March 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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Artemis- Loading up error
by Zohair Hussain 17 Apr '06

17 Apr '06

Hi! I recently had to install ifeffit software package on our network computer. The first time I ran Artemis I was asked to update which I did. However, Artemis did not start after that. The error message that I got is shown in the attached figures artemis-error1a and 1b. Please note that only Artemis doesn't work, all the other softwares (Athena, Hephaestus, TKAtoms etc.) work fine. I tried running the .bat file from the Ifeffit folder but that didn't work either. I also tried to run the artemis.exe file and received the error shown in figure "artemis-error2". Later I unisntalled and re-installed Ifeffit and chose not to do the updates and Artemis is now running fine. I was wondering if anyone has any idea why this is so or if there is a way around installing the updates and still being able to use Artemis??? Thanks, Zohair

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new release (061) of my codes
by Bruce Ravel 07 Apr '06

07 Apr '06

Hi folks, I just made a new release of Athena (0.8.049) and Artemis (0.8.006). A new source tarball is at SourceForge and at my website. An updater for Windows is on Matt's server. There is nothing big in this release, just some bug fixes and a few small usability improvements. See the release notes http://cars9.uchicago.edu/iffwiki/HoraeVersion061 for details. Enjoy, 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/exafs/

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Ifeffit on 10.4
by Emmanuelle Montarges 06 Apr '06

06 Apr '06

Hi everyone Working on MacOs10.4 computer, after several unsuccessful installations of ifeffit package....I have the following message when I try to run Athena from the Terminal window. I downloaded Tk-804.027.tar and installed it in "temp" directory, but I still have the same message...have you ever had this error? ************ Can't load '/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle' for module Tk: dlopen(/Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle, 1): Library not loaded: /usr/X11R6/lib/libX11.6.dylib Referenced from: /Library/Perl/5.8.6/darwin-thread-multi-2level/auto/Tk/Tk.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/DynaLoader.pm line 230. at /Applications/Ifeffit/bin/athena line 52 Compilation failed in require at /Applications/Ifeffit/bin/athena line 52. BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/athena line 52. ********** thanks in advance for your help Emmanuelle MONTARGES-PELLETIER

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Re: [Ifeffit] new release (061) of my codes
by Matt Newville 31 Mar '06

31 Mar '06

Stefano, I'm very confused. Please help me understand what does and does not work for you. Today you said: > 2) If I just type 'ifeffit' from the command line I get the following: > > > stefano% ifeffit > > dyld: Library not loaded: /usr/local/lib/libpgplot.dylib > Referenced from: /Applications/Ifeffit/bin/ifeffit > Reason: image not found > > Trace/BPT trap > Emmanuelle seems to have similar behavior. Of course, you know that this means that no ifeffit applications will run correctly. The messages you sent yesterday implied very strange permission problems and was definitely different than this. What changed? Has the ifeffit command-line program EVER worked for you? Really, I hope this question illustrates my confusion about what does and does not work for you. But you also said today: > just to let people know that for me (OSX 10.4.5) Athena works fine > after installation from ifeffit-1.2.8-Mac10.4.1_pkg.dmg OK... so Ifeffit and athena work??? That is very confusing. It also seems to be very different from Emmanuelle's experience. Hmmm. Then again, if Ifeffit and athena do work, what is the problem you're having? --Matt

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Re: [Ifeffit] new release (061) of my codes
by Matt Newville 31 Mar '06

31 Mar '06

Stefano, I don't know why 'ifeffit i' reports a blank during perl's configuration. Can you verify these from a terminal: A. what does ~> /Applications/Ifeffit/bin/ifeffit -i report? B. Start the command-line ifeffit and type ifeffit> print $&install_dir what does this say? Then again, I don't understand why horae needs to do 'ifeffit -i' on a Mac. It will always be /Applications/Ifeffit/share/ifeffit. --Matt

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Re: [Ifeffit] new release (061) of my codes
by Matt Newville 30 Mar '06

30 Mar '06

HI Stefano, > stefano% ~> /Applications/Ifeffit/bin/ifeffit -i > tcsh: /Users/stefano: Permission denied. But that's implying that you can't even run ifeffit due to permission problems. That makes it seem much more about your system than about Ifeffit. > stefano# ifeffit > stefano# ifeffit> print $&install_dir Hmm, that's weird. The banner message didn't print and the prompt is wrong (it should be "Ifeffit>"). Any ideas why that might be? > stefano# ifeffit> print $&install_dir > su: Illegal variable name. > stefano# print $&install_dir > su: Illegal variable name. Hmm, that's weird too. I'm not sure what wrote "su: Illegal variable name." I'm pretty sure that is not from the ifeffit program. --Matt

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Number of independent points: Artemis & Feffit
by Mauro Rovezzi 30 Mar '06

30 Mar '06

Hi guys, I've noticed a strange behaviour in Artemis during the calculation of N_idp; the value differs from the Feffit one. In fact, with command line feffit (ver. 2.984) N_idp=(2*delta_k*delta_R/pi)+2 but with Artemis the "+2" value disappears. Seen that the procedure is: Artemis-->Ifeffit-->feffit(), why they differs? Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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