October 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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SPAM score=5.6*** Troubles in Running Iffeffit
by Adiraj Srinivas (Dr) 31 Oct '05

31 Oct '05

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=5.6,required=5.3) 8.0 SOFTWARE_APS BODY: Words and phrases for selling software 0.1 HTML_IMAGE_RATIO_06 BODY: HTML has a low ratio of text to image area 0.0 HTML_90_100 BODY: Message is 90% to 100% HTML -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0033] 0.0 HTML_MESSAGE BODY: HTML included in message -------------------- End of SpamAssassin results --------------------- The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

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S02
by Juan Antonio Maciá Agulló 31 Oct '05

31 Oct '05

Hi people, I fitted several supported platinum based catalysts by Artemis. I obtained good R-factors < 0.02 but stranges values of SO2 (<0.30) and I do not know if these low values of SO2 are related with a low coordination number for Pt. I know that particle sizes of these catalysts are very small and then the coordination number is smaller than 12. Thank you very much. JA

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RE: [Ifeffit] Problems with Windows XP Installation.
by Brewer, Luke N 21 Oct '05

21 Oct '05

Bruce, thank you for the solutions. Solution 2 seems to have fixed the problem. I now look forward to learning to run the software. Thanks again, Luke. -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Friday, October 21, 2005 12:36 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Problems with Windows XP Installation. On Friday 21 October 2005 13:14, Brewer, Luke N wrote: > Hello All- > > I have just downloaded and installed the ifeffit.1.2.8.exe package > for Windows XP from a mirror to sourceforge. The installation > appeared to run just fine. I read the note on website about using the > runner.exe instead of the individual executable files. > > When I click on the runner.exe, a window asks me what application I > would like to run (Athena, Artemis, etc.). The window disappears, and > nothing happens for about a minute after which an error window appears > asking me to check the runner.exe.log. The last line of each log > entry reads "timeoutsocket.Timeout: Attempted connect to > ('164.54.160.111', 80) timed out." > > I get the same error each time I try to run the software, regardless > of which application I select. > > Any advice? I would be happy to forward the runner.exe.log to anyone > who can/is willing to help. I think I know the problem -- Matt may have more wisodm. The first version of the runner did not play well without a reliable internet connection. It would seem you have been bitten by this problem. Possible solution #1: If, in fact, you were on a computer with out an internet connection (either by design or because it was temporarily down), make sure the computer is connected and try again. Possible solution #2: Grab this file: http://cars9.uchicago.edu/ifeffit/updates/iff_001.zip and unpack it by hand in C:\Program File\Ifeffit\ (or wherever you installed the whole ifeffit package). That file is the first updater package. It updates the runner as well as Athena, Artemis, and a bunch of documents and example. For more info on how the runner works and how updates happen, see the wiki: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/RunnerProgram HTH, 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/ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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new Tip of the Week
by Bruce Ravel 21 Oct '05

21 Oct '05

Hi! I just posted a new Tip of the Week at http://cars9.uchicago.edu/iffwiki/HoraeTipOfTheWeek This week's bit of magic is Artemis: Quickly plotting paths from the Feff interpretation page Enjoy, 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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Problems with Windows XP Installation.
by Brewer, Luke N 21 Oct '05

21 Oct '05

Hello All- I have just downloaded and installed the ifeffit.1.2.8.exe package for Windows XP from a mirror to sourceforge. The installation appeared to run just fine. I read the note on website about using the runner.exe instead of the individual executable files. When I click on the runner.exe, a window asks me what application I would like to run (Athena, Artemis, etc.). The window disappears, and nothing happens for about a minute after which an error window appears asking me to check the runner.exe.log. The last line of each log entry reads "timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out." I get the same error each time I try to run the software, regardless of which application I select. Any advice? I would be happy to forward the runner.exe.log to anyone who can/is willing to help. Thanks. Luke. Luke N. Brewer, Ph.D. Sandia National Laboratory Materials Characterization Dept.

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L2 vs. L3 edge comparisons
by McCready, Alistair 20 Oct '05

20 Oct '05

OK, a theoretical question whose answer may be straight-forward (and I will probably ridiculed for such a simple question)!! If you analyse, for example, the Pb L3 edge of 2 minerals and you then analyse the Pb L2 edge of the same 2 minerals, will the difference between the edges of 2 minerals be the same, irrespective of the edge you use? Cheers Alistair ------------------------------------------ Dr. Alistair J. McCready Mining & Minerals Saskatchewan Research Council 125-15 Innovation Blvd. Saskatoon, SK, S7N 2X8 Canada Tel: 306 933-7103 Fax: 306 933-7446 email: mccready(a)src.sk.ca "SRC provides Smart Science Solutions" This e-mail and any files transmitted with it are intended only for the named recipients and may contain legally privileged and/or confidential information. If you are not the intended recipient please do not disseminate, distribute or copy this e-mail without the consent of the sender.

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