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

Athena: problems with LCF
by Nina Siebers 05 Aug '11

05 Aug '11

Dear All, I acquired Cd L3-edge spectra of some binary and ternary mixtures in varying proportions and for the individual components. Then, I tried to fit the reference spectra to the spectra of the mixtures using linear combination fitting of Athena to get their abundance. However, results were disappointing despite all spectra were carefully energy calibrated and normalized, so I decided to create simple mathematical ternary mixtures by summing up the spectra of the individual reference spectra (edge step normalized) and tried the fitting again to exclude mixing-failures and check sensitivity of LCF with the idealized spectra. Unfortunately, LCF was also not able to reliable deconvolute these spectra into the individual reference spectra. Does anybody have an explanation for that? It would be nice if somebody could give me information about the mathematical fitting algorithm implemented in Athena. Thanks a lot! Wishes, Nina

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asking questions effectively (yes, *you* need to read this email)
by Bruce Ravel 05 Aug '11

05 Aug '11

Hi everyone, This has been a particularly troubling week for me here on the Ifeffit mailing list. This week we have seen an unusually large number of poorly asked questions. Not bad questions, mind you, just questions that have been asked in a manner that makes it hard to provide a useful response. On Tuesday, someone had a question about a fit in Artemis, but only posted the project file which demonstrated the problem after being prompted to do so. On Wednesday, someone had an issue about LCF fitting in Athena that is contrary to most people's experience with the program. That person did not bother to provide an example project file or any other supporting information to clarify what happened. On Thursday, another person had an Artemis problem which was described in a short and cryptic email. Only after being prompted 3 times to post an example was someone able to be of help. Also on Thursday, we saw the third example in one week of a problem with Artemis, but no example project file to demonstrate the problem. Today, we see someone with a crystallography problem, but we do not see the actual data that would allow someone to reproduce the problem on their own computer. Happily, on Wednesday Paul Bingham posted a clear question and attached Athena and Artemis project files. He very quickly got two useful answers. You do see the lesson here, don't you? If your problem cannot be reproduced on someone else's computer, it is unlikely that you will get a satisfying answer. Don't wait to be prodded. Supply the project file or crystal data that demonstrates the problem *in your first email*. The so-called experts on this list, including me, really do want to help you with your problems. But we are not mind readers. You have to meet us half way. 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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Problem writing Feff 9 input
by Shaner, Ted V 05 Aug '11

05 Aug '11

I have a CIF file that I checked using Mercury to insure that the structure was correct. When I run ATOMS and then use the FEFF.INP file it produces, there seems to be a mistake made. When I view the structure using the JMOL application in FEFF, there are atoms in the wrong locations. FEFF will not run, as atoms are too close together. I tried to remove the atoms, from the list of atoms too close together generated by the executing list, but it does not solve my problem, and the atoms are still in the wrong place. I then tried to cut and paste the coordinates in to a FEFF input file, as was shown how to do when working with non-crystalline materials. This doesn’t work. I also tried to redo the example that Bruce showed, which also won’t open in FEFF, a problem with line 25, though I have been unable to figure out what that problem is. Is there a difference in writing input files for FEFF9? I am at a loss as to why simply cutting and pasting the example doesn’t work. Also, when I try to add coordinates to the FEFF.INP file, I get what looks like a ball in JMOL, and the feff program runs continuously in a loop, with no real calculations being performed. Any help would be greatly appreciated! Thanks, Ted Shaner Department of Chemistry Tulane University Office: Percival-Stern 5016

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Trouble with Artemis
by Morgan Scott 04 Aug '11

04 Aug '11

Hello; Trying to plot a fit in Artemis. My .dat files appear flat on y= zero in the plot window. they open fine in Athena. Any help would be appreciated. regards

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Re: [Ifeffit] Fe K-edge second shell problems
by Scott Calvin 03 Aug '11

