November 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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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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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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writing beam time proposals
by Bruce Ravel 08 Dec '05

08 Dec '05

Hi folks, Yesterday I received an interesting question about writing beam time proposals. I know that proposal review panel members at least from APS and NSLS are readers of this mailing list (perhaps other synchrotrons as well), so I thought it would be interesting to start a thread on proposal writing strategies. The fellow who sent me mail asked: My question is, since I am a student, should my advisor be the official PI applying for time or should I be the PI? Is there any advantage one way or the other? In principle, I think it should not matter. Beam time should be awarded to a quality proposal. What advice do you all have for this proposal writer? What has your experience in applying for beam time? BTW, this fellow had been a student in a recent XAS summer school. I suggested he mention that in his proposal. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance 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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Re: [Ifeffit] Mac installer for 10.4 with horae-048
by Matt Newville 30 Nov '05

30 Nov '05

Stefano, Can you completely delete /Application/Ifeffit and reinstall? I know it sounds brutal, but it;s not going to do anything bad to your System.... --Matt

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Mac installer for 10.4 with horae-048
by Paul Fons 30 Nov '05

30 Nov '05

As the unix auto-update script has been broken due to changes by sourceforge, I have updated the ifeffit installer on sourceforge for Mac OS 10.4 to include the latest revisions (bug fixes to athena). Paul

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Re: Horae-058
by Bruce Ravel 23 Nov '05

23 Nov '05

On Wednesday 23 November 2005 07:35, you wrote: > Greetings from SPring-8 (getting chilly here, but no snow yet). We've got you beat here at the APS. There is snow on the ground right now! The Australian and Brazilian synchrotrons are looking awfully good right now.... > I tried downloading the latest tarball using your horae-update > script. It download a file with the right name, but that only > contains what appear to be sourceforge related web links. In other > words horae_update is broken (much like what happened before). SourceForge redesigned their web site. The screen scraper in horae_update no longer works. I am hesitant to just fix the current code -- it was a hand-built solution and, obviously, much too fragile. A better solution would require either using better html parsing tools from CPAN or figuring out how to gather information from SourceForge without needing to scrape their web pages. I am open to any suggestions or offers of coding help. 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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that didn't take long...
by Bruce Ravel 23 Nov '05

23 Nov '05

Hi folks, I just discovered a fairly serious bug in the version of Athena I just released yesterday. The auto-alignment function is broken. Fortunately, alignment can still be done by hand using the +/- buttons in the alignment dialog. The fix is simple, but I won't be able to post updates until next week. (It's a holiday tomorrow here in the States and I am leaving for the airport soon.) My apologies to anyone who needs that feature in the next few days and especially to Paul who just did a bnch of work to make and post a new OSX installer. 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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new tarball and windows updater
by Bruce Ravel 22 Nov '05

22 Nov '05

Hi folks, Today I made a release that is mostly for maintenence purposes on Athena. Most of the changes have to do with various bug fixes and small UI improvements. Artemis and Hephaestus are unchanged. The new tarball, version 58, is at my site and at SourceForge. I also built a new windows executable and an updater. See http://cars9.uchicago.edu/iffwiki/HoraeVersion058 for details about the release. Thanks to Shelly, Adam, and Norbert for their feedback on this release. 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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graphics help
by crojasa＠unmsm.edu.pe 21 Nov '05

21 Nov '05

Hello help in: why in my graphics the fit curve is more differents that data curve?. If that fit is ok, but the fit curve(red) is very underneath that data curve(blue). Some idea Chachi P.D my graphis is in attachment -- Chachi Rojas GMC FCF UNMSM Tel.Mo.:97499347 email:crojasa@unmsm.edu.pe

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