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

Re: [Ifeffit] Athena: problems with LCF
by Scott Calvin 15 Aug '11

15 Aug '11

Hi Nina, Thank you for bringing your question to the list. As others have said, the problem lies with not having enough data to normalize effectively, and is compounded by not taking control of the normalization process to make sure its relatively consistent. Standard A, for instance, has a post-edge line that cuts very low through the data, as does D. The 1:1 A to D calculated mixture, though, comes across more evenly. This is a problem even with calculated mixtures, as you chose to import the calculated mixture as a mu(E) file, and not as a norm(E) file. In theory, this should be fixable by fixing the edge step of the calculated spectrum to 1, so that it doesn't try to normalize it again. Something's not quite right when I do that, because the calculated average of A and D sometimes slips below both of the other graphs, and an average shouldn't do that. Nevertheless, it gets us close: an LCF fit now gives us 54.5% A and the rest D. Another approach is to remove the "force weights to 1" checkbox. This is often necessary if normalizations are in doubt. That works quite well here, delivering an A to B ratio of 49 to 53. Summary: --It's best to collect data far enough above the edge so that you establish an unambiguous post-edge trendline, if possible. --Post-edge lines should be examined, and changed if they are inconsistent between spectra being used for LCF. It's better to just eyeball normalization than to use radically different trendlines, for instance. I sometimes play around by eye with trendlines to see what range of normalizations they give, and incorporate that in to my final reported uncertainties. --If normalizations are difficult for a particular set of spectra, it is often better to remove the requirement that weights sum to 1. To the degree that normalizations are off, there will be some error in the values that are found, but at least the fitting routine is able to try to compensate for normalization differences by adjusting the weights. In other words, forcing the sum to be 1 when the normalizations are different forces a bad fit. Allowing them to total to anything allows the algorithm to transfer errors in normalization to errors in weighting. Hope that helps! --Scott Calvin Sarah Lawrence College On Aug 15, 2011, at 5:40 AM, Nina Siebers wrote: > Dear All, > > I acquired Cd L3-edge spectra of some binary and ternary mixtures in > varying proportions and for the individual components. The mixtures > were created on Cd-mass basis. 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, the results were > disappointing despite all spectra were carefully energy calibrated and > normalized, so I decided to create simple mathematical binary and > ternary mixtures by summing up the spectra of the individual reference > spectra. After that I did an edge-step normalization in excel and > imported the normalized calculated mixtures into Athena. Then, I tried > the fitting again to exclude mixing-failures and check sensitivity of > LCF with the idealized spectra. Even though the results of the LCF of > the mathematical mixtures were better compared to the real mixtures, > 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. > > Attached is a data file of three mixtures (two ternary and one binary > mixture) including the mathematical mixture created in excel (named > calculated at the end). Mixing ratios are named 1to1to1 (meaning 1:1:1 > of the components in the same order). For the 1:1:1 ternary > mathematical mixture the deconvolution was very good, but the others > need improvement. > > I hope I made my problem clear this time. > > Thanks a lot! > Wishes, > Nina > > > <Mixtures.prj><ATT00001..txt>

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Re: [Ifeffit] how to consider Jahn-Teller distortion?
by Enyuan Hu 09 Aug '11

09 Aug '11

Dear all, Thank you so much for all the suggestions. Dear Matt, thank you for pointing out my rookie mistake and suggested correction. I didn't consider J-T distortion in my new try but the fitting was improved nonetheless. You suggested changing dk from 1 to 4 or 5 for the Kaiser-Bessel window and this has been proved helpful. I guess some appreciation of how the windows function works is needed to really gain insight into why the change of dk is beneficial to the fitting. Also, I was wondering if you can suggest dk values for other windows? Dear Matthew, thank you for your suggestion about using the two shell model. Just like you and Matt pointed out, limited k range poses a great challenge in analyzing J-T distortion. At this point, I do not have enough confidence to implement two shell model. Dear Dominik, thank you for your recommendation of the paper. I looked through it and found that a combination of diagnostic tools was used in that paper. The J-T distortion analysis was based on the results of both XAS and vibrational spectroscopy. Dear Ditty, thank you for your suggestion also. I attached the new fitting file along with the LiCoO3 inp file that you may need. In the new fitting, I actually input the LiMnO2 file (with the same structure as previous LiCoO3) as the sample is more like Fe-doped LiMnO3 (though there're actually substantial doped Ni present and I don't know how to consider that yet). -- Enyuan

