- 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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Re : EXAFS analysis of a sample having two metal centres with different coordination geometry
by Abhijeet Gaur 22 Jul '11

22 Jul '11

<Abhijeet, <This seems like a system which might require more information before using EXAFS analysis. How did you come to the conclusion that there are <two metal centers? You begin by asking how to model two metal centers with different coordination and then in question 3, you lead the list to <believe that there might not be two metal centers? I assume you have found structural data for the sample? You have different geometry as <well as different ligands (atoms). Do the metal centers only contain the absorbing metal or is it mixed? If you had a bit more information <about the material through other methods, I am sure several people could suggest helpful ideas for your analysis. <Chris -- Christopher J. Patridge PhD. 405 NSC - Dept of Chemistry University at Buffalo State University of New York Buffalo, NY 14260 Office:(716)645-4137 Contact:(315)529-0501 <E-mail: patridge at buffalo.edu<http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> Dear Chris, I am sorry for making my problem a bit difficult to understand. Let me clarify the problem: 1. Yes, I have the crystal strcuture of the sample with me, from which I know that there are two metal centers. With this crystal strcuture data, I have generated the theoretical model for the two metal sites. 2. Yes, the metal centers only contain the absorbing metal, i.e., copper but with with different coordination. And my question is whether by using EXAFS analysis of experimetal data, the contribution of two metal center present in sample can be confirmed? Also, is it possible to calculate that how much one metal center contribute to the experimetal data? If, one of the theoretical model does not fit to the experimetal EXAFS data, what does it signify about the corresponding metal center? I hope this will make my problem clear to the members of the mailing list. With thanks Abhijeet Gaur

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EXAFS analysis of a sample having two metal centres with different coordination geometry
by Abhijeet Gaur 21 Jul '11

21 Jul '11

Hi all, I am doing EXAFS analysis of a sample having two metal centres with different coordination geometry. In my sample two (Cu) metal centres are present and these metal centres are surrounded by different ligands (atoms) in different coordination geometry. As I understand the EXAFS data of such sample will have contributions from both the metal centres. So, in order to analyse the EXAFS data, I have generated theoretical model (using Artemis) for both the metal centres. Then, I have fitted these theoretical models to the experimetal data. But, I have some questions regarding this type of analysis as I am not sure whether I going in right direction or not: 1. I have to fit these theoretical models one by one or simultaneously to the experimetal data. 2. How can I confirm that whether the EXAFS data of the sample has contributions from both the metal centres. 3. If one of the model does not fit well to the exp data, does this mean that the corresponding metal centre is not present or the metal centre is present but not contributing. 4. Is it possible to calculate the percentage of contributions from different metal centres to the experimetal data. If someone can suggest some available literature on this problem, it will be really helpful to me. With thanks Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University, Ujjain, India

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Re: [Ifeffit] Scripting - Python
by Andrew Korinda 21 Jul '11

21 Jul '11

Thanks for the help. Sorry it took so long to report back but I can only do must of my work on this on weekends. The corrected code worked great and I'm moving forward again. No message was given when the code wasn't working. Andy Korinda On Nov 1, 2010 1:55 PM, "Matt Newville" <newville(a)cars.uchicago.edu> wrote: Hi Andrew, On Mon, Nov 1, 2010 at 12:01 PM, Andrew Korinda <a-korinda(a)northwestern.edu> wrote: > I'm looking t... This is almost certainly due to space in the filename, and is really more of a problem with the fortran than python (or perl for that matter). That is, with a space in the file name, you should explicitly use read_data(file=...., group=...) This should work better:: import Ifeffit iff = Ifeffit.Ifeffit() ret = iff.ifeffit("read_data(file=C:\Program Files\Ifeffit\examples\Ifeffit\data\cu.xmu, group=c)") If it doesn't, let use know. > >From this experience I have some questions: > > ~First does anyone have some debugging tips for ... There should have been a printed message that might have altered you that the file hadn't been read in correctly: *** read_data: no file name given! was that message not given? > ~Secondly, Does anyone have any example Python scripts for Ifeffit > that they would like to shar... I sort of deliberately have left the base Ifeffit python module bare-bones. It would certainly be possible to add more functionality to that, or distribute add-on packages. It sort of depends what people would find desirable. I have many example scripts using Ifeffit + Python, mostly scripts, not documented, reliable code. Of course, there is also sixpack. I had some older GUIs as well. Would it be helpful to add some small examples on a wiki page? > ~Finally, would I be better off coding in Perl and using Demeter? That's a difficult question. The relative merits of Perl v Python are sort of a topic all on their own. For what it's worth, I believe (far) more people have used Python than Perl, but several very notable Ifeffit programs are written in Perl ;). --Matt PS: The next version of Ifeffit will be in python. Progress is slow, and when it will start to look like an EXAFS analysis program is a fair question. It probably shouldn't sway your decision much. _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.g...

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Bond length to ATOM conversion
by Nicholas.Tse＠csiro.au 15 Jul '11

15 Jul '11

G'day Listed Members, Does anyone know how to convert bond length and bond angles into Cartesian coordinates to input into ATOM in Artemis. The space group is number 176 a P63/m (ie hexagonal dipyramidal) with a a=b=6.3 A, c=3.6 A. Apical Equatorial M-O2 M-O1 O1-O2 O1-O2 O2-O2 O1-M-O2 O1-M-O2 O2-M-O2 Gd(OH)3 2.462(3) 2.465(4) 2.910(6) 2.761(7) 2.879(8) 72.4(1) 68.18(6) 71.6(1) * G. W. Beall and W. O. Milligan, J. Inorg. Nucl. Chem., 1977, vol 39, 65-70 I am currently trying to set up a FEFF file for Gd(OH)3 Sincerely yours, Nicholas

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Re: [Ifeffit] Scripting - Python
by Matt Newville 14 Jul '11

14 Jul '11

Hi Andrew, Hmm, not sure what's going on. It worked for me on one system, but I'll try this on another machine later today. I think the key is to have the folder with ifeffit_12.dll in your PATH. You say you had to edit the use_ifeffit.bat file -- did this have the incorrect paths? A reasonable workaround (and perhaps the distribution should do this) is to copy the dll to C:\Python27\DLL. The trouble with that is that many of the PGPLOT environmental variables might not be set correctly.... but that just means plotting won't work, which might be acceptaable. -Matt On Jul 14, 2011 9:59 AM, "Andrew Korinda" <a-korinda(a)northwestern.edu> wrote:

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Re: [Ifeffit] Opening SSRL data in Athena
by Scott Calvin 08 Jul '11

08 Jul '11

Actually, Athena can open binary SSRL files--I just successfully opened one of Lia's files in Athena. Here's what I did: Under Settings, choose Plugin registry. Check the SSRLB box. From there, it opened fine. Does trying that work for you, Lia? I am using Athena 0.8.061 on a Mac running OS 10.5.8. --Scott Calvin Sarah Lawrence College On Jul 7, 2011, at 6:20 PM, Wayne W Lukens Jr wrote: > Hi Lia, > > Those are binary files from SSRL, which athena cannot open. There > are a few ways that you can deal these files. > > Easiest is to use Six-Pack to work up the data. I believe it will > open SSRL binary files. Six-Pack is a GUI-driven suite of programs > analogous to Athena and Artemis. > > Slightly less easy is to convert your binary data to ascii data, > which can be done on the SSRL computer that you used to collect the > data. At this point, you will have to ask the beamline scientist to > do this for you. You can definitely open the ascii files in Six-Pack. > > Somewhat more difficult is to use EXAFSPAK to work up the data. > These are a suite of programs for EXAFS data analysis that are not > particularly easy to learn. They will open the binary files. > EXAFSPAK is easy to use once you have learned the commands. > > Six-Pack: > > http://home.comcast.net/~sam_webb/sixpack.html > > EXAFSPAK: > > http://ssrl.slac.stanford.edu/exafspak.html > > Sincerely, > > Wayne

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Re: [Ifeffit] Opening SSRL data in Athena (Abhijeet Gaur)
by Abhijeet Gaur 08 Jul '11

08 Jul '11

> Hi Julia, I have also encountered the same problem while analysing the data from SSRL. I can suggest you what I tried and got my data read by Athena. Go to the Setting pannel of the Athena window and then click on Plugin Registry. You will see all types of data format there, then you can check your data format there. Then, you can import your data. Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University Ujjain, India Hello Everyone, I have a question about using Athena to analyze data taken at SSRL beam line 11-2. I can't seem to open the files, a message pops up saying it 'could not be read by ifeffit as a data file'. I have looked around these message threads and in the athena users guide but there doesn't seem to be any information on it. The users guide goes through choosing different data columns and if there is a header or not, but I can't open the data as some sort of text file to see how it is organized. I'm sure its just importing it differently or checking a box or something silly like that, but I would appreciate any guidance. Thank you very much, Lia >

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Re: [Ifeffit] Ifeffit Digest, Vol 101, Issue 7
by Eric Breynaert 08 Jul '11

08 Jul '11

Hey julia, Check the namespace of your SSRL plugins. They should be located at C:\Program Files\Ifeffit\share\perl\Ifeffit\Plugins\Filetype\Athena and they are called SSRLA.pm and SSRLB.pm. You can open the files with notepad. Check if the 1st line (package name, e.g. package Ifeffit::Plugins::Filetype::Athena::SSRLA;) reflects the plugin filename. So the last word has to be SSRLA and SSRLB for respectively SSRLA.pm and SSRLB.pm. If this is not the case , change accordingly. Hope this solves your problem. Eric On 8/07/2011 2:16, 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. Opening SSRL data in Athena (Julia M Klofas) > 2. Re: Opening SSRL data in Athena (segre(a)iit.edu) > 3. Re: Opening SSRL data in Athena (Julia M Klofas) > > Hey julia, > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Jul 2011 16:54:38 -0700 > From: Julia M Klofas<jklofas(a)usgs.gov> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Opening SSRL data in Athena > Message-ID: > <OF693BEABF.DCFC939B-ON882578C6.0083584B-882578C6.00835860(a)usgs.gov> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL:<http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110707/bc6…> > > ------------------------------ > > Message: 2 > Date: Thu, 07 Jul 2011 19:00:25 -0500 > From: "segre(a)iit.edu"<segre(a)agni.phys.iit.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov>, > ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Opening SSRL data in Athena > Message-ID:<fb8b7016-48d6-4d53-a330-7ed2fa9f6544(a)email.android.com> > Content-Type: text/plain; charset="utf-8" > > Hi Julia > > Could you attach the file? I think I know what it is but it would help. > > Carlo > -- Eric Breynaert Centrum voor Oppervlaktechemie en Katalyse Departement Microbiële en moleculaire systemen (M²S) Kasteelpark Arenberg 23 - bus 2461 B-3001 Leuven Tel: +3216321598 Fax: +3216321998

1 0

Opening SSRL data in Athena
by Julia M Klofas 08 Jul '11

08 Jul '11

3 3

request for In metal spectrum
by Brandon Reese 06 Jul '11

06 Jul '11

Hello list members, Does anyone have a scan of In metal taken at room temperature? I need the absorption edge and the EXAFS region, preferably up to 10 1/A or so. There are some potential issues with the spectra I have collected, and I would an independent measurement to compare with mine. Thanks Brandon Reese

1 0

FEFF input files
by Bernt Johannessen 04 Jul '11

04 Jul '11

Dear All, I am looking at using Artemis ("Theory"; "New Atoms page") to create FEFF input files for Gd and Gd2O3. I believe I have got the Gd parameters right: Space group 194 a=b=3.636,c=5.7826 alpha=beta=90,gamma=120 Gd: X=Y=Z=0 And it does give me reasonable paths in the end to work with (see below FEFF.inp file) The Gd2O3 is trickier (space group 206, a=b=c=10.8(?), alpha=beta=gamma=0): How do I determine the X,Y,Z coordinates for the relevant atoms? Regards, Bernt Gd FEFF input file: * This feff6 input file was generated by Artemis 0.8.012 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 3.36 microns, unit edge step: 5.46 microns * specific gravity = 7.888 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00062 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * ----------------------------------------------------------------- * The following crystallographic data were used: * * title ... * space = P 63/m m c * a = 3.6360 b = 3.6360 c = 5.78260 * alpha = 90.0 beta = 90.0 gamma = 120.0 * core = Gd1 edge = L3 * atoms * ! elem x y z tag occ * Gd 0.00000 0.00000 0.00000 Gd1 1.00000 * ----------------------------------------------------------------- TITLE ... HOLE 4 1.0 * Gd L3 edge (7243.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 6.0 *CRITERIA curved plane *DEBYE temp debye-temp NLEG 4 POTENTIALS * ipot Z element 0 64 Gd 1 64 Gd ATOMS * this list contains 23 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Gd1 0.00000 0.00000 0.00000 2.89130 1 Gd1_1 2.89130 0.00000 0.00000 -2.89130 1 Gd1_1 2.89130 3.14887 1.81800 0.00000 1 Gd1_2 3.63600 -3.14887 1.81800 0.00000 1 Gd1_2 3.63600 0.00000 3.63600 0.00000 1 Gd1_2 3.63600 3.14887 -1.81800 0.00000 1 Gd1_2 3.63600 -3.14887 -1.81800 0.00000 1 Gd1_2 3.63600 0.00000 -3.63600 0.00000 1 Gd1_2 3.63600 3.14887 1.81800 2.89130 1 Gd1_3 4.64544 -3.14887 1.81800 2.89130 1 Gd1_3 4.64544 0.00000 3.63600 2.89130 1 Gd1_3 4.64544 3.14887 -1.81800 2.89130 1 Gd1_3 4.64544 -3.14887 -1.81800 2.89130 1 Gd1_3 4.64544 0.00000 -3.63600 2.89130 1 Gd1_3 4.64544 3.14887 1.81800 -2.89130 1 Gd1_3 4.64544 -3.14887 1.81800 -2.89130 1 Gd1_3 4.64544 0.00000 3.63600 -2.89130 1 Gd1_3 4.64544 3.14887 -1.81800 -2.89130 1 Gd1_3 4.64544 -3.14887 -1.81800 -2.89130 1 Gd1_3 4.64544 0.00000 -3.63600 -2.89130 1 Gd1_3 4.64544 0.00000 0.00000 5.78260 1 Gd1_4 5.78260 0.00000 0.00000 -5.78260 1 Gd1_4 5.78260 END [cid:image001.gif@01CC3A6C.C42DB2F0] Bernt Johannessen | Scientist - XAS | Australian Synchrotron p: (03) 8540 4240 | f: (03) 8540 4200 bernt.johannessen(a)synchrotron.org.au<mailto:bernt.johannessen@synchrotron.org.au> | www.synchrotron.org.au 800 Blackburn Road, Clayton, Victoria 3168 <br>This message and any attachments may contain proprietary or confidential information. If you are not the intended recipient or you received the message in error, you must not use, copy or distribute the message. Please notify the sender immediately and destroy the original message. Thank you.

4 4

Problem with Arthemis
by Amayri, Dr. Samer 04 Jul '11

04 Jul '11

Dear colleagues, after I selected in Arthemis "write special output feff8", I had a problem to run this feff8 file (feff.inp) (see please the attached file). I get the following error: Feff 6L.02 Unknown keyword: "EDGE" at line: EDGE L3 See FEFF document for valid keywords. Fatal Error: at RDINP. Could you please help me? Thanks in advance. Samer Amayri __________________________________________________________________ Dr. Samer Amayri Institut für Kernchemie der Universität Mainz Fritz-Strassmann Weg 2 D-55128 Mainz Telefon: +496131 39-25317/25307 (Lab.) Fax-Nr. +496131 39-24510 E-mail: amayri(a)uni-mainz.de<mailto:amayri@uni-mainz.de>

2 1

Fitting bond lengths without a known FEFF file
by Hana 01 Jul '11

01 Jul '11

Dear list experts, Here is another challenging question for me; can someone help? I have soil samples, trying to fit the first shell, I have 3 different optional bond lengths, which might give a lot of information. Now I have two questions: 1. If I do not know of specific structure (XRD implies a very amorphous material), so no specific FEFF file that I can use. what would be my way to determine the parameters for IFEFFIT (Deg, Reff, amp,...)? 2. Is there any option to fit the 3 bond lengths together (no dependency that I can think of...)? Should I fit all pairs, then accordingly assume one component; 'set' it and fit the other two as fractions of 1 (N+(1-N)? Thanks!!

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Re: [Ifeffit] E0 issues
by Scott Calvin 28 Jun '11

28 Jun '11

Hi again, > > Thanks Scott, > I think it is a mistake done by many beginners. To be confident that > I understood you well: so basically the reproducibility of E0 > between samples while fitting to FEFF files mainly depends on the > quality of my calibration. For reproducibility, yes. > Actually, if there is no clear feature in my edges and they are > different in ‘slopes’, I must have either a calibration foil, or a > known standard, measured at the same time; otherwise there is no > good way to get comparable data? Some beamlines are more stable in energy than others. Sometimes it suffices to measure a standard occasionally between measuring data. If the calibration does not drift, or drifts in a predictable way, then you're OK. But if the calibration jumps around by an eV or two, as is not uncommon, then your data inherits that uncertainty unless you measure a reference material at the same time. > Is that right, or the fitting, considering all spectra’s components > will finally lead to a good fit, even with relatively poor > calibration (I will definitely be more careful in the future; but > asking for a set of samples that were mistakenly measured for me > without a standard). This is a different question. If you are fitting to FEFF, then it doesn't matter if the E0's were defined consistently for each sample, or if the calibration drifted. You will most likely float E0 as a free parameter anyway, so the fitting process will adjust for the differences. You do lose the ability to compare the E0's of your different samples, and you lose the ability to constrain them to be the same, but the rest of the fitting process is fine. --Scott Calvin Sarah Lawrence College P.S. Also note that if ifeffit returns an E0 shift of more than about 10 eV, that's a warning sign. Check if that would correspond to an E0 still on or near the rising portion of the edge (a bit past the white line is still OK). If it's not, then the fit is not a good one. If it is, then it's best to choose a new E0 in Athena (or SixPack) that is closer to to where ifeffit wants it; FEFF loses accuracy when the E0 has to be shifted by that much.

2 1

Re: [Ifeffit] E0 issues
by Scott Calvin 27 Jun '11

27 Jun '11

Hi Hana, On Jun 27, 2011, at 2:04 PM, Hana wrote: > I guess my question is obvious to most of you, but after some > practice and reading, the following is still unclear to me > (hopefully some other beginners will benefit): Normally I have > calibrated my spectra using a calibration foil – so energy shift > was done according to that companion standard. Doing a simple > linear combination fit, I have set all spectra to the same E0 value, > somewhere on the edge, above the first derivative maxima (was it a > good practice?). That is a good practice, in my opinion. If you're going to do a linear combination fit, it doesn't really matter how you choose E0, as long as: 1) The spectra are all aligned on the same energy scale 2) The choice of E0 is in some way consistent By using a calibration foil, you have assured #1, and then by simply making E0 the same for all spectra, you have assured #2. > Recently, I found myself actually confused about E0; since my > samples inherently have a phase difference (which is the base to my > ability to differentiate them), how a certain reference point on the > spectrum can be determined? "Reference point" is indeed the correct term. As such, it is somewhat arbitrary, and just needs to be consistent for all spectra being compared. > What can be done when I do not have the calibration foil (especially > for these heavy elements that do not have specific sharp feature)? Consistency is the only requirement. There are many ways to align consistently. If you've got really noisy reference data for some reason, you could even fit some kind of function to the edge and use that, but for reference data that's not usually necessary. > And further, now that I am starting to work on the structural model; > how actually IFEFFIT determined the energy shift when there is no > specific reference point? If you float E0 when fitting to feff files, the reported value is a shift relative to wherever you initially picked it. Thus if you change the initial choice of E0 by 2 eV upward, the shift ifeffit reports should be 2 eV less. Hope that helps... --Scott Calvin Sarah Lawrence College

2 1

E0 issues
by Hana 27 Jun '11

27 Jun '11

I guess my question is obvious to most of you, but after some practice and reading, the following is still unclear to me (hopefully some other beginners will benefit): Normally I have calibrated my spectra using a calibration foil – so energy shift was done according to that companion standard. Doing a simple linear combination fit, I have set all spectra to the same E0 value, somewhere on the edge, above the first derivative maxima (was it a good practice?). Recently, I found myself actually confused about E0; since my samples inherently have a phase difference (which is the base to my ability to differentiate them), how a certain reference point on the spectrum can be determined? What can be done when I do not have the calibration foil (especially for these heavy elements that do not have specific sharp feature)? And further, now that I am starting to work on the structural model; how actually IFEFFIT determined the energy shift when there is no specific reference point? I would be happy to get a better insight.

1 0

Fwd: Icosahedral cluster coordinates
by Scott Calvin 27 Jun '11

27 Jun '11

Hi Zohair, I'm posting this back to the list, because I couldn't solve the problem. I did experiment with your file for a bit; it works fine for the atoms up to 4 angstroms, but ones much past that make feff fail. Maybe someone else can suggest why feff is choking on what appears on inspection to be a valid file. (Note to others on the list: the attached feff.inp file is the one that doesn't work; the pasted one is my original, and does work.) As for atoms being able to work with icosahedral structures, that will probably never be possible. Atoms is designed to work with crystal structures, and icosahedral clusters are not crystals; i.e. they don't have translational symmetry. A separate helper application would have to be written for this kind of cluster. --Scott Calvin Sarah Lawrence College Begin forwarded message: > From: <Zohair.Hussain(a)csiro.au> > Date: June 27, 2011 1:12:06 AM PDT > To: <dr.scott.calvin(a)gmail.com> > Subject: Re: [Ifeffit] Icosahedral cluster coordinates > > Dear Scott, > > I came across an e-mail exchange from 2005 between you and Patrick > Kluth regarding icosahedral clusters and feff files as below. > > I’m trying to fit data collected at the Cu k-edge for Mg65Cu25Gd10 > bulk metallic glass(BMG). It has been reported that BMGs have an > icosahedral structure. A recent paper (attached) gives a > demonstration of that. What I’ve tried to do is to modify the feff > file you made for Patrick to my MgCuGd structure. I attach the > feff.inp file I made for that. > > The problem I’m running into is that when I try and run this > modified feff file through artemis I get an error message (file > attached). I should point out that when I run your feff file for Fe > it runs without any errors. > > I’m wondering if you can either tell me what I’m doing wrong or > guide me to make a feff file from an atoms input file for the MgCuGd > material. > > In the long run, it would be good to know how to make Feff files for > icosahedral structures starting from an atoms input file (I usually > use webatoms for this) as I would be working with various BMG > materials (Al, Ti and Mg based) that should potentially have this > structure. > > I’d be grateful for your help. > > Kind Regards, > > > > Zohair Hussain > Postdoctoral Fellow > > CPSE - CSIRO > Private Bag 33 > Clayton South MDC > Clayton VIC 3169 > Australia > e-mail: zohair.hussain(a)csiro.au > Phone +61 3 9545 7891 > Fax +61 3 9544 1128 > > > > > > [Ifeffit] Icosahedral cluster coordinates > > Scott Calvin SCalvin at slc.edu > Tue Jul 19 19:06:17 CDT 2005 > Previous message: [Ifeffit] Icosahedral cluster coordinates > Next message: [Ifeffit] Icosahedral cluster coordinates > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] > Hi Patrick, > > Hopefully this will do it. A disclaimer: I never actually tested this > on an icosahedral material, and I did the coordinates by hand, so I > can't guarantee it. > > --Scott Calvin > Sarah Lawrence College > > > > > > >I am working with metal clusters and would like to do some FEFF > >calculations on icosahedral clusters. Is there anyone out there who > >has a FEFF input file (or equivalently a list of coordinates) for an > >icosahedral cluster (147 atoms is probably sufficient for my > >purpuses). >

3 2

system iXAFS3.0.3.dmg, cant open arthena project
by diya lee 27 Jun '11

27 Jun '11

Hi, I have a Macbook pro, and I have the iXAFS3.0.3.dmg system installed. But the artemis program could not open arthena project. when i choose open file and select the file ( arthena project), there system either does not respond or only show the first data in the entire project. How could I fix this?Thanks

2 1

Align spectra in Athena
by Dave 24 Jun '11

24 Jun '11

Hi list, Doing my first steps in your world, I am trying to model my data. I am following Kelly's helpful review from 2008 and stuck on apparently simple issue: In order to reduce my deltaE0 (now 9.2), following her advise, I am trying to recall the theoretical spectrum from Artemis to Athena; this was produced by filtering and fitting my data according to the first shell, then fixing all parameters to their best fit, except for enot set to zero, making a sum of all paths under these conditions, saving it as a chi(k) and take it to Athena. Here, to my understanding, I suppose to introduce the 'new-made' chi(k) as a standard and align my data accordingly, save it as a chi(k) and take it back to Artemis to complete the fitting. Unfortunately I cannot make it a standard in Athena, since the whole background options are not available when a chi file is called in. Can someone give a hint? Suggest other ways to better choose E0? Best, Dave

2 1

an error message " You have not used any memory yet"
by Mike Zhu 23 Jun '11

23 Jun '11

Hi All, I had been using Athena for couple of months and had not problem. But recently, I cannot load any new data although I am still able to open project files (*.prj) previously created. Then this error message shows up at the bottom of the Athena window. I tried to reinstall Ifeffit and to install different version of Ifeffit but all failed. I saw a message posted couple of years ago on a similar problem in this email list but it seemed no answer for it. My operating system is Window XP Professional 2000 Service Pack 3. Anyone have a clue how to fix it? Thanks. Best, Mengqiang Zhu

1 0

Averaging of spectra for multiple configurations in Artemis
by Srinivas Tulishetti 22 Jun '11

22 Jun '11

Dear All, I am working on MD - EXAFS for ionic solvation system. I was doing MD-EXAFS for multiple configurations. Each configuration gives different spectrum. So would like get average of all spectra for those multiple configurations. Is it possible to do this in Artemis or iFEFFIT. If it is then, please give your valuable suggestions. Thanking you all. Best, Srinivas Tulishetti

2 1

lfms1
by Francisco Garcia 21 Jun '11

21 Jun '11

Dear users, I have a question about the value lfms1 is the SCF card. What difference does it make if lfms1=0 (solid) versus lfms1=1 (molecule) for hydrated metal ion clusters? My understanding from the manual is that if the metal is the absorber and I am working with cluster, then lfms1=1. However, if the cluster is sufficiently large (radius=6 Ang--8 Ang), then should it be treated as a solid or molecule? Also, how crucial are the hydrogen atoms in the scattering process? Can the EXAFS spectra be computed with only the metal ion and oxygen positions or the hydrogen positions must be included as well? Thank you.

1 0

Fwd: problem with horae installation on ubuntu 11.04
by Bruce Ravel 21 Jun '11

21 Jun '11

Samuel, As you can see, I am forwarding this to the mailing list. It seems to me that you do not have pgplot installed. On ubuntu this package is called "pgplot5". Have you installed it? I would have thought that the pgplot package would have been a dependency of the ifeffit package. Carlo: can you shed any light on Samuel's problem? Rgeards, B ---------- Forwarded Message ---------- Subject: problem with horae installation on ubuntu 11.04 Date: Tuesday, June 21, 2011, 08:19:46 am From: Bickel Sämi <bickels(a)student.ethz.ch> To: "bravel(a)anl.gov" <bravel(a)anl.gov> hi this is probably a stupid question but i'm quite stuck here. i need the athena software but it doesen't load. it termines with the error: > bickels@bickels-laptop:/$ athena > /usr/bin/perl: symbol lookup error: /usr/local/lib/perl/5.10.1/auto/Ifeffit/Ifeffit.so: undefined symbol: pgqndt_ > i tried compiling the ifeffit-perl but it did not work. also i don't know if i got another version of perl.. but i installed ifeffit trough synaptic. im a newbie and this is probably no big issue.. thanks and have a nice day samuel bickel ----------------------------------------- -- 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/

3 3

Re: [Ifeffit] SS and MS contributions to EXAFS
by Scott Calvin 18 Jun '11

18 Jun '11

Hi Francisco, Following up on Matt's comment, a FEFF calculation with default option assigns sigma2 to be 0, and that probably won't result in relative contributions between SS and MS that look much like what happens in the real material. A better strategy would be to read the calculation into Artemis, as Matt suggests, and use a Debye model for the sigma2 for the paths, trying a few different Debye temperatures to get a sense of how it affects the relative contributions. While the Debye model is not an appropriate model for quantitatively fitting most materials, at least it takes a stab at how sigma2 might depend on R, which will help with understanding how important the MS paths are to chi(k). --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 7:21 PM, Matt Newville wrote: > Hi Francisco, > > On Fri, Jun 17, 2011 at 7:34 PM, Francisco Garcia > <garcia.ff.000(a)gmail.com> wrote: >> Dear users, >> >> I would like to quantify the single scattering (SS) and multiple >> scattering (MS) contributions to the EXAFS spectra over a range of k >> values. I adopted the following approach and I would like ask >> experienced users if my approach is sound: >> >> (1) Run a regular EXAFS (default NLEG=8); I assume this includes all >> possible scattering paths. Call the chi(k) data chi.dat >> (2) Run another EXAFS but this time I set NLEG=2. I assume this is >> for >> all SS contributions. Call the chi(k) data chi_ss.dat >> (3) To obtain the MS contribution, I subtracted chi_ss.dat from >> chi.dat >> >> If my approach is faulty, can you tell me how to remedy it? >> >> Thank you. > > That approach would work under the assumption that the atomic > coordinates in the feff.inp file fully described the distribution of > atoms in the system. If, on the other hand, the feff.inp had an > idealized structure, then the approach would model the MS > contributions for that structure. For example, a feff.inp file often > assumes no static or thermal disorder in the system. In that case, > the MS contributions would have no disorder terms (eg, sigma^2) > applied to them. > > An equivalent approach that may be somewhat simpler would be to use > Artemis to run the Feff calculation with NLEG=8 (4 is probably good > enough below 6Ang in most structures), read in all the paths, and sum > the paths with NLEG>2. > > --Matt

1 0

SS and MS contributions to EXAFS
by Francisco Garcia 18 Jun '11

18 Jun '11

Dear users, I would like to quantify the single scattering (SS) and multiple scattering (MS) contributions to the EXAFS spectra over a range of k values. I adopted the following approach and I would like ask experienced users if my approach is sound: (1) Run a regular EXAFS (default NLEG=8); I assume this includes all possible scattering paths. Call the chi(k) data chi.dat (2) Run another EXAFS but this time I set NLEG=2. I assume this is for all SS contributions. Call the chi(k) data chi_ss.dat (3) To obtain the MS contribution, I subtracted chi_ss.dat from chi.dat If my approach is faulty, can you tell me how to remedy it? Thank you.

2 1

Temp effect
by Hana 17 Jun '11

17 Jun '11

Dear EXAFS experts, I am quite a beginner, and that's might be an ignorant question but really important to my work, so I would be happy to get a direction: what would be the right way to weigh in the effect of temperature in soils samples, since solutions like Debye models will not fit to my understanding? specifically, I am trying to compare my measurements(collected at 10K) to literature data of these metals adsorbed on iron oxides (collected at room temperature). I would appreciate any advise, Hana

3 2

Re: [Ifeffit] McMaster correction
by Scott Calvin 17 Jun '11

17 Jun '11

I apologize if I have abused the list while working on my text. I will find a different channel for raising these questions and requests once the current discussion is complete. --Scott On Jun 16, 2011, at 8:11 PM, Matt Newville wrote: > Hope that helps. I have to admit I'm a little uneasy with the > frequency of "I've been pondering..." discussion topics alternating > with requests to review book chapters, and find myself being more > cautious in my response than I would if someone was actually asking a > question. On the other hand, I don't think anyone would object if > you added a button to Athena that normalized the data in a way that > included a correction for the expected decay of mu(E).

2 1

Re: [Ifeffit] McMaster correction
by Scott Calvin 17 Jun '11

17 Jun '11

Thanks, all! Here's what I got out of the discussion: FEFF is calculating the "correct" chi(k), and applying an approximate correction introduces additional sources of error. But the only way to measure chi(k) is to extract it from unnormalized data, and the original definition of chi was an arbitrary, if sensible, one: chi(E) = mu(E)/mu_o(E) - 1. And mu_o(E), while not known with great accuracy, depends only on the element and the edge (perhaps excepting minor contributions from AXAFS). Not applying a correction, whether McMaster or something more accurate (such as the ones Anatoly and John suggested), is equivalent to using the approximation mu_o(E) = mu_o(E_o), which is less accurate than the alternatives. On the other hand, the effect is almost entirely a shift in the absolute (as opposed to relative) value of sigma^2. Considering that, it seems to me that this would be a good option for Athena when calculating chi(k). (I think it would be more problematic to apply when calculating normalized energy-space data, as in that case the correction would depend on instrumental effects and the absorption of other edges in the sample.) So, Bruce, I guess this was first a discussion and then a feature request. :) --Scott Calvin Sarah Lawrence College On Jun 17, 2011, at 4:14 AM, John J. Rehr wrote: > Hi Scott et al., > > Thanks for bringing up this issue. Whether or not McMaster > corrections > are useful does seem to depend on details of the measurement. But > my question is: for the cases where they are useful, can one do > better? As the data & theory get better and better, perhaps we > should try > to extract more accurate cross sections mu(E). For example, is it at > all > of interest to have embedded atom cross-sections to replace the atomic > based Cromer-Liberman cross sections or empirical tables? > > John > > > On Thu, 16 Jun 2011, Scott Calvin wrote: > >> Hi all, >> I've been pondering the McMaster correction recently. >> >> My understanding is that it is a correction because while chi(k) is >> defined >> relative to the embedded-atom background mu_o(E), we almost always >> extract >> it from our data by normalizing by the edge step. Since mu_o(E) drops >> gradually above the edge, the normalization procedure results in >> oscillations that are too small well above edge, which the McMaster >> correction then compensates for. It's also my understanding that this >> correction is the same whether the data is measured in absorption or >> fluorescence, because in this context mu_o(E) refers only to >> absorption due >> to the edge of interest, which is a characteristic of the atom in >> its local >> environment and is thus independent of measurement mode. >> >> So here's my question: why is existing software structured so that >> we have >> to put this factor in by hand? Feff, for instance, could simply >> define >> chi(k) consistently with the usual procedure, so that it was >> normalized by >> the edge step rather than mu_o(E). A card could be set to turn that >> off if a >> user desired. Alternatively, a correction could be done to the >> experimental >> data by Athena, or automatically within the fitting procedure by >> Ifeffit. >> >> Of course, having more than one of those options could cause >> trouble, just >> as the ability to put sigma2 into a feff calculation and in to >> Ifeffit >> sometimes does now. But wouldn't it make sense to have it available >> (perhaps >> even the default) at one of those stages? >> >> --Scott Calvin >> Sarah Lawrence College

1 0

McMaster correction
by Scott Calvin 17 Jun '11

17 Jun '11

Hi all, I've been pondering the McMaster correction recently. My understanding is that it is a correction because while chi(k) is defined relative to the embedded-atom background mu_o(E), we almost always extract it from our data by normalizing by the edge step. Since mu_o(E) drops gradually above the edge, the normalization procedure results in oscillations that are too small well above edge, which the McMaster correction then compensates for. It's also my understanding that this correction is the same whether the data is measured in absorption or fluorescence, because in this context mu_o(E) refers only to absorption due to the edge of interest, which is a characteristic of the atom in its local environment and is thus independent of measurement mode. So here's my question: why is existing software structured so that we have to put this factor in by hand? Feff, for instance, could simply define chi(k) consistently with the usual procedure, so that it was normalized by the edge step rather than mu_o(E). A card could be set to turn that off if a user desired. Alternatively, a correction could be done to the experimental data by Athena, or automatically within the fitting procedure by Ifeffit. Of course, having more than one of those options could cause trouble, just as the ability to put sigma2 into a feff calculation and in to Ifeffit sometimes does now. But wouldn't it make sense to have it available (perhaps even the default) at one of those stages? --Scott Calvin Sarah Lawrence College

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EXAFS modules
by Joshua Kas 14 Jun '11

14 Jun '11

Hi Francisco, This depends on which version of FEFF you are using. The following shows the executables needed for EXAFS in feff9 and feff8. The names are different, so I have put the corresponding module in parentheses. FEFF9 FEFF8 rdinp rdinp atomic ffmod1 (atomic and pot) pot ffmod2 (xsph) xsph ffmod4 (path) path ffmod5 (genfmt) genfmt ffmod6 (ff2x) ff2x Cheers, Josh Kas > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jun 2011 12:22:16 -0700 > From: Francisco Garcia <garcia.ff.000(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] EXAFS modules > Message-ID: <BANLkTimTXXPzOh-sFoYaq_kE3v0pq4BAYA(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear users, > > Which of the following modules are needed to compute only the EXAFS > spectra (that is, chi.dat)?: > > ipot > ixsph > ifms > ipaths > igenfmt > iff2x > > Thank you. > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 100, Issue 9 > *************************************** >

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EXAFS modules
by Francisco Garcia 13 Jun '11

13 Jun '11

Dear users, Which of the following modules are needed to compute only the EXAFS spectra (that is, chi.dat)?: ipot ixsph ifms ipaths igenfmt iff2x Thank you.

