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

Re: [Ifeffit] something is wrong with Ruthenium-Oxygen bond amplitudes
by Scott Calvin 05 Nov '10

05 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 05 Nov '10

05 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 28 Oct '10

28 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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