I have completed the draft of another chapter of my textbook, and am again interested in reviewers (repeat reviewers are fine!). The chapter I've currently got ready is about the parameters of the EXAFS equation, covering physical meaning, effect on graphs, a bit on common constraint schemes, etc.. This will be chapter 10 in the book, and so it's not suitable for absolute beginners. I am interested, though, in hearing from people who are still learning to fit, as well as experts. If you are interested in reviewing the chapter and can get feedback back to me by 4 May, please contact me directly at SCalvin(a)slc.edu . --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Problem with running FEFF in Artemis
by Jatinkumar Rana 15 Apr '11

15 Apr '11

On 15.04.2011 17:29, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: Dear Bruce, Thank you very much for your reply. The feff.inp file with shift (0,0,0) is quite right. I was just alarmed by that message everytime i ran ATOMS. But it is clear now. :-) Thanks a lot. With best regards, Jatin Rana Berlin -- Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

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Soft XAS PhD studentship at the University of Manchester
by Sven Schroeder 15 Apr '11

15 Apr '11

Dear colleagues I would be grateful if you could bring the following PhD opportunity in soft XAS of crystal nucleation from solution to the attention of potential candidates: http://www.jobs.ac.uk/job/ACJ915/4-phd-studentships-available-at-leeds-manc… ================================= Applications close on 16 May 2011 ================================= Background information about the project is available here: http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/I013563/1 and here: http://gow.epsrc.ac.uk/ViewGrant.aspx?GrantRef=EP/I014446/1 Interested candidates can also contact me directly by email. -- Dr Sven L.M. Schroeder (mailto:s.schroeder@manchester.ac.uk) Reader School of Chemical Engineering and Analytical Science (CEAS) The University of Manchester, Manchester M13 9PL, United Kingdom http://www.slmslab.info Also at: School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom Tel +44 (161) 306 4502 Fax +44 (161) 306 8867 Office: Room C57 (Jackson's Mill) DISCLAIMER The views expressed within this message are those of the sender, not those of The University of Manchester or one of its units. While all emails and attachments are scanned for viruses before sending, we cannot accept any responsibility for viruses, so please scan all emails and attachments. This email is intended for the addressee only. If you are not the intended recipient, please notify the sender and delete this email immediately. END OF MESSAGE

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Problem with running FEFF in Artemis
by Jatinkumar Rana 15 Apr '11

15 Apr '11

Dear Ifeffit users, I am facing a strange problem in running ATOMS for the "F d-3 m" space group. It gives me following message : "F d -3 m" appears in the International Tables with multiple choices of origin. If the atoms list seems wrong, you should use a shift vector of: -0.125, -0.125, -0.125 After i add shift vector on ATOMS page and run FEFF in ARTEMIS, it gives me error and shows that many pairs of atoms are close together. The crystallographic data used to run FEFF were obtained using Neutron diffraction experiments. I do not understand the reason for this since i have never come across such a problem. Can anyone help me to comeout of this problem ? I have attached the Artemis project file with this mail for further detail. With best regards, Jatin Rana Berlin -- Jatinkumar Rana Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Institut für angewandte Materialforschung FI-1 Mikrostruktur Hahn-Meitner-Platz 1 D-14109 Berlin Germany Tel: +49 30 8062-43217 Fax: +49 30 8062-43059 eMail: jatinkumar.rana(a)helmholtz-berlin.de **************************************************************************************** Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Vorsitzender des Aufsichtsrats: Prof. Dr. Dr. h.c. mult. Joachim Treusch Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz der Gesellschaft: Berlin Handelsregister: AG Charlottenburg, 89 HRB 5583

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Re: [Ifeffit] Athena question
by Matt Newville 14 Apr '11

14 Apr '11

Hi Ganga, On Thu, Apr 14, 2011 at 5:17 AM, Ganga Hettiarachchi <ganga(a)k-state.edu> wrote: > Matt, > > Have you ever tried to save LC fitting results done using derivatives- we > did as we were doing for any fitting done using nor spectra- that is use > “write a report” option. However it does not save what we see in the LC > fitting graphic window. Why is that? How do we know what’s been saved when > we do that? How can we get it saved to generate stack plots on excel? > I'm not I've ever tried to get the report from a derivative LC fit, so I'll ask the Ifeffit mailing list. Anyone know how to extract this info easily? --Matt

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Re: [Ifeffit] Strategy to obtain cofigurationally averaged EXAFS from MD simulations
by Francisco Garcia 13 Apr '11

13 Apr '11

Dear Anatoly, Thank you very much for your reply. Unfortunately, your PRB references did not solve my problems. I am trying to reproduce the results of Cauet et al [J. Chem. Phys. 132, 194502 (2010)]. I basically have over 500 snapshots of a single Zn2+ ion (absorbing atom) in water (O atoms are the scattering atoms). I have the feff.inp file for each snapshot ready for Artemis. I basically want an efficient way to obtain the chi(k) of data for each snapshot and average the chi(k) as opposed to loading the feff.inp files one by one. Specifically a sample script/example will be of imense help. I could not find much information in the Artemis user manual. I must also state that I am an EXAFS novice so a step by step explanation will help me a lot. Thank you very much.

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