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how to consider Jahn-Teller distortion?
by Enyuan Hu 09 Aug '11

09 Aug '11

Dear all, I'm trying to fit the Fe K-edge EXAFS data and I appreciate that Fe in my sample mainly exists as Fe4+, which is associated with Jahn-Teller distortion. The one shell model that considers Fe residing in the standard octahedral apparently didn't give satisfactory result. I'm sorry that even though I found people do fitting considering Jahn-Teller distortion, I am still not aware of how to carry that out in Artemis. Can someone helps me to look at my fitting and give me some guidance on how to implement fitting that considers Jahn-Teller distortion in Artemis? Thank you. -- Enyuan

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Has anyone got this technical problem during the fit?
by NIRAWAT THAMMAJAK 09 Aug '11

09 Aug '11

Dear All, I was just wondering if some of you may have experienced a problem like this in the fit; I was trying to improve the precision of some fit parameters by doing guess, def, and set. In the 61st fit, I tried to split parameters from constraints that i have made. Then, the program didn't show me the results of the fit. I knew that something might have gone wrong, the program forced me to close. Fortunately, there was a window asking me to save it before closing the project. I opened again the project file after it was safely saved. This time, I could not perform any fitting - the green 'Fit' button was frozen and it's not possible to click it. The red message below showed "Artemis trapped one or more errors! Error message dumped to the screen", but I couldn't see such error message on the screen. I closed the project and opened the file again, the 'Fit' button seemed to work this time. Anyway, I still had that red message below said "Artemis trapped one or more errors!...". After clicking at the data file, the red message was gone and replaced by the number of data points, "22 independent points data points (Nyquist): ...". The numbers of the fit and FT parameters were then shown in the boxes on the left as usual, but the title of data was replaced by "o"! I thought it was okay, then I performed other fits. It worked fine. Until the recent fit that I have it blown up, so I saved and closed the project. Now when I try to open the file, I have got the earlier problem, frozen 'Fit' button. Clicking at data file doesn't help as it used to be. I have tried another saved file in this series of .apj files (same data), they have got the same problem. I have tried open another data file like eto.apj in the demo, it's also got that problem with the red message "Artemis trapped one or more errors!.." too. I don't understand what should have gone wrong with the program. Your help will be very much appreciated. Thank you, Nirawat. -- Nirawat Thammajak DPhil Candidate in Inorganic Chemistry Balliol College Oxford OX1 3BJ United Kingdom

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Re: [Ifeffit] how to consider Jahn-Teller distortion? (Enyuan Hu)
by Ditty Dixon 09 Aug '11

09 Aug '11

Hello Enyuan, I am afraid that you are using LiCoO2, structure data base to fit your Fe structure (look like spinal). The feff calculation you did was completely at the Co edge. If you could re post your questions with modified feff calculation somebody could really help, I also need some input in this regards, as I myself might work in some batteries materials. Best wishes, Ditty On Tue, Aug 9, 2011 at 2:47 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. how to consider Jahn-Teller distortion? (Enyuan Hu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 8 Aug 2011 20:47:52 -0400 > From: Enyuan Hu <bearcharge(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] how to consider Jahn-Teller distortion? > Message-ID: > <CAJud35NE3wkcw4MgrYM+cPzDGjO3gAOp3uRzp9t1uzrypHk1=g(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I'm trying to fit the Fe K-edge EXAFS data and I appreciate that Fe in my > sample mainly exists as Fe4+, which is associated with Jahn-Teller > distortion. The one shell model that considers Fe residing in the standard > octahedral apparently didn't give satisfactory result. I'm sorry that even > though I found people do fitting considering Jahn-Teller distortion, I am > still not aware of how to carry that out in Artemis. Can someone helps me > to > look at my fitting and give me some guidance on how to implement fitting > that considers Jahn-Teller distortion in Artemis? Thank you. > > -- > Enyuan >

