April 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: [Ifeffit] OS X: (was: new release (061) of my codes)
by Matt Newville 28 Nov '06

28 Nov '06

Bruce, everyone Mac-interested: I believe many of the problems that have been seen come from the idea that one can install the binary, and then expect upgrading from source to work. I believe this will always be fragile: Mac OS X does not come with an installed compiler for C or Fortran (they are available). For these machines, the standard 'perl Makefile.PL' will fail. Whether this is the cause of the recent problems is a separate question. The way I see it, there are two ways to go here: A) assume that Mac is "just-another-version-of-Unix" so that installations and upgrading from source should work. B) assume that Mac is as special as Windows, and that ALL installations and upgrades need an actual installer or a simple, foolproof upgrade mechanism that involves no users typing at a terminal. An "upgrade" could simply consist of a zip file of new files, but we'd need a program (like exists for Windows) that did this upgrading semi-automatically. If the perl upgrades were "pure perl" and did not include a compilation, it could probably be made to work more reliably. But I don't quite see that as the right solution, because it still expects upgrades to happen with a different model than the original installation. Personally, I'm not thrilled about having to support option A. Option B means that someone will have to do the work of making and testing binary installers and upgrades. It will probably mean having to stick close to Mac OS X upgrade cycle. But I think we need a consensus on this. Any opinions? --Matt

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XAFS Summer School at APS
by Matt Newville 01 May '06

01 May '06

Hi Folks, There will be an XAFS Summer School at the Advanced Photon Source, Argonne July 26 to July 28, 2006. The school this year will be a little different from the XAFS Schools held over the past few years at the APS and NSLS. This year, we will cover "advanced analysis". The school will be 3 days, there will be no beam time involved, and students will be expected to be familiar with XAFS and data processing (at approximately the level of using Athena). Instructors will include Bruce Ravel, Scott Calvin, Shelly Kelly, and myself. For more details, and to apply for this years XAFS summer school, see http://cars.uchicago.edu/xafs_school/ The application deadline is June 1st. --Matt

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FEFF8
by Ivana Radisavljevic 26 Apr '06

26 Apr '06

Dear Mr. Ravel, I have read in one of the papers of the authors A.I. Lebedev and I.A. Sluchinskaya that Pb scattering form factors in FEFF6 were not precisely determined. As I am dealing with the similar systems, Pb1-xMnxTe(In, Ga) to be precise, could You please tell me if this is also true for the FEFF8 version (if it is true et all)? Another thing that bothers me is that all of the real part Furier transformed EXAFS spectra taken at the tellurium K edge, appear to have the first peak divided. Since there is no direct indication of the sub-shells' existence and having in mind the similar tellurium feature noticed in Your paper "Combined EXAFS and first-principles theory study of Pb1-xGexTe", I am wondering what this feature should represent? I thank You very much in advance, Ivana Radisavljevic Vinca Institute for Nuclear Sciences, Lab 011 P.O. Box. 522, 11001 Belgrade, Serbia and Montenegro Tel. +381 11 2458222/434 Fax. +381 11 3440100 E-mail: iva(a)vin.bg.ac.yu

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(no subject)
by tony vitova 25 Apr '06

25 Apr '06

Hi, I just started to do EXAFS analysis with Artemis and I am not sure if my fit is sufficiently good. It is an attempt to fit the first shell: the first two peaks of LiNbO3 (Nb absorber). Could somebody have a fast look at my Artemis project? I wanted to fix the amplitude and to vary the coordination numbers, thus the places of "N" and "SO2" are changed. Is there another way to do this? Thanks a lot! Tonya --------------------------------- How low will we go? Check out Yahoo! Messengers low PC-to-Phone call rates.

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RE: [Ifeffit] dk setting in Athena
by Kelly, Shelly D. 24 Apr '06

24 Apr '06

Hi Geoff, I don't think that I understand your definition of dk, so I am going to give you mine. A Fourier transform is a complex transformation that requires the data that is being transformed to be defined from -infinity to +infinity. Since our data does not cover this range, we pad the data set with zeros for most of the transformed data range. At the edges in between the actual data range and all the zeros there is a step function, as the data goes from zero to some non-zero number abruptly. A Fourier transform (FT) of a step function is a bunch of signals at all R-values called a FT ripple. This is not a good think to have in your FT. So we spread out the step function by applying a window. The length of the window is defined by dk. In general dk should not be zero. See this presentation for some more discussion of dk. http://www.mesg.anl.gov/Presentations/basics%20of%20exafs%20analysis%202 003.pdf HTH Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Geoff Eldridge > Sent: Monday, April 24, 2006 10:29 AM > To: Ifeffit List > Subject: [Ifeffit] dk setting in Athena > > Hello everyone, > > I've just started doing EXAFS in my research and I have found all your > posts to be very helpful. > > My question is about the dk setting in Athena. I know from earlier > reading that dk affects where the window for the FT is set in k-space > (i.e. a dk setting of one moves the window out further than the k-min > and k-max settings). I believe the purpose of this is to prevent > cutting the tops of peaks out of the FT window. If this is the case, > would a dk setting of 0 then be appropriate provided no parts of peaks > are clipped as shown in a k-space plot with the window shown? > > Thanks, > > Geoff > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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dk setting in Athena
by Geoff Eldridge 24 Apr '06

24 Apr '06

Hello everyone, I've just started doing EXAFS in my research and I have found all your posts to be very helpful. My question is about the dk setting in Athena. I know from earlier reading that dk affects where the window for the FT is set in k-space (i.e. a dk setting of one moves the window out further than the k-min and k-max settings). I believe the purpose of this is to prevent cutting the tops of peaks out of the FT window. If this is the case, would a dk setting of 0 then be appropriate provided no parts of peaks are clipped as shown in a k-space plot with the window shown? Thanks, Geoff

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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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problem compiling ifeffit 1.2.8
by Igor Vasconcelos 12 Apr '06

12 Apr '06

Dear all, I came across the following error when trying to compile ifeffit-1.2.8 (uprading from version 1.2.6) in my Linux FC4 box: ifort -g -c ifftest1.f fortcom: Error: ifftest1.f, line 202: A RETURN statement is invalid in the main program. return -------^ compilation aborted for ifftest1.f (code 1) make[3]: *** [ifftest1.o] Error 1 Does anyone know what the problem might be? Thanks, Igor _________________________________________________________________ Dont just search. Find. Check out the new MSN Search! http://search.msn.click-url.com/go/onm00200636ave/direct/01/

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