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Fe foil at 900 C
by KONG Quingyu 12 Jun '11

12 Jun '11

Hello, We are measuring the kinetic of carbon nanotubes using Fe as catalytic element. To analyze the data, we need the Gamma iron (Fe fcc, iron foil measured with a temperature between 910 and 1400 C) EXAFS spectrum. We appreciate if anyone could send us this spectrum. Thanks a lot in advance, Sincerely Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ________________________________________ 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: Wednesday, June 08, 2011 9:03 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 100, Issue 6 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Question about shift in E0 (Christopher Patridge) 2. Re: Question about shift in E0 (Brandon Reese) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2011 21:55:25 -0400 From: Christopher Patridge <patridge(a)buffalo.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Question about shift in E0 Message-ID: <D53A5E8D-B912-4E7B-A567-2E0BB79B4B06(a)buffalo.edu> Content-Type: text/plain; charset="us-ascii" Brandon, I have a question about your method. You mention that you pick E0 based on the 1st peak of the derivative for each sample then extract chi(k). Have you tried constraining E0 across the set? I have thought that in order to make a good comparison between samples in a set, a common E0 should be chosen in order to replicate closely the background function across the whole set. Constraining may also provide a trend in the fitting. Buena salud, Chris On Jun 6, 2011, at 6:46 PM, Brandon Reese <bjreese(a)gmail.com> wrote: > Kicaj and Matt, > > Thanks for the replies. It is certainly reasonable to ask about the experimental setup, that seems like a good first place to look for oddities. Sorry about using E0 in two different contexts (Athena and Artemis). I'll switch to using E0 for the chosen parameter in Athena's background subtraction and Enot for the guess parameter in Artemis. > > I aligned the scans in Athena using the reference foil absorption edge. I ended up shifting the scans in energy by ~1 eV or less based on the reference foil. I then set the E0 parameter in Athena to the peak of the first derivative. This value varied by about 0.5 eV (or less) between the different samples. This is what I considered when I made the statement about not seeing the oxidation change in the XANES. There is a shift of about 4 eV compared to the reference foil, which I would expect because I am looking at oxides. > > I then extracted the chi(k) into Artemis, and used the same Feff calculations/paths for each sample. In the Artemis fits I am seeing Enot shifts of 1-2 eV, which is a fair bit larger than the error bars. If I chose E0 at peak of the first derivative the Enot came out to be ~7 eV. Since this seemed a little on the big side, I also tried setting E0 to be the top of the white line, in that case Enot came out to be ~1 eV. The Enot shift between samples was about the same either way. Could an argument be made that there is a small shift in the overall oxidation state of the films, possibly contributing to the changes in the conductivity changes in the films? Does anyone have any references about using Enot shifts in this way? > > Scott - The amplitudes of the XANES features are very close. in the normalized spectrum the difference practically 0, and in the derivative the amplitudes are ~5% off. There is bit larger of a difference in amplitude between the samples (in fluorescence) and a pure In2O3 powder (in transmission) of ~10% in the first derivative. The samples are sputtered from oxide sources, so the presence of metallic In should be pretty small. I am interested about your comment on the relative sizes of the first derivative peaks. Comparing my samples to the foil the oxide peak amplitude is bigger than the metal peak by 10% or so. Could this be due to the differences between fluorescence and transmission or not optimizing the experiment to measure the foil? Or could it be due to something else more heinous? > > I noticed on individual fits that the dR for the first shell came out nearly the same (2.162 +/- .007 vs. 2.164) on the two samples, while the Enot's had the 1-2 eV shift between the samples. I tried to fit the two types of samples simultaneously while constraining the dR's (and a few 2nd shell parameters) to be equal to each other and letting the Enot's float. The relative Enot values came out close to what they were before. If I let dR values fit independantly, there was no real change present. In other words the multiple data set fit just made my EB's a bit smaller, but the relative shifts stayed about the same. > > Would there be some reasonable way in a multi-data set fit to constrain the Enot's? > > Brandon > > On Mon, Jun 6, 2011 at 9:04 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > HI Brandon, > > If I understand right (and to echo Darius's questions), it seems like > you measure samples with a metal reference, and aligned the spectra in > Athena so that the references matched. That's a fine way to go. I > would ask: how big were the needed energy shifts? > Are the experimental mu(E) spectra aligned well at this point? If > you're studying metal oxides with different oxygen content, you might > very well see oxidation in the XANES. If I understand correctly, > you're saying you don't see this. > > Then, you extracted the chi(k) from the aligned spectra. How much did > E0 vary for the shifted spectra in this background-subtraction step? > > Then, you pulled these chi(k) into Artemis, and see different E0 > shifts in the fits. This E0 is a little different, in that it is the > E0 shift applied to the Feff calculation to match the experimental > spectra. If you use different paths or different calculations, such > E0 shifts might happen, and wouldn't be highly meaningful. > > I know that's not a complete answer, but hopefully that and Darius's > questions will help, > > --Matt > > PS on Q2: 1/ (kR)^2 vs 1 / kR^2 > > This is probably either a typo, or a different convention based on the > definition of f(k) as the electron scattering amplitude. In the Feff > world, it should be 1/kR^2, but using 1/(kR)^2 would just map f(k) to > k*f(k). > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Postdoc in XAFS at Australian Synchrotron
by Chris Glover 11 Jun '11

11 Jun '11

Hi All, Im hoping this reaches, or could be passed to, interested candidates in a 2 year Postdoc position at the XAS beamline at the Australian Synchrotron. In short the beamline is based on a 1.9T Wiggler with high flux focused beam of ~ 0.2 x 1 mm. It features 2 experimental hutches, the first is a (fixed) 'standard' RT/He transmission / fluorescence setup, and the second flexible for a range of different setups. The main detector on the beamline is a Canberra 100 element Ge pixel array detector and XIA electronics. Optimizing the experimental performance of this detector be the main focus of the Postdocs project. Further information regarding the beamline and the position are available at: http://www.synchrotron.org.au/index.php/aussyncbeamlines/x-ray-absorption-s… http://www.synchrotron.org.au/index.php/about-us/working-at-the-synchrotron… Relocation and repatriation expenses for international candidates will be provided. I would like to clarify that despite rumors and what may be reported in the local and international media, we are not concerned about the long term security and viability of the Australian Synchrotron continued operations. We are, unfortunately, a hot topic with local politics. For any queries or further information please contact me off the list. Regards Chris Glover.

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Question about shift in E0
by Brandon Reese 08 Jun '11

08 Jun '11

Hi all, I am looking at EXAFS of thin film metal oxides. I am varying both metal content and the oxygen content of the films. I aligned the scans with a metal reference foil collected simultaneously. In Artemis, I have noticed that when changing between films with no extra oxygen versus those with extra oxygen there is a shift in the fitted E0 of ~1.5 eV (after aligning to the foil). I tried setting the E0 in Athena to the peak of the 1st derivative and the peak of the white line with the same result (~7 eV difference). I was a little surprised by the offset because in Athena the E0 values varied by <0.5 eV. I am not sure if the argument could be made that this shift is a result in a changing oxidation state because it doesn't show up in the XANES (at least qualitatively). Are there other experimental effects that could cause a shift like this, or is this likely something real in my material? If anyone want to see a representative group of data, let me know. I also have an unrelated quick (I think) question on the EXAFS equation. In some references I see a term 1/(k R)^2 and in others it is 1/(k R^2). I couldn't really see any reason for the difference, unless it is to correct for subtle differences in how the other terms are defined. Thanks Brandon

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Re: [Ifeffit] Question about shift in E0
by Andrew Korinda 07 Jun '11

07 Jun '11

Sorry Brandon, I see now everything I was asking for was I'm the first few emails. Enot is a local atomic shift in E0 as explained before. (sorry I'm not referencing, I only have my phone available this week) What I understand is you have set E0 to 27944 and 27950 then get Enot of -7 and -1 respectively. This leads to a local edge in the EXAFS equation of 27951 in both cases which is what I was getting at previously. But you say ~ so that means you have an real difference between the two, and the opposite of what I was thinking. Sorry if I caused any confusion. Andy Korinda On Jun 7, 2011 6:27 AM, "Brandon Reese" <bjreese(a)gmail.com> wrote: > I was using feff6. Does your comment mean that when fitting Enot with Feff6, > the results should be considered unreliable? I assumed the 0.5 eV shift in > the mu spectra was small enough that the spectrum could be considered > essentially at the same energy. That is why I was surprised with the > (somewhat) larger shift in Artemis. > > Andy, are you asking what the difference is between E0-Enot for the two > samples? If I picked E0 to be 27944 for all the samples( a round number near > the 1st derv peak), Artemis would fit Enot to be ~5.5 for one group of > samples and ~7 for the other group. Approximately the same offset was > present if I let the parameters get chosen automatically, regardless of the > absolute E0 (within reason). Is this what you were asking, or did I > misunderstand? > > Brandon > > Andy, E0-Enot came out to be 2794 > 2011/6/7 "Dr. Dariusz A. Zając" <kicaj(a)ifj.edu.pl> > >> ** >> Hi Brandon, >> that was a reason why I wanted to clarify which parameters you use. >> E0 (as a Fermi level) in Athena can be taken (but do not must) as a valence >> state of measured ion for K edges, whereas in Artemis delE0 can correspond >> to the potential of the one of nearest atoms to the measured one. If you >> talk about Artemis and calculations, would be also helpful to know the >> version of feff. It is known that for version up to 6. can be problem with >> fitting values of Enot. And of course Matt answered you more clearly... >> The difference of 0.5eV between spectra of reference sample can be simply >> related with the energy resolution of the beam (beamline). >> >> Maybe this will helps you more: >> http://cars9.uchicago.edu/pipermail/ifeffit/2004-June/005607.html >> http://cars9.uchicago.edu/pipermail/ifeffit/2006-February/006811.html >> >> kicaj >> >> W dniu 11-06-07 00:46, Brandon Reese pisze: >> >> Kicaj and Matt, >> >> Thanks for the replies. It is certainly reasonable to ask about the >> experimental setup, that seems like a good first place to look for oddities. >> Sorry about using E0 in two different contexts (Athena and Artemis). I'll >> switch to using E0 for the chosen parameter in Athena's background >> subtraction and Enot for the guess parameter in Artemis. >> >> I aligned the scans in Athena using the reference foil absorption edge. I >> ended up shifting the scans in energy by ~1 eV or less based on the >> reference foil. I then set the E0 parameter in Athena to the peak of the >> first derivative. This value varied by about 0.5 eV (or less) between the >> different samples. This is what I considered when I made the statement about >> not seeing the oxidation change in the XANES. There is a shift of about 4 eV >> compared to the reference foil, which I would expect because I am looking at >> oxides. >> >> I then extracted the chi(k) into Artemis, and used the same Feff >> calculations/paths for each sample. In the Artemis fits I am seeing Enot >> shifts of 1-2 eV, which is a fair bit larger than the error bars. If I chose >> E0 at peak of the first derivative the Enot came out to be ~7 eV. Since this >> seemed a little on the big side, I also tried setting E0 to be the top of >> the white line, in that case Enot came out to be ~1 eV. The Enot shift >> between samples was about the same either way. Could an argument be made >> that there is a small shift in the overall oxidation state of the films, >> possibly contributing to the changes in the conductivity changes in the >> films? Does anyone have any references about using Enot shifts in this way? >> >> Scott - The amplitudes of the XANES features are very close. in the >> normalized spectrum the difference practically 0, and in the derivative the >> amplitudes are ~5% off. There is bit larger of a difference in amplitude >> between the samples (in fluorescence) and a pure In2O3 powder (in >> transmission) of ~10% in the first derivative. The samples are sputtered >> from oxide sources, so the presence of metallic In should be pretty small. I >> am interested about your comment on the relative sizes of the first >> derivative peaks. Comparing my samples to the foil the oxide peak amplitude >> is bigger than the metal peak by 10% or so. Could this be due to the >> differences between fluorescence and transmission or not optimizing the >> experiment to measure the foil? Or could it be due to something else more >> heinous? >> >> I noticed on individual fits that the dR for the first shell came out >> nearly the same (2.162 +/- .007 vs. 2.164) on the two samples, while the >> Enot's had the 1-2 eV shift between the samples. I tried to fit the two >> types of samples simultaneously while constraining the dR's (and a few 2nd >> shell parameters) to be equal to each other and letting the Enot's float. >> The relative Enot values came out close to what they were before. If I let >> dR values fit independantly, there was no real change present. In other >> words the multiple data set fit just made my EB's a bit smaller, but the >> relative shifts stayed about the same. >> >> Would there be some reasonable way in a multi-data set fit to constrain the >> Enot's? >> >> Brandon >> >> On Mon, Jun 6, 2011 at 9:04 AM, Matt Newville <newville(a)cars.uchicago.edu >wrote: >> >>> HI Brandon, >>> >>> If I understand right (and to echo Darius's questions), it seems like >>> you measure samples with a metal reference, and aligned the spectra in >>> Athena so that the references matched. That's a fine way to go. I >>> would ask: how big were the needed energy shifts? >>> Are the experimental mu(E) spectra aligned well at this point? If >>> you're studying metal oxides with different oxygen content, you might >>> very well see oxidation in the XANES. If I understand correctly, >>> you're saying you don't see this. >>> >>> Then, you extracted the chi(k) from the aligned spectra. How much did >>> E0 vary for the shifted spectra in this background-subtraction step? >>> >>> Then, you pulled these chi(k) into Artemis, and see different E0 >>> shifts in the fits. This E0 is a little different, in that it is the >>> E0 shift applied to the Feff calculation to match the experimental >>> spectra. If you use different paths or different calculations, such >>> E0 shifts might happen, and wouldn't be highly meaningful. >>> >>> I know that's not a complete answer, but hopefully that and Darius's >>> questions will help, >>> >>> --Matt >>> >>> PS on Q2: 1/ (kR)^2 vs 1 / kR^2 >>> >>> This is probably either a typo, or a different convention based on the >>> definition of f(k) as the electron scattering amplitude. In the Feff >>> world, it should be 1/kR^2, but using 1/(kR)^2 would just map f(k) to >>> k*f(k). >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> >> >> _______________________________________________ >> Ifeffit mailing listIfeffit@millenia.cars.aps.anl.govhttp:// millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >>

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Re: [Ifeffit] Question about shift in E0
by Scott Calvin 06 Jun '11

06 Jun '11

Hi Brandon, I don't find this terribly surprising if your samples are mixtures of a metal and a metal oxide. If you look at the derivative of the XANES spectra of a pure transition metal and its oxides, you'll generally find that the biggest difference is not in the position of the derivative peaks, but in their relative size; for the metal the lower energy derivative peak is much larger than it is for the oxide. A mixture of oxide and metal, therefore, will be primarily evident in XANES through the relative heights of these peaks; sometimes the apparent shift can be very subtle indeed. For example, consider what happens if the first peak in the first derivative is 20 times lower in the oxide than in the metal, and is also 1.5 eV higher in energy. If you have one sample which is 70% metal, and you compare it to a sample which is 40% metal, the tiny contribution of the oxide to the first peak will hardly be visible in either case, and you might see no measurable shift in energy in the XANES for that peak. (You'll see a big change in its amplitude, though.) Likewise, the white line may be dominated by the oxide, and show little shift in the XANES (but once again, a big change in amplitude). An EXAFS fit, however, doesn't suffer from weighting issues in the same way, and may indeed show an E0 shift when the mixture of oxidation states changes. For my description to apply to your system, though, I'd expect you to be seeing substantial changes in the amplitudes of XANES features, even if their position doesn't shift much. Is that the case for your data? --Scott Calvin Sarah Lawrence College On Jun 5, 2011, at 11:56 PM, Brandon Reese wrote: > Hi all, > > I am looking at EXAFS of thin film metal oxides. I am varying both > metal content and the oxygen content of the films. I aligned the > scans with a metal reference foil collected simultaneously. In > Artemis, I have noticed that when changing between films with no > extra oxygen versus those with extra oxygen there is a shift in the > fitted E0 of ~1.5 eV (after aligning to the foil). I tried setting > the E0 in Athena to the peak of the 1st derivative and the peak of > the white line with the same result (~7 eV difference). I was a > little surprised by the offset because in Athena the E0 values > varied by <0.5 eV. I am not sure if the argument could be made that > this shift is a result in a changing oxidation state because it > doesn't show up in the XANES (at least qualitatively). Are there > other experimental effects that could cause a shift like this, or is > this likely something real in my material? If anyone want to see a > representative group of data, let me know. > > >

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Startup Macros
by Emiliano Fonda 31 May '11

31 May '11

Dear all, I would like to write some IFeffit macro and use it in Athena. Actually, I did not find a clean way to load a file with macros at the Athena startup. How can we add our own macros to those that are built-in? Best regards, Emiliano -- Dr. Emiliano Fonda Beamline Scientist (SAMBA) Synchrotron SOLEIL L'Orme des Merisiers Saint Aubin BP48 91192 Gif Sur Yvette CEDEX France Phone +33169359633 Fax +33169359456

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Re: [Ifeffit] more bugs in atoms?
by Gudrun Lisa Bovenkamp 27 May '11

27 May '11

Hi George, I cannot understand how you got this atoms.inp file where the core is stated to be Co1 and there is only Fe. So, I cannot confirm the crystal structure from a database. My problem is solved. I understood that the ATOMS program implemented in Arthemis and ATOMS 2.5 have some bugs that are corrected in ATOMS 3.0 and WebATOMS. When I use those two programs I get a correct crystal structure xyz table in feff.inp. the only reason that I can think of, why your shifting seem to work better is that the atoms.inp file was not representing the correct structure in the first place. This can happen when the situation you wnat to describe is not the situation that was measured by somebody else. Or there is a mistake in the paper. Anyway. Thanks for sharing this idea. Lisa > Date: Thu, 26 May 2011 11:41:08 -0400 >From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] more bugs in atoms? > Message-ID: <BANLkTi=OH=NCJjmwhkE5vLmnTEao8k3avg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Lisa, > > Let me just mention one situation I have encountered using atoms, >and how I > resolved it. I am not sure if this is the result of a bug or not, >but > perhaps you can try applying the approach I took to your own >situation and > see if it can resolve your problem. > > The issue I encountered was running atoms for a monoclinic I2/c >structure, > space group 15. > > Here is the atoms input file: > > ! This atoms input file was generated by Artemis 0.8.014 > ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 > title = ... > space = i 2/c 1 1 > a = 5.51120 b = 5.51120 c = 7.79410 > alpha = 90.0 beta = 90.740 gamma = 90.0 > core = Co1 edge = K rmax = 6.0 > !shift 0.25000 0.25000 0.25000 > atoms > ! elem x y z tag occ. > Fe 0.00000 0.00000 0.00000 Fe1 1.00000 > > If one calculates the Fe-Fe distance between the atom at (0,0,0) and >the > atom at (0, 0, 0.5), from application of the (x, -y, -z+0.5) lattice > translation, one finds a Fe-Fe distance of 3.9705. However, if one >runs the > above atoms input file, this Fe-Fe distance is not found. Instead, a >shift > vector of (0.25, 0.25, 0.25) is needed to get the correct Fe-Fe >distance. > Note, the i2/c space group is listed with only one origin in the > international tables. I determined the necessary shift vector from >trail and > error. It is still unclear to me why it was necessary to include a >shift > vector. So the best suggestion I have is that you can try including > different shift vectors in your own atoms.inp file and see if you >can get > agreement with the crystallography program that way. Since, as I >said, it > isn't clear to me why this fixed my problem, its hard to say if this >is the > same issue you are having, but it may be worth a try. > > It may also be worth while to calculate some atomic distances from >the > lattice positions given in the international tables, and see if >atoms or the > crystallography program is giving you the same thing. > >Finally, let me add on another question for the list here since it is > somewhat related. When one runs the above atoms.inp file with the >(0.25, > 0.25, 0.25) shift vector one finds four Fe1_1 atoms at 3.9701 and >two Fe_2 > atoms at 3.9705. When one then runs Feff, it combines these into a >single >Fe1_1 scattering path with N=6. Is there a command can be placed in >the Feff > input file to tell Feff not to combine identical paths like this? > > Best, > George > >

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Simulation of ion xanes spectra using feff9
by Aurora Clark 27 May '11

27 May '11

Hi; I hope you don¹t mind me posting a question about feff9 to this list, but the feff userlist is defunct. I am trying to learn feff9 by reproducing the work in a JPCA recent paper (JPCA 2011, 115, 2345). I have a calculated structure for U(H2O)8]4+ ion that is nearly identical to that of the paper and so I am using that structure. I have been able to run several test cases for feff9 and I think I have a reasonable understanding of the different cards in feff9 however there are definitely some particulars for these f-element ions that are eluding me. My primary question surround how to deal with ion charge 1. I have tried several options with the ion card, everything from the U having a charge of 4 and the O-atoms zero, to partial charges like 2 and 0.25. However, in each case I get errors that state: ION: Expert option, please read documentation carefully and check your results. ION: Expert option, please read documentation carefully and check your results. U4+-8h2o Now if I run the calculation with no charges on the atoms everything proceeds very smoothly. The manual states that charges typically should not exceed 1 for an atom but in a highly charged system what are you to do? Thank you; Aurora

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Re: [Ifeffit] more bugs in atoms?
by Gudrun Lisa Bovenkamp 26 May '11

26 May '11

Hi George, thanks for responding. I sure imported the same structural information into atoms and the crystal structure program. Lisa > > Hi Lisa, > > I'm not very familiar with PbSO4, so I'm not sure if I can help, but >your > email immediately brought some questions to mind. > >First, did you import the same information into atoms and the crystal > structure program? The way you worded your message made me think >that the > crystal structure program already "knew" the structure of PbSO4, in >which > case perhaps it is using a structure that is slightly different from >the one > you import into atoms. > > Second, what is the source of the structure data you are feeding >into atoms? > In my experience, errors and inconsistencies in the reporting of >structure > data in the literature can lead to unusual results in atoms. > > Best, > George > > >

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Re: [Ifeffit] Can Artemis Simulate a FT Spectrum?
by Palomino, Robert 19 May '11

19 May '11

Matt, Thank you. How would I go about making a theory sum? Would I have to do that in another graphing program or can it be done in Artemis? -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, May 19, 2011 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 99, Issue 17 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. Can Artemis Simulate a FT spectrum? (Palomino, Robert) 2. Re: Can Artemis Simulate a FT spectrum? (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Thu, 19 May 2011 11:38:45 -0400 From: "Palomino, Robert" <rpalomino(a)bnl.gov> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Can Artemis Simulate a FT spectrum? Message-ID: <B32CD18BE9D42745B75847F981879A3602051206(a)exchangemb3.bnl.gov> Content-Type: text/plain; charset="us-ascii" Hi, I was wondering if it was possible for Artemis to simulate a FT spectrum, I have a model and would like to visually see what the simple R-space spectrum would like so see if there are any similarites at all to my sample. I'm not sure if the reason it doesn't converge is because the signal level is too low or if it is the wrong model all together. Robert

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Can Artemis Simulate a FT spectrum?
by Palomino, Robert 19 May '11

19 May '11

Hi, I was wondering if it was possible for Artemis to simulate a FT spectrum, I have a model and would like to visually see what the simple R-space spectrum would like so see if there are any similarites at all to my sample. I'm not sure if the reason it doesn't converge is because the signal level is too low or if it is the wrong model all together. Robert

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Athena (Question about LC fitting)
by Yu-Ting Liu 15 May '11

15 May '11

Hi, Related to this issue, I have a question about whether alignment is necessary for LCF when the oxidation state among sample and standards is different. I used to align spectra of samples and standards before LCF while handling P. However, I got confused about Se. For Se speciation, I prepared six Se species with oxidation state of -2 (FeSe), 0 (elemental Se), 0 (seleno-cystine), 0 (seleno-methionine), 4 (selenite), and 6 (selenate) to fit samples collected from sediments and biofilms. I am wondering whether the shift of spectra due to the alignment would make standards mis-fit spectral features of samples. Thank you so much for the help! Yu-Ting Liu Yu-Ting (Lusia) Liu Postdoctoral Associate Duke University Civil and Environmental Engineering Durham, NC, 27708-0287 ------------------------------------------------------------------------------- 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

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Re: [Ifeffit] Question about transform windows and statistical parameters
by Scott Calvin 13 May '11

13 May '11

Matt, On May 13, 2011, at 8:39 AM, Matt Newville wrote: >> >> After all, the epsilon should be different for different k-ranges, >> as your signal to noise ratio probably changes as a function of k. >> Using the same epsilon doesn't reflect that. > > Without seeing the data in question, this seems like speculation to > me. I'm not at all sure why epsilon (the variation in chi(k)) > should depend strongly on the k-range. In my experience, it usually > does not. The S/N ratio will surely change with k, but that would > surely be dominated by the rapid decay in |chi(k)|, rather than a > change in epsilon. I'm confused. We Fourier transform k-weighted data. Since Ifeffit uses the high-R amplitude to estimate uncertainty, it seems to me that what matters is signal-to-noise, not just noise in the original unweighted chi(k). Am I wrong in that? I may be misunderstanding how epsilon_r is calculated. And epsilon_r is the relevant epsilon for a fit in R space, right? > > I think your assumption that epsilon will depend strongly on k may > not correct. Do you have evidence for this? I would say that it > is not strongly dependent on k, and that reduced chi-square is > useful in comparing fits with different k-ranges. I just tried it on the FeC2O4 chi(k) attached to this post. It's a good example of data where it's not immediately clear to me what the "best" value for kmax is, so it would be tempting to use RCS to compare fits over different k-ranges. I used k-weight 3, and Hanning windows with dk = 1. I chose kmin as 2 and stepped kmax by 0.5, recording epsilon_r for each: kmax epsilon_r 7 0.034840105 7.5 0.041843848 8 0.082627337 8.5 0.087550367 9 0.086032007 9.5 0.085996216 10 0.088679339 10.5 0.090364699 11 0.092509939 11.5 0.108103081 There's a general trend of increasing epsilon_r with an increase in k. There's also a jump of a factor of 2 between 7.5 and 8. Why? Because there's a glitch there, and the glitch adds high-R structure. To make sure there wasn't something odd about this particular chi(k), I took one of the data sets included with the horae distribution: the file y300.chi in the ybco folder. I followed the same procedure as before, except I stepped by 1 inverse angstrom each time, because of the greater data range. kmax epsilon_r 7 0.012866125 8 0.073383695 9 0.078255772 10 0.080016040 11 0.091634572 12 0.105419473 13 0.164341701 14 0.195266957 15 0.224727593 16 0.411139882 17 0.480293296 If anything, the trend is more clear here. > > I find it confusing that you expect the noise in the data to depend > (strongly, even) on k, but not on R. The general wisdom is the > estimate of epsilon from the high-R components is too low, > suggesting that the R dependence is significant. Every time I've > looked, I come to the conclusion that noise in data is either > consistent with "white" or so small as to be difficult to measure. > I believe Corwin Booth's recent work supports the conventional > wisdom that epsilon decreases with R, but I don't recall it > suggesting a significant k dependence. I'm not making any claims as to whether, in general, the noise in the data depends on R. I can speculate about circumstances where low R noise is greater (due, for instance, to temperature fluctuations in cooling water, which are likely to be fairly slow), or where high R noise is greater (an example here would be if whatever system is keeping the beam on the sample vertically as the mono scans is tending to overshoot). But Ifeffit's estimation of epsilon_r demonstrably does not depend on the R-range used for fitting, regardless of the distribution of noise in R. That's a very different thing. Thus, changing the R-range of a fit is completely safe as far as comparing RCS goes. --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Question about transform windows and statistical parameters
by Scott Calvin 13 May '11

13 May '11

Hi Brandon, Matt and Bruce both gave good, thorough answers to your questions this morning. Nevertheless, I'm going to chime in too, because there are some aspects of this issue I'd like to put emphasis on. On May 11, 2011, at 8:46 PM, Brandon Reese wrote: > I tried your suggestion with epsilon and the chi-square values came > out to be very similar values with the different windows. Does this > mean that reporting reduced chi-square values in a paper that > compared several data sets would not be necessary and/or appropriate? Bruce said "no" emphatically, and I say "yes," but I think we've understood the question differently. As Bruce says: > Of course, reduced chi-square can only be compared for fitting > models which compute epsilon the same way or use the same value for > epsilon. That's the key point. I've gotten away from reporting values for reduced chi-square (RCS). That's a personal choice, and is not in accord with the International X-Ray Absorption Society's Error Reporting Recommendation, available here: http://ixs.iit.edu/subcommittee_reports/sc/ I think the difficulty in choosing epsilon is more likely to make a reduced chi-square number confusing than enlightening. But I am moving increasingly toward reporting changes in reduced chi-square between fits on the same data, and applying Hamilton's test to determine if improvements are statistically significant. > Would setting a value for epsilon allow comparisons across > different k-ranges, different (but similar) data sets, or a > combination of the two using the chi-square parameter? > Maybe not. After all, the epsilon should be different for different k- ranges, as your signal to noise ratio probably changes as a function of k. Using the same epsilon doesn't reflect that. > > > In playing around with different windows and dk values my fit > variables generally stayed within the error bars, but the size of > the error bars could change more than a factor 2. Does this mean > that it would make sense to find a window/dk that seems to "work" > for a given group of data and stay consistent when analyzing that > data group? The fact that your variables stay within the error bars is good news. The change in the size of the error bars may be related to a less-than- ideal value for dk you may have used for the Kaiser-Bessel window. But yes, find a window and dk combination that seems to work well and then stay consistent for that analysis. Unless the data is particularly problematic, I'd prefer making a reasoned choice before beginning to fit and then sticking with it; a posteriori choices for that kind of thing make me a little nervous. * * * At the risk of being redundant, four quick examples. Example 1: You change the range of R values in the Fourier transform over which you are fitting a data set. For this example, RCS is a valuable statistic for letting you know whether the fit supports the change in R-range. Example 2: You change the range of k values over which you are fitting your data. For this example, comparing RCS is unlikely to be useful. You are likely trying different k-ranges because you are suspicious about some of the data at the extremes of your range. Including or excluding that data likely implies epsilon should be changed, but by how much? Thus the unreliability of comparing RCS in this case. Example 3: You change constraints on a fit on the same data range. For this example, comparing RCS is very useful. Example 4: You compare fits on the same data range, with the same model, on two different data sets which were collected during the same synchrotron run under similar conditions. For this example, proceed with caution. You may decide to trust Ifeffit's method for estimating epsilon, or you may be able to come up with your own (perhaps basing it on the size of the edge jumps). Hopefully issues like glitches and high-frequency jitter are nearly the same for both samples, which gives you a fighting chance of making reasonable estimates of epsilon. Done with a little care, there may be value in comparing RCS for this kind of case. --Scott Calvin Sarah Lawrence College

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more bugs in atoms?
by Gudrun Lisa Bovenkamp 12 May '11

