February 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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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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RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, How close are the distances for the 6 ligands? It is usually not possible to fit a single peak in the EXAFS spectrum by 6 independent signals. It sound like the distribution of distances for these 6 ligands is incorrect. I suggest that you try to fit just the first peak with one and then with two different shells with unknown coordination numbers and distances. This will give you some more information about what the data indicate the structure is like. If you send me an artemis file, I'll take a peak at it. Shelly skelly(a)anl.gov ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Monday, February 27, 2006 6:31 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Amplitude in Artemis Hi Shelly Unfortunately the coordination number is 1 for all atoms present. I have the crystal structure of the complex, so I am currently including 6 ligating atoms all at distances defined by the structure in the input file. It seems to be the first shell that is causing the problems, with a quickfit first shell artemis fit giving nominally 13 ligating species (which is of course absurd). So I believe something else must be the problem. Cheers Paul ----- Original Message ----- From: Kelly, Shelly D. <mailto:SKelly@anl.gov> To: XAFS Analysis using Ifeffit <mailto:ifeffit@millenia.cars.aps.anl.gov> Sent: Tuesday, February 28, 2006 12:55 AM Subject: RE: [Ifeffit] Amplitude in Artemis Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul ________________________________ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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RE: [Ifeffit] Amplitude in Artemis
by Kelly, Shelly D. 28 Feb '06

28 Feb '06

Hi Paul, It seems possible that one of the other amplitude terms is also incorrect. Scott already mentioned the step height but what about the coordination number? The amplitude of the model is given by coordination number * S02. You mentioned that the S02 value was somewhere between 2 and 4. What is the value for coordination number * S02? If the coordination number is 1, then it is possible that the parameters are switched. Maybe the coordination number should be between 2 and 4 and S02 should be around 1. HTH, Shelly ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Paul Sent: Sunday, February 26, 2006 6:52 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Amplitude in Artemis I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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Amplitude in Artemis
by Paul 27 Feb '06

27 Feb '06

I have just started a PhD and have been given alot of EXAFS data to simulate but I don't know much about artemis. I have tried to fit the data for quite some time now, but can't get any kind of good fit unless the amplitude is above 1. Is there any way amp can be above 1 and rationally explained? Cheers, Paul

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SPAM score=47.4*** Fonts in document pods
by Dave Baker 22 Feb '06

22 Feb '06

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (score=47.4,required=5.3) -2.6 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0000] 50 STOCKS_APS FULL: Hot Stocks Spam -------------------- 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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Re: How to change the spline knots in Athena
by Bruce Ravel 21 Feb '06

21 Feb '06

On Tuesday 21 February 2006 03:08, you wrote: > I am using Athena (0.8.048) software for XAFS analysis. > It is greatly helpful to me for XAFS characterization. > > I have a question on the background estimation. > Spline knots is displayed by "About current group" menu. > Could you tell me how to change the spline knots, if possible. > Changing the knots is useful to suppress the long-range variation. This is the kind of question that is better sent to the mailing list, so I am CCing my answer there. The number of knots is determined by the values of the k-range of the spline fit and by the value of Rbkg. The number of knots is delta_k * Rbkg * 2 / pi and the knots are evenly spaced in k. Ifeffit (and so Athena) does not allow you to move the knots to different locations nor does it allow you add or remove knots. The AUTOBK algorithm works by making a distinction between data and background in terms of Fourier components. Consequently it *cannot* allow you to move the knots or use more knots, since doing so would change the Fourier components included in the background spline. 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/

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error message in help
by Bradley Roberts 21 Feb '06

21 Feb '06

With Ifeffit 1.2.8, Athena 0.8.047, Artemis 0.8.004 running on OS X and plotting correctly, I'm not able to pull up any of the help windows. In either of the GUI programs, when I click on the Help menu and choose Document (or any of the sub-menu items in Athena) X11 beeps in error, and a window opens with the title "pod" and nothing displayed within the window. I mentioned before that I could not get tk::pod to install correctly via CPAN (the response being) Installing tk::pod FAILED windows would pop up during the make test routine that said: Can't find Pod 'perl' with an OK button and that the Text::English and Tk::HistEntry modules were not installed (though they are installed, says CPAN) I recognize that this is probably more of a Perl/CPAN related question but perhaps someone has seen this problem before. -- Bradley Roberts (br2(a)u.washington.edu) Graduate Student, Department of Materials Science & Engineering Roberts Hall 302 Box 352120 University of Washington Seattle, WA 98195 206-616-7485 lab 206-543-3100 fax

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Re: [Ifeffit] pgplot+Kubuntu+/XWINDOW /XSERVE
by Bruce Ravel 21 Feb '06

21 Feb '06

On Monday 20 February 2006 23:48, Denis Testemale wrote: > I've been using Ifeffit+horae (VERY GOOD) stuff for a while on my > previous Mandrake linux distro. I've changed to Kubuntu now. I have > difficulties to install everything on this new laptop. [Please be > aware that I use Linux for quite some time now but still consider > myself as an "everyday beginner"] > > I'm stuck at the installation of PGPLOT. > I've tried then to install from Mat's PGPLOT_install script but ran > into the same kind of error. Here it is: Kubuntu is debian-based and, I think, can use any debian repository. So I think you should be able to use Carlo's debian repository to install the software. Just point kynoptic at the repositories mentioned here: http://cars9.uchicago.edu/~ravel/software/downloads.html#debian Hope that helps, 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/

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