October 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 29 Nov '06

29 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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CuCl: thanks!
by Denis Testemale 30 Oct '06

30 Oct '06

Many thanks for the exhaustive and quick answers. There is still this doubt about the XANES shape, but at least I have some more references to deal with it. Cheers. denis > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. CuCl(solid) spectra? (Denis Testemale) > 2. Re: CuCl(solid) spectra? (Marco A. Alsina) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Oct 2006 11:39:40 +1030 > From: "Denis Testemale" <denis.testemale(a)gmail.com> > Subject: [Ifeffit] CuCl(solid) spectra? > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <4ba19e1a0610291709m1ae4315bx3c16d146a84fd06b(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > G'day! > > I'm looking for a spectrum of CuCl (solid), or a reference where I can see > one. I'm more interested in the XANES than the EXAFS region. I've found > Rumpf et al., Journal of Solid State Chemistry, 163, 158 (2002), but what > puzzles me is that the spectra in the Farrel Lytle database are somewhat > different with a stronger whiteline. Only the spectrum at 77K (from FL > database) does not have this white line, but its poor definition does not > make me feel confident. > Thanks in advance. > Denis > > -- > Denis Testemale > School of Earth and Environmental Sciences, Adelaide University > and > South Australian Museum > North Terrace > 5000 Adelaide > ph: +61 8 8207 7659 >

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CuCl(solid) spectra?
by Denis Testemale 30 Oct '06

30 Oct '06

G'day! I'm looking for a spectrum of CuCl (solid), or a reference where I can see one. I'm more interested in the XANES than the EXAFS region. I've found Rumpf et al., Journal of Solid State Chemistry, 163, 158 (2002), but what puzzles me is that the spectra in the Farrel Lytle database are somewhat different with a stronger whiteline. Only the spectrum at 77K (from FL database) does not have this white line, but its poor definition does not make me feel confident. Thanks in advance. Denis -- Denis Testemale School of Earth and Environmental Sciences, Adelaide University and South Australian Museum North Terrace 5000 Adelaide ph: +61 8 8207 7659

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compiling horae-062a on AMD64
by crojasa＠unmsm.edu.pe 29 Oct '06

29 Oct '06

Hello List I trying install horae-062a on my Slamd64 11.0 ( AMD64 3200+), but it appears a following error; ...... /usr/bin/perl5.8.8 chantler2st.PL chantler.db Can't locate Chemistry/Elements.pm in @INC (@INC contains: /usr/lib/perl5/5.8.8/x86_64-linux /usr/lib/perl5/5.8.8 /usr/lib/perl5/site_perl/5.8.8/x86_64-linux /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl .) at chantler2st.PL line 40. BEGIN failed--compilation aborted at chantler2st.PL line 40. make[1]: *** [chantler.db] Error 2 make[1]: Leaving directory `/usr/local/src/horae-062a/Absorption' make: *** [subdirs] Error 2 Some idea for this error, Either it cannot install Gifefiit. PGplot - Ok Ifeffit - Ok Tk - 95% ok (according to test) Thanks Chachi Rojas Ayala GMC FCF UNMSM Claro:01-97489347 email:crojasa@unmsm.edu.pe

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Artemis import error
by Richard Mayes 25 Oct '06

25 Oct '06

Bruce and all, I'm having trouble importing an Athena project file into Artemis. When I try to import a particular set of data into Artemis as an Athena project file, Artemis keeps giving the errors "Use of uninitialized value in...at artemis line 11223." (where the ... is either hash element or method). I have attached a screenshot (.jpg) of the error message and the offending data as an Athena project file. I can open the rest of my data in Artemis with no problems, even from a file with this data in it, but when I try to open this set of data, it won't work. Any ideas on what the problem is? Rich Mayes

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Re: [Ifeffit] Help with Ag and Pd
by huangwei＠UDel.Edu 24 Oct '06

24 Oct '06

Dear Matt, Many thanks. I download the Ag foil reference and Pd reference. And they are exactly what I want. Thank you very much! Wei

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Help with Ag and Pd
by huangwei＠UDel.Edu 23 Oct '06

23 Oct '06

Dear all feff members, I am a new member here. I have some problems with my Pd-Ag bimetallic samples. I cannot get good EXAFS signals for both Pd and Ag. Can somebody share a good Ag foil and Pd foil reference with me (transmition)? Thank you very much! Wei

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Re: still the spike
by Silvio Levy 19 Oct '06

19 Oct '06

Dear Bruce, OK, I hear you. I'll stop obsessing about the spike and only show chi*k^2 plots in my thesis :-) More seriously -- Your answer helps put things into perspective, and the comparison between the FFT with k-range starting at 0 and 1 is instructive. It's worth noting, however, that in R space there is a hump from R=1 to R=1.4 that (to my knowledge) has no physical explanation, and which is more pronounced when the FT is taken starting at k=0. Should I not worry about this either? Thanks Silvio

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