January 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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Re: [Ifeffit] iXAFS 2 beta 1 released
by Hind Al-Abadleh 28 May '08

28 May '08

Hi Jeff, This is great news. I downloaded the beta version, and got the error message "Apple's X11 for Mac OSX is not installed...". So, I downloaded the latest update for X11 from Apple's website from this page: http://www.apple.com/downloads/macosx/apple/macosx_updates/x11update2006113… And when I tried to install it, an alert message came "this system doesn't need this update". So, now I'm baffled, and truly don't know where to go from here. How would I check my system (OSX 10.4.11) for the X11 already installed? Any advice will be very much appreciated. Thanks, Hind ---------------------------- Hind A. Al-Abadleh, Ph.D. Assistant Professor Chemistry Department, Wilfrid Laurier University Science Building 3020F 75 University Ave. W. Waterloo, Ontario N2L 3C5 Canada Ph.: (519) 884-0710 ext. 2873 Fax: (519) 746-0677 URL: http://www.wlu.ca/science/chemistry/halabadleh/ ---------------------------- >>> terryj(a)iit.edu 12/07/07 12:15 AM >>> Hi All, iXAFS version 2 for Mac OS X 10.4 and above has been released as a beta version. We have tested this version on ppc and intel macs running OS X 10.4 and 10.5. You must have Apple's version of X11 installed in order to use iXAFS. Ken McIvor put in yeoman's work to build the full ifeffit, horea suite as a universal binary. He packaged it as a single drag and drop installation within iXAFS. Ken wanted to post this message but had an illness in the family. Hopefully, we can all thank Ken for his work to get this built in a manner that should work on all modern Macs. A link to download this version of iXAFS can be found at the MRCAT website: http://mrcat.iit.edu We forgot to put in the documentation that the iXAFS shell allows you to run any of the programs from the command line ifeffit, feff6, etc. Jeff _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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2007 APS XAFS School
by Julie Olmsted Cross 04 Apr '08

04 Apr '08

The on-line application for the 2007 APS XAFS School is now available at xafs.org http://www.xafs.org/Workshops/APS2007 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Julie O. Cross Advanced Photon Source Argonne National Lab 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439 tel: 630 327 7825 fax: 630 252 0580 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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saving a window function in Athena/Artemis
by van der Veen Renske 27 Mar '08

27 Mar '08

Hi! Could anyone tell me whether it is possible to save a specific window function together with the data in either Athena or Artemis? Another general question: how can I easily search for specific key words in the archive folders of the mailing list (without going through them individually)? Thanks & happy new year to you all! Renske Renske M. van der Veen PhD student Chergui Group EPFL Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3171 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

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phase shift correction
by Bindu R. 24 Feb '08

24 Feb '08

Could you tell me... Why the peak in the Fourier transform of the experimental spectrum is less than the actual one. Why it is required to include the scattering phase shift correction in the experimental one? As it is expected that the experimental one should show the actual bond length. Bindu Dr.Bindu R. Visiting Scientist DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- Forgot the famous last words? Access your message archive online. Click here.

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Athena installation
by cserhati csaba 29 Jan '08

29 Jan '08

Dear All, I installed the horae66 package on SUSE Linux 10.2. Everything went well, Artemis and Hephaestus works, but when I try to use Athena, I get the following message: unknown color name "Helvetica -12 bold" at /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Tk/Submethods.pm line 37. which looks like true, since 'Helvetica -12 bold' is certainly not a color name. On the other hand I do not have any idea where to go from here. Could you help me out of this please. Regards! -- Cserháti Csaba

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Athena installation
by cserhati csaba 29 Jan '08

29 Jan '08

Dear Bruce, thanks for the fast response. Ihave checked, the perl/Tk version which I use is 804.028 and there is no problem in the athenarc with fonts or colours. I any case I copied it to the end of the mail. The funny thing is, that Artemis works well, so there should not be anything wrong with the perl or Tk. I am not sure for 100% of course. Anyway, thanks! Regards! Csaba # These variables determine the color palette used by Athena. All of the # default values are named colors from X11's rgb.txt file. You can use X11 # named colors, any other named colors that your system recognizes, or # hexadecimal triplets (i.e. "#0000FF" for blue and so on). [colors] marked=darkviolet foreground=black background=cornsilk3 inactivebackground=antiquewhite3 activebackground=cornsilk2 darkbackground=cornsilk3 background2=bisque3 activebackground2=bisque2 disabledforeground=grey50 highlightcolor=blue2 activehighlightcolor=blue3 requiresupdate=steelblue4 button=red4 activebutton=brown3 mbutton=darkviolet activembutton=mediumpurple current=indianred1 frozencurrent=palegreen2 hlist=white single=red4 # These are the fonts used by Athena. There is currently no way of # modifying these within the preferences dialog. You will have to edit the # athenarc file directly. [fonts] smbold=Helvetica 10 bold tiny=Helvetica 8 normal med=Helvetica 12 normal medit=Helvetica 12 italic bold=Helvetica 12 bold boldit=Helvetica 12 bold italic large=Helvetica 14 normal fixed=Courier 12 entry=Courier 10 entrybold=Courier 10 bold small=Helvetica 10 normal -- Cserháti Csaba

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Re: [Ifeffit] Artemis
by Bruce Ravel 23 Jan '08

23 Jan '08

On Sunday 06 January 2008 11:26:53 you wrote: > Is there a way to calculate or read feff7 or FEFF8 paths with the > last version of Artemis? I could not find this information on this page: > > http://cars9.uchicago.edu/~ravel/software/aboutartemis.html > > and this option is not listed in your to-do list. I suppose that > there is a good reason for it! > > Implementing the possibility to read at once several FEFF paths (for > example from the list.dat file) could be useful, I think. Alain, I am CCing this general interest question to the mailing list. Artemis does not actually have a preference for the version of feff that you use. Since Feff is run as an external process, all you need to do is configure Artemis to use your prefered version. * In the Edit menu, select "Edit preferences". * In the Atoms groups, change `template' to "feff7" or "feff8", as you wish. That will have the effect of changing what kind of feff.inp file atoms makes. * In the Feff group, change `feff_executable' to the version of feff you are using. If the executable is not in the execution path, you will need to enter the fully resolved path as the value for that configuration parameter. If you have run feff independently of Artemis and simply wish to import the feffNNNN.dat files, that should work with no regard to the version of Feff that you used. The format of the feffNNNN.dat file did not change between feff6 and feff8. If you are seeing some particular failure of Artemis, then you will need to show me what happens. Without providing enough information for me to reproduce the problem on my own computer, it is not reasonable to expect that I can solve a problem. HTH, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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