03 Aug '11

Hi Paul, Looking at your data, I agree that there does seem to be second-shell scattering present in the signal. Unfortunately, that most likely means that your material is not close to one of the "obvious" model compounds. One possibility to keep in mind is that you may have some kind of overlapping paths in that second "shell"--for example, partially Fe-Na and partially Fe-Ca, or an assortment of Fe-Na's at different distances. A clue can perhaps be obtained by noting the relative height of the peak near 2.3 angstroms compared with the large peak you've fit. As k- weight is raised from 0 to 1 to 2 to 3, the peak at 2.3 angstroms does not grow relative to the first peak. That suggests the scattering may be from another low-Z element like oxygen. So I'd tentatively try an Fe-O path around 2.7 angstroms with its own delR, ss, and N guessed. (Meanwhile, set N_1 to 4 to reduce correlations--you've said you expect the first shell to be tetrahedral.) Good luck--sounds like a stubborn one! --Scott Calvin Sarah Lawrence College On Aug 3, 2011, at 9:49 AM, Paul A Bingham wrote: > Dear Ifeffit users, > > I have been struggling with this problem on and off for many months > and I cannot resolve it - hopefully someone out there can help.... > > I have collected fluorescence Fe K-edge EXAFS of oxide glasses doped > with low levels (0.2%) of Fe. The glasses are typified by their major > components SiO2, Na2O, CaO and also low levels of Fe2O3 and CeO2 > dopants. I'm currently trying to fit the Fe EXAFS. The first shell is > relatively easy to fit and I'm reasonably happy with the fit I > obtained using a tetrahedral Fe3+ standard, in this case FePO4. The > fits are consistent, as I expected to find, with Fe3+ > tetrahedrally-coordinated with four oxygens. > > The problem comes - and here's where I could really use some > suggestions - when I try to fit second Fe-x distance. It seems clear > to me that a second Fe-x distance (and possibly a third) are present > in the data. However, despite expending a great deal of time I am > unable to get a fit that appears anywhere near sensible and robust and > for which the output parameters are sensible. I suspect the second > Fe-x distance (I reckon about 2.8 Angstroms) to be Fe-Na but Fe-Ca, > Fe-Si or Fe-O may also be possible. It's also possible that it is > Fe-Fe or Fe-Ce. > > I have tried all of the "obvious" Fe model compounds (aegirine, > clinopyroxine, etc) and also many others and I simply cannot get > anything approaching a decent fit. The vast majority of distances in > model compounds are Fe-O distances around 1.9-2.1A, then there is > usually a "gap" until about 3.1A. > > I have checked my background subtraction and tried out many different > options, changes and tweaks that I know or can find suggested but I > cannot obtain a fit that is any good. And so I ask my colleagues out > there who are more experienced than I with EXAFS - can anyone help > with this conundrum? > > I have attached the Artemis file with the data and simple one-shell > fit using FePO4 cif file; and the Athena file FYI. > > Thanks in advance for your time and I look forward very much to > reading any suggestions you may have. > > Warm Regards > > Paul Bingham > > -- > Dr. Paul A. Bingham > Immobilisation Science Laboratory > Dept. of Engineering Materials > University of Sheffield > Mappin Street > Sheffield > S1 3JD > UK > > Email: p.a.bingham(a)sheffield.ac.uk > Direct Line: (0114) 2225473 > < > Bingham_Fe_EXAFS_Glass_Ifeffit_Artemis > ><Bingham_Fe_EXAFS_Glass_Ifeffit_Athena.prj><ATT00001..txt>

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Postdoctoral position at Yeshiva University
by Anatoly I Frenkel 03 Aug '11

03 Aug '11

Dear IFEFFIT subscribers: Please find here the info about the job opening: Postdoctoral position at Yeshiva University Physics Department of Yeshiva University in New York City has immediate opening for a postdoctoral research associate position. The postdoc will investigate thermal, structural and electronic properties of nanocatalysts and contribute to the ongoing research in heterogeneous catalysis. He or she will be stationed at Brookhaven National Laboratory (BNL) and work closely with BNL departments (NSLS, Chemistry, Physics/Materials Science and the CFN) as well as the outside collaborators. Required qualifications: expert knowledge of XAFS and x-ray diffraction and experience with nanomaterials characterization. Hands on experience with vibrational spectroscopies (Raman, IR) and electron microscopy is a plus. The research will be performed under the direction of Prof. Anatoly Frenkel primarily at the Synchrotron Catalysis Consortium (http://www.yu.edu/scc) at the National Synchrotron Light Source. Applicants should forward cover letter and CV, and arrange for three letters of recommendation to be sent to Prof. Frenkel at anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

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Fe K-edge second shell problems
by Paul A Bingham 03 Aug '11

