May 2005 - 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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Artemis- Loading up error
by Zohair Hussain 16 Apr '06

16 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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idealized 95-atom Pt cluster
by Charles Chusuei 30 May '05

30 May '05

Hi,,, I'm a new user to Artemis and Atoms. I would like to generate a simulated EXAFS spectrum of an idealized bare 95-atom cluster of Pt (with no ligands attached to it). Looking at Cambridge data files, the largest cluster documented is 18, so I would have to make one up. I would like to arrange the 95 atoms into an idealized sphere with the standard geometry for bulk Pt-Pt bonding that can be predicted from the crystal structure (e.g. metallic radius = 139nm, metallic separation = 277.5nm separation, etc.) I understand this can be done using Artemis and Atoms. I'm relatively new to using the software (prodominantly know how to use Athena for plotting the experimental EXAFS data , not much more). Could anyone provide suggestions on how to get started on this task? E.g. Generating the crystal data and displaying the EXAFS of the resulting bare cluster? Charles

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new windows updater
by Matt Newville 27 May '05

27 May '05

Hi Folks, There's a new Windows updater available (this is #15) with new versions of Athena, Artemis, and Diana that address some of the problems people have reported. Please give them a spin! --Matt

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RE: [Ifeffit] Least Squares Fitting in Athena
by Ravel, Bruce D. 25 May '05

25 May '05

> I have a couple of comments about LSF in Athena and I would like to hear > other people's opinions on the matter. > Also, it would be interesting to know: are there > many people who use Athena to do LSF? > I found that there is some inconsistency with plotting after > the fit is done. In my case nonzero energy shifts are applied to > the fitted data and the standards. The resulting linear combination fit > doesn't look shifted in energy appropriately - visually there is a > mismatch between the data and the fit. On the other hand, R-factor and > Chi^2 are very reasonable. This looks somewhat confusing. > Also, in my experience the obtained fractions in Athena come out slightly > different from those I could get using Sixpack LSF software. In my fits I > used the same constrains/options, same data and references and same data > range. What can be the cause of this? Hi, I have recently seem similar behavior. There are several possible causes for what you are seeing -- the most likely being an error in how the standards are interpolated onto the grid of the unknown data. I have been working hard on the LCF features in Athena recently and have fixed several bugs and added lots of new features. Rather than try particularly hard to address your questions now, I am going to wait and see if they persist after I release the next version of Athena (which will be soon). B

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Least Squares Fitting in Athena
by Stanislav Stoupin 24 May '05

24 May '05

Hello all, I have a couple of comments about LSF in Athena and I would like to hear other people's opinions on the matter. Also, it would be interesting to know: are there many people who use Athena to do LSF? I found that there is some inconsistency with plotting after the fit is done. In my case nonzero energy shifts are applied to the fitted data and the standards. The resulting linear combination fit doesn't look shifted in energy appropriately - visually there is a mismatch between the data and the fit. On the other hand, R-factor and Chi^2 are very reasonable. This looks somewhat confusing. Also, in my experience the obtained fractions in Athena come out slightly different from those I could get using Sixpack LSF software. In my fits I used the same constrains/options, same data and references and same data range. What can be the cause of this? Stanislav Stanislav Stoupin ----------------------------- Research Assistant/PhD student BCPS department Illinois Institute of Technology email: stousta(a)iit.edu voice: 312-567-7983

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Propagation of uncertanties
by Kelly, Shelly D. 17 May '05

17 May '05

Hi Matt and Bruce, I request that Athena reports the uncertainty in the basic EXAFS parameters and not just the fitted variables. For example, the uncertainty in the optimized debye temperature is reported, but the uncertainty in sigma2 value is not currently reported. I could see how this could be done by Athena or by including a new function in IFEFFIT. -What do you think? Thanks Shelly

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Contribution of multiple scattering paths - basic question
by Gerrit Schmithals 13 May '05

13 May '05

Hello, I want to fit a cobalt-porphyrin for which I have an atom.inp-file and EXAFS experimental data at Co K-edge . I started with a simple sum of paths for all paths with a distance below 5 A and an amplitude above 10 (see attachment). If one compares experiment (black curve) with this first fit (red curve) the first shell peaks overlap quite nicely but not the second and third (fourier transforms of the single paths are also drawn as blue and red curves). Then I excluded four paths (the red ones) and did a second sum of path. Now the other shell peaks overlap as well (green curve). The four exluded paths are multiple scattering paths via one nitrogen and one carbon atom. I conclude that the extinction of the second shell peak in the first simulation is due to the fact that these paths have a different phase shift than the other paths with a similar frequency. Do I make a simple error (adjustments of the fitting parameters necessary?) or does that tell me something about the system? I appreciate any help. Regards, Gerrit

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XAFS Summer Schools
by Matt Newville 09 May '05