12 May '11

Hey everybody, For a while I was wondering why I could not get a proper XANES simulation using FEFF (8 or 9). Recently I realized that the xyz list which is created in atoms from the crystal structure is not the same as from a crystal structure program for PbSO4. Can somebody please check this. I attached my feff.imp file including the atoms.imp (which was created by arthemis). Thanks, Lisa * input file was generated by Artemis 0.8.014 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 13.94 microns, unit edge step: 24.69 microns * specific gravity = 5.382 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00039 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * ----------------------------------------------------------------- * The following crystallographic data were used: * * title *-PbSO4 -[PNMA] Anglesite - orthorhombic * title 'James, R W' * title Proceedings of the Royal Society of London, Series A: Mathematical and Physical Sciences (76,1906-) * space = P n m a * a = 8.450 b = 5.380 c = 6.930 * alpha = 90.0 beta = 90.0 gamma = 90.0 * core = Pb edge = L3 * atoms * ! elem x y z tag occ * Pb 0.31530 0.25000 0.33750 1.00000 * S 0.44300 0.25000 -0.19470 1.00000 * O -1.00000 -1.00000 -1.00000 1.00000 * ----------------------------------------------------------------- EDGE L3 S02 1.0 CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 SCF 5.16556 0 15 0.1 EXCHANGE 0 0 0 XANES 6.0 0.07 0.5 FMS 6 *LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 82 Pb -1 -1 0 1 8 O -1 -1 1 2 16 S -1 -1 1 3 82 Pb -1 -1 1 ATOMS * this list contains 156 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Pb 0.00000 1.56072 1.34500 1.12613 3 O_1 2.34799 1.56072 -1.34500 1.12613 3 O_1 2.34799 1.07906 0.00000 3.24185 2 S_1 3.41672 -2.18263 2.69000 -0.22315 2 S_2 3.47128 -2.18263 -2.69000 -0.22315 2 S_2 3.47128 2.04237 2.69000 -0.98960 2 S_3 3.51947 2.04237 -2.69000 -0.98960 2 S_3 3.51947 -2.66429 1.34500 -2.33887 3 O_2 3.79180 -2.66429 -1.34500 -2.33887 3 O_2 3.79180 1.07906 0.00000 -3.68815 2 S_4 3.84276 -3.14594 0.00000 2.47540 2 S_5 4.00307 4.22500 0.00000 -1.21275 1 Pb_1 4.39561 -4.22500 0.00000 -1.21275 1 Pb_1 4.39561 1.56072 4.03500 1.12613 3 O_3 4.47049 1.56072 -4.03500 1.12613 3 O_3 4.47049 -1.10357 2.69000 3.46500 1 Pb_2 4.52329 -1.10357 -2.69000 3.46500 1 Pb_2 4.52329 -1.10357 2.69000 -3.46500 1 Pb_2 4.52329 -1.10357 -2.69000 -3.46500 1 Pb_2 4.52329 3.12143 2.69000 2.25225 1 Pb_3 4.69596 3.12143 -2.69000 2.25225 1 Pb_3 4.69596 -2.66429 4.03500 -2.33887 3 O_4 5.37122 -2.66429 -4.03500 -2.33887 3 O_4 5.37122 0.00000 5.38000 0.00000 1 Pb_4 5.38000 0.00000 -5.38000 0.00000 1 Pb_4 5.38000 -3.14594 0.00000 -4.45460 2 S_6 5.45348 -2.66429 1.34500 4.59112 3 O_5 5.47593 -2.66429 -1.34500 4.59112 3 O_5 5.47593 5.30406 0.00000 2.47540 2 S_7 5.85326 1.56072 1.34500 -5.80387 3 O_6 6.15872 1.56072 -1.34500 -5.80387 3 O_6 6.15872 3.12143 2.69000 -4.67775 1 Pb_5 6.23384 3.12143 -2.69000 -4.67775 1 Pb_5 6.23384 1.07906 5.38000 3.24185 2 S_8 6.37325 1.07906 -5.38000 3.24185 2 S_8 6.37325 -5.32857 2.69000 2.25225 1 Pb_6 6.37984 -5.32857 -2.69000 2.25225 1 Pb_6 6.37984 5.78571 1.34500 -2.33887 3 O_7 6.38387 5.78571 -1.34500 -2.33887 3 O_7 6.38387 1.07906 5.38000 -3.68815 2 S_9 6.61145 1.07906 -5.38000 -3.68815 2 S_9 6.61145 -2.66429 4.03500 4.59112 3 O_8 6.66769 -2.66429 -4.03500 4.59112 3 O_8 6.66769 -3.14594 5.38000 2.47540 2 S_10 6.70589 -3.14594 -5.38000 2.47540 2 S_10 6.70589 6.26736 2.69000 -0.22315 2 S_11 6.82391 6.26736 -2.69000 -0.22315 2 S_11 6.82391 2.04237 2.69000 5.94040 2 S_12 6.83343 2.04237 -2.69000 5.94040 2 S_12 6.83343 5.30406 0.00000 -4.45460 2 S_13 6.92651 0.00000 0.00000 6.93000 1 Pb_7 6.93000 0.00000 0.00000 -6.93000 1 Pb_7 6.93000 4.22500 5.38000 -1.21275 1 Pb_8 6.94736 -4.22500 5.38000 -1.21275 1 Pb_8 6.94736 4.22500 -5.38000 -1.21275 1 Pb_8 6.94736 -4.22500 -5.38000 -1.21275 1 Pb_8 6.94736 1.56072 6.72500 1.12613 3 O_9 6.99497 1.56072 -6.72500 1.12613 3 O_9 6.99497 -6.40764 2.69000 -0.98960 2 S_14 7.01949 -6.40764 -2.69000 -0.98960 2 S_14 7.01949 4.22500 0.00000 5.71725 1 Pb_9 7.10898 -4.22500 0.00000 5.71725 1 Pb_9 7.1089 END

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Athena Artemis
by George Sterbinsky 12 May '11

12 May '11

Hello, I've noticed an odd behavior in Athena and Artemis and I was hoping someone could explain it to me. I've attached an Artemis file Data3.apj and an Athena file Data4.prj. First open Data3.apj. Then from the Artemis file menu choose open, then open Data4.prj and import the Data4.xmu file. Now plot the data in k-space you will see a slight difference between the two spectra, most noticeably above 15 k, so plotting in k^3 is best to see the difference. Now close Artemis and don't save. Open Data4.prj with athena and choose to import only the file Data4.xmu. Save the project as something else. I saved as Data4C.prj, which I have also attached. Close Athena and don't save. Open Data3.apj again. Then from the Artemis file menu choose open, then open Data4C.prj or whatever you may have named the file and import the Data4.xmu file, which should now be the only data file in the project. Now plot the data in k-space and you will find that the two data sets are now the same. The differences at high k are no longer present. Can anyone explain what is going on here? Thank you, George

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Re: [Ifeffit] Athena Artemis
by Scott Calvin 12 May '11

12 May '11

Hi George, I've confirmed the behavior you describe on a Mac running OS 10.5.8, Artemis 0.8.014, Ifeffit 1.2.12, and Athena 0.8.061. It does seem to be a bug or a corrupted file, but I can't figure out what it's actually doing. It's not grabbing the wrong data from the Athena project--none of the other data sets look that close. It sort of seems like it imports a version with a different background subtraction (maybe a different background k-weight, for instance) when you import from the larger project. --Scott Calvin Sarah Lawrence College On May 12, 2011, at 11:18 AM, George Sterbinsky wrote: > Also, for anyone who just wants to see the difference in the two > data sets I've attached a figure. > > George > > On Thu, May 12, 2011 at 1:23 PM, George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu > <mailto:GeorgeSterbinsky@u.northwestern.edu>> wrote: > Hello, > > I've noticed an odd behavior in Athena and Artemis and I was hoping > someone could explain it to me. > > I've attached an Artemis file Data3.apj and an Athena file Data4.prj. > > First open Data3.apj. Then from the Artemis file menu choose open, > then open Data4.prj and import the Data4.xmu file. Now plot the data > in k-space you will see a slight difference between the two spectra, > most noticeably above 15 k, so plotting in k^3 is best to see the > difference. > > Now close Artemis and don't save. Open Data4.prj with athena and > choose to import only the file Data4.xmu. Save the project as > something else. I saved as Data4C.prj, which I have also attached. > > Close Athena and don't save. Open Data3.apj again. Then from the > Artemis file menu choose open, then open Data4C.prj or whatever you > may have named the file and import the Data4.xmu file, which should > now be the only data file in the project. Now plot the data in k- > space and you will find that the two data sets are now the same. The > differences at high k are no longer present. Can anyone explain what > is going on here? > > Thank you, > George > > <DataDiff.pdf><ATT00001..txt>

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Athena (linear combination fitting)
by Dilnesa, Belay 12 May '11

12 May '11

Dear Dr. Ravel, Thanks so much,for information you gave me. I subscribed already in the mailing list. I have a complex system to fit. I have a complex spectra from a hetrogenous sample and a number of reference samples. I am doing EXAFS LCF. To choose from the combinations after fitting is diffcult because the R factor of the first 5 combinations with diffrent reference combinations is similar. And as I see from my fitting the alignement plays really an important role on the LCF. You know when I made allign marked groups based on the standard, it alligns well the enregy but when I see the k-plot, it shifts. And my fitting space is on chi(k) which is sensitive when I allign. It is complex system. The procedures I am trying are, Normalization-allignement-LCF (this procedure alligns the energy well but the chi shifts and this affects my fitting because I am fitting on chi space. The other procedure i checked, Normalization-calibration-LCF (this alligns the energy good but for some spectra it shifts again). When I allign it manually by excel sheet, it works good. Can I use the following procedure...normalization, calibration-allignemet-LCF? I just found a well alligned spectra in E and K plot from this procedure. I will be happy if you comment on those procedure. Thanks so much for the keen help! With best regards, Belay

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Question about transform windows and statistical parameters
by Brandon Reese 12 May '11

12 May '11

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

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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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Question about FEFF6
by goodhei8＠gmail.com 13 Apr '11

13 Apr '11

Dear IFEFFIT Members, I have a strange problem with FEFF calculation. I am not sure if I made some mistakes in FEFF of input file, or FEFF did not handle it well. For Oxygen paths calculated with FEFF in Artemis by 3 input files, the results for O are supposed to be close, but I got a big difference, when I transform them into r space(k 2.5~10,kweight=2 in attachment). There are three input files for FEFF: #1, 6O only on xyz axis #2, + 1P besides 6O #3, + 6P besides 6O For O, #2 and #3 are close(almost same), but #1 is much bigger. (It would make sense to me if #1 #2 are close.) Thank a lot. Best, Jack Song

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Strategy to obtain cofigurationally averaged EXAFS from MD simulations
by Francisco Garcia 12 Apr '11

12 Apr '11

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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XAS/XPS postdoc position at The University of Manchester
by Sven Schroeder 12 Apr '11

12 Apr '11

Dear all I would be grateful if you could bring this XAS/XPS post to the attention of suitable candidates. The post has been funded for 30 months and is available from 1 June 2011. Follow this link: http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/?ref=12… Research Associate (fixed term): Experimental and Computational Soft X-ray Spectroscopy (NEXAFS, XPS) of Corrosion Inhibition with Organic Molecules School of Chemical Engineering and Analytical Science, The University of Manchester Closing date: 06/05/2011 We are seeking to employ a Research Associate within the School of Chemical Engineering and Analytical Science (CEAS) on a full-time basis. The post is fixed-term for a period of 30 months commencing 1st June 2011. This post requires a PhD or equivalent in a relevant discipline (not limited to Physics or Chemistry) based on research in fundamental surface science or catalysis using ultra-high vacuum techniques. Experience with using ab initio soft X-ray spectroscopy data analysis packages such as StoBe, FEFF, CASTEP or similar methods is required. The project focuses on fundamental physicochemical studies of model surface systems in an industrially led project that involves organic chemists, computational chemists and chemical engineers at the Mexican Petroleum Institute (IMP). As such it requires a candidate with the ability to work both on their own initiative as well as a part of teams of varying size, and an ability to travel globally and regularly. Candidates should have an interest in working across the boundary between fundamental academic science and its practical application. Relevant peer-reviewed publications and experience in writing manuscripts for academic journal publications are essential. The candidate will take the lead in analysing the spectroscopic results through a combination of molecular modelling and calculations of core level shifts as well as associated X-ray absorption spectra. He/she will also be responsible for producing reports and presentations, and taking the lead in writing manuscripts for publications. On a day to day basis he/she will liaise directly with relevant contacts at IMP and within the University. Previous experience of operating NEXAFS and XPS equipment on a day to day basis, including minor repairs and vacuum management, would be an advantage. This work will include examination of these corrosion inhibitor/surface systems in simulated real-world environments, using equipment accessible at synchrotron radiation sources in the US and in Europe. The successful candidate will be integrated in the Manchester team, together with another project scientist and the Manchester investigators. He/she will contribute to applications for synchrotron radiation access and logistic coordinating of synchrotron radiation (SR) experiments and act as team leader during SR beamtimes. He/she will also carry out (or supervise) supporting measurements with home laboratory techniques (for example XRD, FTIR, electron microscopies, electrochemical techniques etc). The project requires quarterly reporting and presentations both in project meetings with the industrial partner and at academic conferences. Liaison with relevant contacts at the Mexican partner institute and participation in consortium project meetings twice a year will be required. The post is fixed-term for 30 months, available from 1st June 2011. -- 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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Re: [Ifeffit] Ifeffit Digest, Vol 98, Issue 8
by Guoqiang PAN 10 Apr '11

10 Apr '11

I did as the Bruce's advice, > 1. Check that Module::Build is indeed already on your system by > typing this at the command line: > perl -e "use Module::Build" > If it responds with noting (i.e. no error messages), then you are > fine. > > 2. Edit the files Bundle/LibPerlXrayBundle.pm and remove the line > with Module::Build beneath the "CONTENTS" header. > > 3. Try again. It's OK. Then to run ./build, it's easy to install artemis, athena and hephaestus. Thank you and Matt very much. Guoqiang On Fri, 2011-04-08 at 12:00 -0500, 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. Re: Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14) > (Guoqiang PAN) > 2. Installation Artemis, athena in Fedora 14 (Guoqiang PAN) > 3. Re: Installation Artemis, athena in Fedora 14 (Bruce Ravel) > 4. Re: Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14) > (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 08 Apr 2011 17:21:02 +0800 > From: Guoqiang PAN <gqpan(a)ustc.edu.cn> > To: Matt Newville <newville(a)cars.uchicago.edu> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>, > Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux > (Fedora 14) > Message-ID: <1302254462.5791.25.camel(a)localhost.localdomain> > Content-Type: text/plain; charset="UTF-8" > > Thanks lot to Matt and Bruce. > PGPLOT installation in Fedora 14 Linux case, can only be succeeded using > g77_gcc_aout. I tried every possible choice for fortran-compiler in my > case,only > /usr/local/src/pgplot/makemake /usr/local/src/pgplot linux g77_gcc_aout > could work! > Then PGPLOT_install script will use gfortran as default fortran > compiler, it stopped at > > gfortran -c -O2 -fPIC grexec.f > gfortran -c -O2 -fPIC /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:208.72: > > & RECL=255, FORM='BINARY', IOSTAT=IER) > > 1 > Warning: FORM specifier in OPEN statement at (1) has invalid value > 'BINARY' > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:240.72: > > & RECL=255, FORM='BINARY', IOSTAT=IER) > > 1 > Warning: FORM specifier in OPEN statement at (1) has invalid value > 'BINARY' > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:654.21: > > BLKOUT(0) = 254 > 1 > Error: Arithmetic overflow converting INTEGER(4) to INTEGER(1) at (1). > This check can be disabled with the option -fno-range-check > make: *** [gidriv.o] Error 1 > gfortran -u -Wall -fPIC -O -o > pgpack /usr/local/ifeffit-1.2.11c/pgplot/fonts/pgpack.f > rm -f grfont.dat > ./pgpack </usr/local/ifeffit-1.2.11c/pgplot/fonts/grfont.txt > Characters defined: 996 > Array cells used: 26732 > rm -f pgpack > gfortran -fno-backslash -o > pgdemo1 /usr/local/ifeffit-1.2.11c/pgplot/examples/pgdemo1.f -L`pwd` > -lpgplot_iff -lpng -lz -L/usr/X11R6/lib -lX11 > /usr/bin/ld: cannot find -lpgplot_iff > collect2: ld returned 1 exit status > make: *** [pgdemo1] Error 1 > = Cleaning up and preparing for test > = = = = = = = = = = = = = = = = = = = = = = = = = = > = 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: > = /usr/local/ifeffit-1.2.11c/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 > > > So if I commented out these two lines (line 219 and 220) in > PGPLOT_install > gfortran -v > /dev/null 2>&1 > if [ $? = 0 ] ; then fcompl='gfortran'; fi > PGPLOT_install will be OK! > > As for installation ifeffit, I tried your suggestions > e.g. (./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > -lpgplot_iff -lpng -lz -lX11') or ln -s libpgplot.a libpgplot_iff.a > ,but not successful. It stopped at > > gcc -g -O2 -o ifftest1 ifftest1.o ../lib/libifeffit.a > -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11 > -L/usr/lib/gcc/i686-redhat-linux/4.5.1 > -L/usr/lib/gcc/i686-redhat-linux/4.5.1/../../.. -lgfortran -lm -lgcc_s > /usr/bin/ld: cannot find -lpgplot_iff > collect2: ld returned 1 exit status > make[3]: *** [ifftest1] Error 1 > make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c' > make: *** [all-recursive-am] Error 2 > [root@localhost ifeffit-1.2.11c]# > > I think this also due to the gfortan, and I changed the fortran compiler > to g77: > ./configure --with-fortran=g77 > It is OK! > Best regards, > Guoqiang > > > On Thu, 2011-04-07 at 11:56 -0500, Matt Newville wrote: > > Guoqiang, > > > > Can we take a step back and try to figure out why PGPLOT_install > > didn't work for you? It does work for me on Fedora14. What part of > > PGPLOT_install did not work? > > > > It should be that ./configure --with-pgplot-link='LINKARGS' can be > > used to specify the PGPLOT_LIBS value, say > > > > ./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > > -lpgplot_iff -lpng -lz -lX11' > > > > For PGPLOT installed with PGPLOT_install, or something like > > ./configure --with-pgplot-link='-L/usr/local/pgplot -lpgplot -lpng > > -lz -lX11' > > > > for a PGPLOT installed "by hand". > > > > An important difference between PGPLOT_install and most "by hand" > > installations is that PGPLOT_install will not build a shared library, > > but a static one only. This won't affect building, but can have an > > impact for runtime, as the shared library needs to be found at > > runtime, and so needs to be in the LD_LIBRARY_PATH, or configured with > > ldconfig. > > > > --Matt > > > > > > ------------------------------ > > Message: 2 > Date: Fri, 08 Apr 2011 20:41:54 +0800 > From: Guoqiang PAN <gqpan(a)ustc.edu.cn> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: Bruce Ravel <bravel(a)bnl.gov> > Subject: [Ifeffit] Installation Artemis, athena in Fedora 14 > Message-ID: <1302266514.10181.10.camel(a)localhost.localdomain> > Content-Type: text/plain; charset="UTF-8" > > Hi,all > Main trouble for the installation Artemis, athena etc. in PC Linux > system (in my case is Fedora 14 ) is need to install all perl > pre-requisites from CPAN. Following the install instruction I did as > follows: perl -MCPAN -e 'install Bundle::XasPerlBundle' > But it stopped at 'DAGOLDEN': > > Warning: Prerequisite 'Module::Metadata => 1.000002' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'. > Continuing, but chances to succeed are limited. > Warning: Prerequisite 'CPAN::Meta => 2.110420' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing, > but chances to succeed are limited. > Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > Warning: Prerequisite 'version => 0.87' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > suspicious. Skipping another build attempt, to prevent looping > endlessly. > /usr/local/bin/perl Build --makefile_env_macros 1 > Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled > lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/i686-linux /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm line 10. > Compilation failed in require at lib/Module/Build/Base.pm line 23. > BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23. > Compilation failed in require at lib/Module/Build.pm line 15. > BEGIN failed--compilation aborted at lib/Module/Build.pm line 15. > Compilation failed in require at Build line 42. > BEGIN failed--compilation aborted at Build line 42. > make: *** [all] Error 2 > DAGOLDEN/Module-Build-0.3800.tar.gz > /usr/bin/make -- NOT OK > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > Running make test > Can't test without successful make > Running make install > Make had returned bad status, install seems impossible > > Guoqiang Pan > National Synchrotron Radiation Laboratory > University of Science & Technology of China > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 8 Apr 2011 09:37:01 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Installation Artemis, athena in Fedora 14 > Message-ID: <201104080937.01794.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="utf-8" > > > Guoqiang, > > Module::Build is the tool used to build and install my GUI software. > It is a standard perl module and should already be on your system. I > am surprised that your computer is finding it necessary to try to > download and reinstall it. > > I assume that you are at the step of installing the things I call > LibPerlXray and that you mis-typed. > > I suspect the fault is mine. I probably should not list Module::Build > in the file Bundle/LibPerlXrayBundle.pm. Try the following: > > 1. Check that Module::Build is indeed already on your system by > typing this at the command line: > perl -e "use Module::Build" > If it responds with noting (i.e. no error messages), then you are > fine. > > 2. Edit the files Bundle/LibPerlXrayBundle.pm and remove the line > with Module::Build beneath the "CONTENTS" header. > > 3. Try again. > > I apologize that this is so hard. I just don't have the resources to > test these things on all possible systems, so I rely on the users to > complain when they run into problems. Thanks for being patient. > > B > > > On Friday, April 08, 2011 08:41:54 am Guoqiang PAN wrote: > > Hi,all > > Main trouble for the installation Artemis, athena etc. in PC Linux > > system (in my case is Fedora 14 ) is need to install all perl > > pre-requisites from CPAN. Following the install instruction I did as > > follows: perl -MCPAN -e 'install Bundle::XasPerlBundle' > > But it stopped at 'DAGOLDEN': > > > > Warning: Prerequisite 'Module::Metadata => 1.000002' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > > 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'. > > Continuing, but chances to succeed are limited. > > Warning: Prerequisite 'CPAN::Meta => 2.110420' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing > > 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing, > > but chances to succeed are limited. > > Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > Warning: Prerequisite 'version => 0.87' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for > > 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks > > suspicious. Skipping another build attempt, to prevent looping > > endlessly. > > /usr/local/bin/perl Build --makefile_env_macros 1 > > Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled > > lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1 > > /usr/local/lib/perl5/site_perl/5.10.1/i686-linux > > /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm > > line 10. Compilation failed in require at lib/Module/Build/Base.pm line > > 23. BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23. > > Compilation failed in require at lib/Module/Build.pm line 15. > > BEGIN failed--compilation aborted at lib/Module/Build.pm line 15. > > Compilation failed in require at Build line 42. > > BEGIN failed--compilation aborted at Build line 42. > > make: *** [all] Error 2 > > DAGOLDEN/Module-Build-0.3800.tar.gz > > /usr/bin/make -- NOT OK > > Warning (usually harmless): 'YAML' not installed, will not store > > persistent state > > Running make test > > Can't test without successful make > > Running make install > > Make had returned bad status, install seems impossible > > > > Guoqiang Pan > > National Synchrotron Radiation Laboratory > > University of Science & Technology of China > > -- > > 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/ > > > ------------------------------ > > Message: 4 > Date: Fri, 8 Apr 2011 09:53:08 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: gqpan(a)ustc.edu.cn > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>, > Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] Fwd: Re: Fwd: ifeffit installation in Linux > (Fedora 14) > Message-ID: <BANLkTi=TERxR=UPKNfpdaybr6hsKtBFBrA(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Guoqiang, > > Ah, I see and sorry for the trouble, especially I have had a fix (so > that gfortran is used) for this for a while now. I believe you have > a reasonable solution, but the PGPLOT_install script in the svn > repository works better. I tried this on Fedora14 x86_64 yesterday > revealed another problem, that I think I have fixed. I'll try to get > that resolved and post a new PGPLOT_install script, and upload a > ifeffit 1.2.11d tarball. > > Thanks > > --Matt > > > > On Fri, Apr 8, 2011 at 4:21 AM, Guoqiang PAN <gqpan(a)ustc.edu.cn> wrote: > > Thanks lot to Matt and Bruce. > > PGPLOT installation in Fedora 14 Linux case, can only be succeeded using > > g77_gcc_aout. I tried every possible choice for fortran-compiler in my > > case,only > > /usr/local/src/pgplot/makemake /usr/local/src/pgplot linux g77_gcc_aout > > could work! > > Then PGPLOT_install script will use gfortran as default fortran > > compiler, it stopped at > > > > gfortran -c -O2 -fPIC grexec.f > > gfortran -c -O2 -fPIC /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f > > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:208.72: > > > > ? ? & ? ? ? ? RECL=255, FORM='BINARY', IOSTAT=IER) > > > > 1 > > Warning: FORM specifier in OPEN statement at (1) has invalid value > > 'BINARY' > > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:240.72: > > > > ? ? & ? ? ? ? ? ? ? RECL=255, FORM='BINARY', IOSTAT=IER) > > > > 1 > > Warning: FORM specifier in OPEN statement at (1) has invalid value > > 'BINARY' > > /usr/local/ifeffit-1.2.11c/pgplot/drivers/gidriv.f:654.21: > > > > ? ? ? ? BLKOUT(0) = 254 > > ? ? ? ? ? ? ? ? ? ? 1 > > Error: Arithmetic overflow converting INTEGER(4) to INTEGER(1) at (1). > > This check can be disabled with the option -fno-range-check > > make: *** [gidriv.o] Error 1 > > gfortran -u -Wall -fPIC -O -o > > pgpack /usr/local/ifeffit-1.2.11c/pgplot/fonts/pgpack.f > > rm -f grfont.dat > > ./pgpack </usr/local/ifeffit-1.2.11c/pgplot/fonts/grfont.txt > > ?Characters defined: ? 996 > > ?Array cells used: ? 26732 > > rm -f pgpack > > gfortran -fno-backslash -o > > pgdemo1 /usr/local/ifeffit-1.2.11c/pgplot/examples/pgdemo1.f -L`pwd` > > -lpgplot_iff -lpng -lz -L/usr/X11R6/lib -lX11 > > /usr/bin/ld: cannot find -lpgplot_iff > > collect2: ld returned 1 exit status > > make: *** [pgdemo1] Error 1 > > ?= Cleaning up and preparing for test > > ?= = = = = = = = = = = = = = = = = = = = = = = = = = > > ?= 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: > > ?= ? ?/usr/local/ifeffit-1.2.11c/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 > > > > > > So if I commented out these two lines ?(line 219 and 220) in > > PGPLOT_install > > ? ?gfortran -v > /dev/null 2>&1 > > ? ?if [ $? = 0 ] ; then ?fcompl='gfortran'; fi > > PGPLOT_install will be OK! > > > > As for installation ifeffit, I tried your suggestions > > e.g. (./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > > -lpgplot_iff -lpng -lz -lX11') or ln -s libpgplot.a libpgplot_iff.a > > ,but not successful. It stopped at > > > > gcc ?-g -O2 ?-o ifftest1 ?ifftest1.o ../lib/libifeffit.a > > -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11 > > -L/usr/lib/gcc/i686-redhat-linux/4.5.1 > > -L/usr/lib/gcc/i686-redhat-linux/4.5.1/../../.. -lgfortran -lm -lgcc_s > > /usr/bin/ld: cannot find -lpgplot_iff > > collect2: ld returned 1 exit status > > make[3]: *** [ifftest1] Error 1 > > make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test' > > make[2]: *** [all-recursive] Error 1 > > make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src' > > make[1]: *** [all-recursive] Error 1 > > make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c' > > make: *** [all-recursive-am] Error 2 > > [root@localhost ifeffit-1.2.11c]# > > > > I think this also due to the gfortan, and I changed the fortran compiler > > to g77: > > ./configure --with-fortran=g77 > > It is OK! > > Best regards, > > Guoqiang > > > > > > On Thu, 2011-04-07 at 11:56 -0500, Matt Newville wrote: > >> Guoqiang, > >> > >> Can we take a step back and try to figure out why PGPLOT_install > >> didn't work for you? ?It does work for me on Fedora14. ? What part of > >> PGPLOT_install did not work? > >> > >> It should be that ./configure --with-pgplot-link='LINKARGS' can be > >> used to specify the PGPLOT_LIBS value, say > >> > >> ? ? ./configure --with-pgplot-link='-L/usr/local/share/ifeffit/pgplot > >> -lpgplot_iff -lpng -lz -lX11' > >> > >> For PGPLOT installed with PGPLOT_install, or something like > >> ? ? ./configure --with-pgplot-link='-L/usr/local/pgplot -lpgplot -lpng > >> -lz -lX11' > >> > >> for a PGPLOT installed "by hand". > >> > >> An important difference between PGPLOT_install and most "by hand" > >> installations is that PGPLOT_install will not build a shared library, > >> but a static one only. ?This won't affect building, but can have an > >> impact for runtime, as the shared library needs to be found at > >> runtime, and so needs to be in the LD_LIBRARY_PATH, or configured with > >> ldconfig. > >> > >> --Matt > > > > > > > > > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 98, Issue 8 > **************************************

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Fwd: Re: Fwd: ifeffit installation in Linux (Fedora 14)
by Bruce Ravel 08 Apr '11

08 Apr '11

---------- Forwarded Message ---------- Subject: Re: Fwd: ifeffit installation in Linux (Fedora 14) Date: Thursday, April 07, 2011, 10:52:57 am From: Bruce Ravel <bravel(a)bnl.gov> To: gqpan(a)ustc.edu.cn On Thursday, April 07, 2011 10:23:20 am you wrote: > Thank you very much for your rapid reply. > Yes, I tried first with pgplot using > ./configure --with-pgplot=/usr/local/pgplot/, but failed with the 'make' > ../lib/libifeffit.a(iff_cursor.o): In function `iff_zoom_': > /usr/local/ifeffit-1.2.11c/src/lib/iff_cursor.f:134: undefined reference > to `pgband_' > /usr/local/ifeffit-1.2.11c/src/lib/iff_cursor.f:138: undefined reference > to `pgband_' > collect2: ld returned 1 exit status > make[3]: *** [ifftest1] Error 1 > make[3]: Leaving directory `/usr/local/ifeffit-1.2.11c/src/test' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/usr/local/ifeffit-1.2.11c/src' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/usr/local/ifeffit-1.2.11c' > make: *** [all-recursive-am] Error 2 > (more details in my previous make.log file) > Then I tried with ./configure --without-pgplot, which can > be done without any problem. That's the problem. > Regards, > Guoqiang Hmmm...... so it seems not to be linking with libpgplot.a. Odd. I notice on my computer that the pgplot library is called libpgplot_iff.a and that the Makefile in src/lib/ has this line: PGPLOT_LIBS = -L/usr/local/share/ifeffit/pgplot -lpgplot_iff -lpng -lz -lX11 I also see that Matt's PGPLOT_install script changes one of pgplot's files to use the installation location specified in PGPLOT_install as default location (i.e. the one that would be specified by setting the PGPLOT_DIR environment variable). The script then renames the library to have the "_iff". There are a number of ways to address. Here is one relatively simple suggestion: 1. cd to the location of libpgplot.a on your computer 2. make a symbolic link to libpgplot.a like so: ln -s libpgplot.a libpgplot_iff.a 3. set the PGPLOT_DIR environment variable to the directory containing libpgplot.a. This can be done either typing export PGPLOT_DIR=/location/of/pgplot at the commend line or putting it in a login script to make it permanent. (Of course, replace /location/of/pgplot with the correct thing on your computer.) 4. cd back to the location of the ifeffit source and try again to build it. All that is, of course, untested on my end. But I think it should work. If not, we'll keep trying until we figure it out! 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/ ----------------------------------------- -- 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/

3 3

Installation Artemis, athena in Fedora 14
by Guoqiang PAN 08 Apr '11

08 Apr '11

Hi,all Main trouble for the installation Artemis, athena etc. in PC Linux system (in my case is Fedora 14 ) is need to install all perl pre-requisites from CPAN. Following the install instruction I did as follows: perl -MCPAN -e 'install Bundle::XasPerlBundle' But it stopped at 'DAGOLDEN': Warning: Prerequisite 'Module::Metadata => 1.000002' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing 'DAGOLDEN/Module-Metadata-1.000004.tar.gz' with 'make_test => NO'. Continuing, but chances to succeed are limited. Warning: Prerequisite 'CPAN::Meta => 2.110420' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' failed when processing 'DAGOLDEN/CPAN-Meta-2.110930.tar.gz' with 'make_test => NO'. Continuing, but chances to succeed are limited. Warning: Prerequisite 'ExtUtils::CBuilder => 0.27' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. Warning: Prerequisite 'Parse::CPAN::Meta => 1.4401' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. Warning: Prerequisite 'version => 0.87' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. Warning: Prerequisite 'ExtUtils::ParseXS => 2.21' for 'DAGOLDEN/Module-Build-0.3800.tar.gz' already built but the result looks suspicious. Skipping another build attempt, to prevent looping endlessly. /usr/local/bin/perl Build --makefile_env_macros 1 Can't locate Module/Metadata.pm in @INC (@INC contains: t/lib t/bundled lib /usr/local/lib/perl5/5.10.1/i686-linux /usr/local/lib/perl5/5.10.1 /usr/local/lib/perl5/site_perl/5.10.1/i686-linux /usr/local/lib/perl5/site_perl/5.10.1 .) at lib/Module/Build/ModuleInfo.pm line 10. Compilation failed in require at lib/Module/Build/Base.pm line 23. BEGIN failed--compilation aborted at lib/Module/Build/Base.pm line 23. Compilation failed in require at lib/Module/Build.pm line 15. BEGIN failed--compilation aborted at lib/Module/Build.pm line 15. Compilation failed in require at Build line 42. BEGIN failed--compilation aborted at Build line 42. make: *** [all] Error 2 DAGOLDEN/Module-Build-0.3800.tar.gz /usr/bin/make -- NOT OK Warning (usually harmless): 'YAML' not installed, will not store persistent state Running make test Can't test without successful make Running make install Make had returned bad status, install seems impossible Guoqiang Pan National Synchrotron Radiation Laboratory University of Science & Technology of China

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Fwd: ifeffit installation in Linux (Fedora 14)
by Bruce Ravel 07 Apr '11

07 Apr '11

Guoqiang, First off, I am responding to you on the Ifeffit mailing list, which is the appropraite venue for questions about Ifeffit and related software. please use the mailing list for all future correspondance. I am not completely clear on what you are asking about, but I suspect that your problem is that Ifeffit isn't plotting anything. That is, I suspect that you have managed to compile pgplot and you have managed to compile Ifeffit, but you do not have pgplot and ifeffit talking to one another. The reason for this is that you said $ ./configure --without-pgplot This builds Ifeffit without pgplot support. What I think you want to do is to use the "--with-pgplot=dir" argument for "configure". That, you should do something like $ ./configure --with-pgplot=/usr/local/share/pgplot where you would, of course, specify, the actual installation location of pgplot on your computer. You will then need to remake and reinstall ifeffit. If that doesn't solve the problem, try asking again on the mailing list, where other knowledgeable people can offer their advice as well. Regards, 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] Third cumulant in DWF
by Joshua Kas 05 Apr '11

05 Apr '11

Hi all, I agree that adding debye waller factors in feff might be confusing, however, it can be useful if you are using a model for the DW factors that is not included in ifeffit, i.e., the spring constant, equation of motion, or dynamical matrix based methods. If these (or any of the other models in feff) are used, it will not change the path parameters used by ifeffit. The DWFs are only used in constructing chi(k), but the DWFs are printed out for each path so that they can be used in ifeffit/artemis if needed. Cheers, Josh > On Monday, April 04, 2011 06:51:23 pm Matthew Marcus wrote: > > Another question is whether, if you add a sigma2 to feff.inp, what > > does FEFF do? > > Ick! As good of a question as that might be, I have to recommend > against that practice in the strongest possible terms. Adding > sigma^2 <> 0 (or S0^2 <> 1, for that matter) to a Feff calculation > intended for use with Ifeffit/Artemis is highly likely to be highly > confusing. > > 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/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 98, Issue 4 > ************************************** >

1 0

Third cumulant in DWF
by Ping, Yuan 05 Apr '11

05 Apr '11

Dear IFEFFIT experts: Is it possible to add a k^3 term in the phase for fitting to take into account anharmonic effect? The fitted coefficient will be proportional to the 3rd cumulant of Debye-Waller factor. I work with high-temperature high-pressure systems where anharmonic effect is not negligible. Thanks. Yuan Ping

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2011 XAFS Summer school
by sumitk＠barc.gov.in 05 Apr '11

05 Apr '11

Dear Members, I am interested to attend the 2011 APS/IIT XAFS Summer school. I have written to Dr. Bunker for details but however, i am not able to reach him. I have already written (e-mail) to him on bunker(a)iit.edu site but i did not get reply. If dr. Bunker is on the mail list, i expect to reach him through this or if some member has the correct e-mail id of him, it will be of help to me to reach him. Thanking Sumit Kumar Scientific Officer Radiochemistry Division Bhabha Atomic Research Centre Mumbai, India-400 085. Phone: +91-22-2559 0640 (O).