03 Aug '11

Dear Ifeffit users, I have been struggling with this problem on and off for many months and I cannot resolve it - hopefully someone out there can help.... I have collected fluorescence Fe K-edge EXAFS of oxide glasses doped with low levels (0.2%) of Fe. The glasses are typified by their major components SiO2, Na2O, CaO and also low levels of Fe2O3 and CeO2 dopants. I'm currently trying to fit the Fe EXAFS. The first shell is relatively easy to fit and I'm reasonably happy with the fit I obtained using a tetrahedral Fe3+ standard, in this case FePO4. The fits are consistent, as I expected to find, with Fe3+ tetrahedrally-coordinated with four oxygens. The problem comes - and here's where I could really use some suggestions - when I try to fit second Fe-x distance. It seems clear to me that a second Fe-x distance (and possibly a third) are present in the data. However, despite expending a great deal of time I am unable to get a fit that appears anywhere near sensible and robust and for which the output parameters are sensible. I suspect the second Fe-x distance (I reckon about 2.8 Angstroms) to be Fe-Na but Fe-Ca, Fe-Si or Fe-O may also be possible. It's also possible that it is Fe-Fe or Fe-Ce. I have tried all of the "obvious" Fe model compounds (aegirine, clinopyroxine, etc) and also many others and I simply cannot get anything approaching a decent fit. The vast majority of distances in model compounds are Fe-O distances around 1.9-2.1A, then there is usually a "gap" until about 3.1A. I have checked my background subtraction and tried out many different options, changes and tweaks that I know or can find suggested but I cannot obtain a fit that is any good. And so I ask my colleagues out there who are more experienced than I with EXAFS - can anyone help with this conundrum? I have attached the Artemis file with the data and simple one-shell fit using FePO4 cif file; and the Athena file FYI. Thanks in advance for your time and I look forward very much to reading any suggestions you may have. Warm Regards Paul Bingham -- Dr. Paul A. Bingham Immobilisation Science Laboratory Dept. of Engineering Materials University of Sheffield Mappin Street Sheffield S1 3JD UK Email: p.a.bingham(a)sheffield.ac.uk Direct Line: (0114) 2225473

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Invitation to connect on LinkedIn
by Somaditya Sen 03 Aug '11

03 Aug '11

LinkedIn ------------ ifeffit, I'd like to add you to my professional network on LinkedIn. - Somaditya Somaditya Sen Research Associate at Physics Dept., UWM Greater Milwaukee Area Confirm that you know Somaditya Sen https://www.linkedin.com/e/o6ijfu-gqwaay89-k/isd/3744123338/3Yn0HeKq/ -- (c) 2011, LinkedIn Corporation

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Re: [Ifeffit] Question on GDS values: amp
by Scott Calvin 02 Aug '11

02 Aug '11

Hi Nic, On Aug 2, 2011, at 6:41 AM, Nicholas.Tse(a)csiro.au wrote: > Just a sidenote, is the general workflow for fitting XAFS data the > following: > > Fit first shell and get reasonable Enot and Amp and then make set > them, then incrementally add more of the scatter paths and adjust > the delR for each path correspondingly. Adjusting degeneracy for > atom assuming there are slight differences in the atoms spacing. > > I know the question is very trivial but I don't seem to be able to > find a general guideline for knowing when the fitting process is > over in these type of analysis. As for your side note, there are several workflows that have success. The most appropriate one depends both on your level of knowledge about the material and your personal preference. I don't particularly favor the one you describe, though, because it's an attempt to fit a few parameters at a time to avoid wrestling with correlations. That doesn't end up actually avoiding correlations; it just locks them in. For instance, if you first guess amp, find a "best fit" value, set it, and then run a fit with something else varied (say, a degeneracy), then you've artificially broken the correlation between amp and degeneracy. But you've done it in a completely arbitrary way...you haven't really explored the space of the two varied jointly. (Of course, if you're only doing a single shell, you can't vary both S02 and N, because they correlate completely. But you certainly can't pretend you can by first varying S02 with N fixed, and then varying N with S02 fixed!) The two most prevalent valid fitting strategies I've seen are: "Bottom up." (That's my name for it. I've also heard it called "shell by shell.") In this strategy, you start with a single shell with few constraints; perhaps you guess N (taking S02 from a standard), E0, delR, and ss. You try different nearest-neighbors and see what works best. As you begin to gain knowledge about the system, you add more distant shells and begin to add reasonable constraints. In a biological system where you've determined nearest neighbors are sulfur, for instance, then your knowledge of the particular system may suggest what ligands are present, which might provide information about second nearest-neighbors. For instance, the number of second nearest-neighbor carbons might be equal to the number of near-neighbor sulfurs, constraining some of the degeneracies. "Top down." Start with a highly-constrained, multi-shell fit. For instance, you might include all important paths out to 5 angstroms, with the only free parameters S02. E0, and a sigma2 parameter or two. If the fit appears qualitatively close, constraints can then be relaxed to more realistically model the particular features of the material (as one example, you can vary degeneracies to allow for vacancies or nanoscale effects). If the fit does not appear qualitatively close initially, it is probably the wrong starting material. (Amplitudes are often far off initially with this approach, and there may be small phase shifts, but the first few big peaks should be roughly in the right place. A minor variation on this approach is to start with a sum of paths rather than fit at all.) Note that both strategies end up in the same place: a modestly constrained multi-shell fit. (And no, that's not always possible-- sometimes first shell information is all you can get.) When do you use each? If your material is a modestly modified version of a known crystal, top down is a good way to go. For instance, you might have a doped zinc oxide. You know the structure of zinc oxide; the question is the effect of the dopant. Why waste effort trying to fit just a nearest-neighbor first, which can be quite difficult, when you think you know the rough structure out to several angstroms? On the other hand, for something like a protein you probably don't initially know much about the structure at all. Then bottom up works better. Many problems, such as some environmental problems, fall in between the two, and either approach might be effective. A strategy that I've sometimes seen used by beginners in workshops, which is not a good idea, is to fit one shell, get the results, set the values of those parameters to the result of the fit, add another shell, and so on. This is a misunderstanding of the bottom up approach! Rather than using information from outer shells to achieve better fits on the inner shells (or vice-versa), you lock in distortions and make it difficult to evaluate statistically-related measures such as error bars. Hopefully that helps! --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Question on GDS values: amp
by Bruce Ravel 02 Aug '11

