January 2007 - 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] statistical vicissitudes and dead links
by Kelly, Shelly D. 26 Jan '07

26 Jan '07

Hi Paul, Here is a PDF version of the relevant pages from Dani's thesis. Shelly --------------------------- Shelly Kelly Argonne National Laboratory Bldg 203, RM E113 9700 S. Cass Ave Argonne, IL 60439 Molecular Environmental Science Group www.mesg.anl.gov skelly(a)anl.gov phone: 630-252-7376 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Paul Fons > Sent: Saturday, January 20, 2007 7:38 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] statistical vicissitudes and dead links > > Hi Shelly, > I noticed that the link you posted either is dead or doesn't work > from outside anl (the message from the server is ambiguous). > > Paul > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Multiple k-weight fitting
by David C. Schmitter 22 Jan '07

22 Jan '07

Hi everyone. I am currently trying to reduce the correlations between N and sigma squared. I have been told that multiple k-weight fitting is the way to go about this; but I am curious what the best method is to try and do this using Artemis. Is it simply a matter of clicking the other weighting options available? If so, what should I be looking for to determine whether my parameters are correct or not? I am not sure if this is a redundant question in terms of the mailing list; but I am a relatively new user and cannot remember seeing anything about it yet. Thanks. Dave Schmitter David C. Schmitter Dept. of Physics and Astronomy Nebraska Center for Materials and Nanoscience University of Nebraska Lincoln dschmitt(a)unlserve.unl.edu (402) 472-5094

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Re: [Ifeffit] statistical vicissitudes
by Kelly, Shelly D. 21 Jan '07

21 Jan '07

Hi Aaron, In EXAFS the expected deviation in RCS(reduced chi square) is sqrt(2/nu) So one fit is better than another fit if their difference is greater than twice the fluctuation in the RCS values (RCS1-RCS2)/RCS2 > 2 sqrt(2/nu) We divide by RCS2 because our RCS-values are poorly scaled. {in your link to the nist pages F = RCS1/RCS2 -1 and the statistically significant variation in F is 2 * sqrt(2/nu)} If there are different values for nu in the two models then (RCS1-RCS2) > 2sqrt(RCS2^2/nu2 + RCS1^2/nu1) I think that the best explanation of these tests are given in Dani Haskel's thesis pg 39 - 41 http://www.aps.anl.gov/xfd/people/haskel/dani.html and Bevington, P. R.; Robinson, D. K. Data Reduction and Error Analysis for the Physical Sciences; 2 ed.; McGraw-Hill: New York, 1992. 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 Aaron Slowey > Sent: Thursday, January 18, 2007 4:50 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] statistical vicissitudes > > Hello - > > The use of R-factors and reduced-chi-squared values, it's computations > by IFEFFIT have been made clear by past writings, but the use of > reduced-chi-squared as a comparative statistic has not, to my > knowledge, been completely well-documented. > > Not withstanding the three disconnects between classical statistics > and the realities of EXAFS mentioned in the IFEFFIT faq section > > http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling#head- > ed63cbd00d0b85def31ada3a695873243d08a76a > > can > > Is the criterion provided by Kelly et al. (2001) J. Phys. Chem. B 105(27) > > http://www.mesg.anl.gov/pdf/JPC2001samms.pdf > > namely, redchi-sq_1 / redchi-sq_2) - 1 > 2 * (2 / deg_of_freedom)^0.5, > > derived from the F-test formalism and, if so, how? > > I tried to derive the above equation based on the F-test formalism > provided by NIST: > > http://www.itl.nist.gov/div898/handbook/prc/section3/prc32.htm > > but was unsuccessfull. The Kemner et al. paper referenced by Kelly et > al. to explain the statistical basis for the above equation does not > clearly do so. > > I request that someone please provide a reference to a *first > principles* basis for criteria to compare reduced-chi-square values of > alternate EXAFS fits. > > Aaron > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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statistical vicissitudes
by Aaron Slowey 18 Jan '07

18 Jan '07

Hello - The use of R-factors and reduced-chi-squared values, it's computations by IFEFFIT have been made clear by past writings, but the use of reduced-chi-squared as a comparative statistic has not, to my knowledge, been completely well-documented. Not withstanding the three disconnects between classical statistics and the realities of EXAFS mentioned in the IFEFFIT faq section http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling#head-ed63cbd00d0b85def… can Is the criterion provided by Kelly et al. (2001) J. Phys. Chem. B 105(27) http://www.mesg.anl.gov/pdf/JPC2001samms.pdf namely, redchi-sq_1 / redchi-sq_2) - 1 > 2 * (2 / deg_of_freedom)^0.5, derived from the F-test formalism and, if so, how? I tried to derive the above equation based on the F-test formalism provided by NIST: http://www.itl.nist.gov/div898/handbook/prc/section3/prc32.htm but was unsuccessfull. The Kemner et al. paper referenced by Kelly et al. to explain the statistical basis for the above equation does not clearly do so. I request that someone please provide a reference to a *first principles* basis for criteria to compare reduced-chi-square values of alternate EXAFS fits. Aaron

