December 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

9 21

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

12 22

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 >

8 9

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

4 5

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 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

5 9

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.

6 8

Re: [Ifeffit] Path updating in Artemis
by Silvio Levy 31 Dec '07

31 Dec '07

Dear Bruce, in fact this is the very first shortcoming I notice in Artemis. It's a terrific piece of software. And I'm writing to propose a workaround, which I hope would be quick to implement (in any case easier than any heuristic that may eventually solve the problem in Demeter). Just as you can export and import artemis.variables file, allowing batch control over the GDS list, I'd like to have the same for parameter assignments. See below for a suggested file format, taken directly from the "Path parameter math expressions" screen. The key is that upon rereading, paths would be identified by their number -- their order in the file would be irrelevant. Hence resyncing would require only three quick steps: exporting the parameters to a file, editing the "Path number" lines to coincide with the Interpretation column, and reading the file back in again! The export/import steps might appear under the Theory menu, like the corresponding operation under the GDS menu. What do you think? Silvio ****** [A missing line might leave the parameter value untouched, while a line with nothing after the colon would unset the corresponding value.] Path number: 1 Title: [C] % whatever appears in the Data & Paths list label: N: 1 SO2: amp delE0: enot delR: delr sigma^2: ss Ei: 3rd: 4th: Path number: 2 Title: [S] label:

1 0

Re: [Ifeffit] Path updating in Artemis
by Silvio Levy 31 Dec '07

31 Dec '07

> Modify the feff.inp file, run feff, import paths, > parametrize them. Thanks Bruce. The problem here is "parametrize them". This is too tedious a process to carry out every time two paths switch places. So I've been discarding and rereading only the paths that change numbers; still tedious, but doable. Incidentally, I have not been able to use "Export these path parameters / to selected paths" - it either does nothing or, worse, it exports the parameters to all paths. (Perhaps I don't understand the meaning of "selected" in this context.) Silvio

2 1

Path updating in Artemis
by Silvio Levy 31 Dec '07

31 Dec '07

Dear List (and especially Bruce) I recently restarted using Artemis after a hiatus. I seem to be confused about a key procedure used to worked before (unless I'm deluded). I load in an Athena project (a single curve to be fitted), and then a feff file that contains an approximation to my atomic positions (8 atoms). Then I run feff via artemis, and I guess/set/def the variables for each path. The paths to sulfur use the variables ampS, delrS, ssS; those to carbon use ampC, delrC, etc. (Not all variables are floated independently, but I like to keep the names separate and express dependencies explicitly.) Now suppose I tweak my feff data (in the feff.inp tab of Artemis) and rerun feff. If I DON'T import any paths at the end, as recommended by the dialog, the Reff, amp, etc. associated with each path in the "Data & Paths" panel remain unchanged, while the data for the paths in "Interpretation" panel get updated. The two columns are now out of sync, and pressing the Fit button merely redoes the computation using the old paths. If I rerun feff and DO import paths at the end, I end up with duplicate paths; the new ones have the the right Reff etc., but they use the default variables rather than the ones that I laboriously associated with the earlier paths. How can I get paths that have the variable scheme I created, but new data for each feff run? The only way I seem to be able to do this is by closing the project and reopening it. But I could swear that earlier this was not the case. What am I missing? Silvio

2 1

Fwd: How to fit the XAFS of alloy?
by Scott Calvin 28 Dec '07

28 Dec '07

Hi Kefan, I have forwarded your message to the Ifeffit mailing list. If you are not yet a member of that list, you can join at: http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit --Scott Calvin Sarah Lawrence College Begin forwarded message: > From: wang.kefan(a)gmail.com > Date: December 27, 2007 8:09:50 PM EST > To: SCalvin(a)slc.edu > Subject: How to fit the XAFS of alloy? > > Dear Scott Calvin > > Merry Christmas! > I want to fit the Ge-K edge XAFS of Si_xGe_1-x(May include O), and > where can I find practical processing example? There's so many > materials needed to be read, and I would ask you for some suggests > rather than search alone. :) Thank you very much! > > Best Regards > -- > Kefan Wang > School of Physics and Electronics > Henan University, 475004, P.R. China > E-mail: kfwang(a)henu.edu.cn; wang.kefan(a)gmail.com

1 0