02 Aug '11

Nic, I think that you have rediscovered something many of us have found before you. If your fit is wonky -- an E0 of >50 for instance -- that usually means you have made a mistake in your starting structure. In this case, there was a problem in the crystal data. Sonetimes one presumes, say, a sulfide when the sample is actually oxidized. Sometimes one makes the absorption edge mistake I suggested. The moral is that, if your fits are wonky, that is usually telling you something about your initial assumptions. To say that another way, a screwy fit is usually useful information and a hint that you need to reexamine your work carefully. I also want to point out that when you described your problem in words, you got a bunch of interesring, but ultimately unhelpful guesses. When you provided enough information that someone else could reproduce the problem, Dominic was able to provide you the right answer. That's a lesson for everyone reading this email! B -- Dominik Samuelis <d.samuelis(a)fkf.mpg.de> wrote: Dear Nic, I've had a short look into your Artemis file. First of all, it seems that something's wrong with the Gd2O3 structure data in your feff.inp. Running feff on your feff.inp gives this error: Feff 8.40 ... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 8 14 8 2.24848E+00 2.70250E+00 0.00000E+00 14 2.47549E+00 2.70250E+00 0.00000E+00 Run continues in case you really meant it. WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 9 15 9 -2.24848E+00 -2.70250E+00 0.00000E+00 15 -2.47549E+00 -2.70250E+00 0.00000E+00 Run continues in case you really meant it. [...] It seems that all your "Gd2" atoms have a duplicate in your "Gd3" atoms, shifted only by ~0.2 angstroms in either x,y, or z direction. Looking further at your feff.inp, already your ATOMS input somehow looks broken: (your ATOMS list) * Gd 0.25000 0.25000 0.25000 Gd1 1.00000 * Gd 0.02100 0.00000 0.25000 Gd2 1.00000 * Gd 0.54200 0.00000 0.25000 Gd3 1.00000 * O 0.12500 0.12500 0.37500 O1 1.00000 * O 0.12500 0.37500 0.37500 O2 (my list, cif file from ICSD, Shuenn et al., J. Chin. Chem. Soc. 57 (2010), 938) Gd 0.25 0.25 0.25 Gd1 1.000 * (8b position) O 0.3904 0.1513 0.379 O1 1.000 * (48e position) Gd 0.9710 0 0.25 Gd2 1.000 * (24d position) Using this crystal data, I was able to fit your data reasonably well (didn't tweak to make the fit perfect though...) - see attached file! I've also attached the .cif file that I've used, in case you want to compare with yours. BTW, enot values of >20 eV shouldn't really happen in any fit. Best regards, Dominik On 02.08.2011 04:42, Nicholas.Tse(a)csiro.au wrote: > Thank you all the suggestions. > > I believe the ATOM model used is representative of what it should be. I generated the FEFF file from the CIF file from the American Mineralogist X'stal DB. The generated FEFF has the edge L3 that should be fine. A simple summation of the scatter paths does roughly produce the pattern for the sample, except for the amplitudes. > > The enot was found to be 53.8995 +/- 2.7632. > > I have also included the .prj and .apj files for your inspection. > > Regards, > > Nic > > > > >_____________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Max Planck Institute for Solid State Research Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

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