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Final Deadline for NASCCSC Oral Presentations
by Carlo Segre 03 Apr '11

03 Apr '11

Hello: The final abstract deadline for oral presentations to the 2011 North American Core Shell Spectroscopy Conference is today, Sunday, April 3, 2011. Poster abstracts will continue to be accepted after tonight. The Second Annual North American Core Shell Spectroscopy Conference will be held jointly with the Denver X-ray Conference in Colorado Springs August 1-5, 2011. The conference is centrally located, making it easily accessible from the entire continent and it is excellent opportunity to have young scientists present to the Core Shell Spectroscopy community. We hope that you can attend and make this event an ongoing success. More information can be found at http://www.dxcicdd.com/cssc/ Hope to see you there! 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://www.iit.edu/~segre segre(a)debian.org

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Final Deadline for NASCCSC Abstracts
by Carlo Segre 31 Mar '11

31 Mar '11

Hello: The final abstract deadline for the 2011 North American Core Shell Spectroscopy Conference has been extended to Sunday, April 3, 2011. The Second Annual North american Core Shell Spectroscopy Conference will be held jointly with the Denver X-ray Conference in Colorado Springs August 1-5, 2011. The conference is centrally located, making it easily accessible from the entire continent and it is excellent opportunity to have young scientists present to the Core Shell Spectroscopy community. We hope that you can attend and make this event an ongoing success. More information can be found at http://www.dxcicdd.com/cssc/ Hope to see you there! 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://www.iit.edu/~segre segre(a)debian.org

1 0

Again some questions related to IFEFFIT_ ARTEMIS computer package program
by Nicolae Aldea 30 Mar '11

30 Mar '11

Dear Professor "Matt Newville The first I would like to thank for your mails sent me on Tue Mar 22, 2011 and On Sun, Mar 27, 2011. Now, I have had success for entering to ifeffit(a)millenia.cars.aps.anl.gov My new questions are: 1) Should I introduce in GDS degen parameter for fitting beside amp, enot, delr and ss? What happened when I want to obtain coordination number (CN) associated to some coordination shell. I thank that there is a difference some time between CN and degen. In some cases they are the same. Many journals as you know report CN. For a coordination shell I think that we have some times more paths, is it rue or false? Does dgen associate only for a path ? 2) I could to view the feffXXXX.dat in according with your indication in own folder of computer package program c:\Document andSettings\USERNAME\Application Data\horae\stash, but can I save directly them? I did not find a direct bottom for saving them, is it true or I did not see it? 3) The exafs signal is a real function from math. point of view. So, FT[chi(k)]= real_RDF_even(r)+i*RDF_odd(r). Then IFT[real_RDF_even(r)+i*RDF_odd(r)] = chi_real(k)+ i*zero, where i=sqrt(-1), is it true ? In affirmative case why you have in ARTEMIS plot region the both components ? Is not the imaginary part zero ? from math p. v. the module of chi(r) is a symmetrical signal. Even, we take into account only a region [rmin:rmax] for RDF(r) we obtain for IFT of RDF(r) only a real signal. Thanking you I advance I remain, Nick Aldea

4 3

PhD position at KIT, INE in Germany
by tony vitova 25 Mar '11

25 Mar '11

Dear all, We are looking for a PhD candidate, who will work in a professional and friendly atmosphere in a young research group at the Karlsruhe Institute of Technology, Institute for Nuclear Waste Disposal with outstanding tradition in actinide research. The interested person should have background in physics, chemistry or related natural sciences, strong interest in instrumentation, method development and spectroscopy. Please see the attachment for additional information. many greetings from Karlsruhe Tonya

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NACSSC - Still 2 weeks for abstract submission
by Carlo Segre 22 Mar '11

22 Mar '11

Hello All: The Abstract Deadline has been extended for an additional 2 weeks until April 1, 2011, for oral presentations at the North American Core Shell Spectroscopy Conference to be held in conjunction with the 2011 Denver X-Ray Conference from August 1-5, 2011. http://www.dxcicdd.com/03/DXC_abstract.asp This conference is centrally located and an excellent opportunity for students and postdoctoral researchers to participate. This year, we are specifically interested in having presentations relating to 5f electron systems and catalysis. This conference is a great opportunity to meet with other practitioners of core-shell spectroscopy as well as a broader x-ray diffraction and fluorescence community. 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://www.iit.edu/~segre segre(a)debian.org

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Please give us help
by 松浦真 21 Mar '11

21 Mar '11

Dear IFFEFIT members I'm a member of this mailing list and I engage in XAFS research in Tohoku University, in Japan. As you know incredible earthquake and subsequent Tsunami, the scale of which has never happened for hundreds years, has attacked Japan on March 11. More than 20 thousands of peoples are killed by this disaster and even now many victims are dieing being unable to extend a helping hand. Furthermore Tsunmai attacked Fukusima's nuclear reactors and residents within 30 km are evacuated due to radiational contamination. Through disparate effort thousands of fuel rods are successfully cooling down well, but straggling will still continue now. Japan faces triple crisis; earthquake, Tsunami and nuclear disaster, which have been never happened in our history after the second World War. Tohoku University in Sendai has suffered incredible damage by this earthquake. Though actual damage is not clear yet, I think it takes more than decade until complete reconstruction. Synchrotron radiation facility of KEK Tsukuba also seems to suffer serious damage. XAFS researchers in Japan now face to a unprecedented difficulty. I guess the damage of this disaster in Japan amounts total about 5 x 10^6 million US$. I believe Japanese can concur this disaster in future. But we need help to save numerous victims due to earthquake,Tsunami and nuclear disasters and need to help for reconstruction. I wish the colleges of XAFS in the world to notice this serious situation in Japan and I wish to appeal to other people to help Japanese. Thank you for your collaboration. Makoto Matsuura IMR, Tohoku University

2 2

Looking for reviewers for XAFS textbook chapters
by Scott Calvin 09 Mar '11

09 Mar '11

Hi all, I am looking for people interested in reviewing portions of the XAFS textbook I am working on. I am particularly hoping that some people less experienced in XAFS will volunteer, so that I can get feedback on how well it teaches and how well it covers the topics you'd like to know more about. Experts are also welcome! The first chapter I've got ready is the chapter on sample preparation. If you are interested in reviewing this chapter and can get feedback back to me within two weeks, please email me at SCalvin(a)slc.edu . --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Looking for reviewers for XAFS textbook chapters
by Scott Calvin 08 Mar '11

08 Mar '11

Darn it! I did not mean to send the packet to the whole list. If anyone is interested in reviewing, please send a request to SCalvin(a)slc.edu . I apologize for spamming you all with a multi-MB file. --Scott On Mar 8, 2011, at 12:24 PM, Scott Calvin wrote: > Great! > > I'm attaching the review packet. The page numbering is a bit > chaotic, because it's actually several documents stitched together: > > The copyright notice. My publisher is allowing me to distribute > review copies, but only on the condition that reviewers not > redistribute them. > A detailed table of contents. This is more detailed than the final > version will be, but gives context to reviewers as to what will be > covered elsewhere. > An excerpt from the preface explaining the origin of the cartoon > characters. (Yes, there are cartoon characters...) > An introduction to the cartoon characters. > Chapter 3, on sample preparation. > References > > In the chapter, I've placed numbers along the margin to aid in > making comments. For example, you might want to comment on page 18, > lines 6-7. The numbers won't appear in the final version. > > If you have any questions about the context of the chapter, the > intended audience, or whatever, feel free to ask! > > --Scott Calvin > Sarah Lawrence College > <XAFSforEveryone_Chapter3_v2.pdf> > > On Mar 8, 2011, at 11:27 AM, Prof. Dr. Peter Leinweber wrote: > >> hello, i am interested in reviewing this. i am not experienced but i >> want to learn more. >> i look forward to hearing from you, peter leinweber >> >> Am 08.03.2011 04:13, schrieb Scott Calvin: >>> Hi all, >>> >>> I am looking for people interested in reviewing portions of the XAFS >>> textbook I am working on. I am particularly hoping that some people >>> less experienced in XAFS will volunteer, so that I can get >>> feedback on >>> how well it teaches and how well it covers the topics you'd like to >>> know more about. Experts are also welcome! >>> >>> The first chapter I've got ready is the chapter on sample >>> preparation. >>> If you are interested in reviewing this chapter and can get feedback >>> back to me within two weeks, please email me at SCalvin(a)slc.edu . >>> >>> --Scott Calvin >>> Sarah Lawrence College >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >> >> >> -- >> Prof. Dr. Peter Leinweber >> Soil Science >> Institute for Land Use >> University of Rostock >> D-18051 Rostock/Germany >> Tel.: +49 381 498 3120 >> Fax: +49 381 498 3122 >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

1 0

FEFF6L input keyword question
by YOON Zin Seok 03 Mar '11

03 Mar '11

Dear FEFF users, Hi, I am a beginner of FEFF6L. Usually depending on the manual provided by web site, I am managing to calculate spectrum, and there are too many difficulties...I would like to be advised from you, senior members. I have three questions. (1) I would like to control the temperature. In the manual, I see DEBYE 190 315 (Calculate Debye-Waller factors for Cu at 190 K??). Can I change the temperature simply by modifying the number "190"? Can I find a reference paper for this? (2) Where can I find Debye-Waller factors in the output files? (3) How can I change the ionic state? I would like to compare the output file, chi dat., between SF6 and SF6+ molecules. I hope I could have answers for my questions... Best wishes, Zin

3 2

International Workshop on Improving Data Quality and Quantity , for XAFS Experiments (Q2XAFS2011), Tsukuba, Apr. 12-13, 2011
by Yohei Uemura 02 Mar '11

02 Mar '11

Dear ifeffit mailing list users, This is Yohei Uemura at Photon Factory, KEK, Japan. "Q2XAFS" workshop is going to be held on 12-13 April 2011 in Photon Factory, Tsukuba, Japan. This workshop aims to have worldwide discussions about measurements and data collection of XAFS to improve data quality and quantity. There will be also presentations about XAFS experiments on bio-systems and recent beamline developments. Please read the message from the organisers below. **************************************************************** Dear Colleagues It is our pleasure to inform you that "International Workshop on Improving Data Quality and Quantity for XAFS Experiments (Q2XAFS2011)" will be held during April 12-13, 2011 in Tsukuba, Japan. As you have been of great significance in the related topics of XAFS, we would be honored to ask your attendance and participation in our efforts aimed at quality and quantity improvements. We will welcome your early registration (reduced fee) at the Q2XAFS2011 web (http://pfwww.kek.jp/Q2XAFS2011/index.html) by February 28. The workshop is jointly organized by the IUCr XAFS Commission and the IXAS, inviting outstanding researchers representing synchrotron radiation facilities all over the world. Q2XAFS2011 focuses on Q2 (quality and quantity) control of EXAFS data collection, analyzing and exchange. Our goal is to assess the current status, to find fundamental problems and to propose a solution through standards and/or recommendation. The workshop will provide opportunities to fully discuss and exchange opinions on important categories of Q2 control. As the topics of the workshop are strongly dependent on beamlines and experimental stations, participation of experienced scientists based at facilities is essential. In particular, we will have a dedicated session for standard data format that would dramatically improve efficiency and security of data collection and exchange. Your participation in the workshop will be greatly appreciated. We look forward to seeing you in Tsukuba. Sincerely, yours Soich Wakatsuki, Chair of Q2XAFS2011, Director of Photon Factory Isabella Ascone, IUCr XAFS Commission, Chair Hiroyuki Oyanagi, IXAS, Chair **************************************************************** -- =========================================== 上村洋平所属: 高エネルギー加速器研究機構　物質構造科学研究所放射光科学研究施設（Photon Factory) 住所: 茨城県つくば市大穂1-1 Yohe'i Uemura (Ph.D) Affiliation : Photon Factory, Institute of Materials Science, KEK Adress : 1-1 Oho, Tsukuba-Shi, Ibaraki, Japan 305-0801 TEL&FAX: 029-879-6105 PHS: 029-864-5200 + 4956 Email : yuemura(a)post.kek.jp ===========================================

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Purple & Red E Derivatives
by Andrew Korinda 25 Feb '11

25 Feb '11

While working in Athena today I noticed something peculiar while looking at the derivative plots of mu(E) data. When I plot the current group (red button) the plot can be spiky. However, when I plot as marked group (purple button) everything is much smoother and more rounded. Smoothed data will do the same thing. It always happens whether I have mu(E) or norm(E) selected. I have never noticed a difference in how any of the other plots current when switching between marked and active plotting. I didn't see anything in the documentation about how the derivatives are calculated so I'm turning to all of you. Have any of you noticed this? Does anyone know if there is a difference in how the derivatives are calculated in each plotting function? Andy Korinda Notestein Lab Northwestern University

4 6

parseval's theorem and athena
by kirshstein＠googlemail.com 17 Feb '11

17 Feb '11

Hello, I would like to use parseval's theorem (as described in a document called: Error Reporting Recommendations: A Report of the Standards and Criteria Committee, Adopted by the IXS Standards and Criteria Committee July 26, 2000 ) to quantify the statistical noise in my spectra. In section 3 (as shown in the attachment), it says that for the formula to work, the forward FT has to be normalized by sqrt(deltak/Pi). (delta k is the spacing of points in k space) What is the normalization used for FFT in athena? if it is not sqrt(deltak/Pi), what is it? how does the parseval theorem formula need to be modified as a function of FT normalization? Many thanks for answers! Regina

2 3

FEFF question Te K edge
by Andrea L Foster 16 Feb '11

16 Feb '11

Hello All, sorry if this is not the correct venue...I tried to join a feffusers list I saw at http://leonardo.phys.washington.edu/feff/html/mailing_list.html but I got bounces when I subscribed and tried to post. my problem is below, and I'm sure one of the many knowledgeable folks on this group can help: I am starting to run FEFF6L calculations for Tellurium phases. I used published structure report of calaverite (AuTe2) and Na2TeO3_5H2O to generate ATOMS.INP files which I then used to generate FEFF.inp files. These two very different Te minerals gave me the following error when running FEFF6L (following is a copy of a little of the FEFF output): Running "C:\Program Files\Ifeffit\bin\feff6l.exe" feff.inp Feff 6L.02 Disodium Tellurite 5-hydrate Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... ...I have stopped copying the FEFF output there. I do not think that the problem is with the crystal structures as they are pretty simple (though human error is never to be minimized, especially mine ;). ATOMS returned no errors when it ran. The interatomic distances generated in feff match those reported in the crystal structure report...and the coordination numbers appear to be correct (for example the sodium tellurite structure should have 3 closest oxygen neighbors, and does, at the correct distances)... so I don' t know how to troubleshoot this error when nothing appears wrong geometrically. I have attached the 2 feff.inp files (which list the xtal structure info) in case that helps. They are slightly renamed. thanks for any help, andrea ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andrea L. Foster, Ph.D. U.S.G.S. WMESC 345 Middlfield Rd., MS 901 Menlo Park, CA 94025 T: 650-329-5437 F: 650-329-5491

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Re: [Ifeffit] Fe in glassy ceramics
by Scott Calvin 16 Feb '11

16 Feb '11

Hi Andrei, It's not unreasonable to model such a thing. Use a highly constrained model for the spinel, not allowing coordination numbers to float and using very few sigma2 parameters. I've published a model like that for fitting spinels here: http://prb.aps.org/abstract/PRB/v66/i22/e224405 My model is more complicated than yours needs to be, because you don't really have site disorder; all the sites are Fe. Then multiply the amplitudes by a guessed parameter representing the fraction of the iron that is in the spinel phase. The remaining amplitude gets used for the glassy phase, which can possibly be fit by a single iron-oxygen path, which can be cloned from one of the spinel near neighbor paths, but now with most parameters floated. You may very well need to fix S02 based on the value from a standard. Fit over a wide range in the Fourier transform, so that you take advantage of high R peaks to pin down the spinel part. Worth a shot, anyway. The key is being aggressive with assumptions and constraints, and then being honest about how that affects your uncertainties in the end. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Feb 16, 2011, at 4:53 AM, Andrei Shiryaev wrote: > Dear colleagues, > > Probably similar questions were already asked, but nevertheless I > would appreciate some advice how to solve the problem. > > We are looking at Fe environment in complex glasses, which underwent > partial crystallization. A fraction of Fe has precipitated as spinel- > like nanocrystals, another fraction remains in glass. Spinel itself > is already challenging for XAFS, but our task is to understand the > Fe fraction in glass (e.g., Fe-O bond length). > > We do not know the exact composition of the crystalline phases, thus > we can not record a suitable standard. Does anybody have an idea how > could we try to separate the Fe in glass from Fe(cryst) contributions? > > I fully realize that the problem is ill-posed, perhaps, some people > had somehow solved this problem. > > Thanks a lot, > Andrei Shiryaev > > Instituteof Physical Chemistry > Moscow > Russia

1 0

Fe in glassy ceramics
by Andrei Shiryaev 16 Feb '11

16 Feb '11

Dear colleagues, Probably similar questions were already asked, but nevertheless I would appreciate some advice how to solve the problem. We are looking at Fe environment in complex glasses, which underwent partial crystallization. A fraction of Fe has precipitated as spinel-like nanocrystals, another fraction remains in glass. Spinel itself is already challenging for XAFS, but our task is to understand the Fe fraction in glass (e.g., Fe-O bond length). We do not know the exact composition of the crystalline phases, thus we can not record a suitable standard. Does anybody have an idea how could we try to separate the Fe in glass from Fe(cryst) contributions? I fully realize that the problem is ill-posed, perhaps, some people had somehow solved this problem. Thanks a lot, Andrei Shiryaev Instituteof Physical Chemistry Moscow Russia

2 1

compiling feff 9
by Eugenio Otal 11 Feb '11

11 Feb '11

Hello, I am trying to compile the feff9 with ifort linux compiler but I find that the code is split in more than one file unlike feff84 that is only one file, feff84.f. I read the manual and I cannot find any help in feff9 manual, in feff84 manual there are more information but it is also not so useful. Would you help me to know how to compile the code with all this files. Kind Regards, euG 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - - Dr. Eugenio H. Otal Solid State Chemistry and Catalysis Laboratory, Empa - Swiss Federal Laboratories for Materials Science and Technology, Ueberlandstrasse 129, CH-8600 Duebendorf, Switzerland, Tel +41 44 823 41 31, Fax +41 44 823 40 19, eugenio.otal(a)empa.ch, www.empa.ch/abt131,

1 0

Reminder: NASCCSC Abstracts Deadline
by Carlo Segre 08 Feb '11

08 Feb '11

Hello All: In case you had not seen this notice, the Second Annual North american Core Shell Spectroscopy Conference will be held jointly with the Denver X-ray Conference in Colorado Springs this on August 1-5. This years conference will have special sessions on catalysis and 5f electron systems. Abstract sumissions will be open probably until March 1, 2011. More information can be found at http://www.dxcicdd.com/cssc/ Hope to see you there! 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://www.iit.edu/~segre segre(a)debian.org

1 0

R dependence of S02
by Scott Calvin 05 Feb '11

05 Feb '11

Hi all, I've been pondering how much R dependence we should expect to see in S02; that is, how much R dependence is shown by intrinsic losses. I've looked at quite a bit of the literature, not to mention old threads from this mailing list. One recent (2002) reference is this one by Campbell et al.: http://prb.aps.org/pdf/PRB/v65/i6/e064107 My understanding is that S02 is intended to account for intrinsic losses; that is, those that are determined when the core hole forms. Extrinsic losses, such as inelastic scattering of the photoelectron and the effect of the core-hole lifetime, are accounted for by a mean free path term. The mathematics of how ifeffit implements this are here: http://cars9.uchicago.edu/~newville/feffit/feffit.ps Intrinsic losses are dependent on k for at least two reasons. One is that the cross-section of the intrinsic effects themselves depends on the energy of the incident x-ray. This is evident if one thinks in terms of shake-up and shake-off events. But another reason is that shake-up and shake-off events rob some energy from the primary photoelectron. At low k, ten or twenty electron volts can alter the phase of the primary photoelectron significantly, and thus shake-up and shake-off events will tend to cancel each other out. But at high k, the energy robbed from the photoelectron is less significant, because the EXAFS oscillations are more spread out in energy. Thus, shake-up and shake-off events, while still occurring, will not suppress the EXAFS amplitude as much at high k. S02 therefore gradually rises through most of the EXAFS region to reach a limiting value of 1 well above the top of the EXAFS region. The latter effect--the fact that removing a specified amount of energy from the primary photoelectron has less of an effect at high k than at low--also implies an R dependence. Low R oscillations are further apart in energy than high R oscillations, and thus over a specified k range low R oscillations should be less affected. In other words, S02 should show a modest decrease with increasing R over typical EXAFS ranges. Some papers, in particular those with John Rehr as an author, confirm that S02 should have an R dependence, but don't discuss the implications much. While ifeffit allows for floating ei, a parameter related to the mean free path, as I understand it that will still give a damping of the amplitude that is exponential in R. It seems to me that the S02 dependence on R, in contrast, is likely to be more gentle. Why is this important? Several authors, including myself, have analyzed crystallite size and/ or morphology by comparing the coordination number of successive scattering shells. This is potentially much more accurate than just finding the first-shell coordination number, because it is independent of any amplitude effects that are independent of R, such as normalization errors and many experimental effects. Errors in the mean free path are a bit more significant, but the exponential dependence of the mean free path gives it a very different shape than effects from size and morphology. But an R-dependence of S02 would be troubling, as the functional form might look a bit more like a size effect. So one question is this: does anyone have an order-of-magnitude estimate of how much R dependence to expect in S02 over the EXAFS range? If over a range of 2 to 6 angstroms S02 changed by even a few percent, that could have a significant effect on the kind of size analyses I mentioned in the preceding paragraph. Of course, another question is if I've completely blown it anywhere in my discussion above; I've just been puzzling this out over the last few days! --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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EXAFS fitting method
by Abhijeet Gaur 30 Jan '11

30 Jan '11

Hi all, As I understand, the EXAFS fitting procedure using Artemis, for generating a theoretical model requires the crystal structure parameter like space group, cell parameters and *specially* *atom coordinates* etc. For this we have to perform XRD measurements of single crystals of the samples. I have some questions (1) In case we dont have the XRD data of a sample then how can the EXAFS analysis be done of that sample? (2) If we have already performed the XRD on the sample then by doing EXAFS what additional information are we getting ? (3) If the answer to the first question is that - *use the crystal structure of a * * similar sample,* then what are the conditions under which we can use the known crystal structure of one sample for other samples ? Thanks in advance Abhijeet Gaur

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Fwd: Horae-70 installation problem
by Bruce Ravel 18 Jan '11

18 Jan '11

Hi all, Has anyone here ever used security enhanced linux? I got the following bug report from an SELinux user which includes an error message from one of SELinux security systems. Never having used SELinux myself, I don't quite understand the problem Dr. Pan is observing once he uses chcon to change the security state of the ifeffit library. And I don't have a machine on which to explore this problem. I am hoping someone here might be more knowledgable than I. If anyone can offer any assistance to Dr. Pan, that would be great. Thanks, B ---------- Forwarded Message ---------- Subject: Horae-70 installation problem Date: Saturday, January 15, 2011, 01:34:29 am From: Guoqiang PAN <gqpan(a)ustc.edu.cn> To: Bruce Ravel <bravel(a)bnl.gov> Dear Dr. Ravel Hi, thank you very much for the horae-70 for artemis, athema and hephaestus XAFS software. Due to the detail for the installation, I have installed in my PC linux of Fedora Core 10. When artemis has been installed, it was failed to run correctly. There is a detailed explanation of it in the attachment. I fixed it using chcon -t textrel_shlib_t '/usr/local/lib/perl5/site_perl/5.10.1/i686-linux/auto/Ifeffit/Ifeffit.so' Afterwards, it seems work, but the data in the interface panel could not be changed,please refer to the attached snapshot pictures. My system information as follows: [gqpan@localhost horae-070]$ uname -a Linux localhost.localdomain 2.6.27.5-117.fc10.i686 #1 SMP Tue Nov 18 12:19:59 EST 2008 i686 i686 i386 GNU/Linux Thank you for your help! Best regards! Guoqiang PAN National synchrotron Radiation Laboratory University of Science & Technology of China ----------------------------------------- -- 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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Liquid gold-Latex suspension measurements
by Julian Kaiser 14 Jan '11

14 Jan '11

Dear Colleagues, I would like to measure some Gold-Nanoparticles that are embedded in a kind of polymer-matrix consisting of a polystyrene-core and some polyelectrolyte-chains. The total amount of gold in the suspension will be 0.025-0.05 percent by weight. The idea is to place the sample in a polystyrene cuvette with approximately 1 mm diameter (sample) and (2x) 1 mm (polystyrene). We've tried once to measure in transmission mode, where we had some problems maybe due to the absorption of water and polystyrene. Measurements in fluorescence mode might also cause problems by self-absorption and the absorption of the polystyrene again. Does anybody have good experience with liquid measurements of diluted samples? Best regards, Julian ========================================= Julian Kaiser Helmholtz-Zentrum Berlin für Materialien und Energie Hahn-Meitner-Platz 1, D-14109 Berlin Tel. +49 30 8062 - 43029 Mail: Julian.Kaiser(a)helmholtz-berlin.de ========================================= Helmholtz-Zentrum Berlin für Materialien und Energie GmbH 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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error
by JeongEunSuk 12 Jan '11

12 Jan '11

Hi all I fitted ZnMgO to know whether Mg is sited on Zn position. the method of fitting as following; 1st : to fit with some Mg located on Zn site. 2nd: to fit with some Mg which position is different from Zn cite The parameters for Mg like bonding length, disorder and others were set. When I was fitting, there are only 8 parameters in both two method. So that independent data point and variables are same. Both 1st and 2nd had same R-factor but reduced chi-square of 1st was lager than that of 2nd. It has been known that R-factor is independent of error( uncertainty in the measurement) but reduced chi-squrare is inverse proportional to error^2. So I think that same R-factor and different reduced chi-square for two method mean the fittings of two method are not different, but error used in reduced chi-square is different. I want to know how the error used in reduced chi-square is decided in FEFFIT code.

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Re: [Ifeffit] Cadmium K-edge
by Alan Du 12 Jan '11

12 Jan '11

Hi Bhoopesh and Scott, I should have given a description of my project. Yes Scott, the work is to investigate the binding mechanisms of aqueous cadmium onto sodium titanate nanotubes. Spectrum of Sample 1 and 2 obtained from merging 9 scans and 4 scans, respectively. A quick check in Athena and, indeed, the white line of Samples are higher than CdO. I'm not sure the reason behind it though. It is likely that cadmium binds to the surface of substrate rather than inside the bulk. The lack of distinct peaks after 1.8 Å means that there are not many scatters around the absorber? Bhoopesh, as requested, I have attached the real part of FT ( http://img585.imageshack.us/i/ftreal.jpg/) I haven't got a chance to interpret them. >From preliminary fitting of Sample 1, the major and minor peaks at 1.8 and 2.3 Å could be described by a Cd-O path (CdO). This interests me because Sample 2 does not have a peak at 2.3 Å, meaning there is another single scattering path for Sample 2?. The peaks at 3 Å were fitted with Cd-Ti path (CdTiO3). No multiple scattering paths used. The best fit goes something like this: **************************************************************************** Independent points = 13.166992187 Number of variables = 8.000000000 Chi-square = 1534.709946959 Reduced Chi-square = 297.021921317 R-factor = 0.000128095 Measurement uncertainty (k) = 0.000060423 Measurement uncertainty (R) = 0.004455442 Number of data sets = 1.000000000 Guess parameters +/- uncertainties (initial guess): amp = 0.9242390 +/- 0.0509920 (1.0000) enot = 1.3950420 +/- 0.5425380 (0.0000) delr = -0.0872060 +/- 0.0051060 (0.0000) ss = 0.0113250 +/- 0.0008480 (0.0030) amp_2 = 0.2441320 +/- 0.1905250 (1.0000) enot_2 = 22.5261260 +/- 4.5990590 (0.0000) delr_2 = 0.2510860 +/- 0.0719080 (0.0000) ss_2 = 0.0274690 +/- 0.0128040 (0.0030) Correlations between variables: amp_2 and ss_2 --> 0.9342 enot_2 and delr_2 --> 0.9133 amp and ss --> 0.8865 enot and delr --> 0.8632 amp_2 and delr_2 --> 0.3040 delr_2 and ss_2 --> 0.2888 All other correlations are below 0.25 k-range = 2.000 - 9.000 dk = 1.000 k-window = hanning k-weight = 3 R-range = 1.000 - 4.000 dR = 0.000 R-window = hanning fitting space = R background function = none phase correction = none R-factor for this data set = 0.00270 *********************************************************************************** The above enot_2 is on the high side. I am not entirely familiar with the parameters yet. Are there other parameters I should worry about? Cheers, Alan J. DU Nanyang Technological University, Singapore

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sample preparation for liquid samples
by Polzer, Frank 11 Jan '11

11 Jan '11

Dear all, I would like to measure manganese oxide nanoparticles at the Mn K edge. The nanoparticles are affixed to polystyrene latex carrier particles (PS) and the whole composite material (MnO2@PS with ca. 5 m-% MnO2 in the composite) is dispersed in water. Therefore we consider measuring the composite material in the dried state as a powder as well as in the dispersed state in water. The sample preparation for powders to me is quite straight forward, but I would really appreciate if somebody could share his experience with sample preparation and measurements of liquid samples. I think that aqueous samples are best measured in the fluorescence mode. That's why I am concerned of problems like self-absorption and so on. Can anybody tell my what is a good concentration range to overcome effects like self-absorption and how to get good fluorescence data in general? And what kind of sampler holder or materials (cuvettes, etc.) are best suited for aqueous samples? I am looking forward to receiving some helpful replies! Cheers, Frank Dipl. Chem. Frank Polzer F-I2 - Soft Matter and Functional Materials Helmholtzzentrum Berlin für Materialien und Energie Lise-Meitner-Campus Hahn-Meitner-Platz 1 14109 - Berlin Tel.: +49 30 8062-43830 Fax: +49 30 8062-42308 frank.polzer(a)helmholtz-berlin.de<mailto:frank.polzer@helmholtz-berlin.de> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V Vorsitzender des Aufsichtsrates: Prof. Dr. Dr. h.c. mult. Joachim Treusch, Stellvertretende Vorsitzende: Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn- Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Prof. Dr. Dr. h.c. Wolfgang Eberhardt, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] Athena crash during LCA
by Scott Calvin 08 Jan '11

08 Jan '11

Hi Matt and Jeff, I just upgraded to 0.8.061, and it works in that version, so apparently whatever the bug was has been fixed. Thanks for checking it out for me! --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Jan 8, 2011, at 7:08 AM, Matt Newville wrote: > Hi Scott, > > Like for Jeff, the chi(k) LCA fit works for me with Athea 0.8.061 on > OSX 10.6. If I had to make a guess or recommendation for something > to try it would be this: > > Standard2 extends to pretty far out in K (>20Ang^-1) and Standard2 is > pretty glitchy beyond 12Ang^-1 or so. You might try truncating the > data and/or removing the obvious glitches before doing the background > subtraction and LCA fit. > Again, that's a guess. > > Does the latest iXAFS3 not work for you on 10.5.8? I haven't tried > it, but the intention was that it would work on 10.5. > > --Matt >

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Athena crash during LCA
by Scott Calvin 08 Jan '11

08 Jan '11

Hi all, Athena has been crashing for me during one particular linear combination analysis, and I'm wondering if any of you have an explanation. A project file which demonstrates the problem is attached. I am using Athena 0.8.054 with ifeffit 1.2.10 on a MacBook Pro using OS 10.5.8. The behavior can be seen by trying to fit the Data group by using a linear combination of Standard 1 and Standard 2 in chi(k). It gets as far as "plotting in k-space from group 'Data'...done!' and then hangs, with the watch icon remaining indefinitely. This doesn't happen in norm(E) or deriv(E) fits, and doesn't happen when Standard 1 is not used. But Standard 1 appears to have uncorrupted chi(k) data when plotted directly. Standard 1 is from one of the XDAC lines at NSLS, as are the standards that work. I've tried saving Standard 1 and reading it in as a new group, but no luck. I've also looked at the data in Standard 1, and I don't see anything out of place, such as a place where the energy backs up. I've tried starting the chi(k) file with zero values, truncating the end values, and changing the background spline to end at the same point the data does. And it always hangs at the same point. Any ideas? I'd like to use this data for a workshop next week! --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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Re: [Ifeffit] Athena crash during LCA
by Scott Calvin 08 Jan '11

08 Jan '11

Jeff--sorry, I guess my grammar got a little convoluted. It DOES work with norm(E) and deriv(E) fitting for me as well. It does NOT work with chi(k) fitting for me. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Jan 7, 2011, at 7:58 PM, Jeff Terry wrote: > Did not try really hard to work with it. > > Fitting Data as norm(E) from -20.000 to 30.000 > > Fit included 98 data points and 3 variables > R-factor = 0.000263 > chi-square = 0.04347 > reduced chi-square = 0.0004482 > > group weight > ======================================= > 2: Standard 1 1.000(0.000) > 3: Standard 2 0.455(0.000) > > > group e0 shift > ======================================= > 2: Standard 1 -0.905( 0.000) > 3: Standard 2 -0.905( 0.000) > > > > <PastedGraphic-1.pdf> > > On Jan 7, 2011, at 8:07 PM, Scott Calvin wrote: > >> Hi all, >> >> Athena has been crashing for me during one particular linear >> combination analysis, and I'm wondering if any of you have an >> explanation. A project file which demonstrates the problem is >> attached. I am using Athena 0.8.054 with ifeffit 1.2.10 on a >> MacBook Pro using OS 10.5.8. >> >> The behavior can be seen by trying to fit the Data group by using a >> linear combination of Standard 1 and Standard 2 in chi(k). It gets >> as far as "plotting in k-space from group 'Data'...done!' and then >> hangs, with the watch icon remaining indefinitely. This doesn't >> happen in norm(E) or deriv(E) fits, and doesn't happen when >> Standard 1 is not used. But Standard 1 appears to have uncorrupted >> chi(k) data when plotted directly. Standard 1 is from one of the >> XDAC lines at NSLS, as are the standards that work. >> >> I've tried saving Standard 1 and reading it in as a new group, but >> no luck. I've also looked at the data in Standard 1, and I don't >> see anything out of place, such as a place where the energy backs >> up. I've tried starting the chi(k) file with zero values, >> truncating the end values, and changing the background spline to >> end at the same point the data does. And it always hangs at the >> same point. >> >> Any ideas? I'd like to use this data for a workshop next week! >> >> --Scott Calvin >> Faculty at Sarah Lawrence College >> Currently on sabbatical at Stanford Synchrotron Radiation Laboratory >> >> <LCACrash.prj> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Re: [Ifeffit] Problem with Athena
by Bruce Ravel 07 Jan '11