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SSRL data format
by Matthew Ginder-Vogel 17 Jan '07

17 Jan '07

Hi All, Sam Webb's "SamView" which is part of SixPACK opens SSRL data files and you can then save them in ASCII format. I think he he has the source code posted on his website. Matt On 1/17/07, ifeffit-request(a)millenia.cars.aps.anl.gov < ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: opening SSRL data with Athena (Tsu-Chien Weng) > 2. Re: opening SSRL data with Athena (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 17 Jan 2007 09:57:05 +0100 > From: Tsu-Chien Weng <tsuchien.weng(a)esrf.fr> > Subject: Re: [Ifeffit] opening SSRL data with Athena > To: bravel(a)anl.gov > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <45ADE4E1.9020902(a)esrf.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, Bruce, > > I have written codes in MATLAB to convert ASCII data into SSRL's binary > data in > order to use EXAFSPAK. The binary format is guessed by dumping the > data. Maybe > someone can use it as a start and come up with a plugin for Athena. > > > > Bruce Ravel wrote: > > > > Question 3 at this FAQ page: > > http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions > > explains in some detail what kind of data Athena is able to read. > > Obviously SSRL's binary format cannot be imported without the use of a > > plugin. > > > > It would be possible, in principle, to write a plugin that is capable > > of reading the SSRL binary format. However, to my knowledge (which > > certainly may be faulty) the technical details of the SSRL format are > > not published any place where I can find them. That's something of an > > impediment. ;-) > > > > It would most certainly help to convert to an ascii format. Not > > having worked at SSRL since my grad school days, I don't really know > > how to do so. Your beamline scientist should be able to help you with > > that. Perhaps someone on the list will know the details. > > > > B > > > > > -- > Tsu-Chien WENG > European Synchrotron Radiation Facility > 6, rue Jules Horowitz, EXPH Sect-26 > 38043 Grenoble, FRANCE > Tel: +33(0)438.88.19.82 > Fax: +33(0)476.88.27.84 >

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Re: opening SSRL data with Athena
by Bruce Ravel 17 Jan '07

17 Jan '07

On Friday 12 January 2007 15:20, Aaron Slowey wrote: > I'm running IFEFFIT, Athena, etc. on my Intel Mac after using the the > recent installer provided by MRCAT. I've opened Athena successfully > and was able to load a GSECARS data file, but I am unable to load > SSRL binary data files (original file from a VMS beamline computer). > > Would it help to convert the SSRL binaries to ASCII files? If so, how > can I do that? Aaron, There are enough people in the Ifeffit-using community who are SSRL users and who might be interested in this question. SO I am CCing my answer to the mailing list. Question 3 at this FAQ page: http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions explains in some detail what kind of data Athena is able to read. Obviously SSRL's binary format cannot be imported without the use of a plugin. It would be possible, in principle, to write a plugin that is capable of reading the SSRL binary format. However, to my knowledge (which certainly may be faulty) the technical details of the SSRL format are not published any place where I can find them. That's something of an impediment. ;-) It would most certainly help to convert to an ascii format. Not having worked at SSRL since my grad school days, I don't really know how to do so. Your beamline scientist should be able to help you with that. Perhaps someone on the list will know the details. 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/

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Projekt with the "flatten-problem"
by Jens Kruse 14 Jan '07

14 Jan '07

Hi, find attached an example with the "flatten-problem". thanks a lot, jens "Hi, I have a normalization problem with Athena. If I turn on the "flatten" option in the background removal section, Athena creates in some of the normalized spectra a step in the pre-edge range. How can I get rid of it? Thanks, jens"

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Re: [Ifeffit] Re: opening SSRL data with Athena
by Silvio Levy 14 Jan '07

14 Jan '07

Here is how I converted my SSRL-collected data so as to be able to import them into Athena. (By the way, when you collect the data you can specify that you want them in ASCII, but I did not know that at the time.) 1. Install EXAFSPAK, the SSRL-grown Exafs data analysis suite. 2. Run the MVIEW command on each file with instructions to save the output in ASCII. Although the command is interactive, you can run it in quasi-batch mode -- you just have to quit from each window as pops up. This way you can cycle through 100 files or more in a couple of minutes. For example, on Linux, I ran the following shell script for files collected in transmission mode. The key command is mview /num=1-6 /den=1 /write=output-file input-file ********************** #!/bin/sh cd Raw # directory where the SSRL binary files reside for i in `cat list-of-files-to-be-converted` do mview /num=1-6 /den=1 /write=../ASCII/$i $i done # this prints 7 columns (the first being a repeat of energy) # In Athena, select num=5,den=6 for sample, num=6,den=7 for reference ********************** Hope this helps! Silvio Levy

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