November 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: question on Athena data import
by Jay Brandes 11 Dec '06

11 Dec '06

Ended up looking at the older threads and the fix posted a few months ago, to use the program textwrangler and save in UNIX text format, worked. The problem seems to be that the normal Mac text handling programs do not have this option and Athena requires it. Just looking at the files in another text editing program does not reveal the problem. Anyway, problem solved.

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OS X Mactel
by Carlo Segre 01 Dec '06

01 Dec '06

Hello All: Jeff Terry's tar archive with installable binaries of Ifeffit and horae for OS X Mactel has been put on the MRCAT web site http://mrcat.iit.edu/iXAFS.tar.gz Instructions for installation are in the tarball. An installer is being developed but please test this version. Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Problem opening old artemis files
by Igor Vasconcelos 30 Nov '06

30 Nov '06

Dear all, As I described in the previous email: >I installed the most recent "sarge" package in my Kubuntu box with no >problems. However, I haven't succeeded opening my Artemis files I created >about 5 months ago under Fedora 3. >I don't really know whether this comes >from a version incompatibility or it is a linux distribution related >problem. I am attaching a file with info trapped by Artemis. I'd appreciate if someone, most likely Bruce :-), could help me figure this out. Thanks, Igor _________________________________________________________________ Share your latest news with your friends with the Windows Live Spaces friends module. http://clk.atdmt.com/MSN/go/msnnkwsp0070000001msn/direct/01/?href=http://sp…

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Re: question on Athena data import
by Bruce Ravel 30 Nov '06

30 Nov '06

On Thursday 30 November 2006 10:09, Jay Brandes wrote: > Dear Dr Ravel- I have been using your program Athena for XANES and > EXAFS analysis and have liked it alot. I am having a very > frustrating problem, however. I have some older data that is in text > format and cannot get Athena to import it. I have tried taking the > data examples and replacing the data with my own and I only get the > error message "...has fewer than 10 data points. I have tried copying > the format exactly as far as I can see it in my text editing > programs, but no go. Tab delineated, space delineated, etc., don't > work either. This is very simple 2 column data. The documentation > doesn't seem to indicate that there should be any problems. I use Mac > OS X 10.4. Any advice would be greatly appreciated! Hi Jay, I am taking the liberty of CCing my answer to the mailing list. I am happy to answer this sort of question, but I prefer that it be asked on the mailing list so that others may benefit by the exchange. I have written some guidelines on how to report problems with the software: http://cars9.uchicago.edu/~ravel/software/bugs.html The reason I am pointing this out is that I am better able to help users who familiarize themselves with the suggestions on that page. Without an example of the troublesome data file, I cannot replicate the problem on my computer and therefore cannot offer reliable advice. All that said, the Ifeffit FAQ might be helpful to you. In particular, questions 3 and 4 on this page: http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions are probably directly relevant to your problem. 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 horae Debian packages
by Carlo Segre 30 Nov '06

30 Nov '06

Hello All: The horae-063 Debian packages have been built. For the "sarge" release, you can find it at my repository deb http://fermi.phys.iit.edu/debian/sarge binary/ For the "sid" (unstable) release, it has been uploaded to the Debian mirrors and should be available within 24 hours or so. For the "etch" (testing) release, I hope that it will make it into the contrib section before release at the end of December. It takes about 10 days. If you just can't wait, let me know. Finally, I know that the "etch" and "sid" Debian packages will not install in Ubuntu (along with ifeffit too). Is there any interest in getting these included in Ubuntu? If so, please let me know and I will see about it. I have not tried as of yet since I don't know any Ubuntu developers yet. Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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OS X Mactel
by Magnus Bergknut 29 Nov '06

29 Nov '06

Hi ³If anyone would like to test the OS X Mactel version, please drop me an email and I will send you a link to it.² I would greatly appreciate a link in order to try the Mactel build. Best Regards /Magnus ---------------------------------------------------- Magnus Bergknut, PhD SLU Institutionen för Skogsekologi Petrus Laestadius väg 901 83 Umeå Swedish University of Agricultural Sciences, SLU Department of Forest Ecology Petrus Laestadius vag S-901 83 Umeå SWEDEN Phone: +46 90 786 8230 ---------------------------------------------------- ########################################### This message has been scanned by F-Secure Anti-Virus for Microsoft Exchange. For more information, connect to http://www.f-secure.com/

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ifeffit on Intel Mac?
by Magnus Bergknut 29 Nov '06

29 Nov '06

Hello Sorry to intrude like this, but is there any information regarding ifeffit on Intel Mac? Best Regards /Magnus ---------------------------------------------------- Magnus Bergknut, PhD SLU Institutionen för Skogsekologi Petrus Laestadius väg 901 83 Umeå Swedish University of Agricultural Sciences, SLU Department of Forest Ecology Petrus Laestadius vag S-901 83 Umeå SWEDEN Phone: +46 90 786 8230 ---------------------------------------------------- ########################################### This message has been scanned by F-Secure Anti-Virus for Microsoft Exchange. For more information, connect to http://www.f-secure.com/

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SIXpack now in Debian
by Carlo Segre 29 Nov '06

29 Nov '06

Hello All: The latest version of SIXpack is now in Debian "sid" (unstable). I still am keeping "sarge" and "etch" versions on my archive but I hope that sixpack will make it into "etch" before the release. As of today, I have also built version for ubuntu "dapper" and "edgy". The archives are at: Debian: deb http://fermi.phys.iit.edu/debian/sarge binary/ deb http://fermi.phys.iit.edu/debian/etch binary/ Ubuntu: deb http://fermi.phys.iit.edu/debian/dapper binary/ deb http://fermi.phys.iit.edu/debian/edgy binary/ Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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