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Re: [Ifeffit] asking questions effectively (yes, *you* need to read this email)
by Scott Calvin 08 Aug '11

08 Aug '11

One addition to Bruce's appeal: for some subscribers to the list, large attachments are a problem. For instance, some people are still working at dial-up speeds (due to the US' rural digital divide, I was one of those recently), or even have limits on the amount of data they can download in a month. The question, then, is what is a "large" attachment? We've had some discussion of that on the list previously, and never arrived at a hard- and-fast rule. Nonetheless, let me suggest that anything below 1 megabyte is fine--in fact, it should be encouraged so that we can help with the kind of questions Bruce just enumerated. Paul's files, for instance, were 214 KB, or 0.24 MB. I suggest, therefore, that if you have a project file that is large because, for instance, it has many, many fits in its history, please re-save it in a smaller version, and attach that. You should also be careful with screenshots that they are not needlessly large--e.g. saved in a resolution far beyond what is necessary. In the occasional case that the problem or question requires a large file to manifest, such as that described by Nirawat yesterday, some other arrangement needs to be worked out. It's possible, for instance, to use a service such as Dropbox to make the file available without actually attaching it to an email. --Scott Calvin Sarah Lawrence College On Aug 5, 2011, at 3:25 PM, Bruce Ravel wrote: > > 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 >

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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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Question on GDS values: amp
by Nicholas.Tse＠csiro.au 02 Aug '11

02 Aug '11

Dear All, Just wondering what could I do to make the amp guess value as a positive number? If I run it and let it float (i.e. guess), the amp becomes negative in the resulting fits, but the fit has nice delr and ss values (i.e. make sense). If I restrict the amp value to 1, everything else doesn't fit. I am only fitting the first nearest neighbour in a measured standard; Gadolinium oxide. Regards, Nic Nicholas Tse Postgraduate Student, University of Melbourne CSIRO Materials Science and Engineering. Phone: +61 3 9545 2626 | Mobile: 0403 782 805 nicholas.tse(a)csiro.au<mailto:nicholas.tse@csiro.au> | www.csiro.au<http://www.csiro.au> | www.csiro.au/cmse<http://www.csiro.au/cmht> Address: Ian Wark Laboratories, Bayview Ave Clayton 3169 VIC [Postal: Private Bag 10, Clayton South VIC 3169] [Deliveries: Gate 3 Normanby Road, Clayton VIC 3168] Please consider the environment before printing this email.

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Re: [Ifeffit] Question on GDS values: amp
by Scott Calvin 01 Aug '11

01 Aug '11

Hi Nic, The delr and ss values may adopt reasonable values with a negative amp, but they're almost certainly not the right values. A negative amp turns the chi(k) upside-down. To make it ft, the other parameters then have to shift the graph over by half an oscillation, yielding values of E0 and delR that are wrong. It is unusual that a first-shell fit to a standard doesn't seem to be giving a qualitatively reasonable result with an amp of 1. What happens if you do a sum of the most important paths without a fit? Does the fit look qualitatively correct over a large range of R? (The amplitudes will of course be substantially off without a fit.) It sounds like something substantial is wrong: either the material isn't actually dadolinium oxide, or the structure you're using for the feff calculation isn't right (is there more than one crystallographic setting?), or there was serious distortion in the measurement (perhaps a thick, concentrated standard was measured in fluorescence without correction). --Scott Calvin Sarah Lawrence College On Aug 1, 2011, at 12:36 AM, Nicholas.Tse(a)csiro.au wrote: > Dear All, > > Just wondering what could I do to make the amp guess value as a > positive number? If I run it and let it float (i.e. guess), the amp > becomes negative in the resulting fits, but the fit has nice delr > and ss values (i.e. make sense). If I restrict the amp value to 1, > everything else doesn’t fit. I am only fitting the first nearest > neighbour in a measured standard; Gadolinium oxide. > > Regards, > > Nic >