07 Jan '11

Hi Samer, I am CCing my response to the Ifeffit mailing list. I ask that questions about the software be directed to the mailing list rather than to me personally. The file that you attached is from the SSRL Data Collector. This is one of the formats supported by a filetype plugin. See http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/plugin.html As explained on that page, from the "Settings" menu, select "Plugin registry", then click on the button labeled "SSRLA". Athena will then be able to import your file. If you do not have that plugin on your computer for some reason (for example, if you are running a somewhat old version of Athena), a copy can be found at http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… Place that file in C:\Program File\Ifeffit\horae\Ifeffit\Plugins\Filetype\Athena\ if you are a windows user or in $HOME/.horae/Ifeffit/Plugins/Filetype/Athena/ on linux. There is a similar location on a Mac, but I don't know its path off the top of my head. B On Friday, January 07, 2011 05:46:13 am you wrote: > Dear Mr. Bruce, > > > > At first I wish you a happy new year and a very successful 2011! > > I have problem with opening the Roble files with Athena (see pleas attached > file). > > I get the following error: the file could not be read by ifeffit as data > file. > > Our Athena version is 0.8.061. > > > > Could you please help me? > > 　 > > Thanks in advance. > > > > With best wishes, > > > > Samer Amayri > __________________________________________________________________ > Dr. Samer Amayri > Institut für Kernchemie > der Universität Mainz > Fritz-Strassmann Weg 2 > D-55128 Mainz > Telefon: +496131 39-25317/25307 (Lab.) > Handy: 017621805879 > Fax-Nr. +496131 39-24510 > E-mail: amayri(a)uni-mainz.de<mailto:amayri@uni-mainz.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/

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Re: [Ifeffit] Cadmium K-edge
by Scott Calvin 06 Jan '11

06 Jan '11

Hi Alan, (To the list: I discussed Alan's system a bit with him when he came to SSRL, but don't recall the details. That's why in this reply I have a little more knowledge about it than what he posted yesterday.) I suspect the peak at 2.3 A does indeed represent structure of some kind. Your k-space data for sample 1 has very little noise, so I don't think it's spurious in that sense. What strikes me about your data is that the FT's have so little structure beyond the 1.8 A peak. I don't recall exactly the nature of your system: it was cadmium loaded on to the surface of a substrate, but I don't recall what the substrate was. If it's low-Z (for example, silica), then the scattering off of whatever the oxygen is bonded to (in my example, silicon) would show up pretty weakly, and that could be the peak at 2.3 A. It's absence in sample 2 could represent the cadmium ion being less selective about what surface site it bonds to, so that the Cd-Si distance (in my example) varies and the peak washes out. That's all just an example of the kind of thing that could be responsible for what you're seeing. I agree that a good plan is to use a Cd-O structure to at least let you model the first peak. For the second peak, though, you may have to take more inspiration from the structure of the substrate than the structure of Cd-O. It's also intriguing that the white line in your sample is larger than in the CdO standard from the database. Someone with more XANES experience than I might be able to suggest why that is--something about these being bound to the surface? Is my recollection of your system correct? If so, what was the substrate? --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Jan 5, 2011, at 11:23 PM, Alan Du wrote: > > Hi all, > > I processed my XAS data and compare them with standards from Farrel > Lytle Database. (http://img717.imageshack.us/i/xasw.jpg/) > > In the RSF, both sample 1 and 2 has a major peak at R = ca. 1.8 A. > sample 1 has an additional peak at R = ca. 2.3 A. I wonder if this > tiny peak is significant. > > It seems both samples has peak positions similar to those of CdO > standard, which sound logical because the cadmium will bind to the > surface oxygen of the material. > > I looking at fitting sample 1 and 2 using whatever crystallographic > info of CdO I can get my hands on. > > Wonder if the plan make sense. > > Happy new year, > Alan

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Cadmium K-edge
by Alan Du 06 Jan '11

06 Jan '11

Hi all, I processed my XAS data and compare them with standards from Farrel Lytle Database. (http://img717.imageshack.us/i/xasw.jpg/) In the RSF, both sample 1 and 2 has a major peak at R = ca. 1.8 A. sample 1 has an additional peak at R = ca. 2.3 A. I wonder if this tiny peak is significant. It seems both samples has peak positions similar to those of CdO standard, which sound logical because the cadmium will bind to the surface oxygen of the material. I looking at fitting sample 1 and 2 using whatever crystallographic info of CdO I can get my hands on. Wonder if the plan make sense. Happy new year, Alan

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Ifeffit "print" command question
by Kelly, Tony D Ctr USAF AETC AFIT/ENP 31 Dec '10

31 Dec '10

To whom it may concern, I have recently downloaded Ifeffit for Mac OS X from your website. I am hoping to be able to use it with EXAFS data as the FEFF6 website led me to your application. I am currently working through the tutorial. However, every time I try to use the print command to make a literal string statement, all I get is 0.0000 back. Example: print " the square root of ", number, " is ", sqrt(number) 0.0 99.0000000 0.0000000 9.94987437 print "Hi mom" 0.000000000 Any thoughts? Thanks, Tony Tony Kelly, M.S. DTRA PhD Student Department of Engineering Physics Air Force Institute of Technology Office: (937)255-3636 ext 7300

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RE : Ifeffit Digest, Vol 94, Issue 5
by KONG Quingyu 21 Dec '10

21 Dec '10

Dear Colleagues, We are measuring EXAFS of Mo foil and Bi2O3 in a dispersive EXAFS beamline, to calibrate the energy we need the standard EXAFS spectra (in energy, not in pixel) of these two samples. We appreciate to anyone who can send us the standard EXAFS spectra of them. Thanks a lot in advance, Sincerely, Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr -------- Message d'origine-------- De: ifeffit-bounces(a)millenia.cars.aps.anl.gov de la part de ifeffit-request(a)millenia.cars.aps.anl.gov Date: sam. 18/12/2010 19:00 À: ifeffit(a)millenia.cars.aps.anl.gov Objet : Ifeffit Digest, Vol 94, Issue 5 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Ifeffit Digest, Vol 94, Issue 4 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Sat, 18 Dec 2010 08:33:20 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: KONG Quingyu <quingyu.kong(a)synchrotron-soleil.fr>, XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 94, Issue 4 Message-ID: <AANLkTimiw7fCxQHUO3CsZ3A4qBs0RVqLamjfG__BHquQ(a)mail.gmail.com> Content-Type: text/plain; charset=GB2312 Hi Qingyu, Sorry the attachment didn't make it to you. It's also at http://cars9.uchicago.edu/gsecars/Data/XAFS_Standards/ --Matt 2010/12/18 KONG Quingyu <quingyu.kong(a)synchrotron-soleil.fr>: > Dear Matt, > > Many thanks for your kind help. > > However, I can not find the file you sent to me. Would you please send them again with an attached file. > > Best regards, > Qingyu > > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > > > > ________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov ?? ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 18/12/2010 (???) 04:05 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 94, Issue 4 > > > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: RE : Ifeffit Digest, Vol 94, Issue 2 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Dec 2010 21:05:28 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] RE : Ifeffit Digest, Vol 94, Issue 2 > Message-ID: > <AANLkTikuj5+as8e=0+_P-LWH03WhpMW1QrK7PCXpc-VF(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Qingyu, > > I haven't analyzed this data carefully, but attached is an Athena > Project File of some room temperature data on W metal from a > powder-on-tape sample, Si(111) mono, W L3 edge, APS bending magnet > line. I don't have ready details on the absolute calibration, but > the edge energy is reasonably close to the book value. Also included > are EXAFS for WO2 and WO3 (also room temperature, powder-on-tape, > measured under the same conditions). The data for the metal and WO2 > look good out to 17 inverse Angstroms. The WO3 data looks a litle > noisier than the other two, and dies off by 12 inverse Angstroms. > > Hope that helps, > > --Matt > > 2010/12/17 KONG Quingyu <quingyu.kong(a)synchrotron-soleil.fr>: >> Dear Colleague, >> >> Anyone who has an EXAFS spectrum of Tungsten(W), please send me a copy. >> Thanks a lot in advance. >> >> Qingyu Kong >> >> >> Beamline ODE >> Soci?t? civile Synchrotron SOLEIL >> L'Orme des Merisiers >> Saint-Aubin - BP 48 >> 91192 GIF-sur-YVETTE CEDEX >> Tel: +33 (0)1 69 35 97 84 (office) >> ? ? ? +33 (0)1 69 35 97 16 (beamline) >> email: kong(a)synchrotron-soleil.fr >> >> >> >> >> >> >> -------- Message d'origine-------- >> De: ifeffit-bounces(a)millenia.cars.aps.anl.gov de la part de ifeffit-request(a)millenia.cars.aps.anl.gov >> Date: jeu. 16/12/2010 19:00 >> ?: ifeffit(a)millenia.cars.aps.anl.gov >> Objet : Ifeffit Digest, Vol 94, Issue 2 >> >> 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. Soft XAS Postdoc position at The University of Manchester >> ? ? ?(Sven Schroeder) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 15 Dec 2010 20:35:41 +0000 >> From: Sven Schroeder <S.Schroeder(a)manchester.ac.uk> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: [Ifeffit] Soft XAS Postdoc position at The University of >> ? ? ? ?Manchester >> Message-ID: >> ? ? ? ?<7457E57E2F521447AC5A411883C1CF71070D15(a)MBXP07.ds.man.ac.uk> >> Content-Type: text/plain; charset="us-ascii" >> >> Dear colleagues >> >> I would be grateful if you could bring this post to the attention of suitable candidates. The post has been funded for 33 months and will be supervised jointly by myself and Rob Lindsay in the School of Materials. >> >> Best regards, >> >> Sven >> >> -- >> >> Research Associate >> School of Chemical Engineering & Analytical Science / School of Materials >> The University of Manchester >> >> High-Pressure Soft X-ray Synchrotron Spectroscopy of Adsorbed Large Organic Molecules for Corrosion Inhibition >> >> Closing date: 11/01/2011 >> Reference: EPS/11323 >> >> http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/index.h… >> >> We are seeking to employ a Postdoctoral Research Associate within the School of Chemical Engineering and Analytical Science and the School of Materials on a full-time basis. >> >> A PhD in a relevant scientific discipline and several years of hands-on experience in experimental X-ray spectroscopy (XPS, NEXAFS, other surface techniques) are required. The project focuses on fundamental physicochemical studies of model surface systems to an industrially relevant project involving organic chemists, computational chemists and chemical engineers at the Mexican Petroleum Institute (IMP). As such it requires a candidate with the ability to work both on own initiative as well as a part of teams of varying size. Candidates should have an interest in working across the boundary between fundamental academic science and its practical application. Relevant peer-reviewed publications and experience in writing manuscripts for academic journal publications are essential. The post requires an ability to travel globally and regularly. Experience of using ab initio soft X-ray spectroscopy data analysis packages, including StoBe, FEFF, and CASTEP, or similar computatio! n! > al! >> ?methods would be an advantage. >> >> -- >> 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 <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 >> >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 94, Issue 2 >> ************************************** >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

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Re: [Ifeffit] Ifeffit Digest, Vol 94, Issue 4
by Matt Newville 18 Dec '10

18 Dec '10

Hi Qingyu, Sorry the attachment didn't make it to you. It's also at http://cars9.uchicago.edu/gsecars/Data/XAFS_Standards/ --Matt 2010/12/18 KONG Quingyu <quingyu.kong(a)synchrotron-soleil.fr>: > Dear Matt, > > Many thanks for your kind help. > > However, I can not find the file you sent to me. Would you please send them again with an attached file. > > Best regards, > Qingyu > > > Beamline ODE > Société civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > > > > ________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov 代表 ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: 18/12/2010 (星期六) 04:05 > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 94, Issue 4 > > > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: RE : Ifeffit Digest, Vol 94, Issue 2 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Dec 2010 21:05:28 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] RE : Ifeffit Digest, Vol 94, Issue 2 > Message-ID: > <AANLkTikuj5+as8e=0+_P-LWH03WhpMW1QrK7PCXpc-VF(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Qingyu, > > I haven't analyzed this data carefully, but attached is an Athena > Project File of some room temperature data on W metal from a > powder-on-tape sample, Si(111) mono, W L3 edge, APS bending magnet > line. I don't have ready details on the absolute calibration, but > the edge energy is reasonably close to the book value. Also included > are EXAFS for WO2 and WO3 (also room temperature, powder-on-tape, > measured under the same conditions). The data for the metal and WO2 > look good out to 17 inverse Angstroms. The WO3 data looks a litle > noisier than the other two, and dies off by 12 inverse Angstroms. > > Hope that helps, > > --Matt > > 2010/12/17 KONG Quingyu <quingyu.kong(a)synchrotron-soleil.fr>: >> Dear Colleague, >> >> Anyone who has an EXAFS spectrum of Tungsten(W), please send me a copy. >> Thanks a lot in advance. >> >> Qingyu Kong >> >> >> Beamline ODE >> Soci?t? civile Synchrotron SOLEIL >> L'Orme des Merisiers >> Saint-Aubin - BP 48 >> 91192 GIF-sur-YVETTE CEDEX >> Tel: +33 (0)1 69 35 97 84 (office) >> ? ? ? +33 (0)1 69 35 97 16 (beamline) >> email: kong(a)synchrotron-soleil.fr >> >> >> >> >> >> >> -------- Message d'origine-------- >> De: ifeffit-bounces(a)millenia.cars.aps.anl.gov de la part de ifeffit-request(a)millenia.cars.aps.anl.gov >> Date: jeu. 16/12/2010 19:00 >> ?: ifeffit(a)millenia.cars.aps.anl.gov >> Objet : Ifeffit Digest, Vol 94, Issue 2 >> >> 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. Soft XAS Postdoc position at The University of Manchester >> ? ? ?(Sven Schroeder) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 15 Dec 2010 20:35:41 +0000 >> From: Sven Schroeder <S.Schroeder(a)manchester.ac.uk> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: [Ifeffit] Soft XAS Postdoc position at The University of >> ? ? ? ?Manchester >> Message-ID: >> ? ? ? ?<7457E57E2F521447AC5A411883C1CF71070D15(a)MBXP07.ds.man.ac.uk> >> Content-Type: text/plain; charset="us-ascii" >> >> Dear colleagues >> >> I would be grateful if you could bring this post to the attention of suitable candidates. The post has been funded for 33 months and will be supervised jointly by myself and Rob Lindsay in the School of Materials. >> >> Best regards, >> >> Sven >> >> -- >> >> Research Associate >> School of Chemical Engineering & Analytical Science / School of Materials >> The University of Manchester >> >> High-Pressure Soft X-ray Synchrotron Spectroscopy of Adsorbed Large Organic Molecules for Corrosion Inhibition >> >> Closing date: 11/01/2011 >> Reference: EPS/11323 >> >> http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/index.h… >> >> We are seeking to employ a Postdoctoral Research Associate within the School of Chemical Engineering and Analytical Science and the School of Materials on a full-time basis. >> >> A PhD in a relevant scientific discipline and several years of hands-on experience in experimental X-ray spectroscopy (XPS, NEXAFS, other surface techniques) are required. The project focuses on fundamental physicochemical studies of model surface systems to an industrially relevant project involving organic chemists, computational chemists and chemical engineers at the Mexican Petroleum Institute (IMP). As such it requires a candidate with the ability to work both on own initiative as well as a part of teams of varying size. Candidates should have an interest in working across the boundary between fundamental academic science and its practical application. Relevant peer-reviewed publications and experience in writing manuscripts for academic journal publications are essential. The post requires an ability to travel globally and regularly. Experience of using ab initio soft X-ray spectroscopy data analysis packages, including StoBe, FEFF, and CASTEP, or similar computation! > al! >> ?methods would be an advantage. >> >> -- >> 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 <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 >> >> >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 94, Issue 2 >> ************************************** >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

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Re: [Ifeffit] RE : Ifeffit Digest, Vol 94, Issue 2
by Matt Newville 18 Dec '10

18 Dec '10

Dear Qingyu, I haven't analyzed this data carefully, but attached is an Athena Project File of some room temperature data on W metal from a powder-on-tape sample, Si(111) mono, W L3 edge, APS bending magnet line. I don't have ready details on the absolute calibration, but the edge energy is reasonably close to the book value. Also included are EXAFS for WO2 and WO3 (also room temperature, powder-on-tape, measured under the same conditions). The data for the metal and WO2 look good out to 17 inverse Angstroms. The WO3 data looks a litle noisier than the other two, and dies off by 12 inverse Angstroms. Hope that helps, --Matt 2010/12/17 KONG Quingyu <quingyu.kong(a)synchrotron-soleil.fr>: > Dear Colleague, > > Anyone who has an EXAFS spectrum of Tungsten(W), please send me a copy. > Thanks a lot in advance. > > Qingyu Kong > > > Beamline ODE > Société civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > > > > > > -------- Message d'origine-------- > De: ifeffit-bounces(a)millenia.cars.aps.anl.gov de la part de ifeffit-request(a)millenia.cars.aps.anl.gov > Date: jeu. 16/12/2010 19:00 > À: ifeffit(a)millenia.cars.aps.anl.gov > Objet : Ifeffit Digest, Vol 94, Issue 2 > > 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. Soft XAS Postdoc position at The University of Manchester > (Sven Schroeder) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 15 Dec 2010 20:35:41 +0000 > From: Sven Schroeder <S.Schroeder(a)manchester.ac.uk> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Soft XAS Postdoc position at The University of > Manchester > Message-ID: > <7457E57E2F521447AC5A411883C1CF71070D15(a)MBXP07.ds.man.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear colleagues > > I would be grateful if you could bring this post to the attention of suitable candidates. The post has been funded for 33 months and will be supervised jointly by myself and Rob Lindsay in the School of Materials. > > Best regards, > > Sven > > -- > > Research Associate > School of Chemical Engineering & Analytical Science / School of Materials > The University of Manchester > > High-Pressure Soft X-ray Synchrotron Spectroscopy of Adsorbed Large Organic Molecules for Corrosion Inhibition > > Closing date: 11/01/2011 > Reference: EPS/11323 > > http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/index.h… > > We are seeking to employ a Postdoctoral Research Associate within the School of Chemical Engineering and Analytical Science and the School of Materials on a full-time basis. > > A PhD in a relevant scientific discipline and several years of hands-on experience in experimental X-ray spectroscopy (XPS, NEXAFS, other surface techniques) are required. The project focuses on fundamental physicochemical studies of model surface systems to an industrially relevant project involving organic chemists, computational chemists and chemical engineers at the Mexican Petroleum Institute (IMP). As such it requires a candidate with the ability to work both on own initiative as well as a part of teams of varying size. Candidates should have an interest in working across the boundary between fundamental academic science and its practical application. Relevant peer-reviewed publications and experience in writing manuscripts for academic journal publications are essential. The post requires an ability to travel globally and regularly. Experience of using ab initio soft X-ray spectroscopy data analysis packages, including StoBe, FEFF, and CASTEP, or similar computational! > methods would be an advantage. > > -- > 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 > > > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 94, Issue 2 > ************************************** > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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RE : Ifeffit Digest, Vol 94, Issue 2
by KONG Quingyu 17 Dec '10

17 Dec '10

Dear Colleague, Anyone who has an EXAFS spectrum of Tungsten(W), please send me a copy. Thanks a lot in advance. Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr -------- Message d'origine-------- De: ifeffit-bounces(a)millenia.cars.aps.anl.gov de la part de ifeffit-request(a)millenia.cars.aps.anl.gov Date: jeu. 16/12/2010 19:00 À: ifeffit(a)millenia.cars.aps.anl.gov Objet : Ifeffit Digest, Vol 94, Issue 2 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. Soft XAS Postdoc position at The University of Manchester (Sven Schroeder) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Dec 2010 20:35:41 +0000 From: Sven Schroeder <S.Schroeder(a)manchester.ac.uk> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Soft XAS Postdoc position at The University of Manchester Message-ID: <7457E57E2F521447AC5A411883C1CF71070D15(a)MBXP07.ds.man.ac.uk> Content-Type: text/plain; charset="us-ascii" Dear colleagues I would be grateful if you could bring this post to the attention of suitable candidates. The post has been funded for 33 months and will be supervised jointly by myself and Rob Lindsay in the School of Materials. Best regards, Sven -- Research Associate School of Chemical Engineering & Analytical Science / School of Materials The University of Manchester High-Pressure Soft X-ray Synchrotron Spectroscopy of Adsorbed Large Organic Molecules for Corrosion Inhibition Closing date: 11/01/2011 Reference: EPS/11323 http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/index.h… We are seeking to employ a Postdoctoral Research Associate within the School of Chemical Engineering and Analytical Science and the School of Materials on a full-time basis. A PhD in a relevant scientific discipline and several years of hands-on experience in experimental X-ray spectroscopy (XPS, NEXAFS, other surface techniques) are required. The project focuses on fundamental physicochemical studies of model surface systems to an industrially relevant project involving organic chemists, computational chemists and chemical engineers at the Mexican Petroleum Institute (IMP). As such it requires a candidate with the ability to work both on own initiative as well as a part of teams of varying size. Candidates should have an interest in working across the boundary between fundamental academic science and its practical application. Relevant peer-reviewed publications and experience in writing manuscripts for academic journal publications are essential. The post requires an ability to travel globally and regularly. Experience of using ab initio soft X-ray spectroscopy data analysis packages, including StoBe, FEFF, and CASTEP, or similar computational! methods would be an advantage. -- 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 ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 94, Issue 2 **************************************

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Soft XAS Postdoc position at The University of Manchester
by Sven Schroeder 15 Dec '10

15 Dec '10

Dear colleagues I would be grateful if you could bring this post to the attention of suitable candidates. The post has been funded for 33 months and will be supervised jointly by myself and Rob Lindsay in the School of Materials. Best regards, Sven -- Research Associate School of Chemical Engineering & Analytical Science / School of Materials The University of Manchester High-Pressure Soft X-ray Synchrotron Spectroscopy of Adsorbed Large Organic Molecules for Corrosion Inhibition Closing date: 11/01/2011 Reference: EPS/11323 http://www.manchester.ac.uk/aboutus/jobs/vacancies/research/vacancy/index.h… We are seeking to employ a Postdoctoral Research Associate within the School of Chemical Engineering and Analytical Science and the School of Materials on a full-time basis. A PhD in a relevant scientific discipline and several years of hands-on experience in experimental X-ray spectroscopy (XPS, NEXAFS, other surface techniques) are required. The project focuses on fundamental physicochemical studies of model surface systems to an industrially relevant project involving organic chemists, computational chemists and chemical engineers at the Mexican Petroleum Institute (IMP). As such it requires a candidate with the ability to work both on own initiative as well as a part of teams of varying size. Candidates should have an interest in working across the boundary between fundamental academic science and its practical application. Relevant peer-reviewed publications and experience in writing manuscripts for academic journal publications are essential. The post requires an ability to travel globally and regularly. Experience of using ab initio soft X-ray spectroscopy data analysis packages, including StoBe, FEFF, and CASTEP, or similar computational methods would be an advantage. -- 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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On Macro Lytle File Group
by Alan Du 09 Dec '10

09 Dec '10

Hi IFEFFIT Users, I major in environmental science and my research is studying the adsorption of aqueous cadmium on TiO2 solid. I am new to EXAFS and currently trying to fit my Cd K-edge spectra with some Cd experimental standards. The Farrel Lytle Database have some Cd spectra which seems useful and I would like to extract them from their "raw" state. The macro is given in the FAQ/Data Handling section of IFEFFIT, but I am not sure of how to go about using the macro or any other macro. Ctrl 5 in Athena is all I know. Can anyone advise me on this? # macro lytle file group 4000 read_data ($1, group=$2, label='steps i0 i1 i2') set (dspace = 1.92017, stpdeg = $3) set (r2d = 57.29577951, hc = 12398.61) set $2.energy = hc / (2 * dspace) / sin($2.steps / (r2d * stpdeg)) set $2.xmut = -log($2.i1/$2.i0) set $2.xmuf = ($2.i2/$2.i0) pre_edge $2.energy, $2.xmut end macro Cheers, Alan -- Alan Jianhong DU Research Student Nanyang Technological University, Singapore School of Civil & Environmental Engineering Blk N1, N1-B4b-04, 50 Nanyang Avenue, Singapore 639798 Mobile: +65 9621 6991 Fax: +65 6861 5254

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iXAFS
by George Sterbinsky 29 Nov '10

29 Nov '10

Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for Leopard before installing the new version. Is it sufficient to just drag iXAFS.app to the trash or is there a better way to make sure everything gets removed? Thank you, George

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Re: [Ifeffit] Distortion of transmission spectra due to particle size
by Scott Calvin 26 Nov '10

26 Nov '10

Let me try again. First of all, perhaps you missed that after my first post, I acknowledged that my statement in the first post was mistaken? In fact, I later said: > So there's nothing wrong with the arguments in Lu and Stern, > Scarrow, etc.--it's the notion I had that we use multiple layers of > tape to improve uniformity that's mistaken. The Lu and Stern paper, which I now agree with, comes up with an equation I have attached as a png file. That equation is derived for spheres of diameter D in a monolayer. It does, incidentally, include a typo; the part inside the ln should start with mu_2^2/mu_1^2. But that's just typographical, and doesn't affect their subsequent argument. Lu and Stern then make the following claim: > Finally, the attenuation in N layers is given by (I/I0)^N, where I > is the transmitted intensity through one layer. Chi_eff for N layers > is then the same as for a single layer since N will cancel in the > final result. That's the statement I initially thought was incorrect, and thought was equivalent to a non-random stacking of layers. Since I'm now convinced that the statement is correct, I don't want to get bogged down in a discussion of why I still find it a bit puzzling. Other than my first post, no one else in this thread has yet challenged the Lu and Stern statement, and some, such as Matthew Marcus, have supported it. The statement can be rephrased to say that, for a given particle diameter D, the ratio of chi_eff to chi_real is independent of the number of layers; that is, the distortion due to nonuniformity is not reduced by adding additional identical layers. I found this conclusion so startling that at first I rejected it. Several others in this thread indicated that they too tended to think that additional identical layers would reduce distortions in the spectrum due to nonuniformity. I then tested this principle that emerges from the Lu and Stern paper in two other situations, and found that it holds in those as well. Here are the details: The first case I'll examine is a Gaussian distribution of standard deviation sigma and average width x_o, with a distribution narrow enough so that we can ignore the negative-thickness tail. Grant Bunker has investigated this case, for example on page 88 of his new textbook. The derivation is straightforward, and he finds that (mu x)_eff = mu x_o - (mu sigma)^2/2 Your simulation beautifully demonstrates that when I use N layers of this type, we can expect that the new mean thickness x_new = N x_o, and sigma_new = sqrt(N) sigma. This gives: (mu x)_new_eff = mu N x_o - [mu sqrt(N) sigma]^2/2 = N [mu x_o - (mu sigma)^2/2] = N (mu x)_eff Thus the new spectrum is exactly the same shape as the old spectrum-- just scaled up by a factor of N. Therefore, after normalization, the spectrum of the multi-layer sample will be exactly the same as for the single layer. (Note that this analysis does not include the effect of signal to noise, harmonics, etc.). Thus the distortion due to nonuniformity is independent of the number of identical layers used. My next thought was to see if this was a peculiarity of normally distributed samples and monolayers of spheres. After all, extremely nonuniform samples will tend to approach a Gaussian thickness distribution as more layers are randomly stacked up--perhaps they asymptotically approach the distortion present in the Gaussian case? So I investigated pinholes. This time I did the calculation all the way from scratch, just to make sure I understood all the assumptions. Take a sample that has a fraction p of pinholes, with the remaining 1- p of the sample being of uniform thickness x. In that case, I = p I_o + (1-p) I_o exp(-mu x) mu_eff = ln (I/I_o) = ln [p + (1-p) exp(-mu x)] Now take two layers of that type, with the pinholes randomly distributed. A fraction p^2 will still be pinhole, a fraction 2p(1-p) will have thickness x, and a fraction (1-p)^2 will have thickness x^2. So now I/I_o = p^2 + 2p(1-p) exp(-mu x) + (1-p)^2 exp(-2 mu x) mu_eff = ln[p^2 + 2p(1-p) exp(-mu x) + (1-p)^2 exp(-2 mu x)] = ln[p+(1- p)exp(-mu x)]^2 = 2ln[p + (1-p) exp(-mu x)] And that is exactly twice the mu_eff of the single layer--i.e., after normalization it will be identical. Any distortions caused by pinholes will be identical, despite the fraction of sample having pinholes all the way through dropping from p to p^2. Some in our community already realized that, but I didn't. In fact, I'd go so far as to say I was shocked by the result. Judging by some of the advice that is routinely given about sample preparation, I suspect that this may come as a surprise to many others as well. Hopefully that establishes what my understanding currently is. Beyond that, we seem to be miscommunicating on some questions of terminology: On Nov 24, 2010, at 12:04 PM, Matt Newville wrote: > Scott, > > You said: >> the distortion from nonuniformity is as bad for four strips >> stacked as for the single strip. > > As I showed earlier, a four layer sample is more uniform than a one > layer sample, whether the total thickness is preserved or the > thickness per layer is preserved. > >> For 1% pinholes: >> # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | >> # 1 | 1.0 | 0.990 | 0.099 | >> # 5 | 1.0 | 4.950 | 0.225 | >> # 25 | 1.0 | 24.750 | 0.500 | > > Yes, the sample with 25 layers has a more uniform thickness. > >> As before, the standard deviation increases as square root of N. >> Using a >> cumulant expansion (admittedly slightly funky for such a broad >> distribution) necessarily yields the same result as the Gaussian >> distribution: the shape of the measured spectrum is independent of >> the >> number of layers used! And as it turns out, an exact calculation >> (i.e. not >> using a cumulant expansion) also yields the same result of >> independence. > > OK... The shape is the same, but the relative widths change. > > 24.75 +/- 0.50 is a more uniform distribution than 0.99 +/- .099. > Perhaps this is what is confusing you? The thicker sample is more uniform (in the sense of fractional uniformity), but the distortion in the normalized mu(E) due to the nonuniformity is identical. That is exactly what is surprising, and what I initially did not believe. Now I am firmly convinced that it is true. > >> So Lu and Stern got it right. But the idea that we can mitigate >> pinholes by >> adding more layers is wrong. > > Adding more layers does make a sample of more uniform thickness. > Perhaps "mitigate pinholes" means something different to you? By "mitigate pinholes" I mean that we can obtain a normalized energy spectrum that is closer to the mu(E) we are trying to measure. But we can't do that by adding more identically distributed layers if the thick and thin spots are randomly stacked--we end up with exactly the same normalized mu(E). (As usual, this analysis neglects signal to noise, harmonics, and the like.) I used a lot of words there to try to be precise. But basically, stacking two layers of tape with the hope that pinholes will tend to be cancelled out will not work. > > In your original message (in which you set out to "track down" a piece > of "incorrect lore") you said that Lu and Stern assumed that layers > were stacked "so that thick spots are always over thick and thin spots > over thin". They did not assume that. Given that initial > misunderstanding, and the fact that you haven't shown any calculations > or simulations, it's a bit hard for me to fathom what you think Lu and > Stern "got right" or wrong. They got everything right. I was trying to save a different piece of lore that I think is even more widely disseminated--that stacking thin layers of tape reduces the amount of distortion due to nonuniformity as compared to one thin layer of tape. I thought I had shown calculations (the Gaussian case), and Jeremy has shown simulations which confirm the result for the pinhole case. > The main point of their work is that it is better to use more > layers to get to a given thickness. You seem to have some objection > to this, but I cannot figure out what you're trying to say. I agree that your statement is a true one which is also consistent with their paper, but would respectfully differ as to what the main point of the paper is. The abstract reads: > Powdered samples samples are commonly used to measure the extended X- > ray absorption fine structure (EXAFS) and near-edge structure. It is > shown that sizes of particles typically employed produce significant > reduction in the EXAFS amplitude for concentrated samples. The > distortion is calculated and found to be in good agreement with > measurements on FeSi2 samples. To obtain accurate EXAFS amplitudes > on powdered samples it is necessary to use particles significantly > smaller than 400 mesh when the atom of interest is concentrated. The use of increasing number of layers as the particles are sieved more finely is done to provide a controlled experiment in which differences in signal to noise and thickness effects are not a factor. Suggesting that it is better to use more layers to get a given thickness is an indirect way of getting at the real issue, which is particle size. For a given particle size, multiple layers provide no help whatsoever with nonuniformity-related distortions, but merely allow for the desired signal to noise. Lu and Stern provide the correct emphasis in their paper. It is only some of the subsequent XAFS practitioners, including myself until about 24 hours ago, who placed the stress on the multiple layers per se as addressing the uniformity issue. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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Re: [Ifeffit] Distortion of transmission spectra due to particle size
by Scott Calvin 24 Nov '10

