September 2006 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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New Method for Normalization?
by Barton, David (DG) 30 Mar '09

30 Mar '09

XANES Aficionados, I know most users on this list are hard-core EXAFS analysts, but some of us use XANES analysis to decipher mixed phases or use it to get structural clues when data quality isn't sufficient for EXAFS analysis. Anyway, I have a question for those interested in quantitative analysis of XANES or those that are willing to offer an opinion on methods to normalize raw spectra to get reliable, repeatable comparisons of near-edge features. Has anyone considered using the methods of Penner-Hahn to normalize their data to get reliable intensities of near-edge features? The reference to their method of normalization is below: J. Synchrotron Rad. (2005). 12, 506-510 [doi:10.1107/S0909049504034193] "A method for normalization of X-ray absorption spectra" T.-C. Weng, G. S. Waldo and J. E. Penner-Hahn It is my understanding the Ifeffit uses a linear function to remove the pre-edge and a quadratic for the post-edge and that the Athena's flatten is a subtraction of these functions. This is an excellent method under most scenarios since the background is usually fairly smooth and can be well approximated by a quadratic equation. Personally, I have had only a few rare cases where the quadratic function on the post-edge was not sufficient to reliably normalize the data and in those cases a third-order polynomial was sufficient. Does anyone else have an opinion on using alternative normalization routines? Dave _________________________________ David Barton The Dow Chemical Company

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Re: [Ifeffit] OS X: (was: new release (061) of my codes)
by Matt Newville 29 Nov '06

29 Nov '06

Bruce, everyone Mac-interested: I believe many of the problems that have been seen come from the idea that one can install the binary, and then expect upgrading from source to work. I believe this will always be fragile: Mac OS X does not come with an installed compiler for C or Fortran (they are available). For these machines, the standard 'perl Makefile.PL' will fail. Whether this is the cause of the recent problems is a separate question. The way I see it, there are two ways to go here: A) assume that Mac is "just-another-version-of-Unix" so that installations and upgrading from source should work. B) assume that Mac is as special as Windows, and that ALL installations and upgrades need an actual installer or a simple, foolproof upgrade mechanism that involves no users typing at a terminal. An "upgrade" could simply consist of a zip file of new files, but we'd need a program (like exists for Windows) that did this upgrading semi-automatically. If the perl upgrades were "pure perl" and did not include a compilation, it could probably be made to work more reliably. But I don't quite see that as the right solution, because it still expects upgrades to happen with a different model than the original installation. Personally, I'm not thrilled about having to support option A. Option B means that someone will have to do the work of making and testing binary installers and upgrades. It will probably mean having to stick close to Mac OS X upgrade cycle. But I think we need a consensus on this. Any opinions? --Matt

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Consistency criterion
by Juan Antonio Maciá Agulló 29 Sep '06

29 Sep '06

Hi all, Scott answered my question about consistency but now I have a new doubt. I have two fits (one in k1 and other in k3 weights) with fitted parameters that have uncertainty ranges overlaped, then... in principle, they are consitent, right? But the fit in k1 weight have a R-factor too high (0.06) and therefore is not a good fit. So I do not know if I can say that they are consistent even so. Thank you very much Best regards, JA >I read in Artemis manual that a good fit must be consistent for different >k-weights. When two fits (one with k1 and other with k3) are consistent? I >mean, which is maximum allowed difference, 1%, 5%...between these two fits? Ideally, the fitted parameters should have uncertainty ranges that overlap. For example, one bond length might be 2.03 +/- 0.04 angstroms, and the equivalent bond length using a different k-weight might be 2.09 +/- 0.03 angstroms.