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Portable Ifeffit packet + portable python
by jack song 01 Aug '11

01 Aug '11

Dear all, I made a portable version of Ifeffit, which is updated to the latest version. To run a program x, please double click RunXxx.bat file. There are also 3 portable python (2.5, 2.6, 2.7) with Ifeffit module. Please extract it to the same folder. (extract here as folderA\IfeffitPortable, folderA\PythonPortablexxx) Download below, IfeffitPortable: http://dl.dropbox.com/u/2776935/IfeffitPortable.zip<http://dl.dropbox.com/u/2776935/IfeffitPortable.zip> Python 2.5 portable: http://dl.dropbox.com/u/2776935/PythonPortable_1.1_py2.5.4.zip Python 2.6 portable: http://dl.dropbox.com/u/2776935/PythonPortable_1.1_py2.6.1.zip Python 2.7 portable: http://dl.dropbox.com/u/2776935/PythonPortable2.7.2.1.zip If there is a problem, please let me know. I will make more information available later. PS, if you need a dropbox, which I highly recommend. Please click my refer link http://db.tt/WRHqYkA, which will increase my box 250MB. Best, Jack Song

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FEFF6L.02 - missing path?
by Pawel Zajdel 29 Jul '11

29 Jul '11

Hi Matt, OK, I got the point and it is clear now. Thanks Pawel > As you've probably read in the Feff documentation, Feff has a couple > of filters that it uses: one fast and less accurate to eliminate > really unimportant scattering paths to make the path-finding mechanism > more efficient, and one slightly more accurate one to decide later > which paths to calculate the EXAFS for. At this point, both of these > optimizations seems less-than-critical, and just turning them off > completely (CRITERIA 0 0) is not so bad, especially for moderately > ordered systems like your crystal structure.

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Re: [Ifeffit] problems in installing PGPLOT in UBUNTU
by Enyuan Hu 29 Jul '11

29 Jul '11

Dear Matt, I checked the log file but didn't see any error message. I don't know if it's because I succeeded in installing Athena and Artemis following Carlo's suggestion and the log file is thereby updated. Here's the content of the log file: "#!/bin/sh # PGPLOT install log # system = linux == linux g77_gcc # prefix = /usr/local/ # fortran compiler = gfortran gzip -dc pgplot5.2.tar.gz | tar xf - mkdir -p /usr/local//share/ifeffit/pgplot/ # driver.list written to /usr/local//share/ifeffit/pgplot//drivers.list # starting build cd /usr/local//share/ifeffit/pgplot// rm -f grfont.dat pgplot.doc pgxwin_server lib*pgplot* pgdemo* /home/enyuan/ifeffit-1.2.11d/pgplot/makemake /home/enyuan/ifeffit-1.2.11d/pgplot linux g77_gcc # customizing grgil.f for ifeffit sed 's|/usr/local/pgplot/|/usr/local//share/ifeffit/pgplot/|g' /home/enyuan/ifeffit-1.2.11d/pgplot/src/grgfil.f > /home/enyuan/ifeffit-1.2.11d/pgplot/src/grgfil_iff.f mv makefile Tmp sed 's|grgfil|grgfil_iff|g' Tmp > makefile sed 's|libpgplot|libpgplot_iff|g' makefile > Tmp sed 's|-lpgplot|-lpgplot_iff|g' Tmp > makefile # customizing xwdriv.c for ifeffit sed 's|getenv("PGPLOT_DIR")|'"/usr/local//share/ifeffit/pgplot/"'|g' /home/enyuan/ifeffit-1.2.11d/pgplot/drivers/xwdriv.c > /home/enyuan/ifeffit-1.2.11d/pgplot/drivers/xwdriv_iff.c mv makefile Tmp sed 's|xwdriv|xwdriv_iff|g' Tmp > makefile # fix png driver mv makefile Tmp sed 's|pndriv.o : ./png.h|#### pndriv.o : ./png.h|g' Tmp > makefile make FCOMPL= gfortran FFLAGC=-O1 libpgplot_iff.a make FCOMPL= gfortran grfont.dat prog pgplot.doc pgxwin_server cpg make clean " I hope the length is not too bothering and thank you very much for the help! -- Enyuan

