September 2008 - 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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Ifeffit Ok on BlueWhite64, ...
by Chachi Rojas 03 Feb '09

03 Feb '09

Hi Matt Ifeffit run perfectely (thanks Matt) after installed by your scripts on RC1. Now, a question for Bruce try to install horae-065, but, error message is below: ---------- === The Ifeffit wrapper, Athena, Artemis, and Hephaestus === This is linux. Checking dependencies ... Tk is not installed. Download the latest from http://search.cpan.org/search?module=Tk Failed dependencies. Not installing athena and artemis. ------ Tk modules (version 8.4.15) were installed on /usr, but perl Makefile.PL it does not recognize Some idea Ch. > Date: Wed, 22 Aug 2007 15:56:26 -0500 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: [Ifeffit] Ifeffit and gfortran (was: iffefit compile on > BlueWhite64) > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0708221356y37280877v86ac576fe9b6b96c(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Chachi, all > > I believe I have a source kit that will build correctly for you using > gfortran. I've tested on three different generations of Fedora/Redhat > linux systems, one with only g77, one with only gfortran, and one with > both, and the installation now works on all of them. > > Please try > http://cars9.uchicago.edu/~ifeffit/src/ifeffit-1.2.10_rc1.tar.gz > > With this tar ball, you will need to install pgplot: > tar xvzf ifeffit-1.2.10_rc1.tar.gz > cd ifeffit-1.2.10 > sh PGPLOT_install > ./configure > make > make install > > (doing the two 'install steps' with sufficient privilege). Again, you > need to install PGPLOT with the provided script. Both the PGPLOT and > Ifeffit installations will use gfortran if available, and g77 if > gfortran is not available. I think it would not be too difficult to > attempt to use Intel's ifort compiler or g95, though I do not know > that it's needed-- all linux distribution come with gcc so have > easy-to-use packages for gfortran (and, for "legacy", g77). > > I did get horae-065 and the python wrappers to build with no trouble > (once the Tk modules were installed) on all systems, though I haven't > done much more than trivial testing. > > Since I tested only on a few linux boxes, I'd be interested in hearing > reports for other systems. > > I'll wait a few days (or more) to hear reports before uploading this > as ifeffit-1.2.10. > > --Matt >

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update for Windows, fixing problems with Athena/Artemis
by Matt Newville 01 Oct '08

01 Oct '08

Hi Folks, I just put up a Windows updater with new versions of Athena and Artemis which (should / seems to) fix the "Athena is stuck" problems seen be various people. Details on what else changed are below. All windows users with Ifeffit 1.2.10 and 1.2.11 should install this update. If you're still using an older version, beware that this update will be binary incompatible with that version, and you should upgrade to 1.2.11 before installing this update. If you've been having troubles with Athena/Artemis "getting stuck" and these persist after installing this update, please let us know!! --Matt =========== This update to Ifeffit 1.2.11 for Windows corrects several problems with the prior release related to building the Athena et al executables against the wrong version of the Ifeffit library. This update includes newly rebuilt executables for Athena, Artemis, Hephaestus, and Atoms. Additionally, the following features have been added to Athena: 1. Filename are sorted when importing multiple files. 2. Corrected a problem related to importing chi(k) data that do not start at 0. 3. Filetype plugins have been added for: - SSRL binary files - SSRL ASCII files - SSRL MicroEXAFS files - files from the CLS HXMA beamline - files from Photon Factory beamline 12C Enjoy! Bruce Ravel 25 Sep. 2008 ===========

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Independence of scattering paths?
by van der Veen Renske 01 Oct '08

01 Oct '08

Hello! I have a question concerning the independence of scattering pathways. I fitted the EXAFS signal of a molecule consisting of 30 atoms (the related FEFF calculation is called calc 1). To see the effect of the surrounding solvent molecules in the chi(k) data, I added an O-atom in the coordinate list of the FEFF input file at an arbitrary distance from the absorbing atom (in this case Pt) and I re-ran FEFF (calc 2). As a check within calc 2, I generated the sum of the same scattering paths that were used in the fitting model of calc 1 using the therein obtained structural fit parameters. The new O-atom was not included in this sum. I expected the sum within calc 2 to be identical to the fit of calc 1 based on the fact that the original atoms can not sense the presence of the new O-atom (independence of scattering paths). BUT: the resulting sum was significantly different from the fit! Am I overlooking something here? Aren't the calculated backscatter amplitudes and phases independent from each other? I am using Artemis version 0.8.007, Windows XP, Ifeffit 1.2.9. Thank you! Best regards, Renske Renske M. van der Veen PhD student EPFL / PSI Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3151 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