24 Nov '10

Matt, Your second simulation confirms what I said: > The standard deviation in thickness from point to point in a stack > of N tapes generally increases as the square root of N (typical > statistical behavior). Now follow that through, using, for example, Grant Bunker's formula for the distortion caused by a Gaussian distribution: (mu x)eff = mu x_o - (mu sigma)^2/2 where sigma is the standard deviation of the thickness. So if sigma goes as square root of N, and x_o goes as N, the fractional attenuation of the measured absorption stays constant, and the shape of the measured spectrum stays constant. There is thus no reduction in the distortion of the spectrum by measuring additional layers. Your pinholes simulation, on the other hand, is not the scenario I was describing. I agree it is better to have more thin layers rather than fewer thick layers. My question was whether it is better to have many thin layers compared to fewer thin layers. For the "brush sample on tape" method of sample preparation, this is more like the question we face when we prepare a sample. Our choice is not to spread a given amount of sample over more tapes, because we're already spreading as thin as we can. Our choice is whether to use more tapes of the same thickness. We don't have to rerun your simulation to see the effect of using tapes of the same thickness. All that happens is that the average thickness and the standard deviation gets multiplied by the number of layers. So now the results are: For 10% pinholes, the results are: # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | # 1 | 10.0 | 0.900 | 0.300 | # 5 | 10.0 | 4.500 | 0.675 | # 25 | 10.0 | 22.500 | 1.500 | For 5% pinholes: # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | # 1 | 5.0 | 0.950 | 0.218 | # 5 | 5.0 | 4.750 | 0.485 | # 25 | 5.0 | 23.750 | 1.100 | For 1% pinholes: # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | # 1 | 1.0 | 0.990 | 0.099 | # 5 | 1.0 | 4.950 | 0.225 | # 25 | 1.0 | 24.750 | 0.500 | As before, the standard deviation increases as square root of N. Using a cumulant expansion (admittedly slightly funky for such a broad distribution) necessarily yields the same result as the Gaussian distribution: the shape of the measured spectrum is independent of the number of layers used! And as it turns out, an exact calculation (i.e. not using a cumulant expansion) also yields the same result of independence. So Lu and Stern got it right. But the idea that we can mitigate pinholes by adding more layers is wrong. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 24, 2010, at 6:05 AM, Matt Newville wrote: > Scott, > >> OK, I've got it straight now. The answer is yes, the distortion from >> nonuniformity is as bad for four strips stacked as for the single >> strip. > > I don't think that's correct. > >> This is surprising to me, but the mathematics is fairly clear. >> Stacking >> multiple layers of tape rather than using one thin layer improves >> the signal >> to noise ratio, but does nothing for uniformity. So there's nothing >> wrong >> with the arguments in Lu and Stern, Scarrow, etc.--it's the notion >> I had >> that we use multiple layers of tape to improve uniformity that's >> mistaken. > > Stacking multiple layers does improve sample uniformity. > > Below is a simple simulation of a sample of unity thickness with > randomly placed pinholes. First this makes a sample that is 1 layer > of N cells, with each cell either having thickness of 1 or 0. Then it > makes a sample of the same size and total thickness, but made of 5 > independent layers, with each layer having the same fraction of > randomly placed pinholes, so that total thickness for each cell could > be 1, 0.8, 0.6, 0.4, 0.2, or 0. Then it makes a sample with 25 > layers. > > The simulation below is in python. I do hope the code is > straightforward enough so that anyone interested can follow. The way > in which pinholes are randomly selected by the code may not be > obvious, so I'll say hear that the "numpy.random.shuffle" function is > like shuffling a deck of cards, and works on its array argument > in-place. > > For 10% pinholes, the results are: > # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | > # 1 | 10.0 | 0.900 | 0.300 | > # 5 | 10.0 | 0.900 | 0.135 | > # 25 | 10.0 | 0.900 | 0.060 | > > For 5% pinholes: > # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | > # 1 | 5.0 | 0.950 | 0.218 | > # 5 | 5.0 | 0.950 | 0.097 | > # 25 | 5.0 | 0.950 | 0.044 | > > For 1% pinholes: > # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | > # 1 | 1.0 | 0.990 | 0.099 | > # 5 | 1.0 | 0.990 | 0.045 | > # 25 | 1.0 | 0.990 | 0.020 | > > Multiple layers of smaller particles gives a more uniform thickness > than fewer layers of larger particles. The standard deviation of the > thickness goes as 1/sqrt(N_layers). In addition, one can see that 5 > layers of 5% pinholes is about as uniform 1 layer with 1% pinholes. > Does any of this seem surprising or incorrect to you? > > Now let's try your case of 1 layer of thickness 0.4 with 4 layers of > thickness 0.4, with 1% pinholes. In the code below, the simulation > would look like > # one layer of thickness=0.4 > sample = 0.4 * make_layer(ncells, ph_frac) > print format % (1, 100*ph_frac, sample.mean(), sample.std()) > > # four layers of thickness=0.4 > layer1 = 0.4 * make_layer(ncells, ph_frac) > layer2 = 0.4 * make_layer(ncells, ph_frac) > layer3 = 0.4 * make_layer(ncells, ph_frac) > layer4 = 0.4 * make_layer(ncells, ph_frac) > sample = layer1 + layer2 + layer3 + layer4 > print format % (4, 100*ph_frac, sample.mean(), sample.std()) > > and the results are: > # N_layers | % Pinholes | Ave Thickness | Thickness Std Dev | > # 1 | 1.0 | 0.396 | 0.040 | > # 4 | 1.0 | 1.584 | 0.080 | > > The sample with 4 layers had its average thickness increase by a > factor of 4, while the standard deviation of that thickness only > doubled. The sample is twice as uniform. > > OK, that's a simple model and of thickness only. Lu and Stern did a > more complete analysis and made actual measurements of the effect of > thickness on XAFS amplitudes. They *showed* that many thin layers is > better than fewer thick layers. > > Perhaps I am not understanding the points you're trying to make, but I > think I am not the only one confused by what you are saying. > > --Matt >

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Re: [Ifeffit] Distortion of transmission spectra due to particle size
by Scott Calvin 24 Nov '10

24 Nov '10

Some follow-up. This, for example, is from an excellent workshop presentation by Rob Scarrow: > Errors from large particles are independent of thickness > The relative (%) variation in thickness depends on the ratio > (particle diameter / avg. thickness), so it is tempting to increase > the avg. thickness (i.e. increase μx) as an alternative to reducing > the particle diameter. > However, simulations of MnO2 spectra for average Δμ0x = 1, 2 or 3 > show that the errors in derived pre-edge peak heights and EXAFS > amplitude factors are significant when diameter > 0.2 / Δμ0, but > that they are not affected by the average sample thickness. (Δμ0 > refers to the edge jump) > The equation at right is given by Heald (quoting earlier work by > Stern and Lu). D is particle diameter, μ1 is for just below the > edge, and Δμ =μ(above edge) - μ1. I've seen similar claims elsewhere, although Scarrow's is particularly clear and unambiguous. The equation Scarrow gives is indeed the one from Lu and Stern, and the simulations are based on that equation. That Lu-Stern equation is derived for a monolayer of spheres, and then experimentally tested with multiple layers of tape. I'm still trying to work through the math to see how it works for multiple layers. I'm not convinced that the N divides out as is claimed in the article. As Matt says, it wasn't their main point. There is no question that if the particle size is large compared to an absorption length there will be nonuniformity and thus distortions. But compare a monolayer of particles with a diameter equal to 0.4 absorption lengths with four strips of tape of that kind stacked. Do we really think the distortion due to nonuniformity will be as bad in the latter case as in the first? In practice, I think many transmission samples fall in roughly that regime, so the question isn't just academic. I'll keep trying to work through the math and let you know what I find. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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maximum number of paths in Artemis
by Bruce Ravel 23 Nov '10

23 Nov '10

Yuan, It seems unwise to post a new question at the end of a long and active thread. Presumably you are looking for an answer -- hiding your question at the end of another thread does not seem like a good way to get that answer. That said, the answer to the question of how to get more than 512 paths depends on your operating system. For Mac: See http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2010-October/009673.html For Windows: You will need the ifeffit dll compiled with more paths. Matt, does such a thing exist for the current version of the dll? If you are using linux, let us know. It is not hard to recompile everything to do what you need. I can write up a short howto. 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] Transmission EXAFS sample
by Jatinkumar Rana 23 Nov '10

23 Nov '10

On 22.11.2010 19:00, 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. Re: Transmission EXAFS sample (Scott Calvin) > 2. Re: Transmission EXAFS sample (Scott Calvin) > 3. maximum number of paths in Artemis (Yuan Ping) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 22 Nov 2010 07:13:42 -0800 > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<5B5040D9-F501-4BA0-8F24-38630B43B943(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > To my mind, when considering sample preparation the important thing is > not so much the "right" thickness, as knowing the effects to guard > against as the thickness deviates toward the thin or thick side. > > As transmission samples become thicker, the problem of "unwanted" > photons becomes more severe. Those photons may be harmonics, photons > scattered into the It detector, or photons from the tails of the > resolution curve of the monochromator. > > As transmission samples become thinner, uniformity becomes more of an > issue. If you play with the equations, you'll see that if your sample > is a mixture of regions that have a thickness of 1.0 absorption > lengths and regions that have a thickness of 2.0 absorption lengths, > the spectrum is less distorted than if it is a mixture of 0.5 and 1.0 > absorption lengths. > > So if a sample is on the thick side, it is particularly important to > guard against harmonics in the beam and scattered photons. If it is on > the thin side, it is particularly important to guard against > nonuniformity. > > To put it another way, problems are synergistic. With a well- > conditioned beam, a uniform sample, and linear detectors, the > thickness almost doesn't matter (within reason)--at a modern beamline, > a total absorption of even 0.05 or 4.0 will work. > > But as each of those conditions deviates from the ideal, distortions > become much more severe. > > There's an old joke about someone on a diet going in to a fast food > joint and asking for a double bacon cheeseburger, a large fries...and > a diet Coke. In XAFS measurements, that attitude actually kind of > works, because of the synergies I just discussed. > > Personally, I trust my ability to condition the beam and minimize > scattering more than I trust my ability to make a uniform sample, so I > lean a little toward the thicker side. > > --Scott Calvin > Faculty at Sarah Lawrence College > Currently on sabbatical at Stanford Synchrotron Radiation Laboratory > > > > On Nov 22, 2010, at 5:13 AM, Welter, Edmund wrote: > > >> Dear Jatin, >> >> the optimum mued of 2.x is not just derived by simple photon counting >> statistics. As Matt pointed out, for transmission measurements at a >> synchrotron beamline in conventional scanning mode this is seldom a >> matter. Nevertheless, one should avoid to measure subtle changes of >> absorption at the extreme ends, that is, transmission near 0 % or >> 100 %. >> In optical photometry this is described by the more or less famous >> "Ringbom plots" which describe the dependency of the accuracy of >> quantitative analysis by absorption measurements (usually but not >> necessarily in the UV/Vis) from the total absorption of the sample. >> >> This time the number is only near to 42, the optimum transmission is >> 36.8 % (mue = 1). So, to achieve the highest accuracy in the >> determination of small Delta c (c = concentration) you should try to >> measure samples with transmissions near to this value (actually the >> minimum is broad and transmissions between 0.2 and 0.7 are ok). In our >> case, we are not interested in the concentration of the absorber, >> but we >> are also interested in (very) small changes of the transmission resp. >> absorption in our samples. Or, using Bouger, Lambert Beer's law, in >> our >> case mue (-ln(I1/I0) is a function of the absorption coefficient >> (mue0). >> The concentration of the absorber and the thickness (d) of the sample >> are constant. >> >> -ln(I1/I0) = mue0 * c * d >> >> But then: If the optimum is a mue between 0.35 and 1.6 why are we all >> measuring successfully (ok, more or less ;-) using samples having a >> mue >> between 2 and 3? ...and 0.35 seems desperately small to me! Maybe >> sample >> homogeneity is an issue? >> >> Cheers, >> Edmund Welter >> >> >> > > > ------------------------------ > > Message: 2 > Date: Mon, 22 Nov 2010 07:16:06 -0800 > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<3730BF4F-966F-46E3-9784-B5FB8EF5310D(a)gmail.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > > On Nov 22, 2010, at 7:09 AM, Jatinkumar Rana wrote: > >>> >> Hi Scott, >> >> Sorry for mixing up the things. >> >> For the case, when i have very limited amount of sample that i can not >> cover 1sq.cm area, you, Matt and others have given very very clear >> explanation about possible solutions and the probable effects on data >> quality. I am really very thankful to all of you for sharing your >> experience and expertise. >> >> My last post was with reference to the case when i have enough powders >> (i.e., reference oxide compounds). It is just to be ensured that i am >> doing things 100% exactly in a same way it has to be done. >> >> With best regards, >> Jatin >> >> -- >> Jatinkumar Rana >> >> > Yes, Jatin, the procedure you described is fine. There is no "right" > way to make samples, although there are many wrong ways. > > --Scott Calvin > Faculty at Sarah Lawrence College > Currently on sabbatical at Stanford Synchrotron Radiation Laboratory >

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Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 22 Nov '10

22 Nov '10

On Nov 21, 2010, at 2:45 AM, Jatinkumar Rana wrote: >> >> > Hi Scott, > > Yes I have assumed the sample cross section area to be 1 sq. cm. and > then calculated the amount of sample required for that. > > What i planned is following : > > I would calculate the amount of sample required for 1sq.cm area, take > that amount of sample and make it very fine paste using mortar and > pestle, and then apply it uniformly on a piece of kapton tape. Then > fold > the tape over and over again in such a way that final bunch of tapes > will yield to 1 sq.cm. area containing the required amount of sample. > > Will it be the right approach ?? OR I can take randomly few milligrams > of powder (i.e. not strictly as per calculation) and make a several > uniform layers of tape ?? > > With best regards, > Jatin > > -- Hi Jatin, I'm not sure I understand. If you have enough sample for the 1 square centimeter target, then there shouldn't be a problem, right? I was assuming from your initial question that you weren't going to have enough sample to do that. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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Distortion of transmission spectra due to particle size
by Scott Calvin 22 Nov '10

22 Nov '10

Hi all, I'm tracking down a piece of EXAFS lore which I think is incorrect. I've seen it said that you cannot compensate for the distortion introduced by large particle sizes by making the sample thicker. Certainly thick samples have their own set of issues (e.g. "thickness effects" from harmonics), but I've seen the claim that the mathematics of the distortions introduced by nonuniformity means that there is a particle-size distortion that is independent of thickness. This claim is sometimes accompanied by an equation giving chi_eff/chi_real as a function of particle size diameter D and various absorption coefficients. I've eventually traced this equation back to a paper by Lu and Stern from 1983, have walked through the derivation, and believe there is a flaw in the logic that has led to the erroneous--and widely quoted-- conclusion that thickness cannot compensate for particle size. The paper, for those who want to follow along, is K. Lu and E. A. Stern, "Size effect of powdered sample on EXAFS amplitude," Nucl. Instrm. and Meth. 212, 475-478 (1983). They calculate the intensity transmitted by a spherical particle, and from there calculate the attenuation in the normalized EXAFS signal for a beam passing through that particle. They then, however, extend this to multiple layers of particles by the following argument: "Finally, the attenuation in N layers is given by (I/I0)^N, where I is the transmitted intensity through one layer. Xeff for N layers is then the same as for a single layer since N will cancel in the final result." This is not the case, is it? It seems to me that their analysis assumes that the spheres in subsequent layers line up with the spheres in previous ones, so that thick spots are always over thick and thin spots over thin. It's little wonder, then, that making the sample thicker does not improve the uniformity according to that analysis. I've done a calculation for the effects of uniformity in a somewhat different way, and found that it is indeed true that multiple layers on particles show less distortion due to nonuniformity that a single layer of particles of the same size, just as one would intuitively imagine, and in contrast to Lu and Stern. Do you agree that the extrapolation to multiple layers in the original Lu and Stern paper is not correct, or have I misled myself somehow? --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory P.S. None of this should be taken as an endorsement of overly thick samples! Harmonics and the like are a concern regardless of the uniformity issue.

5 4

Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 22 Nov '10

22 Nov '10

To my mind, when considering sample preparation the important thing is not so much the "right" thickness, as knowing the effects to guard against as the thickness deviates toward the thin or thick side. As transmission samples become thicker, the problem of "unwanted" photons becomes more severe. Those photons may be harmonics, photons scattered into the It detector, or photons from the tails of the resolution curve of the monochromator. As transmission samples become thinner, uniformity becomes more of an issue. If you play with the equations, you'll see that if your sample is a mixture of regions that have a thickness of 1.0 absorption lengths and regions that have a thickness of 2.0 absorption lengths, the spectrum is less distorted than if it is a mixture of 0.5 and 1.0 absorption lengths. So if a sample is on the thick side, it is particularly important to guard against harmonics in the beam and scattered photons. If it is on the thin side, it is particularly important to guard against nonuniformity. To put it another way, problems are synergistic. With a well- conditioned beam, a uniform sample, and linear detectors, the thickness almost doesn't matter (within reason)--at a modern beamline, a total absorption of even 0.05 or 4.0 will work. But as each of those conditions deviates from the ideal, distortions become much more severe. There's an old joke about someone on a diet going in to a fast food joint and asking for a double bacon cheeseburger, a large fries...and a diet Coke. In XAFS measurements, that attitude actually kind of works, because of the synergies I just discussed. Personally, I trust my ability to condition the beam and minimize scattering more than I trust my ability to make a uniform sample, so I lean a little toward the thicker side. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 22, 2010, at 5:13 AM, Welter, Edmund wrote: > Dear Jatin, > > the optimum mued of 2.x is not just derived by simple photon counting > statistics. As Matt pointed out, for transmission measurements at a > synchrotron beamline in conventional scanning mode this is seldom a > matter. Nevertheless, one should avoid to measure subtle changes of > absorption at the extreme ends, that is, transmission near 0 % or > 100 %. > In optical photometry this is described by the more or less famous > "Ringbom plots" which describe the dependency of the accuracy of > quantitative analysis by absorption measurements (usually but not > necessarily in the UV/Vis) from the total absorption of the sample. > > This time the number is only near to 42, the optimum transmission is > 36.8 % (mue = 1). So, to achieve the highest accuracy in the > determination of small Delta c (c = concentration) you should try to > measure samples with transmissions near to this value (actually the > minimum is broad and transmissions between 0.2 and 0.7 are ok). In our > case, we are not interested in the concentration of the absorber, > but we > are also interested in (very) small changes of the transmission resp. > absorption in our samples. Or, using Bouger, Lambert Beer's law, in > our > case mue (-ln(I1/I0) is a function of the absorption coefficient > (mue0). > The concentration of the absorber and the thickness (d) of the sample > are constant. > > -ln(I1/I0) = mue0 * c * d > > But then: If the optimum is a mue between 0.35 and 1.6 why are we all > measuring successfully (ok, more or less ;-) using samples having a > mue > between 2 and 3? ...and 0.35 seems desperately small to me! Maybe > sample > homogeneity is an issue? > > Cheers, > Edmund Welter > >

2 1

Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 22 Nov '10

22 Nov '10

On Nov 22, 2010, at 7:09 AM, Jatinkumar Rana wrote: >> > Hi Scott, > > Sorry for mixing up the things. > > For the case, when i have very limited amount of sample that i can not > cover 1sq.cm area, you, Matt and others have given very very clear > explanation about possible solutions and the probable effects on data > quality. I am really very thankful to all of you for sharing your > experience and expertise. > > My last post was with reference to the case when i have enough powders > (i.e., reference oxide compounds). It is just to be ensured that i am > doing things 100% exactly in a same way it has to be done. > > With best regards, > Jatin > > -- > Jatinkumar Rana > Yes, Jatin, the procedure you described is fine. There is no "right" way to make samples, although there are many wrong ways. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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Re: [Ifeffit] Transmission EXAFS sample
by Jatinkumar Rana 22 Nov '10

22 Nov '10

On 21.11.2010 19:00, 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. Re: Transmission EXAFS sample (Jatinkumar Rana) > 2. Re: Transmission EXAFS sample (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Nov 2010 11:44:25 +0100 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To:ifeffit@millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<4CE8F809.3040208(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 20.11.2010 19:00,ifeffit-request@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. Re: Transmission EXAFS sample (Scott Calvin) >> 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 19 Nov 2010 10:30:37 -0800 >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<DEC4127B-B536-4A85-BED3-2799D5B596C4(a)gmail.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Hi Jatin, >> >> Matt covered most of what I would say, but I'll add a few comments of >> my own. >> >> I'm not sure how you arrived at the conclusion that you have only a >> few percent of what you need--you must be assuming a sample area >> somehow. I have frequently made transmission measurements on samples >> where I only had a few milligrams available. Generally, I did it by >> spreading it on a layer of tape as well as I could and then folding >> the tape over and over again--sometimes to make as many as 16 layers. >> (Of course, that many layers is not advisable if you're below 6 keV or >> so, as the absorption of the tape itself would kill the signal). Even >> if there are lots of pinholes because you can't cover the tape >> effectively, 16 layers from folding will make them cancel out fairly >> well. I can then narrow the beam a bit to match the size of my sample. >> Flux isn't really the issue here, so I don't even need a focussed >> beamline--I can just narrow the slits. >> >> Two other tips: >> >> 1) Realize that even with a tiny amount of sample that much of it >> won't end up on the tape. The process of brushing on tape is designed >> to separate the small grains from the big ones, with only the small >> ones ending up on tape. Allow that to happen! >> >> 2) You can sometimes get a second piece of tape to have some sample on >> it by putting it sticky side down on your mortar and peeling it back. >> A thin layer of dust from the sample will stick to the tape, and give >> you a little more absorption and a bit more of a uniform distribution. >> If you stack that with the primary piece of tape and then fold a few >> times, you may end up in pretty good shape, as long as you're not >> operating at a low enough energy so that all the layers of tape are a >> problem.. >> >> This procedure doesn't give me the best data I've ever seen, but it's >> often not bad. >> >> --Scott Calvin >> Sarah Lawrence College >> >> On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: >> >> >> >>> Dear Jatin, >>> >>> The idea that the optimum absorption length (mu*t) for transmission >>> experiments is 2.3 assumes that the errors in the measurement are due >>> to counting statistics of the x-rays. For any synchrotron experiment, >>> the number of x-rays in the transmission chamber is high enough that >>> the noise from counting statistics is rarely significant. This means >>> that using a value of 2.3 is really not that important. >>> >>> The more important issues are >>> a) having a uniform sample. >>> b) not having (mu*t) so high that higher-order harmonics dominate >>> the transmission measurement. >>> >>> For transmission measurements, it's difficult to overstate the >>> importance of a uniform sample. For an ideal thickness, I would say >>> that the better rules of thumb than mu*t = 2.3 are to aim for an edge >>> step of 0.1 to 1.0, and a total absorption less than 3.0. >>> >>> If you only have enough material for an edge step as low as 0.02 (as >>> you imply), then measuring in fluorescence or electron emission is >>> probably a better choice. Such a sample won't be severely affected by >>> "self-absorption" (or "over absorption" to use the term this mailing >>> list prefers) in the fluorescence measurement. I would recommend >>> simultaneously measuring transmission and florescence for such a >>> sample. >>> >>> My concern about a very thin sample is uniformity. Specifically, is >>> the grain size really well below mu/0.02 so that a collection of >>> particles can give a uniform thickness? Since you didn't give any >>> details of the system, it's hard to guess. >>> >>> Is it feasible to pack that material into a smaller area so that the >>> thickness is increased and use a smaller x-ray beam? >>> >>> >>> >>>> -- Can my sample be only few percentage of the "actual amount" (i.e. >>>> calculated based on above fact) required, and still i can perform >>>> transmission EXAFS ? How would this affect my data ? (I guess, it >>>> will be >>>> heavily dominated by noise) >>>> >>>> >>> I would guess that a sample with mu*t of 0.02 would be dominated by >>> pinholes. >>> >>> >>> >>>> -- What if, i have required amount of sample but since material's >>>> density is >>>> so high that it yields only small volume of powder (for a given >>>> weight), >>>> that it can not be covered up on multiple layers of Kapton tape to >>>> ensure >>>> pinhole-free sample ? >>>> >>>> >>> If you cannot get the grain size small enough to have many overlapping >>> grains in the sample, the sample won't be uniform enough for good >>> transmission data. The techniques of using multiple layers of mixing >>> with a low-Z binder don't solve this problem. These do help to make a >>> uniform collection of overlapping grains, but don't make the grains >>> smaller. >>> >>> I would recommend trying to increase the thickness at the expense of >>> cross-sectional area, and/or measuring in both transmission and >>> fluorescence. >>> >>> Hope that helps, >>> >>> --Matt >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 19 Nov 2010 23:21:43 -0500 >> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<69bc35f1-e92c-426c-8786-e2a5c881fae8@blur> >> Content-Type: text/plain; charset="us-ascii"; Format="Flowed"; >> DelSp="Yes" >> >> That's probably how they discovered graphene, by trying to make exafs >> sample. >> Anatoly >> >> Sent from my mobile phone, please forgive typos. >> >> -----Original message----- >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Fri, Nov 19, 2010 18:30:37 GMT+00:00 >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> >> >>

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Re: [Ifeffit] Ifeffit Digest, Vol 93, Issue 16
by Jatinkumar Rana 22 Nov '10

22 Nov '10

On 21.11.2010 19:00, 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. Re: Transmission EXAFS sample (Jatinkumar Rana) > 2. Re: Transmission EXAFS sample (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Nov 2010 11:44:25 +0100 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<4CE8F809.3040208(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 20.11.2010 19:00, 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. Re: Transmission EXAFS sample (Scott Calvin) >> 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 19 Nov 2010 10:30:37 -0800 >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<DEC4127B-B536-4A85-BED3-2799D5B596C4(a)gmail.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Hi Jatin, >> >> Matt covered most of what I would say, but I'll add a few comments of >> my own. >> >> I'm not sure how you arrived at the conclusion that you have only a >> few percent of what you need--you must be assuming a sample area >> somehow. I have frequently made transmission measurements on samples >> where I only had a few milligrams available. Generally, I did it by >> spreading it on a layer of tape as well as I could and then folding >> the tape over and over again--sometimes to make as many as 16 layers. >> (Of course, that many layers is not advisable if you're below 6 keV or >> so, as the absorption of the tape itself would kill the signal). Even >> if there are lots of pinholes because you can't cover the tape >> effectively, 16 layers from folding will make them cancel out fairly >> well. I can then narrow the beam a bit to match the size of my sample. >> Flux isn't really the issue here, so I don't even need a focussed >> beamline--I can just narrow the slits. >> >> Two other tips: >> >> 1) Realize that even with a tiny amount of sample that much of it >> won't end up on the tape. The process of brushing on tape is designed >> to separate the small grains from the big ones, with only the small >> ones ending up on tape. Allow that to happen! >> >> 2) You can sometimes get a second piece of tape to have some sample on >> it by putting it sticky side down on your mortar and peeling it back. >> A thin layer of dust from the sample will stick to the tape, and give >> you a little more absorption and a bit more of a uniform distribution. >> If you stack that with the primary piece of tape and then fold a few >> times, you may end up in pretty good shape, as long as you're not >> operating at a low enough energy so that all the layers of tape are a >> problem.. >> >> This procedure doesn't give me the best data I've ever seen, but it's >> often not bad. >> >> --Scott Calvin >> Sarah Lawrence College >> >> On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: >> >> >> >>> Dear Jatin, >>> >>> The idea that the optimum absorption length (mu*t) for transmission >>> experiments is 2.3 assumes that the errors in the measurement are due >>> to counting statistics of the x-rays. For any synchrotron experiment, >>> the number of x-rays in the transmission chamber is high enough that >>> the noise from counting statistics is rarely significant. This means >>> that using a value of 2.3 is really not that important. >>> >>> The more important issues are >>> a) having a uniform sample. >>> b) not having (mu*t) so high that higher-order harmonics dominate >>> the transmission measurement. >>> >>> For transmission measurements, it's difficult to overstate the >>> importance of a uniform sample. For an ideal thickness, I would say >>> that the better rules of thumb than mu*t = 2.3 are to aim for an edge >>> step of 0.1 to 1.0, and a total absorption less than 3.0. >>> >>> If you only have enough material for an edge step as low as 0.02 (as >>> you imply), then measuring in fluorescence or electron emission is >>> probably a better choice. Such a sample won't be severely affected by >>> "self-absorption" (or "over absorption" to use the term this mailing >>> list prefers) in the fluorescence measurement. I would recommend >>> simultaneously measuring transmission and florescence for such a >>> sample. >>> >>> My concern about a very thin sample is uniformity. Specifically, is >>> the grain size really well below mu/0.02 so that a collection of >>> particles can give a uniform thickness? Since you didn't give any >>> details of the system, it's hard to guess. >>> >>> Is it feasible to pack that material into a smaller area so that the >>> thickness is increased and use a smaller x-ray beam? >>> >>> >>> >>>> -- Can my sample be only few percentage of the "actual amount" (i.e. >>>> calculated based on above fact) required, and still i can perform >>>> transmission EXAFS ? How would this affect my data ? (I guess, it >>>> will be >>>> heavily dominated by noise) >>>> >>>> >>> I would guess that a sample with mu*t of 0.02 would be dominated by >>> pinholes. >>> >>> >>> >>>> -- What if, i have required amount of sample but since material's >>>> density is >>>> so high that it yields only small volume of powder (for a given >>>> weight), >>>> that it can not be covered up on multiple layers of Kapton tape to >>>> ensure >>>> pinhole-free sample ? >>>> >>>> >>> If you cannot get the grain size small enough to have many overlapping >>> grains in the sample, the sample won't be uniform enough for good >>> transmission data. The techniques of using multiple layers of mixing >>> with a low-Z binder don't solve this problem. These do help to make a >>> uniform collection of overlapping grains, but don't make the grains >>> smaller. >>> >>> I would recommend trying to increase the thickness at the expense of >>> cross-sectional area, and/or measuring in both transmission and >>> fluorescence. >>> >>> Hope that helps, >>> >>> --Matt >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >> >> ------------------------------ >> >> Message: 2 >> Date: Fri, 19 Nov 2010 23:21:43 -0500 >> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> Message-ID:<69bc35f1-e92c-426c-8786-e2a5c881fae8@blur> >> Content-Type: text/plain; charset="us-ascii"; Format="Flowed"; >> DelSp="Yes" >> >> That's probably how they discovered graphene, by trying to make exafs >> sample. >> Anatoly >> >> Sent from my mobile phone, please forgive typos. >> >> -----Original message----- >> From: Scott Calvin<dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Fri, Nov 19, 2010 18:30:37 GMT+00:00 >> Subject: Re: [Ifeffit] Transmission EXAFS sample >> >> >>

1 0

Re: [Ifeffit] Transmission EXAFS sample
by Jatinkumar Rana 21 Nov '10

21 Nov '10

On 20.11.2010 19:00, 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. Re: Transmission EXAFS sample (Scott Calvin) > 2. Re: Transmission EXAFS sample (Frenkel, Anatoly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 19 Nov 2010 10:30:37 -0800 > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<DEC4127B-B536-4A85-BED3-2799D5B596C4(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Hi Jatin, > > Matt covered most of what I would say, but I'll add a few comments of > my own. > > I'm not sure how you arrived at the conclusion that you have only a > few percent of what you need--you must be assuming a sample area > somehow. I have frequently made transmission measurements on samples > where I only had a few milligrams available. Generally, I did it by > spreading it on a layer of tape as well as I could and then folding > the tape over and over again--sometimes to make as many as 16 layers. > (Of course, that many layers is not advisable if you're below 6 keV or > so, as the absorption of the tape itself would kill the signal). Even > if there are lots of pinholes because you can't cover the tape > effectively, 16 layers from folding will make them cancel out fairly > well. I can then narrow the beam a bit to match the size of my sample. > Flux isn't really the issue here, so I don't even need a focussed > beamline--I can just narrow the slits. > > Two other tips: > > 1) Realize that even with a tiny amount of sample that much of it > won't end up on the tape. The process of brushing on tape is designed > to separate the small grains from the big ones, with only the small > ones ending up on tape. Allow that to happen! > > 2) You can sometimes get a second piece of tape to have some sample on > it by putting it sticky side down on your mortar and peeling it back. > A thin layer of dust from the sample will stick to the tape, and give > you a little more absorption and a bit more of a uniform distribution. > If you stack that with the primary piece of tape and then fold a few > times, you may end up in pretty good shape, as long as you're not > operating at a low enough energy so that all the layers of tape are a > problem.. > > This procedure doesn't give me the best data I've ever seen, but it's > often not bad. > > --Scott Calvin > Sarah Lawrence College > > On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: > > >> Dear Jatin, >> >> The idea that the optimum absorption length (mu*t) for transmission >> experiments is 2.3 assumes that the errors in the measurement are due >> to counting statistics of the x-rays. For any synchrotron experiment, >> the number of x-rays in the transmission chamber is high enough that >> the noise from counting statistics is rarely significant. This means >> that using a value of 2.3 is really not that important. >> >> The more important issues are >> a) having a uniform sample. >> b) not having (mu*t) so high that higher-order harmonics dominate >> the transmission measurement. >> >> For transmission measurements, it's difficult to overstate the >> importance of a uniform sample. For an ideal thickness, I would say >> that the better rules of thumb than mu*t = 2.3 are to aim for an edge >> step of 0.1 to 1.0, and a total absorption less than 3.0. >> >> If you only have enough material for an edge step as low as 0.02 (as >> you imply), then measuring in fluorescence or electron emission is >> probably a better choice. Such a sample won't be severely affected by >> "self-absorption" (or "over absorption" to use the term this mailing >> list prefers) in the fluorescence measurement. I would recommend >> simultaneously measuring transmission and florescence for such a >> sample. >> >> My concern about a very thin sample is uniformity. Specifically, is >> the grain size really well below mu/0.02 so that a collection of >> particles can give a uniform thickness? Since you didn't give any >> details of the system, it's hard to guess. >> >> Is it feasible to pack that material into a smaller area so that the >> thickness is increased and use a smaller x-ray beam? >> >> >>> -- Can my sample be only few percentage of the "actual amount" (i.e. >>> calculated based on above fact) required, and still i can perform >>> transmission EXAFS ? How would this affect my data ? (I guess, it >>> will be >>> heavily dominated by noise) >>> >> I would guess that a sample with mu*t of 0.02 would be dominated by >> pinholes. >> >> >>> -- What if, i have required amount of sample but since material's >>> density is >>> so high that it yields only small volume of powder (for a given >>> weight), >>> that it can not be covered up on multiple layers of Kapton tape to >>> ensure >>> pinhole-free sample ? >>> >> If you cannot get the grain size small enough to have many overlapping >> grains in the sample, the sample won't be uniform enough for good >> transmission data. The techniques of using multiple layers of mixing >> with a low-Z binder don't solve this problem. These do help to make a >> uniform collection of overlapping grains, but don't make the grains >> smaller. >> >> I would recommend trying to increase the thickness at the expense of >> cross-sectional area, and/or measuring in both transmission and >> fluorescence. >> >> Hope that helps, >> >> --Matt >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > Message: 2 > Date: Fri, 19 Nov 2010 23:21:43 -0500 > From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Transmission EXAFS sample > Message-ID:<69bc35f1-e92c-426c-8786-e2a5c881fae8@blur> > Content-Type: text/plain; charset="us-ascii"; Format="Flowed"; > DelSp="Yes" > > That's probably how they discovered graphene, by trying to make exafs > sample. > Anatoly > > Sent from my mobile phone, please forgive typos. > > -----Original message----- > From: Scott Calvin<dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Fri, Nov 19, 2010 18:30:37 GMT+00:00 > Subject: Re: [Ifeffit] Transmission EXAFS sample > > >

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Re: [Ifeffit] Transmission EXAFS sample
by Scott Calvin 20 Nov '10

20 Nov '10

Hi Jatin, Matt covered most of what I would say, but I'll add a few comments of my own. I'm not sure how you arrived at the conclusion that you have only a few percent of what you need--you must be assuming a sample area somehow. I have frequently made transmission measurements on samples where I only had a few milligrams available. Generally, I did it by spreading it on a layer of tape as well as I could and then folding the tape over and over again--sometimes to make as many as 16 layers. (Of course, that many layers is not advisable if you're below 6 keV or so, as the absorption of the tape itself would kill the signal). Even if there are lots of pinholes because you can't cover the tape effectively, 16 layers from folding will make them cancel out fairly well. I can then narrow the beam a bit to match the size of my sample. Flux isn't really the issue here, so I don't even need a focussed beamline--I can just narrow the slits. Two other tips: 1) Realize that even with a tiny amount of sample that much of it won't end up on the tape. The process of brushing on tape is designed to separate the small grains from the big ones, with only the small ones ending up on tape. Allow that to happen! 2) You can sometimes get a second piece of tape to have some sample on it by putting it sticky side down on your mortar and peeling it back. A thin layer of dust from the sample will stick to the tape, and give you a little more absorption and a bit more of a uniform distribution. If you stack that with the primary piece of tape and then fold a few times, you may end up in pretty good shape, as long as you're not operating at a low enough energy so that all the layers of tape are a problem.. This procedure doesn't give me the best data I've ever seen, but it's often not bad. --Scott Calvin Sarah Lawrence College On Nov 19, 2010, at 8:13 AM, Matt Newville wrote: > Dear Jatin, > > The idea that the optimum absorption length (mu*t) for transmission > experiments is 2.3 assumes that the errors in the measurement are due > to counting statistics of the x-rays. For any synchrotron experiment, > the number of x-rays in the transmission chamber is high enough that > the noise from counting statistics is rarely significant. This means > that using a value of 2.3 is really not that important. > > The more important issues are > a) having a uniform sample. > b) not having (mu*t) so high that higher-order harmonics dominate > the transmission measurement. > > For transmission measurements, it's difficult to overstate the > importance of a uniform sample. For an ideal thickness, I would say > that the better rules of thumb than mu*t = 2.3 are to aim for an edge > step of 0.1 to 1.0, and a total absorption less than 3.0. > > If you only have enough material for an edge step as low as 0.02 (as > you imply), then measuring in fluorescence or electron emission is > probably a better choice. Such a sample won't be severely affected by > "self-absorption" (or "over absorption" to use the term this mailing > list prefers) in the fluorescence measurement. I would recommend > simultaneously measuring transmission and florescence for such a > sample. > > My concern about a very thin sample is uniformity. Specifically, is > the grain size really well below mu/0.02 so that a collection of > particles can give a uniform thickness? Since you didn't give any > details of the system, it's hard to guess. > > Is it feasible to pack that material into a smaller area so that the > thickness is increased and use a smaller x-ray beam? > >> -- Can my sample be only few percentage of the "actual amount" (i.e. >> calculated based on above fact) required, and still i can perform >> transmission EXAFS ? How would this affect my data ? (I guess, it >> will be >> heavily dominated by noise) > > I would guess that a sample with mu*t of 0.02 would be dominated by > pinholes. > >> -- What if, i have required amount of sample but since material's >> density is >> so high that it yields only small volume of powder (for a given >> weight), >> that it can not be covered up on multiple layers of Kapton tape to >> ensure >> pinhole-free sample ? > > If you cannot get the grain size small enough to have many overlapping > grains in the sample, the sample won't be uniform enough for good > transmission data. The techniques of using multiple layers of mixing > with a low-Z binder don't solve this problem. These do help to make a > uniform collection of overlapping grains, but don't make the grains > smaller. > > I would recommend trying to increase the thickness at the expense of > cross-sectional area, and/or measuring in both transmission and > fluorescence. > > Hope that helps, > > --Matt > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Transmission EXAFS sample
by Jatinkumar Rana 19 Nov '10