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Re: [Ifeffit] FEFF6L.02 - missing path?
by Pawel Zajdel 29 Jul '11

29 Jul '11

Matt, Thanks for the explanation. In this case, next two questions. 1. Is there a way to say it was rejected other than re-running feff with CRITERIA 0 0? I expected it to show in Feff.run file with "neglected" flag. My "default" Feff.run file says " Curved wave chi amplitude ratio 4.00% Discard feff.dat for paths with cw ratio < 2.67%" and the "neglected" flag is present for those with <2.67%. 2. Also there is still one path left (all paths No# 10 Se-Zn-Se) with cw ratio 2.83, which passes the <2.67 criterion but is weaker than the two paths that are rejected before it with amps 3.952 and 3.999. In other words - when using "default" generated feff.inp, which paths in Feff.run are reported as neglected and which are not reported at all? Best Pawel >> Message: 1 > Date: Thu, 28 Jul 2011 18:25:56 -0400 > From: Pawe? Zajdel <pawel.zajdel(a)us.edu.pl> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] FEFF6L.02 - missing path? > Message-ID: <5EB6FA326A714E6BAD00215CBFB556AE@NewLapek> > Content-Type: text/plain; charset="iso-8859-2"; Format="flowed" > > Dear All, > > I am facing a strange issue while playing with EXAFS for a spinel type > structure. I tried two typical examples: MgAl2O4 and ZnCr2Se4 with > octahedral site K edge of Al or Cr. > The MgAl2O4 is fine but for ZnCr2Se4, FEFF seems to omit one scattering > path. It is not reported as being rejected by <2.6% amp criterion, so I > wonder, while it is not shown. > This is path 3 (as seen in MgAl2O4), which goes from Cr/Al to anion, then > over the "octahedron" edge to another anion and back to Cr/Al. > For oxide Reff=3.2251 > <cut from feff.run> > path cw ratio deg nleg reff > 1 100.000 6.000 2 1.9371 > 2 37.913 6.000 2 2.8853 > 3 10.687 12.000 3 3.2251 <-- It's here > 4 9.664 2.000 2 3.3444 > </cut> > For selenide Reff=4.2354 > <cut from feff.run> > path cw ratio deg nleg reff > 1 100.000 6.000 2 2.5248 > 2 47.173 6.000 2 3.7084 <-- should be after this > one. > 3 25.382 6.000 2 4.3485 > </cut> > I am attaching two atoms.inp files, which may help. It is space grup 227, > standard setting (2), atom list is correct. > I am using Ifeffit 1.2.11c with Feff 6L.02. It s present under WinVista > and > Linux on two different machines. > Am I missing something? > I would appreciate any suggestions. > > Best > Pawel > Message: 2 > Date: Thu, 28 Jul 2011 21:27:57 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] FEFF6L.02 - missing path? > Message-ID: > <CA+7ESbpzXoP+OkH2Nq14DY-W4SP-cgCnh_0=+b7OhSvLMG80xA(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Pawel, > > For these two structures, the location of the anions (Se for ZnCr2Se4 > and O for MgAl2O4) are not in in exactly the same location in the unit > cell. The nearly identical double scattering paths: > Al->O->O->Al > and > Cr->Se->Se->Cr > each have small estimated scattering amplitudes ("Zabinsky Curved Wave > Importance Factors"). The Cr->Se->Se->Cr path is filtered out with > the default settings, and so not included in the path list, while the > Al->O->O->Al path is not filtered out. > > You can guarantee to see all the paths if you put > CRITERIA 0 0 > > in the feff.inp file. > > For a more detailed reason of why Al->O->O->Al has an estimated > amplitude of 10.7 (and so not filtered out) while the Cr->Se->Se->Cr > has an estimated amplitude of 3.9 (and so is filtered out), there are > a few points to consider: > > 1. The amplitude reported is relative to the strongest scattering > path, which always has amplitude 100. In both cases, this is the > first shell Al->O->Al and Cr->Se->Cr. Se is a stronger back-scatterer > than O. > > 2. Both absorber and scatterer are heavier in the Zn-Cr-Se case > than the Mg-Al-O case, and the the heavier atoms are more point-like > in their electron density. > > 3. The Se atoms are closer to 0.25, 0.25, 0.25 in the unit cell > than the O atoms. This makes the Cr->Se->Se->Cr path have a > scattering angle beta a little closer to 90 degrees, which gives less > scattering amplitude. > > I think all three of these conspire to give the Cr->Se->Se->Cr path > less amplitude than the Al->O->O->Al path. > > Hope that helps, > > --Matt > -- dr Pawel Zajdel Division of Physics of Crystals Institute of Physics University of Silesia Uniwersytecka 4 40-007 Katowice Poland [48]323591978

