February 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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Query regarding inequivalent sites in the EXAFS fitting
by Bindu R. 29 Feb '08

29 Feb '08

Dear Bruce, Could you please tell me if there is an option to do the EXAFS fitting for a compound having the absorbing atoms at two inequivalent crystallographic sites. For example, In Ca3Co2O6 compound, the Co ion occupies two inequivalent crystallographic sites with the Co1-O bond distance at 1.960 and Co2-O at 2.09 Ang. How does one invoke the contribution of both the bond distances in the first shell fitting? Best regards Bindu Dr.Bindu R. Visiting Fellow DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Mobile-919892536830 --------------------------------- 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.

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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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Re: [Ifeffit] thanks for your posting
by Matt Newville 23 Feb '08

23 Feb '08

Hi Mustafa, On Fri, Feb 22, 2008 at 1:13 PM, Mustafa Hussein <mustafa.hussein86(a)yahoo.com> wrote: > Dear Prof Newville, > > Thanks for your reply. I have some questions, I am listing them below, OK. I'm going to forward with to the mailing list as well. > I am simulating the excited state dynamics of two platinum atoms, can I > specify two atoms as absorbing atoms? or I have to re-run the calculation > again to average over the two sites of absorption? You have to re-run the calculation again. > I used the Atoms.inp Archive, but I did not arrive at a molecule that might > be similar to mine. > So I need to build an input file? it is okay, I think I can deal with shell > scripting. That's fine. Using Pt metal might be a good place to start too. > What is meant by HOLE? and the values 1 and 1.0 are the default or they can > be changed? and at what basis? In HOLE 1 1.0 the first '1' means "Use the K edge (1s electron)" which is one of the most common edges used for EXAFS. For Pt you may want to simulate the more-commonly-measured L3 edge, which would use HOLE 4 The '1.0' means "multiply by a constant factor of 1.0", which is there to allow one to put in a factor (usually called S02) that multiplies the calculated EXAFS. For now, leave it as 1.0 -- it can be dealt with later or ignored for a pure simulation. There is some documentation for this on the Feff web page. > What do the 0.00000 coordinates for the absorbing atom mean? I suppose they > mean the atom is centered in a computational box or something, I do not know > exactly!! Feff needs only atomic coordinates of a "cluster of atoms" -- it could be a molecule, part of a crystalline solid, or coordinates from a simulation for a liqud, glass, etc. It does not need or implicitly impose periodic boundary conditions. So the coordinates are all in Angstroms, but relative to some arbitrary origin. It's common to put the absorbing atom at 0,0,0, but it is not necessary: "ipot = 0" specifies the absorbing atom. If you can generate x,y,z coordinates in Angstroms from your simulation, just use those. > You input six oxygen atoms, what are they? all bonded to two Mn atoms?? or > they are pertinent to solvent molecules? For the example I gave, those oxygens were bonded to the Mn. For EXAFS it generally does not matter a great deal whether the atoms are bonded or not, though for a gas or liquid 'residence time' is a factor, and the cluster should reflect a "snapshot" of the atomic arrangement on the timescale of the EXAFS measurement (which is femto-seconds). In many cases, the solvent is visible, especially for metals in water -- the hydration shell is seen. > I quote "generally feff needs no more than a few hundred atoms", of the > molecule in question, or including solvent molecules too? Actually, I am > doing my simulation in the gas phase, would this be okay with the input > requirements? Oh, sure. One potential (pun intended, sorry!) issue is that Feff does a real space calculation of the atomic potentials for the atoms in your cluster. For a gas phase (or non-condensed molecule) the 'emptiness' on the outside of the cluster can make the calculation a little less reliable. In my experience, I often put a few extra waters (well, O atoms) around a small molecule just to help the calculation. Also, note that for Feff6 that comes with Ifeffit/Artemis, it's recommended to take out all the H atoms -- they aren't see by the x-rays anyway and make the potentials calculation harder. I'm hope someone from the mailing list might be able to add more insight on simulations for small molecules.... Hope that helps, --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 60, Issue 4
by joshua jason kas 22 Feb '08

22 Feb '08

Another way to get feff to run is to define the stoichiometry. I found that the following cards work. Change the SCF definition to the following SCF 3.46808 0 30 0.05 and change the potential definition to POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 26 Fe -1 -1 1 1 26 Fe -1 -1 1000 2 29 Cu -1 -1 1 This makes feff assume that there are many Fe atoms for each Cu atom, which was what I was assuming from your feff.inp. Cheers, Josh > Message: 1 > Date: Thu, 21 Feb 2008 13:52:31 -0600 > From: "Matt Newville" <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] problem with feff.inp > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <b8522e3d0802211152p6fa9c908v24ba67bc2dfc81b2(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > It looks like the SCF calculation is having a hard time with the new > potential. The input file you sent only has atoms out to 2.48 Ang > (though perhaps you truncated it when posting???), but the > > SCF 4 0 30 0.2 1 > > in your feff.inp means to make a self-consistent potential out to 4 > Ang. Without any atoms out that far, I can imagine it would have > problems. I think you'll probably need a larger cluster than a > single shell for a reasonable XANES simulation. > > Hope that helps, > > --Matt >

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