19 Nov '10

Dear all, I have very basic question about the sample preparation for EXAFS. It is well understood and proven by several researchers that the optimum amount of sample (per unit area) required for EXAFS is determined by the fact that the total absorbtion of the entire sample above the absorption edge (of interest) should be between 2 to 2.5, more precisely, it should be 2.3. The reason which forces me to put this question to a mailing list is that, i treat my sample through a process which yields only few percentage of the total amount of sample required for EXAFS. I would prefer to measure EXAFS in transmission mode with samples prepared on several layers of Kapton tape which are bound together to ensure pinhole free sample. My questions are : -- Can my sample be only few percentage of the "actual amount" (i.e. calculated based on above fact) required, and still i can perform transmission EXAFS ? How would this affect my data ? (I guess, it will be heavily dominated by noise) -- What if, i have required amount of sample but since material's density is so high that it yields only small volume of powder (for a given weight), that it can not be covered up on multiple layers of Kapton tape to ensure pinhole-free sample ? I look forward to any comments or suggestions as this would help me improvise the quality of my data. With best regards, Jatin -- 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] Origin of terminology "self-absorption"
by Scott Calvin 17 Nov '10

17 Nov '10

I tried a few searches, but rapidly get lost in other uses of the term. My guess is we borrowed it from some other spectroscopy, much the way we borrowed "Debye-Waller factor" from XRD, and then proceeded to change its meaning. But it would be nice to be able to track that down. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory On Nov 16, 2010, at 10:54 AM, Matthew Marcus wrote: > It's definitely a misnomer. I use "overabsorption" and encourage > others to do so. I suppose to track it down would require going > back over the seminal papers on the subject. > mam > > On 11/16/2010 10:19 AM, Scott Calvin wrote: >> Hi all, >> >> As some of you know, I'm currently working on a textbook on XAFS >> analysis. Because of that, I'm going to occasionally pose some >> questions for the list that may seem a bit random. I hope none of >> you mind me using the list in this way; the questions may seem to >> come out of left field, but I think they will still be of interest >> to many. >> >> With that said, here's my question for today: >> >> What is the origin of the use of "self-absorption" to describe the >> suppression of fine-structure observed in thick, concentrated >> samples measured in fluorescence? I understand the physics of the >> effect itself, my question is the curious wording. Compared to a >> thin concentrated sample, the effect might better be described as >> "saturation," while compared to a thick dilute sample, it's >> actually related to a lack of absorption by other elements. >> >> --Scott Calvin >> Faculty at Sarah Lawrence College >> Currently on sabbatical at Stanford Synchrotron Radiation Laboratory >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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UO2 thin films on STO
by mohamed sobhy 16 Nov '10

16 Nov '10

Dear All I would like to grow UO2 thin films on STO (SrTiO3) substrate but I found that Sr K-edge 16105 and U L3-edge is 17166. Do you think there will be any interference? Best, Mohamed

4 3

Origin of terminology "self-absorption"
by Scott Calvin 16 Nov '10

16 Nov '10

Hi all, As some of you know, I'm currently working on a textbook on XAFS analysis. Because of that, I'm going to occasionally pose some questions for the list that may seem a bit random. I hope none of you mind me using the list in this way; the questions may seem to come out of left field, but I think they will still be of interest to many. With that said, here's my question for today: What is the origin of the use of "self-absorption" to describe the suppression of fine-structure observed in thick, concentrated samples measured in fluorescence? I understand the physics of the effect itself, my question is the curious wording. Compared to a thin concentrated sample, the effect might better be described as "saturation," while compared to a thick dilute sample, it's actually related to a lack of absorption by other elements. --Scott Calvin Faculty at Sarah Lawrence College Currently on sabbatical at Stanford Synchrotron Radiation Laboratory

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help
by Aaron Yevick 12 Nov '10

12 Nov '10

Hi all, I downloaded Artemis twice, from both cars.uchicago and sourceforge. Both times I downloaded the latest, 1.2.11.exe. When it installed, I opened Artemis and was prompted to install several updates. I clicked Install Updates, and both times it says: downloading fetching update 10 (iff_010.zip).... downloaded iff_010.zip OK. expanding file iff_010.zip and goes no further in an hour. I quit. When it runs, along the bottom it says the version is 0.8.012 (c) 2002-2008, which I was told is not the latest version (is that true?) My operating system is Windows 7 Professional. Can anybody offer suggestions as to why this happens? Does it matter if I don't have these updates? Aaron

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Re: [Ifeffit] something is wrong with Ruthenium-Oxygen bond amplitudes
by Scott Calvin 06 Nov '10

06 Nov '10

Hi Maria, What was the physical form of the samples (powder, thin film, etc.) and how were they measured (transmission, fluorescence, ...)? Sometimes this kind of thing can stem from sample/beamline/data effects. --Scott Calvin Sarah Lawrence College On Nov 5, 2010, at 5:50 PM, María Elena Montero Cabrera wrote: > Hello friends, > > Hopping someone could help us. We are having some problems in > fitting Ru K-edge in a Ruthenium-cuprate sample on Artemis, with > path functions obtained using FEFF 8.4, where we got amplitude > values of less than 0.50 for Ru-O first shells. We think this value > probably is wrong, although there are some publications where some > oxygen deficiency is studied and recorded as true. The ATOMS input > data was found to be ok due to the Rietveld analysis results told us > these are good. The reason we think we may be wrong with something > during the fitting appeared because we tried to fit our reference > sample of RuO2 (measured under same conditions as the experiment of > Ru-Cu at SSRL) and we came to the same results, even worst, of > amplitude lower than 0.40. We are attaching the Artemis files so you > can take a look on it and give us some light to continue with our > analysis. > Thanking in advance, take care

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something is wrong with Ruthenium-Oxygen bond amplitudes
by María Elena Montero Cabrera 06 Nov '10

06 Nov '10

Hello friends, Hopping someone could help us. We are having some problems in fitting Ru K-edge in a Ruthenium-cuprate sample on Artemis, with path functions obtained using FEFF 8.4, where we got amplitude values of less than 0.50 for Ru-O first shells. We think this value probably is wrong, although there are some publications where some oxygen deficiency is studied and recorded as true. The ATOMS input data was found to be ok due to the Rietveld analysis results told us these are good. The reason we think we may be wrong with something during the fitting appeared because we tried to fit our reference sample of RuO2 (measured under same conditions as the experiment of Ru-Cu at SSRL) and we came to the same results, even worst, of amplitude lower than 0.40. We are attaching the Artemis files so you can take a look on it and give us some light to continue with our analysis. Thanking in advance, take care -- María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31109, Chih. México Tel (614) 4391123

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Re: [Ifeffit] feff question
by Joshua Kas 04 Nov '10

04 Nov '10

Hi George, The obsolete warning is probably not a big deal, however, the compilation should be tested since compiling with gfortran has not been well tested for feff7. If you can get an old version of g77, you won't have issues. Otherwise, I would use the following command when running gfortran. gfortran -finit-local-zero -o feff702 feff702.f This may not work with your version of gfortran (-finit-local-zero is not in the manual) but if it does, the compiled feff will be less likely to have runtime errors. Cheers, Josh Kas I installed gfortran-4.2.3.dmg file on top of the gfortran-42-5577.pkg and > can now see "gfortran" in '/usr/local/bin'. I am also able to compile > simple > fortran code, but when I attempt to run Feff7 I get the following message: > > bash-3.2$ /usr/local/bin/gfortran -o feff702 feff702.f > feff702.f:12161.72: > > if (den.eq.0) pause 'failure in polint' > 1 > Warning: Obsolete: PAUSE statement at (1) > feff702.f:12226.72: > > if (den.eq.0) pause 'failure in polint' > 1 > Warning: Obsolete: PAUSE statement at (1) > bash-3.2$ > > Any idea as to what the problem is now? > > Thank you, > George > > > > On Wed, Nov 3, 2010 at 3:45 PM, Matt Newville <newville(a)cars.uchicago.edu > >wrote: > > > Hi George, > > > > On Wed, Nov 3, 2010 at 2:37 PM, George Sterbinsky > > <GeorgeSterbinsky(a)u.northwestern.edu> wrote: > > > I've also noticed that there is not a file or directory called gfortran > > in > > > '/usr/local/bin'. This is what made me think I may also need to install > > the > > > gfortran-4.2.3.dmg file. If I do not see a file or directory called > > gfortran > > > in '/usr/local/bin' does this indicate that gfortran is not installed? > Is > > it > > > possible that gfortran-42-5577.pkg placed it somewhere else? > > > > Yes, those are all possible. You need to install gfortran, find out > > where it is, and then run it to compile and link feff702 into an > > executable. It sounds like you might want to get a local unix-savvy > > person who can help you.... > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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feff question
by George Sterbinsky 03 Nov '10

03 Nov '10

Hi, I am hoping someone can explain to me how to run Feff 7 on a mac (OSX version 10.5.8) starting from the feff702.f file. Thank you, George

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Scripting - Python
by Andrew Korinda 01 Nov '10

01 Nov '10

I'm looking to introduce some scripting routines to some of my EXAFS fitting work. Looking around I ran across the Python module and downloaded that. The shell works fine, as does enter commands directly into Ifeffit, however I'm not getting the read and write commands to work from within Python scripts. Example: iff.ifeffit("read_data(C:\Program Files\Ifeffit\examples\Ifeffit\data\cu10k.chi,group=c)") returns -1. >From this experience I have some questions: ~First does anyone have some debugging tips for cross talk problems? The Fortran return values are fine, but would returning the echo_buffer or a log file be more helpful? ~Secondly, Does anyone have any example Python scripts for Ifeffit that they would like to share? I'm new to Python and haven't done programming for a while and I'd like to get a better idea of what's all possible, and how. I was looking at Matt Newville's message back in 2008 about defining a library for Athena in Python and his 2001 paper but couldn't find much else. ~Finally, would I be better off coding in Perl and using Demeter? Thanks everyone, Andy Korinda Notestein Lab Chemical & Biological Engineering Northwestern University

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"Hard tests failed in fovrg"
by srihari velaga 29 Oct '10

29 Oct '10

Hi all, I am trying to fit Cd kedge EXAFS data of CdO and CdO-CaO solid solution. Like many others I ended with “Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small“error. Professor John, mentioned this may be due to insufficient grid size in calculating the phase shifts and he advised to post the "feff.inp", to have a look at it. But I have 38 feff.inp files in total (corresponding to CdO, solid solutions of CdO-CaO at various compositions and for dopents as well). I feel it will be hard to look into this may files, for any one. I will be thankful if anyone help me, in how to overcome this problem. Here with I am attaching the "feff.inp" of CdO. Please tell me how to modify feff.inp file such that I can do myself for the rest of feff files Thanks in advance. Srihari. V VELAGA.SRIHARI, DAE RESEARCH FELLOW, X-RAY AND CRYSTAL GROWTH SECTION, MATERIAL SCIENCE DIVISION, INDIRA GANDHI CENTRE FOR ATOMIC RESEARCH, KALPAKKAM,TAMILNADU-603102, INDIA.

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Scott Calvin 25 Oct '10

25 Oct '10

Yes; it's a case of trying to distinguish between a few boulders and lots of pebbles; the total volume isn't the issue. What I'm looking at is something like surface/volume ratio, but with "surface" being path-dependent and gradual. For a nearest-neighbor path, only the top monolayer of atoms are on the surface. For a 5 angstrom path, the transition region from "surface" to "core" extends 5 angstroms in. But that more sophisticated definition of "surface" doesn't change the fact that the dominant dependence is 1/R, so that should address the issue. --Scott Calvin Sarah Lawrence College On Oct 25, 2010, at 4:43 AM, Matt Newville wrote: > Hi Scott, > > That's a pretty amazing use case. > > But I'm not sure I understand the issue exactly right. I would have > thought the volume (r**3) was the important physical parameter, and > that a 1000nm particle would dominate the spectra over 3nm particles. > Or is it that you are trying to distinguish between 1 very large > crystal or 100s of smaller crystals? Perhaps the effect you're > really trying to account for is the surface/volume ratio? If so, I > think using Matthew Marcus's suggestion of using 1/r (with a safety > margin) makes the most sense. > > --Matt >

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Re: [Ifeffit] LCF analysis
by Scott Calvin 25 Oct '10

25 Oct '10

On Oct 25, 2010, at 8:25 AM, Wayne W Lukens Jr wrote: > A more useful way to look at this is that the probabilities that A, > B and C are present are 99.99999999%, 93%, and 77%, respectively. An excellent post, Wayne, but I don't think that last statement is quite right. If the F-test gives a probability of 0.23 for material C, I believe it's saying that there is a 23% that, given the noise level in the data, the fit would indicate that C was present when it was not. That is not the same thing as saying there is a 77% chance of C being present. To see this, imagine very, very noisy data. Including C in the fit might very well improve the fit in the sense of an R-factor--maybe, in fact, there's a 45% chance of a modest improvement with a given set of very noisy data, even if there's no C present. That does not mean that a result like that should lead to the conclusion that C is more likely than not present (55%). --Scott Calvin Sarah Lawrence College

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LCF analysis
by Luxton.Todd＠epamail.epa.gov 25 Oct '10

25 Oct '10

I have a general question for the group. How do you conduct your LCF fitting routine? Do most people allow Eo to vary for the standards, or force the weights of all of the combinations to 1? How do people judge a significant improvement to the resulting goodness of fit parameters? I am aware of most of the pitfalls associated with LCF analysis of XAFS data (over fitting data with too many standards, not having information to support the use of a standard in the fit, ect.). What I am really interested in is how people fit and judge the quality of a fit after collecting all of the necessary background information? Or, what is the process/routine people go through during LCF analysis? I have looked at older threads on the IFEFFIT web page, but I was unable to find a description of the general process people follow. Additionally, if anyone is aware of a reference discussing the potential problems and/or solutions to fitting data using LCF that would be great. All the Best Todd

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Asymmetric error bars in IFeffit
by Scott Calvin 25 Oct '10

25 Oct '10

Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber- scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Scott Calvin 25 Oct '10

25 Oct '10

I don't think it's at all strange, Anatoly, and I think Matthew's solution is the right one--it seems obvious in retrospect that the parameter that Ifeffit should evaluate is 1/R, but apparently it wasn't obvious to me on Friday. :) As for obtaining N instead of R, the beauty of both of our algorithms is that they don't depend on finding N; they depend on finding the ratio of N's for different shells. Finding N accurately is notoriously challenging: you need some way of getting S02, you need to have the normalization right, and you're sunk if there are data quality issues like an inhomogeneous sample, uncorrected self-absorption, or significant beam harmonics. But finding the ratio of N for two or more different shells doesn't depend so strongly on any of those things. Since my method implicitly involves multiple ratios of coordination numbers, it is not so clear how to invert it. In any case, I expect Matthew's solution to work, and will pursue it further on Monday. --Scott Calvin Sarah Lawrence College On Oct 24, 2010, at 5:59 PM, Frenkel, Anatoly wrote: > Scott, > It is a strange result. Suppose you fit a bulk metal foil and vary > the 1nn coordination number. You will not get 12 +/- 1000. You will > get about 12 +/- 0.3 depending on the data quality and the k range, > and on the amplitude factor you fix constant. Then, suppose you take > your formula for a particle radius from your JAP article and > propagate this uncertainty to get the radius uncertainty. That would > give you a huge error because you are in the flat region of the N(R) > function and R does bit affect N. > The meaning of your large error bar is, I think, that you are in > such a large limit of sizes that they cannot be inverted to get N > and thus the errors cannot be propagated to find Delta R. > Why don't you try to obtain N instead of R? You will get much > smaller error bars and you can find the lower R limit from your N(R) > equation (by plugging in N - deltaN you will find R - delta R). > > The right limit is infinity as you pointed out. > > Anatoly > > ________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Sent: Fri Oct 22 16:23:08 2010 > Subject: [Ifeffit] Asymmetric error bars in IFeffit > > Hi all, > > I'm puzzling over an issue with my latest analysis, and it seemed > like the sort of thing where this mailing list might have some good > ideas. > > First, a little background on the analysis. It is a simultaneous fit > to four samples, made of various combinations of three phases. > Mossbauer has established which samples include which phases. One of > the phases itself has two crystallographically inequivalent > absorbing sites. The result is that the fit includes 12 Feff > calculations, four data sets, and 1000 paths. Remarkably, everything > works quite well, yielding a satisfying and informative fit. > Depending on the details, the fit takes about 90 minutes to run. > Kudos to Ifeffit and Horae for making such a thing possible! > > Several of the parameters that the fit finds are "characteristic > crystallite radii" for the individual phases. In my published fits, > I often include a factor that accounts for the fact that a phase is > nanoscale in a crude way: it assumes the phase is present as spheres > of uniform radius and applies a suppression factor to the > coordination numbers of the paths as a function of that radius and > of the absorber-scatterer distance. Even though this model is rarely > strictly correct in terms of morphology and size dispersion, it > gives a first-order approximation to the effect of the reduced > coordination numbers found in nanoscale materials. Some people, > notably Anatoly Frenkel, have published models which deal with this > effect much more realistically. But those techniques also require > more fitted variables and work best with fairly well-behaved > samples. I tend to work with "messy" chemical samples of free > nanoparticles where the assumption of sphericity isn't terrible, and > the size dispersion is difficult to model accurately. > > At any rate, the project I'm currently working on includes a fitted > characteristic radius of the type I've described for each of the > phases in each of the samples. And again, it seems to work pretty > well, yielding values that are plausible and largely stable. > > That's the background information. Now for my question: > > The effect of the characteristic radius on the spectrum is a > strongly nonlinear function of that radius. For example, the > difference between the EXAFS spectra of 100 nm and 1000 nm single > crystals due to the coordination number effect is completely > negligible. The difference between 1 nm and 10 nm crystals, however, > is huge. > > So for very small crystallites, IFeffit reports perfectly reasonable > error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat > larger crystallites, however, it tends to report values like 10 +/- > 500 nm. I understand why it does that: it's evaluating how much the > parameter would have to change by to have a given impact on the chi > square of the fit. And it turns out that once you get to about 10 > nm, the size could go arbitrarily higher than that and not change > the spectrum much at all. But it couldn't go that much lower without > affecting the spectrum. So what IFeffit means is something like "the > best fit value is 10 nm, and it is probable that the value is at > least 4 nm." But it's operating under the assumption that the > dependence of chi-square on the parameter is parabolic, so it comes > up with a compromise between a 6 nm error bar on the low side and an > infinitely large error bar on the high side. Compromising with > infinity, however, rarely yields sensible results. > > Thus my question is if anyone can think of a way to extract some > sense of these asymmetric error bars from IFeffit. Here are > possibilities I've considered: > > --Fit something like the log of the characteristic radius, rather > than the radius itself. That creates an asymmetric error bar for the > radius, but the asymmetry the new error bar possesses has no > relationship to the uncertainty it "should" possess. This seems to > me like it's just a way of sweeping the problem under the rug and is > potentially misleading. > > --Rerun the fits setting the variable in question to different > values to probe how far up or down it can go and have the same > effect on the fit. But since I've got nine of these factors, and > each fit takes more than an hour, the computer time required seems > prohibitive! > > --Somehow parameterize the guessed variable so that it does tend to > have symmetric error bars, and then calculate the characteristic > radius and its error bars from that. But it's not at all clear what > that parameterization would be. > > --Ask the IFeffit mailing list for ideas! > > Thanks! > > --Scott Calvin > Sarah Lawrence College > <ATT00001..txt>

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Frenkel, Anatoly 25 Oct '10

25 Oct '10

Scott, It is a strange result. Suppose you fit a bulk metal foil and vary the 1nn coordination number. You will not get 12 +/- 1000. You will get about 12 +/- 0.3 depending on the data quality and the k range, and on the amplitude factor you fix constant. Then, suppose you take your formula for a particle radius from your JAP article and propagate this uncertainty to get the radius uncertainty. That would give you a huge error because you are in the flat region of the N(R) function and R does bit affect N. The meaning of your large error bar is, I think, that you are in such a large limit of sizes that they cannot be inverted to get N and thus the errors cannot be propagated to find Delta R. Why don't you try to obtain N instead of R? You will get much smaller error bars and you can find the lower R limit from your N(R) equation (by plugging in N - deltaN you will find R - delta R). The right limit is infinity as you pointed out. Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Frenkel, Anatoly 23 Oct '10

23 Oct '10

Matthew, if you relied on FEFF as one part of the complex calculation, where the other part was the experimentally extracted one, you could've as well done everything with just FEFF. Why didn't you? A. ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 18:01:17 2010 Subject: Re: [Ifeffit] Asymmetric error bars in IFeffit Another reason, from my point of view, is that FEFF wasn't accurate enough to use on its own without references. Also, it still can be argued that the process of data reduction and filtering produces distortions which aren't captured by using FEFF alone. Further, if one is comparing very similar systems, e.g. bulk and nano of the same stuff, then with the exception of multiple scattering, the one system should be an ideal reference for the other. A trick I used to do: Suppose, for instance, that I wanted to fit a shell of Zn surrounded by Si (not an actual case). There's no Si-rich zinc silicide to use as a reference, but it's not too hard to make theta-CuAl2, a compound in which all Cu atoms are surrounded by Al in the first shell (this was done). From this, amp and phase functions could be extracted which refer to Cu looking at Al (Cu->Al). Next, to transform this into the desired Zn->Si, I would do FEFF calculations on identical structures with the atoms changed around and take: A(Zn->Si, semi-empirical) = A(Cu->Al, expt)*[A(Zn->Si, FEFF)/A(Cu->Al, FEFF)] phi(Zn->Si, semi-empirical) = phi(Cu->Al, expt)+[Phi(Zn->Si, FEFF)-phi(Cu->Al, FEFF)] with A, phi being amplitude and phase for a given shell, and appropriate account being taken of the distance differences involved. This makes sense if you consider A~ = A*exp(i*phi) to be one of the factors in a complex chi~ such that chi = Im(chi~), and you're essentially making a correction to ln(A~). Yes, this was low-rent and subject to errors, but it seemed to make sense provided one didn't try to take it too far, for instance trying to change Al for Au or an oxide for a metal. Brings back memories, not all of them fond :-) mam ----- Original Message ----- From: Frenkel, Anatoly <mailto:frenkel@bnl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov Sent: Friday, October 22, 2010 2:38 PM Subject: Re: [Ifeffit] Asymmetric error bars in IFeffit On a related subject, now I understand why we use the concept of chemical transferability of amplitudes and phases by recycling the same FEFF path for different systems. The true reason is historic: back then it took one hour for one FEFF calculation.... Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Asymmetric error bars in IFeffit
by Frenkel, Anatoly 22 Oct '10

22 Oct '10

On a related subject, now I understand why we use the concept of chemical transferability of amplitudes and phases by recycling the same FEFF path for different systems. The true reason is historic: back then it took one hour for one FEFF calculation.... Anatoly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Oct 22 16:23:08 2010 Subject: [Ifeffit] Asymmetric error bars in IFeffit Hi all, I'm puzzling over an issue with my latest analysis, and it seemed like the sort of thing where this mailing list might have some good ideas. First, a little background on the analysis. It is a simultaneous fit to four samples, made of various combinations of three phases. Mossbauer has established which samples include which phases. One of the phases itself has two crystallographically inequivalent absorbing sites. The result is that the fit includes 12 Feff calculations, four data sets, and 1000 paths. Remarkably, everything works quite well, yielding a satisfying and informative fit. Depending on the details, the fit takes about 90 minutes to run. Kudos to Ifeffit and Horae for making such a thing possible! Several of the parameters that the fit finds are "characteristic crystallite radii" for the individual phases. In my published fits, I often include a factor that accounts for the fact that a phase is nanoscale in a crude way: it assumes the phase is present as spheres of uniform radius and applies a suppression factor to the coordination numbers of the paths as a function of that radius and of the absorber-scatterer distance. Even though this model is rarely strictly correct in terms of morphology and size dispersion, it gives a first-order approximation to the effect of the reduced coordination numbers found in nanoscale materials. Some people, notably Anatoly Frenkel, have published models which deal with this effect much more realistically. But those techniques also require more fitted variables and work best with fairly well-behaved samples. I tend to work with "messy" chemical samples of free nanoparticles where the assumption of sphericity isn't terrible, and the size dispersion is difficult to model accurately. At any rate, the project I'm currently working on includes a fitted characteristic radius of the type I've described for each of the phases in each of the samples. And again, it seems to work pretty well, yielding values that are plausible and largely stable. That's the background information. Now for my question: The effect of the characteristic radius on the spectrum is a strongly nonlinear function of that radius. For example, the difference between the EXAFS spectra of 100 nm and 1000 nm single crystals due to the coordination number effect is completely negligible. The difference between 1 nm and 10 nm crystals, however, is huge. So for very small crystallites, IFeffit reports perfectly reasonable error bars: the radius is 0.7 +/- 0.3 nm, for instance. For somewhat larger crystallites, however, it tends to report values like 10 +/- 500 nm. I understand why it does that: it's evaluating how much the parameter would have to change by to have a given impact on the chi square of the fit. And it turns out that once you get to about 10 nm, the size could go arbitrarily higher than that and not change the spectrum much at all. But it couldn't go that much lower without affecting the spectrum. So what IFeffit means is something like "the best fit value is 10 nm, and it is probable that the value is at least 4 nm." But it's operating under the assumption that the dependence of chi-square on the parameter is parabolic, so it comes up with a compromise between a 6 nm error bar on the low side and an infinitely large error bar on the high side. Compromising with infinity, however, rarely yields sensible results. Thus my question is if anyone can think of a way to extract some sense of these asymmetric error bars from IFeffit. Here are possibilities I've considered: --Fit something like the log of the characteristic radius, rather than the radius itself. That creates an asymmetric error bar for the radius, but the asymmetry the new error bar possesses has no relationship to the uncertainty it "should" possess. This seems to me like it's just a way of sweeping the problem under the rug and is potentially misleading. --Rerun the fits setting the variable in question to different values to probe how far up or down it can go and have the same effect on the fit. But since I've got nine of these factors, and each fit takes more than an hour, the computer time required seems prohibitive! --Somehow parameterize the guessed variable so that it does tend to have symmetric error bars, and then calculate the characteristic radius and its error bars from that. But it's not at all clear what that parameterization would be. --Ask the IFeffit mailing list for ideas! Thanks! --Scott Calvin Sarah Lawrence College

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Zn foil data
by Jonathan L Keating 21 Oct '10

21 Oct '10

Dear All Firstly, lots of thanks to the contributors of the mailing list for providing such a great platform to discuss and help with exafs analysis. I have a request and wonder if anybody may have some Zn XAS foil data with data extending beyond 13 inverse Angstroms in k-space? Many Thanks Jon

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Re: [Ifeffit] calibration/aligment...2 (Scott Calvin)
by ornella smila castro 15 Oct '10

15 Oct '10

Dear Scott, this is exactly why I was confused about alignment, since I want to see that shift!! Thank you so much for your precious help. it is very clear now.. With best wishes, Ornella > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 92, Issue 13 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Thu, 14 Oct 2010 17:54:36 -0500 > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: calibration/aligment...2 (Scott Calvin) > 2. Re: MPSE (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 14 Oct 2010 11:37:43 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] calibration/aligment...2 > Message-ID: <04C38483-D6F6-4F2D-B206-AFFB25B30429(a)gmail.edu> > Content-Type: text/plain; charset="us-ascii"; Format="flowed"; > DelSp="yes" > > Thanks, Ornella, that clarifies what you're doing. > > My recommendation is to look closely at the 6 reference spectra and > see if there appears to be a systematic energy shift between them. For > example, each spectrum might be shifted by about 0.3 eV from the > spectrum before it. Or the first two spectra might appear aligned, but > then the third through sixth are shifted by 1.5 eV. In either of those > cases, you should align them. In my second example, I might throw out > the second spectrum as an additional precaution (if the shift occurred > "all at once," it might have occurred during the scan before which it > appears). In either case, it doesn't really matter which scan you > choose to align to (and calibrate, if you have a way of doing that). > > If, on the other hand, the 6 reference spectra appear to basically > overplot except for random noise, I would not try to align them further. > > I would treat the 6 spectra for the electrolysed solution similarly-- > align them to each other if there is a systematic energy shift. > > What you should not do, in my opinion, is to align the electrolysed > scans to the reference scans. You actually expect there to be a > chemical shift between the two sets of data, and aligning one to the > other would remove that! > > --Scott Calvin > Sarah Lawrence College > > On Oct 14, 2010, at 11:00 AM, ornella smila castro wrote: > > > Hi Matt and Scott, > > > > First, thank you so much for replying to my questions. > > I realised that I should have been a bit more accurate on the type > > of experiments I am doing. > > To start with, I am doing electrochemistry combined with EXAFS. I am > > using an integrated electrolysis/EXAFS cell. Our experiments are as > > follow: in the case of this experiment in particular, we have a > > solution of ruthenium-based compound that we flow through a channel > > through which the beam passes and that we call "reference". we > > record let's say 6 spectra in a row (we use a flow in order to avoid > > beam damage on our sample).we didn't do any reference spectra (if > > you mean running a scan of a Ru foil before starting the actual > > experiment). then, we make up a new solution but this time we > > electrolysed the solution (by applying a potential) in order to get > > the cationic produced species. (the obtained spectra will therefore > > be a mixture of the neutral and the cationic species). and we record > > as well a set of 6 spectra. > > Here is what I did and what I was wondering if it was the right > > thing to do: I have considered the first spectra of the first set of > > scans as the reference for calibration/alignment. is it ok? > > Thus, I am wondering if when I process the second set of data > > (electrolysed solution), which spectra I should take as a starting > > point for calibrating/aligning my second series of scans: the one I > > used for the first serie or the first of the second set of scans? > > > > I hope this is clear... > > > > Thanks again for your help, > > Ornella > >

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Re: [Ifeffit] MPSE
by Joshua Kas 14 Oct '10

14 Oct '10

Hi Mehmet, The documentation in feff9 for MPSE is (obviously) not very good. What you will need, to start, is a calculation of the bulk loss function L(E) = -Im[1/epsilon(E)] for your material. I can discuss the details with you over email if you like. Cheers, Josh Kas joshua.j.kas(a)gmail.com > Dear all, > > > > i want to run FEFF with the many pole self energy MPSE. In the > documentation > to FEFF9 is written that I have to use the formula detailed in > 'EpsInvFormula.ps' to calculate the optical constants. > > Where can I get this file? > > > > Many thanks > > > > Mehmet from University Duisburg-Essen in Germany > > > >

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Re: [Ifeffit] calibration/aligment...2
by Scott Calvin 14 Oct '10

14 Oct '10

Thanks, Ornella, that clarifies what you're doing. My recommendation is to look closely at the 6 reference spectra and see if there appears to be a systematic energy shift between them. For example, each spectrum might be shifted by about 0.3 eV from the spectrum before it. Or the first two spectra might appear aligned, but then the third through sixth are shifted by 1.5 eV. In either of those cases, you should align them. In my second example, I might throw out the second spectrum as an additional precaution (if the shift occurred "all at once," it might have occurred during the scan before which it appears). In either case, it doesn't really matter which scan you choose to align to (and calibrate, if you have a way of doing that). If, on the other hand, the 6 reference spectra appear to basically overplot except for random noise, I would not try to align them further. I would treat the 6 spectra for the electrolysed solution similarly-- align them to each other if there is a systematic energy shift. What you should not do, in my opinion, is to align the electrolysed scans to the reference scans. You actually expect there to be a chemical shift between the two sets of data, and aligning one to the other would remove that! --Scott Calvin Sarah Lawrence College On Oct 14, 2010, at 11:00 AM, ornella smila castro wrote: > Hi Matt and Scott, > > First, thank you so much for replying to my questions. > I realised that I should have been a bit more accurate on the type > of experiments I am doing. > To start with, I am doing electrochemistry combined with EXAFS. I am > using an integrated electrolysis/EXAFS cell. Our experiments are as > follow: in the case of this experiment in particular, we have a > solution of ruthenium-based compound that we flow through a channel > through which the beam passes and that we call "reference". we > record let's say 6 spectra in a row (we use a flow in order to avoid > beam damage on our sample).we didn't do any reference spectra (if > you mean running a scan of a Ru foil before starting the actual > experiment). then, we make up a new solution but this time we > electrolysed the solution (by applying a potential) in order to get > the cationic produced species. (the obtained spectra will therefore > be a mixture of the neutral and the cationic species). and we record > as well a set of 6 spectra. > Here is what I did and what I was wondering if it was the right > thing to do: I have considered the first spectra of the first set of > scans as the reference for calibration/alignment. is it ok? > Thus, I am wondering if when I process the second set of data > (electrolysed solution), which spectra I should take as a starting > point for calibrating/aligning my second series of scans: the one I > used for the first serie or the first of the second set of scans? > > I hope this is clear... > > Thanks again for your help, > Ornella

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Re: [Ifeffit] calibration/aligment...2
by ornella smila castro 14 Oct '10