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problems in installing PGPLOT in UBUNTU
by Enyuan Hu 29 Jul '11

29 Jul '11

Dear all, Has anyone met a problem when installing PGPLOT in UBUNTU? I fellowed the prescribed recipe in http://cars9.uchicago.edu/~ifeffit/src/INSTALL but always encounter problem when trying to get PGPLOT installed. The message is like this: "= Uh-oh. PGPLOT is missing some important files! = It looks like PGPLOT failed during building or = is only partially installed. = = Please consult the PGPLOT installation instructions = in the subdirectory pgplot/, and the log file: = /home/enyuan/ifeffit-1.2.11d/PGPLOT_install.log = which contains a full list of commands run. = = You may want to repeat these steps by hand or = consult the PGPLOT installations instructions = in install-unix.txt " I'm a newbie to UBUNTU so I would really appreciate it if the answer can consider my ignorance and be as simple as possible :) BTW, the motivation I'm switching to UBUNTU is the video of doctor Bruce lecturing on vimeo.comwhich were done in the environment of Demeter...juicy!! -- Enyuan

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Peak fitting analysis
by Abhijeet Gaur 29 Jul '11

29 Jul '11

Hi all, I am doing XAFS analysis of some Cu(II) samples. As well known Cu(II) samples shows a pre-edge feature at around 8976 eV, characterstic of Cu(II) spectra. I am trying to perform peak fitting analysis of this pre-edge feature to determine its intensity as it is related to the coordination. I am trying Peak fitting analysis with Athena, but unable to get some results. May be I am doing something wrong. The Athena project is attached herewith. With thanks Abhijeet Gaur

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FEFF6L.02 - missing path?
by Paweł Zajdel 29 Jul '11

29 Jul '11

Dear All, I am facing a strange issue while playing with EXAFS for a spinel type structure. I tried two typical examples: MgAl2O4 and ZnCr2Se4 with octahedral site K edge of Al or Cr. The MgAl2O4 is fine but for ZnCr2Se4, FEFF seems to omit one scattering path. It is not reported as being rejected by <2.6% amp criterion, so I wonder, while it is not shown. This is path 3 (as seen in MgAl2O4), which goes from Cr/Al to anion, then over the "octahedron" edge to another anion and back to Cr/Al. For oxide Reff=3.2251 <cut from feff.run> path cw ratio deg nleg reff 1 100.000 6.000 2 1.9371 2 37.913 6.000 2 2.8853 3 10.687 12.000 3 3.2251 <-- It's here 4 9.664 2.000 2 3.3444 </cut> For selenide Reff=4.2354 <cut from feff.run> path cw ratio deg nleg reff 1 100.000 6.000 2 2.5248 2 47.173 6.000 2 3.7084 <-- should be after this one. 3 25.382 6.000 2 4.3485 </cut> I am attaching two atoms.inp files, which may help. It is space grup 227, standard setting (2), atom list is correct. I am using Ifeffit 1.2.11c with Feff 6L.02. It s present under WinVista and Linux on two different machines. Am I missing something? I would appreciate any suggestions. Best Pawel -- dr Pawel Zajdel Division of Physics of Crystals Institute of Physics University of Silesia Uniwersytecka 4 40-007 Katowice Poland [48]323591978

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