09 May '05

Hi Folks, I thought I'd mention a couple of summer schools and XAFS courses that are happening this summer. I know many of you have attended summer schools or XAFS workshops in the past, and there are many people on this list who are fairly new to XAFS and synchrotron work in general. First, there will be a four-day XAFS school at Advanced Photon Source, Argonne, IL from July 26 to 30. More Information is at http://cars.uchicago.edu/xafs_school/ (Both Bruce and I will be involved with this). The application deadline for this is June 10, 2005. I believe there will also be an EXAFS Course at NSLS, Brookhaven Lab, NY in October, 2005: http://www.nsls.bnl.gov/newsroom/events/workshops/exafs/ In addition, there are also annual synchrotron based summer schools covering a range of techniques at Argonne National Lab, and a joint summer school between SSRL (Stanford) and ALS (Berkeley). I think the deadline for these may have passed. But there are quite a few other workshops, courses, and summer schools, including outside the US. A more complete list is at http://lightsources.org/cms/?pid=1000510 Cheers, --Matt PS: If you know of other courses, etc feel free to advertise them here.

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Re: athena for OSX.4
by Paul Fons 09 May '05

09 May '05

Please excuse me for forwarding a copy to the list in case there are others out there that have run into the same problem. For all those who want to be Tigers (Mac OS 10.4), here is a brief summary of the installation procedure. I should add that there is not an installer that will do everything at once, but the procedure is really pretty easy. I have not tried installing horae on a brand new system, I have only tried (and succeeded) in making a previously functional horae-051 under Mac OS 10.3 work properly under Mac OS (Tiger) 10.4. The errors you see are generated because there is a new version of perl installed (5.8.6) which doesn't know about Perl/Tk, the graphics system that Bruce uses for all of his packages. The solution is simple, you must download and install Perl/Tk and then reinstall horae. After that everything just works again. The build procedure is nearly automatic, but you need to have installed the developer tools (which are included on the Tiger installation DVD). First you need to download Tk from CPAN (the server where free Perl software is hosted). Here is the procedure. 0. I assume you had an installed and functional horae running under 10.3 and did an upgrade to 10.4 1. Download the source for Tk by a. make a new (temporary) scratch directory mkdir temp; cd temp b. download Tk going in your browser of choice go to the web page: http://search.cpan.org/~ni-s/Tk-804.027/ and hitting the download button on that page (the file will be named Tk-804-2.027.tar.gz) c. uncompress the file in your scratch directory tar zxf /the-path-to-your-download-directory/ Tk-804-2.027.tar.gz d. change to the Tk directory, compile, and install the new Tk cd Tk-804.027 perl Makefile.PL make sudo make install e. now you must download and install the latest version of horae via Bruce's web page go to the site http://leonardo.phys.washington.edu/~ravel/ software/downloads.html#unix and use the download link for horae-051.tar.gz f. decompress and install the new horae source cd ../temp (move up from the Tk directory to the top level of your new temporary directory) tar zxf /the-path-to-your-download-directory/ horae-051.tar.gz cd horae-051 perl Makefile.PL make sudo make install That's it. You are done. I just popped up a X11 window (you did remember to install the X11 program which is an optional install on the Tiger DVD accessible using the "Customize" button in the installer, right?) and typed artemis & and poof, artemis appeared. Note that if you did a clean install you should still be able to get everything working by downloading Matt's installer and installing the 10.3 copy (it won't work out of the box) and then following the above procedure. I have not verified this, however, so caveat empor as the Romans said... Hope this helps. Paul On May 10, 2005, at 3:08 AM, denauwer(a)tele2.fr wrote: > Dear Paul, > > We have contacted Bruce because we want to use Athena on Mac OSX.4 > and it is not working. We have tried from the terminal and we got > the following message: > > "Can't load '/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/ > Event/Event.b > undle' for module Tk::Event: dlopen(/Library/Perl/5.8.1/darwin- > thread-multi-2lev > el/auto/Tk/Event/Event.bundle, 1): Library not loaded: /System/ > Library/Perl/5.8. > 1/darwin-thread-multi-2level/CORE/libperl.dylib > Referenced from: /Library/Perl/5.8.1/darwin-thread-multi-2level/ > auto/Tk/Event/ > Event.bundle > Reason: image not found at /System/Library/Perl/5.8.6/darwin- > thread-multi-2lev > el/XSLoader.pm line 68. > at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 10 > Compilation failed in require at /Library/Perl/5.8.1/darwin-thread- > multi-2level/ > Tk.pm line 13. > BEGIN failed--compilation aborted at /Library/Perl/5.8.1/darwin- > thread-multi-2le > vel/Tk.pm line 13. > Compilation failed in require at /Applications/Ifeffit/bin/athena > line 53. > BEGIN failed--compilation aborted at /Applications/Ifeffit/bin/ > athena line 53. > Undefined subroutine &Tk::Event::CleanupGlue called at /Library/ > Perl/5.8.1/darwi > n-thread-multi-2level/Tk/Event.pm line 3. > END failed--call queue aborted at /Applications/Ifeffit/bin/athena > line 53." > > Could you if you have time, please, explain what we have to do to > fix this problem? > > Thank you for your help, > Christophe Den Auwer > > > Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８茨城県つくば市東１−１−1 つくば中央第４近接場光応用工学センターポール・フォンス主任研究官

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