14 Oct '10

Hi Matt and Scott, First, thank you so much for replying to my questions. I realised that I should have been a bit more accurate on the type of experiments I am doing. To start with, I am doing electrochemistry combined with EXAFS. I am using an integrated electrolysis/EXAFS cell. Our experiments are as follow: in the case of this experiment in particular, we have a solution of ruthenium-based compound that we flow through a channel through which the beam passes and that we call "reference". we record let's say 6 spectra in a row (we use a flow in order to avoid beam damage on our sample).we didn't do any reference spectra (if you mean running a scan of a Ru foil before starting the actual experiment). then, we make up a new solution but this time we electrolysed the solution (by applying a potential) in order to get the cationic produced species. (the obtained spectra will therefore be a mixture of the neutral and the cationic species). and we record as well a set of 6 spectra. Here is what I did and what I was wondering if it was the right thing to do: I have considered the first spectra of the first set of scans as the reference for calibration/alignment. is it ok? Thus, I am wondering if when I process the second set of data (electrolysed solution), which spectra I should take as a starting point for calibrating/aligning my second series of scans: the one I used for the first serie or the first of the second set of scans? I hope this is clear... Thanks again for your help, Ornella > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 92, Issue 11 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Thu, 14 Oct 2010 12:00:01 -0500 > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. MPSE (Mehmet Kaya) > 2. calibration/alignment (ornella smila castro) > 3. Re: calibration/alignment (Scott Calvin) > 4. Re: calibration/alignment (Matt Newville) > 5. Re: calibration/alignment (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Oct 2010 12:23:06 +0200 > From: "Mehmet Kaya" <mehmet.kaya(a)uni-due.de> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] MPSE > Message-ID: <000401cb6ac0$a110d0d0$e3327270$@kaya@uni-due.de> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > > > i want to run FEFF with the many pole self energy MPSE. In the documentation > to FEFF9 is written that I have to use the formula detailed in > 'EpsInvFormula.ps' to calculate the optical constants. > > Where can I get this file? > > > > Many thanks > > > > Mehmet from University Duisburg-Essen in Germany > > > >

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Re: [Ifeffit] calibration/alignment
by Scott Calvin 14 Oct '10

14 Oct '10

On Oct 14, 2010, at 7:39 AM, Matt Newville wrote: > If you're just getting started, I would say to not worry about energy > alignment until it becomes an obvious problem. A cautionary tale (with details made up, since I don't remember them!) from when I was just starting out as to what constitutes an "obvious problem": I collected five transmission EXAFS scans on the same sample. The scans were on top of each other when I looked at the graph, so I merged them...and proceeded to get somewhat screwy fits. The problem? I only looked at the graph across the whole spectra--say, 1500 eV. It turns out there was about a 0.7 eV shift between each scan and the next one, for a total of roughly 3 eV . That was small enough so as to be invisible when looked at on that scale. When I looked at just the XANES, though, the shift did become "obvious." I aligned the spectra and merged them, and suddenly the problems in the fit went away! Since then, I've seen the same thing happen with students to whom I am teaching the technique. On the other hand, there's no magic "blessing" given by the process of alignment. Suppose I have ten scans of very noisy data, and no reference. If I used the auto-align procedure in Athena, it sometimes shifts a scan 0.3 eV one way, sometimes 0.2 eV the other way, with no apparent rhyme or reason. Looking at the graphs, even zoomed in, just shows a bunch of noisy data roughly on top of each other. In that case, there's no reason to believe there are actual shifts between scans, and I would NOT align them prior to merging. Finally, beamline scientists usually have a very good idea whether their line is prone to drifts. Ask them! --Scott Calvin Sarah Lawrence College

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calibration/alignment
by ornella smila castro 14 Oct '10

14 Oct '10

Hi everyone, I am trying to do some data processing with Athena but I am already stuck at the first step. The thing is: I read the worked example section of the "Athena's user guide" and on the example on the iron foil, it is mentioned to calibrate the data at the right energy (until here evrything is fine) but then it is said to align the data. Can anyone explain to me what does "alignment" exactly means, and what is the aim of "aligning the data". The data that I have collected were through a channel through which a solution flow (~200 microliters/hr) so I am not convinced that alignment makes sense. Many thanks, Ornel

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Re: [Ifeffit] calibration/alignment
by Scott Calvin 14 Oct '10

14 Oct '10

Hi Ornel, Alignment is used to compensate for monochromators that do not maintain stable energy calibration between scans. In conventional measurements, you'll generally have several scans that are supposed to be of the same sample under identical conditions, and those scans may need to be aligned with each other. That is not the case for a time series, which is what I think you are saying you have. So in a time series, how do you compensate for any energy drift of the monochromator? If you are recording a simultaneous reference spectrum, you can align the reference spectra to each other. (Athena automatically will shift the sample spectra by the same amount that the reference spectra are shifted.) If you have a time series but don't have a simultaneous reference spectra, it becomes tougher. If you collected a reference spectrum before and after the time series, you could try to interpolate any shift that's seen, although that's dicey; shifts sometimes occur in jumps. But if there's no shift, you're probably OK! If you have a time series and no reference at all, or a reference only before the series, you're out of luck. You're relying then on the assumption of energy stability, which on some beamlines might be OK...but it is best to confirm that by at least measuring a reference before and after. --Scott Calvin Sarah Lawrence College On Oct 14, 2010, at 2:46 AM, ornella smila castro wrote: > Hi everyone, > > I am trying to do some data processing with Athena but I am already > stuck at the first step. The thing is: I read the worked example > section of the "Athena's user guide" and on the example on the iron > foil, it is mentioned to calibrate the data at the right energy > (until here evrything is fine) but then it is said to align the > data. Can anyone explain to me what does "alignment" exactly means, > and what is the aim of "aligning the data". The data that I have > collected were through a channel through which a solution flow (~200 > microliters/hr) so I am not convinced that alignment makes sense. > > Many thanks, > Ornel > <ATT00001..txt>

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MPSE
by Mehmet Kaya 13 Oct '10

13 Oct '10

Dear all, i want to run FEFF with the many pole self energy MPSE. In the documentation to FEFF9 is written that I have to use the formula detailed in 'EpsInvFormula.ps' to calculate the optical constants. Where can I get this file? Many thanks Mehmet from University Duisburg-Essen in Germany

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 12 Oct '10

12 Oct '10

Hi Matt, Thank you very much. I have gone through the chapter in your Tutorial and things are more convincing now. With best regards, Jatin Rana HZB Berlin On 09.10.2010 19:00, 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. Re: schemes for delr and sigma2 for multiple scattering paths > (Matt Newville) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Jatinkumar Rana) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 8 Oct 2010 13:13:23 -0500 > From: Matt Newville<newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID: > <AANLkTimBJbC9EqyUs31kiHuU9F+fHSVv+ib5oXBKq5Kb(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Jatin, > > I tried to answer both of these question in chapter 3 of > http://xafs.org/Tutorials?action=AttachFile&do=view&target=Newville_xas_fun… > > Does the explanation there help? If not, do you have any suggestions > for making it clearer? > > The basic physics is that an absorbed x-ray creates a photo-electron > which will scatter from its neighbors. A portion of the scattered > portion (so, a small amount) of that photo-electron will return to the > absorbing atom. But Pauli's exclusion principle tells us that if an > electron is at the absorbing atom, and has the same energy (and other > quantum numbers) as the outgoing photo-electron, the outgoing > photo-electron cannot be created in the first place. Thus, the > scattering of the photo-electron from the neighbors affects whether > the photo-electron can be created, and so whether the x-ray will be > absorbed. > > The effect can be either destructive or constructive, as with nearly > any wave-like phenomenon. It does seem a bit circular that the > photo-electron scattering affects the existence of the photo-electron, > but quantum mechanics leads to many much stranger behaviors. > > --Matt > > > ------------------------------ > > Message: 2 > Date: Sat, 09 Oct 2010 09:41:12 +0200 > From: Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID:<4CB01C98.4020103(a)helmholtz-berlin.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hello Chris, Bruce, > > Thank you so very much for your detailed explanations. > > With best regards, > Jatin Rana > HZB Berlin > > > > > > On 08.10.2010 19:00, 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. Re: schemes for delr and sigma2 for multiple scattering paths >> (Chris Patridge) >> 2. Re: schemes for delr and sigma2 for multiple scattering paths >> (Bruce Ravel) >> 3. Re: schemes for delr and sigma2 for multiple scattering paths >> (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 8 Oct 2010 10:09:34 -0400 >> From: Chris Patridge<patridge(a)buffalo.edu> >> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple >> scattering paths >> Message-ID:<68FC92BB-B842-48F2-8596-7675D168EB16(a)buffalo.edu> >> Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes >> >> Hello Jatin, >> >> I don't confess expertise but i think the absorption coeff. relates to >> the overlap between the initial and final wavefunction. Therefore the >> interference between outgoing and backscattering modulates the final >> wavefunction which manifests as the exafs fluctuations past the edge >> which in turn changes the It signal so we can use the difference >> between Io and It to measure exafs data. Any additional comments are >> welcomed if I am mistaken as I said I am not an expert. >> >> Buena salud, >> >> Chris Patridge >> >> >> On Oct 8, 2010, at 9:30 AM, Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de >> > wrote: >> >> >> >>> Hi Scott, >>> >>> Nice to see you back-in-action from holidays. Thank you very much >>> for your suggestions. >>> >>> Since last few days i was trying to visualize the physical process >>> going on inside an absorbing atom when we measure EXAFS, i met few >>> really basic questions, which of course, could be due to lack of my >>> understandings. Therefore, I tried to go through literatures and >>> EXAFS books but i am not satisfied. >>> >>> Therefore, i decided to put them to mailing list >>> >>> My first question is : >>> >>> In EXAFS, the oscillations are due to the intereference between the >>> outgoing photo electron from absorbing atom and incoming >>> backscattered photoelectron from the scatterer. Depending upon, how >>> much they are out of phase w.r.t each other we get oscillations in >>> EXAFS curve. These oscillations are nothing but the variation in the >>> absobtion coefficient of sample as the energy of incident photon is >>> varied. >>> >>> I wonder, how, the intereference between the photo electrons is >>> related to absorbtion coefficient of sample ?? >>> >>> because, It = I0 * exp (-ut) >>> >>> My second question is : >>> >>> While measuring EXAFS at beamline, we only measure the intial >>> intensity (Io) and the transmitted intenstiy from sample (It). In >>> other words, we only measure the number of photons before and after >>> the sample and variation in abs.coeffi.(u) is related to variation >>> in It. >>> >>> How interference between photoelectrons will be reflected as >>> variation in abs.coeffi. (u) of sample while we never measure photo >>> electrons in EXAFS?? >>> >>> We only measure Io and It. >>> >>> Also, whether the intereference between photo electrons is >>> constructive or destructive, the incident photon will lose its >>> energy once it knocks an electron from say K-shell of absorbing atom >>> and hence photon is said to have absorbed. >>> >>> I will be really thankful to you for your valuable explanation. >>> >>> With Best regards, >>> Jatin Rana >>> HZB, Berlin >>> >>> >>> >>> >>> >>> On 07.10.2010 19:00, 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. Re: Multiple scattering paths in fitting (Frenkel, Anatoly) >>>> 2. Re: schemes for delr and sigma2 for multiple scattering >>>> paths >>>> (Scott Calvin) >>>> >>>> >>>> --- >>>> ------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Thu, 7 Oct 2010 09:38:26 -0400 >>>> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >>>> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >>>> Subject: Re: [Ifeffit] Multiple scattering paths in fitting >>>> Message-ID: >>>> <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> For relationships between sigma2 for MS and SS paths, some are >>>> listed in the Appendix to this article: >>>> >>>> P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). >>>> >>>> Anatoly >>>> >>>> >>>> >>>>

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 09 Oct '10

09 Oct '10

Hello Chris, Bruce, Thank you so very much for your detailed explanations. With best regards, Jatin Rana HZB Berlin On 08.10.2010 19:00, 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. Re: schemes for delr and sigma2 for multiple scattering paths > (Chris Patridge) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Bruce Ravel) > 3. Re: schemes for delr and sigma2 for multiple scattering paths > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 8 Oct 2010 10:09:34 -0400 > From: Chris Patridge<patridge(a)buffalo.edu> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] schemes for delr and sigma2 for multiple > scattering paths > Message-ID:<68FC92BB-B842-48F2-8596-7675D168EB16(a)buffalo.edu> > Content-Type: text/plain; charset=us-ascii; format=flowed; delsp=yes > > Hello Jatin, > > I don't confess expertise but i think the absorption coeff. relates to > the overlap between the initial and final wavefunction. Therefore the > interference between outgoing and backscattering modulates the final > wavefunction which manifests as the exafs fluctuations past the edge > which in turn changes the It signal so we can use the difference > between Io and It to measure exafs data. Any additional comments are > welcomed if I am mistaken as I said I am not an expert. > > Buena salud, > > Chris Patridge > > > On Oct 8, 2010, at 9:30 AM, Jatinkumar Rana<jatinkumar.rana(a)helmholtz-berlin.de > > wrote: > > >> Hi Scott, >> >> Nice to see you back-in-action from holidays. Thank you very much >> for your suggestions. >> >> Since last few days i was trying to visualize the physical process >> going on inside an absorbing atom when we measure EXAFS, i met few >> really basic questions, which of course, could be due to lack of my >> understandings. Therefore, I tried to go through literatures and >> EXAFS books but i am not satisfied. >> >> Therefore, i decided to put them to mailing list >> >> My first question is : >> >> In EXAFS, the oscillations are due to the intereference between the >> outgoing photo electron from absorbing atom and incoming >> backscattered photoelectron from the scatterer. Depending upon, how >> much they are out of phase w.r.t each other we get oscillations in >> EXAFS curve. These oscillations are nothing but the variation in the >> absobtion coefficient of sample as the energy of incident photon is >> varied. >> >> I wonder, how, the intereference between the photo electrons is >> related to absorbtion coefficient of sample ?? >> >> because, It = I0 * exp (-ut) >> >> My second question is : >> >> While measuring EXAFS at beamline, we only measure the intial >> intensity (Io) and the transmitted intenstiy from sample (It). In >> other words, we only measure the number of photons before and after >> the sample and variation in abs.coeffi.(u) is related to variation >> in It. >> >> How interference between photoelectrons will be reflected as >> variation in abs.coeffi. (u) of sample while we never measure photo >> electrons in EXAFS?? >> >> We only measure Io and It. >> >> Also, whether the intereference between photo electrons is >> constructive or destructive, the incident photon will lose its >> energy once it knocks an electron from say K-shell of absorbing atom >> and hence photon is said to have absorbed. >> >> I will be really thankful to you for your valuable explanation. >> >> With Best regards, >> Jatin Rana >> HZB, Berlin >> >> >> >> >> >> On 07.10.2010 19:00, 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. Re: Multiple scattering paths in fitting (Frenkel, Anatoly) >>> 2. Re: schemes for delr and sigma2 for multiple scattering >>> paths >>> (Scott Calvin) >>> >>> >>> --- >>> ------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Thu, 7 Oct 2010 09:38:26 -0400 >>> From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> >>> To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] Multiple scattering paths in fitting >>> Message-ID: >>> <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> For relationships between sigma2 for MS and SS paths, some are >>> listed in the Appendix to this article: >>> >>> P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). >>> >>> Anatoly >>> >>> >>> >>>

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 08 Oct '10

08 Oct '10

Hi Scott, Nice to see you back-in-action from holidays. Thank you very much for your suggestions. Since last few days i was trying to visualize the physical process going on inside an absorbing atom when we measure EXAFS, i met few really basic questions, which of course, could be due to lack of my understandings. Therefore, I tried to go through literatures and EXAFS books but i am not satisfied. Therefore, i decided to put them to mailing list My first question is : In EXAFS, the oscillations are due to the intereference between the outgoing photo electron from absorbing atom and incoming backscattered photoelectron from the scatterer. Depending upon, how much they are out of phase w.r.t each other we get oscillations in EXAFS curve. These oscillations are nothing but the variation in the absobtion coefficient of sample as the energy of incident photon is varied. I wonder, how, the intereference between the photo electrons is related to absorbtion coefficient of sample ?? because, It = I0 * exp (-ut) My second question is : While measuring EXAFS at beamline, we only measure the intial intensity (Io) and the transmitted intenstiy from sample (It). In other words, we only measure the number of photons before and after the sample and variation in abs.coeffi.(u) is related to variation in It. How interference between photoelectrons will be reflected as variation in abs.coeffi. (u) of sample while we never measure photo electrons in EXAFS?? We only measure Io and It. Also, whether the intereference between photo electrons is constructive or destructive, the incident photon will lose its energy once it knocks an electron from say K-shell of absorbing atom and hence photon is said to have absorbed. I will be really thankful to you for your valuable explanation. With Best regards, Jatin Rana HZB, Berlin On 07.10.2010 19:00, 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. Re: Multiple scattering paths in fitting (Frenkel, Anatoly) > 2. Re: schemes for delr and sigma2 for multiple scattering paths > (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 7 Oct 2010 09:38:26 -0400 > From: "Frenkel, Anatoly"<frenkel(a)bnl.gov> > To: "XAFS Analysis using Ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Multiple scattering paths in fitting > Message-ID: > <CCBF39F82283424BBB90EA208CD9DE80014175C7(a)exchangemb5.bnl.gov> > Content-Type: text/plain; charset="iso-8859-1" > > For relationships between sigma2 for MS and SS paths, some are listed in the Appendix to this article: > > P. Shanthakumar, et al, Physical Review B 74, 174103 (2006). > > Anatoly > > > >

4 4

Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
by Scott Calvin 07 Oct '10

07 Oct '10

Not at all unusual, Han Sen. If you think about the EXAFS equation, you'll see that sigma^2 and amplitude primarily affect the amplitude of the signal, while distances affect the position of the peak in the Fourier transform (or equivalently, the spacing of peaks in chi(k)). So sigma^2 and amplitude can trade off without affecting distance- based aspects of the fit much. That's why I suggested you try forcing the sigma^2 to a "reasonable" value to see what happened to your fit. Sometimes none of the aspects of the fit you're interested in depend strongly on the sigma^2 of low- amplitude paths--particularly if what you're interest in is distances or information that is in part derived from distances, like phase identification. In those cases, the anomalous sigma^2 can be a "yellow flag" (think about what might be causing it and decide if it's a problem to your scientific case) rather than a "red flag" (drop everything and resolve the problem before proceeding). Also, note from the EXAFS equation that sigma^2 is weighted by k^2, and amplitude is not. If fits using different k-weights result in significantly different values of sigma^2, that can be a clue that the issue is actually one of amplitude, as in your case. At any rate, I'm glad you solved your issue in such a satisfying way! --Scott Calvin Sarah Lawrence College On Oct 7, 2010, at 11:22 AM, Han Sen Soo wrote: > Hello Shelly and Scott, > Thank you both again for your suggestions. It seems that after > making the MS path more linear in my cif file, the FEFF calculation > increased the amplitude value of the path and dramatically > increased the sigma^2 value in the fit. Strangely, the fit values > for the distances remain pretty much the same and the statistical > figures of merit have improved, but the sigma^2 values are now much > more reasonable (about twice as large, but I have a more triangular > than linear model, so you're right Scott, your explanation does not > work for my case). I guess the increased amplitude made a difference? > > Hello Abhijeet, I used a rudimentary geometrical way to get my bond > angles. For a 3 atom triangle M-O-A, the effective MS path length > (R_MOA) is twice the sum of the individual bond distances. So if you > have the R_MOA, R_MO, and R_MA distances from your fits, you can use > R_MOA - R_MO - R_MA to get the O-A bond length. And with the 3 sides > of the triangle, you can use the geometrical Cosine Rule to get any > of the 3 bond angles. This is just geometry so I don't know what the > error propagation for this would be. > > Thanks again everyone! > han sen

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin/Shelly Kelly/Abhijeet Gaur); Re: Ifeffit Digest, Vol 92, Issue 5
by Han Sen Soo 07 Oct '10

07 Oct '10

Hello Shelly and Scott, Thank you both again for your suggestions. It seems that after making the MS path more linear in my cif file, the FEFF calculation increased the amplitude value of the path and dramatically increased the sigma^2 value in the fit. Strangely, the fit values for the distances remain pretty much the same and the statistical figures of merit have improved, but the sigma^2 values are now much more reasonable (about twice as large, but I have a more triangular than linear model, so you're right Scott, your explanation does not work for my case). I guess the increased amplitude made a difference? Hello Abhijeet, I used a rudimentary geometrical way to get my bond angles. For a 3 atom triangle M-O-A, the effective MS path length (R_MOA) is twice the sum of the individual bond distances. So if you have the R_MOA, R_MO, and R_MA distances from your fits, you can use R_MOA - R_MO - R_MA to get the O-A bond length. And with the 3 sides of the triangle, you can use the geometrical Cosine Rule to get any of the 3 bond angles. This is just geometry so I don't know what the error propagation for this would be. Thanks again everyone! han sen On Oct 7, 2010, at 6:36 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. Re: More than 256 paths on Mac OS 10.5? (Scott Calvin) > 2. Re: sigma^2 values for multiple scattering paths (Scott > Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Han Sen Soo) > 3. Re: sigma^2 values for multiple scattering paths (Scott > Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 (Scott Calvin) > 4. Multiple scattering paths in fitting (Abhijeet Gaur) > 5. schemes for delr and sigma2 for multiple scattering paths > (Jatinkumar Rana) > 6. Re: Multiple scattering paths in fitting (Frenkel, Anatoly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 6 Oct 2010 10:01:27 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] More than 256 paths on Mac OS 10.5? > Message-ID: <6DD333D2-F58C-4E55-AB0D-430483EF97F4(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Thanks, Matt! > > --Scott Calvin > Sarah Lawrence College > > On Oct 6, 2010, at 9:08 AM, Matt Newville wrote: > >> Hi Scott, >> >> >> The attached zip file has dynamic libraries (and static program >> ifeffit) built with 1024 paths and feff files. It contains the files >> >> lib/libifeffit.dylib >> lib/libifeffit.so >> bin/ifeffit >> >> The zip file should be unzipped under >> /Applications/iXAFS.app/Contents/Resources/local/ >> to overwrite the above files. You should be able to open the iXAFS >> Shell and type >> >> cd /Applications/iXAFS.app/Contents/Resources/local/ >> unzip ~/Downloads/iXAFS_1024paths.zip >> athena >> >> >> Athena and Artemis will automatically use the new dynamic library. >> > > > > ------------------------------ > > Message: 2 > Date: Wed, 6 Oct 2010 10:36:25 -0700 > From: Han Sen Soo <hssoo(a)lbl.gov> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths > (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 > Message-ID: <BC995EC7-578E-4256-9D62-DE5E73831893(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hello Scott, > Just to make sure I understand what you mean, are you saying that in your 3 atom system, the S1 and S2 atoms have relatively fixed locations but A may have large vibrational amplitudes in the A-S1 and A-S2 directions? So the round-trip 3 atom MS path has a small sigma^2 value since the variation in the A-S1-S2-A path is dictated by the more or less fixed S1 and S2 end-points (with minimal perpendicular contribution), whereas the 2 individual SS paths have large sigma^2 value due to the large A-S vibrations? > > I tried setting the sigma^2 value to a reasonable number for the MS path and it appears to increase the R factor slightly and tries to maximize the floating degeneracy I set (with a restrain to be physically reasonable based on my model). It does not look as good but at least it seems more plausible. I will try out Shelly's suggestions to see if they work too. I guess what I wanted to find out is whether the model I included is telling me that something is terribly wrong. > > Thank you all again for your responses! > han sen > > On Oct 6, 2010, at 10:00 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. Re: sigma^2 values for multiple scattering paths (Scott Calvin) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 6 Oct 2010 09:39:49 -0700 >> From: Scott Calvin <dr.scott.calvin(a)gmail.com> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Cc: "Dr.Scott.Calvin(a)gmail.com" <Dr.Scott.Calvin(a)gmail.com> >> Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths >> Message-ID: <AB39966C-893D-4947-BED2-A26FC6534315(a)gmail.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Although I agree with the main points that Bruce makes, I do want to >> comment on one piece: >> >> On Oct 6, 2010, at 7:03 AM, Bruce Ravel wrote: >> >>> . >>> >>> In no case can I understand a physical explanation for the the MS >>> sigma^2 being smaller than for the SS. >> >> Actually, there is a physical situation where something like that can >> occur, although it sounds like it's not the one that Han Sen has. >> >> Consider an absorbing atom rattling around in a relatively fixed cage >> or lattice. And then consider a linear (or near-linear) arrangement: >> >> S1 -- A -- S2 >> >> One multiple scattering path that can sometimes have a sizable >> contribution is A --> S1 --> S2 --> A. This path will have a sigma^2 >> that is a bit larger than the single-scattering path S1 --> S2 --> S1, >> because of the perpendicular component of the motion of A. >> >> But it's quite frequently the case that S1 --> S2 --> S1 is not >> modeled in a fit, because the S edge is not measured. >> >> On the other hand, the single scattering paths A --> S1 --> A and A -- >>> S2 --> A ARE included in the fit. Those two have high sigma^2's, >> because A is rattling around a lot. >> >> Under that circumstance, a multiple-scattering path included in the >> fit may indeed have a lower sigma^2 than the single-scattering paths >> included in the fit. >> >> The moral, of course, is that it's not hard to think physically about >> what sigma^2 means for a multiple scattering path. If one appears to >> have an "unphysically" small sigma2, then the explanation is probably >> one of the ones given by Bruce or Shelly. >> >> One more thought on this. How much does it change your fit, Han Sen, >> if you set the sigma^2 for the multiple-scattering path to some >> "reasonable" value. If the scientific information you want from your >> fit is not sensitive to exactly what sigma^2 the MS path gets, and is >> not significantly different when given a "reasonable" value than when >> allowed to find its "best-fit" value, then there's probably no need to >> resolve the issue. In my experience, this is often the case with low- >> amplitude MS paths: the fit is improved by their inclusion, but may >> not be particularly sensitive to the details of their path parameters. >> >> --Scott Calvin >> Sarah Lawrence College >> >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 92, Issue 4 >> ************************************** > > > > > ------------------------------ > > Message: 3 > Date: Wed, 6 Oct 2010 10:51:59 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths > (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4 > Message-ID: <CBC93BEC-49EA-40CB-B700-4CD1E421D1A5(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > On Oct 6, 2010, at 10:41 AM, Han Sen Soo wrote: > >> Hello Scott, >> Just to make sure I understand what you mean, are you saying that in >> your 3 atom system, the S1 and S2 atoms have relatively fixed >> locations but A may have large vibrational amplitudes in the A-S1 >> and A-S2 directions? So the round-trip 3 atom MS path has a small >> sigma^2 value since the variation in the A-S1-S2-A path is dictated >> by the more or less fixed S1 and S2 end-points (with minimal >> perpendicular contribution), whereas the 2 individual SS paths have >> large sigma^2 value due to the large A-S vibrations? >> > > Yes--you explained it far better than I did. :) > > --Scott Calvin > Sarah Lawrence College > > > > ------------------------------ > > Message: 4 > Date: Thu, 7 Oct 2010 12:51:01 +0530 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Multiple scattering paths in fitting > Message-ID: > <AANLkTim8q3nucice-cVa-F2jpqCR=abDbkKk=AJj2X87(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > I just read the discussion on "sigma^2 values for multiple > scattering paths ". One thing is clear that inclusion of multiple scattering > path may increase the quality of fit. I have also some questions related to > MS paths. > 1. What else information can be obtained from multiple scattering paths? > 2. What values of delr should be relevant for MS paths. > 3. How can we determine the bond-angles from multiple-sacttering paths using > Artemis fitting method. > > With thanks > Abhijeet Gaur > School of Studies in Physics > Vikram University, Ujjain. >

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Re: [Ifeffit] schemes for delr and sigma2 for multiple scattering paths
by Scott Calvin 07 Oct '10

07 Oct '10

Jatin, IF the uniform expansion model is valid for single scattering paths, then it is for multiple scattering paths as well. For some materials, particularly those with cubic space groups, that's got a good chance of being a useful model. Others tends to distort with changes in temperature, doping, etc., and it may not work as well. But even in those cases, if you've decided how to constrain the delr for single- scattering paths, you'll do reasonably well by using some kind of appropriate average of the delr's for related single-scattering paths. --Scott Calvin Sarah Lawrence College On Oct 7, 2010, at 3:05 AM, Jatinkumar Rana wrote: > Dear all, > > It is reasonable to assign a constant fraction by which unit cell > expands at a given temperature of XAFS measuremnt and so the variation > in the path lengths for every single scattering paths could be > assigned > as delr = alpha * Reff. Similarly, one can assign sigma2 value for > each > single scattering path depending on both type of scatterer and its > distance from the absorbing atom. > > Now coming to multiple scattering paths, Sigma2 for multiple > scattering > paths can be constrained based on the sigma2 of related single > scattering paths and a definite path-geometry-dependent scheme > (Triangle, collinear, reversed etc.) could be applied. > > Is there any such scheme for delr of multiple scattering paths ? or we > can simply assume that all paths (single scattering and multiple > scattering) undergo uniform expansion by a factor alpha. > > Thank you so much in advance for your valuable time... > > With best regards, > Jatin Rana > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Multiple scattering paths in fitting
by Abhijeet Gaur 07 Oct '10

07 Oct '10

Hi all, I just read the discussion on "sigma^2 values for multiple scattering paths ". One thing is clear that inclusion of multiple scattering path may increase the quality of fit. I have also some questions related to MS paths. 1. What else information can be obtained from multiple scattering paths? 2. What values of delr should be relevant for MS paths. 3. How can we determine the bond-angles from multiple-sacttering paths using Artemis fitting method. With thanks Abhijeet Gaur School of Studies in Physics Vikram University, Ujjain.

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schemes for delr and sigma2 for multiple scattering paths
by Jatinkumar Rana 07 Oct '10

07 Oct '10

Dear all, It is reasonable to assign a constant fraction by which unit cell expands at a given temperature of XAFS measuremnt and so the variation in the path lengths for every single scattering paths could be assigned as delr = alpha * Reff. Similarly, one can assign sigma2 value for each single scattering path depending on both type of scatterer and its distance from the absorbing atom. Now coming to multiple scattering paths, Sigma2 for multiple scattering paths can be constrained based on the sigma2 of related single scattering paths and a definite path-geometry-dependent scheme (Triangle, collinear, reversed etc.) could be applied. Is there any such scheme for delr of multiple scattering paths ? or we can simply assume that all paths (single scattering and multiple scattering) undergo uniform expansion by a factor alpha. Thank you so much in advance for your valuable time... With best regards, Jatin Rana

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
by Scott Calvin 06 Oct '10

06 Oct '10

On Oct 6, 2010, at 10:41 AM, Han Sen Soo wrote: > Hello Scott, > Just to make sure I understand what you mean, are you saying that in > your 3 atom system, the S1 and S2 atoms have relatively fixed > locations but A may have large vibrational amplitudes in the A-S1 > and A-S2 directions? So the round-trip 3 atom MS path has a small > sigma^2 value since the variation in the A-S1-S2-A path is dictated > by the more or less fixed S1 and S2 end-points (with minimal > perpendicular contribution), whereas the 2 individual SS paths have > large sigma^2 value due to the large A-S vibrations? > Yes--you explained it far better than I did. :) --Scott Calvin Sarah Lawrence College

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Re: [Ifeffit] sigma^2 values for multiple scattering paths (Scott Calvin); Re: Ifeffit Digest, Vol 92, Issue 4
by Han Sen Soo 06 Oct '10

06 Oct '10

Hello Scott, Just to make sure I understand what you mean, are you saying that in your 3 atom system, the S1 and S2 atoms have relatively fixed locations but A may have large vibrational amplitudes in the A-S1 and A-S2 directions? So the round-trip 3 atom MS path has a small sigma^2 value since the variation in the A-S1-S2-A path is dictated by the more or less fixed S1 and S2 end-points (with minimal perpendicular contribution), whereas the 2 individual SS paths have large sigma^2 value due to the large A-S vibrations? I tried setting the sigma^2 value to a reasonable number for the MS path and it appears to increase the R factor slightly and tries to maximize the floating degeneracy I set (with a restrain to be physically reasonable based on my model). It does not look as good but at least it seems more plausible. I will try out Shelly's suggestions to see if they work too. I guess what I wanted to find out is whether the model I included is telling me that something is terribly wrong. Thank you all again for your responses! han sen On Oct 6, 2010, at 10:00 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. Re: sigma^2 values for multiple scattering paths (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 6 Oct 2010 09:39:49 -0700 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: "Dr.Scott.Calvin(a)gmail.com" <Dr.Scott.Calvin(a)gmail.com> > Subject: Re: [Ifeffit] sigma^2 values for multiple scattering paths > Message-ID: <AB39966C-893D-4947-BED2-A26FC6534315(a)gmail.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > Although I agree with the main points that Bruce makes, I do want to > comment on one piece: > > On Oct 6, 2010, at 7:03 AM, Bruce Ravel wrote: > >> . >> >> In no case can I understand a physical explanation for the the MS >> sigma^2 being smaller than for the SS. > > Actually, there is a physical situation where something like that can > occur, although it sounds like it's not the one that Han Sen has. > > Consider an absorbing atom rattling around in a relatively fixed cage > or lattice. And then consider a linear (or near-linear) arrangement: > > S1 -- A -- S2 > > One multiple scattering path that can sometimes have a sizable > contribution is A --> S1 --> S2 --> A. This path will have a sigma^2 > that is a bit larger than the single-scattering path S1 --> S2 --> S1, > because of the perpendicular component of the motion of A. > > But it's quite frequently the case that S1 --> S2 --> S1 is not > modeled in a fit, because the S edge is not measured. > > On the other hand, the single scattering paths A --> S1 --> A and A -- >> S2 --> A ARE included in the fit. Those two have high sigma^2's, > because A is rattling around a lot. > > Under that circumstance, a multiple-scattering path included in the > fit may indeed have a lower sigma^2 than the single-scattering paths > included in the fit. > > The moral, of course, is that it's not hard to think physically about > what sigma^2 means for a multiple scattering path. If one appears to > have an "unphysically" small sigma2, then the explanation is probably > one of the ones given by Bruce or Shelly. > > One more thought on this. How much does it change your fit, Han Sen, > if you set the sigma^2 for the multiple-scattering path to some > "reasonable" value. If the scientific information you want from your > fit is not sensitive to exactly what sigma^2 the MS path gets, and is > not significantly different when given a "reasonable" value than when > allowed to find its "best-fit" value, then there's probably no need to > resolve the issue. In my experience, this is often the case with low- > amplitude MS paths: the fit is improved by their inclusion, but may > not be particularly sensitive to the details of their path parameters. > > --Scott Calvin > Sarah Lawrence College > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 92, Issue 4 > **************************************

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Re: [Ifeffit] More than 256 paths on Mac OS 10.5?
by Scott Calvin 06 Oct '10

06 Oct '10

Thanks, Matt! --Scott Calvin Sarah Lawrence College On Oct 6, 2010, at 9:08 AM, Matt Newville wrote: > Hi Scott, > > > The attached zip file has dynamic libraries (and static program > ifeffit) built with 1024 paths and feff files. It contains the files > > lib/libifeffit.dylib > lib/libifeffit.so > bin/ifeffit > > The zip file should be unzipped under > /Applications/iXAFS.app/Contents/Resources/local/ > to overwrite the above files. You should be able to open the iXAFS > Shell and type > > cd /Applications/iXAFS.app/Contents/Resources/local/ > unzip ~/Downloads/iXAFS_1024paths.zip > athena > > > Athena and Artemis will automatically use the new dynamic library. >

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