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Incorporating FEFF8 into IFEFFIT
by Richard Mayes 28 Sep '06

28 Sep '06

Bruce, I have just recieved a copy of FEFF8. Is there a way to incorporate it into Artemis on the windows version of IFEFFIT? In theory, we should be able to play a "shell game" with the names of the executable files and get FEFF8 to work while IFEFFIT thinks it's running FEFF6l (by changing the FEFF6l.exe file to something else, and rename the FEFF8 file to FEFF6l.exe) and then replace the DAT files to those for FEFF8. Is this possible or is it just better to run FEFF8 independently and import the .inp files into Artemis? Rich Mayes Barnes Group Dept. of Chemistry Univ. of Tennessee Knoxville, TN 37996

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Phase corrected Fourier transforms
by Juan Antonio Maciá Agulló 27 Sep '06

27 Sep '06

Hi all, I have read Phase corrected Fourier transforms in Athena manual and now I have a big doubt, ¿phase correction or not in a publication? I have read also that this correction is different (more complete) in Artemis and I am not sure if I should correct also in Artemis and which path should I use and why. I saw many papers dealing with EXAFS fits and they showed a "calculated" bond distance, I think it is: d = Reff + deltaR, right? I also ask for a paper where I can find that deltaE is ok (even for high-Z backscatterers) if deltaE < 10eV. I have high correlations between ss and SO2, and deltaR and deltaE. I tried different fits but I can not eliminate them, then...is the fit wrong? Sorry for these easy questions but I am a novice in XAFS. Thank you very much. Best regards, JA

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Re: [Ifeffit] Artemis error message
by Matt Newville 20 Sep '06

20 Sep '06

Hi Stefano, Did you try using /Applications/Ifeffit/bin/feff6 as the preferred feff executable in Artemis? That's what the error message was suggesting you try. Can you verify that you have /Applications/Ifeffit/bin/feff6? --Matt

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Artemis import from the text file
by Victor.Streltsov＠csiro.au 19 Sep '06

19 Sep '06

Hi All, I have the following Artemis problem: when I export variables to text file and then read them back into new Artemis run/project (import variables from the text file), Artemis cuts parts of the expressions starting from multiplication sign '*'. I tried different text editors and character coding as well as different platforms (Windows XP, Linux FC4). It always does the same thing with imported math expressions. It doesn't like '*' character. I am puzzled. I would appreciate your help and any suggestions. Thanks Victor Dr Victor Streltsov CSIRO Molecular & Health Technologies 343 Royal Parade Parkville VIC 3052 Australia Phone: +61 3 96627311 Fax: +61 3 96627101 victor.streltsov(a)csiro.au

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Short questions
by Juan Antonio Maciá Agulló 15 Sep '06

15 Sep '06

Hi Ifeffit people, I have a couple of short questions for you. I used the "Scott Calvin's rule" (number of variables < 2/3*Nip) to calculate the maximum number of allowed free parameters but I read that some people use the Nyquist theorem, which are the differences between them? and, which one is more correct? And finally, how are errors calculated in Artemis for the parameters N (coordination number), deltaE0, S02, deltaR and sigma^2? Thanks a lot JA

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FW: PhD position@LWV/PSI
by Degueldre Claude A. 12 Sep '06

12 Sep '06

-----Original Message----- From: Bruce Ravel [mailto:bravel@anl.gov] Sent: Montag, 11. September 2006 17:22 To: Degueldre Claude A. Subject: Re: PhD position@LWV/PSI URGENT AND FOR INFORMATION COULD YOU PLEASE VENTILATE THE INFO... We have 1 position free for doctorant with main topic EXAFS. You find the job below: http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was=l iste&kategorie=doktoranden With the KS 4334 If you have any candidate, please let me know... We need to evaluate candidates on Sep. 25. All the best CLAUDE DEGUELDRE ----------------------------------------------------- On Monday 11 September 2006 10:07, you wrote: > Bruce > We have 1 position free for doctorant with main topic EXAFS. You find > the job below: > http://pa.web.psi.ch/pages/offenestellen/d/index_offenestellen.php?was > =l > iste&kategorie=doktoranden > With the KS 4334 > If you have any candidate, please let me know... > We need to evaluate candidates on Sep. 25. > All the best Hi Claude, I don't know anyone who can fill the spot in the next two weeks, unfortunately. I think you should post this job opening on the Ifeffit mailing list. Matt and I consider that an excellent use of the mailing list. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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