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Re: [Ifeffit] Independence of scattering paths? (van der Veen Renske)
by Frommer Jakob 30 Sep '08

30 Sep '08

Hi Renske, I am not sure whether I fully understand your question but here is my *two-cent-explanation*: FEFF's first step is to calculate the potentials - since it is a real space code based on the muffin-tin approximation the surrounding of an atom determines the actual scattering potential (even if you are not doing a self-consistent calculation). Since the potentials in turn determine the backscattering amplitudes and phase shifts, placing an additional atom randomly in a structure is certainly not a good idea. A possible work-around may be to find a *similar* (but known) structure with oxygen ligands and combine these two calculations in artemis (for multiple scattering however the geometry can matter a lot). If your solvent contains oxygen already you may (at least as a first approximation and for single scattering) just duplicate that path in artemis. Regards Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry

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plot linetypes option in athena windows version
by Malte Schulz 22 Sep '08

22 Sep '08

Hi there, I would like to export graphics from Athena to use them in my b&w printed thesis. Therefore it would be really useful to have Athena cycle through linetypes instead of colors. I found the "linetypes" option in the "plot" section of the preferences menu. However it doesn't seem to have any effect. I am using Athena v. 0.8.056 for windows. Malte

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export from large Athena projects
by shiryaev＠crys.ras.ru 19 Sep '08

19 Sep '08

Hi, It seems that there is a problem in exporting normalised data files from large (i.e. >10 curves) Athena projects: Exported data are cut in energy. When one exports the files one by one, this problem does not occurs. All the best, Andrei

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[ATOMS] supercell input file
by Mauro Rovezzi 19 Sep '08

19 Sep '08

Dear all, I would like to submit to your attention a problem with Atoms that I still do not understand. What I would like to do is to generate a FEFF input file starting from a supercell, that is repeating the unit cell NXxNYxNZ times and create the crystal with the resulting box. An example is given in the attached _test-atoms.inp_ created following this procedure: from wurtzite GaN (a,c cell parameters) that we describe with 2 atoms I reduce the symmetry and I use 4 atoms, then I create a 72 atoms supercell - 4*(3x3x2) - that has 3ax3ax2c dimensions and finally I tell atoms to use "P1" space group in order to replicate the supercell in x,y,z space and shift at the center the absorbing atom. Here the *problem*: the resulting _test-feff8.inp_ present good values of distances but strangely it has generated an additional Fe potential (there is just 1 Fe absorbing atom in the box/list). This is annoying because I have to remove manually the wrong "ipot" to run FEFF. Is it a stupid mistake generating the Atoms input file or is it an odd behaviour? Cheers, Mauro PS: Atoms 3.0.1 (linux) 05/08/15 PPS: Do not pay attention to coordinates and distances, these are just test-files! -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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XANES peak fitting
by Dominik Samuelis 18 Sep '08

18 Sep '08

Dear Jenny, although it doesn't exactly look like the software in your attached word file (this probably is some special XPS instrument software), peak fitting can very nicely be done with the Athena program (Analysis -> Peak fit). It's got all the features that you'd expect from a peak fitting software (difference plot, component plot, the possibility to fix certain values, and an almost arbitrary number of gaussians :-) ). If you are not restricted to the ifeffit package, the Peak Fitting Module in OriginLab's Origin Pro also produces nice results. It's not free software, though. Cheers, dominik Am 18.09.2008 um 21:45 schrieb ifeffit- request(a)millenia.cars.aps.anl.gov: > From: Jenny Cai <jennyh_cai(a)yahoo.ca> > Subject: [Ifeffit] XANES peak fitting > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <407251.2113.qm(a)web88208.mail.re2.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Hi guys, > > Could anyone tell me which software in Ifeffit package can do peak > fitting like the one shown in the attached file? > > Thank you in advance! > > Jenny Cai > -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

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