May 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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XAS School at the APS
by Bruce Ravel 02 Jun '06

02 Jun '06

Hi folks, We are almost at the application deadline for this summer's XAS school at the APS. Here is the URL: http://cars9.uchicago.edu/xafs_school/ This year's course is July 26-28. This will be an "advanced topics" class. The material covered will be geared toward people who have some background already in XAS and XAS data analysis and wish to sharpen their skills, expand their knowledge, and learn some of the tricks of the trade that the experts use in their own research. If you are interested -- please apply, but do so soon because time is running out! Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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new Debian package of SixPack
by Carlo Segre 26 May '06

26 May '06

I have uploaded a Debian package of the new version of Sam Webb's SixPack. It should also look for Ubuntu variants (use the "sid" version) Use the following apt lines for the different releases. deb http://fermi.phys.iit.edu/debian/sarge binary/ deb http://fermi.phys.iit.edu/debian/etch binary/ deb http://fermi.phys.iit.edu/debian/sid binary/ P.S. - will also produce Ifeffit 1.2.9 packages after Memorial Day. There are some unexpected changes in the Debian version of pgplot5 which I have to work through... Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 Carlo.Segre(a)iit.edu http://www.iit.edu/~segre

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Can ifeffit be run in MAC OS X based on Intel Processor?
by Jingen Xiang 25 May '06

25 May '06

Hi, guys I tried to install the ifeffit to my macbook (intel processor). But it's failed to run the athena which is software based on ifeffit. The version of ifeffit is "ifeffit-1.2.8-Mac10.4_horae61a_pkg.dmg". This version software works well in iBook (PowerPC). Who knows whether ifeffit can be run in MAC OS X based on Intel Processor? Thank you very much! Jingen

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residual in non-equally spaced data
by Francesco Giannici 21 May '06

21 May '06

Hope it'n not a known bug. Anyway, I have to report a strange behavior in Artemis 0.8.006 & Ifeffit 1.2.8 (everything updated today). I have extracted a chi(k) with EDA, which returns non-equally spaced data (equally-spaced in energy, I think), but the fix_chik macro in Artemis fixes everything (or so it seems) interpolating the data over an equally-spaced grid. Next, when I try to plot the residual functions, both in k and R-space, very weird things appear. Anyway, as expected, if I do myself the interpolation and I use the clean data, everything is ok. Bye, -- Francesco Giannici Dept. of Inorganic Chemistry University of Palermo giannici at pa dot ismn dot cnr dot it

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Re: from I.Demchenko - Institute of Physics PAS (question about FEFF6, 8)
by Bruce Ravel 17 May '06

17 May '06

Hi Iraida, I am sending my answer to the mailing list -- in part because it is an interesting and relevant question and in part because I am not sure I know the correct answer to your question. On Wednesday 17 May 2006 08:02, you wrote: > Dear Bruce, > > After reading on site http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > about possible differences in calculations by FEFF6 and FEFF8 I've tested > my models by both FEFF programs. And now, perhaps I'm making a stupid > mistake in atom.inp file and next in feff.inp files.or I have a problem. I > need to examine GaxMn1-xAs samples with the concentration of Mn about 1-2% > (for example). The measurements were done for K edge of Mn. Within the > initial model Ga atoms are replaced by Mn. My atom.inp file is present > below: > > title = GaAs:Mn (Mn_Ga model) > space = F -4 3 M > a = 5.65330 > core = Ga > edge = K > rmax = 6.0 > out = feff.inp > atoms > ! elem x y z tag > Ga 0.00000 0.00000 0.00000 > As 0.25000 0.25000 0.25000 > > Then in the feff.inp file in "potentials" card I change the central Ga atom > to Mn (in connection with the small concentration of Mn (1-2%) I didn't add > any Mn atoms in the second and third coordination shells). For this model > in the elementary cell we have: 48.4372% of Ga atoms; 50% of As atoms and > 1.56% of Mn atoms. Our cluster is limited to 6 Å (rmax = 6.0). > > POTENTIALS > * ipot z [ label l_scmt l_fms stoichiometry ] > 0 25 Mn -1 -1 0 > 1 33 As -1 -1 1 > 2 31 Ga -1 -1 1 > > ATOMS > 0.00000 0.00000 0.00000 0 Mn 0.00000 > -1.41332 -1.41332 1.41332 1 As 2.44795 > -1.41332 1.41332 -1.41332 1 As 2.44795 > 1.41332 -1.41332 -1.41332 1 As 2.44795 > 1.41332 1.41332 1.41332 1 As 2.44795 > -2.82665 0.00000 -2.82665 2 Ga 3.99749 > 2.82665 -2.82665 0.00000 2 Ga 3.99749 > 0.00000 -2.82665 2.82665 2 Ga 3.99749 > -2.82665 -2.82665 0.00000 2 Ga 3.99749 > 0.00000 2.82665 2.82665 2 Ga 3.99749 > 0.00000 2.82665 -2.82665 2 Ga 3.99749 > 2.82665 0.00000 2.82665 2 Ga 3.99749 > -2.82665 0.00000 2.82665 2 Ga 3.99749 > 0.00000 -2.82665 -2.82665 2 Ga 3.99749 > -2.82665 2.82665 0.00000 2 Ga 3.99749 > 2.82665 0.00000 -2.82665 2 Ga 3.99749 > 2.82665 2.82665 0.00000 2 Ga 3.99749 > .......... > .......... > > Then I do the calculations by FEFF6 and FEFF8 programs, respectively. > > In the table you'll find the differences in Amp for calculations done by > FEFF6 and FEFF8 programs (there are values only for the first three single > scat.). > > # degen reff Amp Scat. path > 1 4 2.448 100 feff6 Mn-As > 100 feff8 > 2 12 3.998 88.07 feff6 Mn-Ga > 101.44 feff8 > 5 12 4.688 64.42 feff6 Mn-As > 67.22 feff8 > > > > My question is: why do we have such big differences in Amp? Should I prefer > the calculations done by FEFF6 program? Asimilar question to this came up recently on the mailing list: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-March/002368.html And here is my response, explaining my best memory of how that amplitude term is computed http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2006-March/002405.html Jeremy and Feng also give useful responses to the original question in that thread. The bottom line is, I think, that the amplitude term is a very imprecise measure of the actual size and importance of a path. What's more, the exact details of how it is inaccurately calculated may be different in Feff6 and Feff8 (although I do not know that for a fact). What seems like a much more relevant comparison between the two is how they actually compare when plotted. So, import both the feff6 and feff8 calculations into Artemis and compare the two calculations path by path in k-space AND in R-space. When you do that, how different are they? And where in k- and R-space are the differences most pronounced? That will, I think, be a much more accurate comparison of the two calculations. Hope that helps, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Re: Athena won't read my NSLS x10c data
by Bruce Ravel 15 May '06

15 May '06

On Monday 15 May 2006 12:58, you wrote: > Dear Bruce, > > I downloaded the ifeffit-1.2.8.exe installer from > cars.uchicago.edu/ifeffit/download.html to my PC running Windows XP version > 2002, SP1. I can launch Athena (version 0.8.046 obtained through the > download) using either the desktop icon or the runner.exe, but when I try > to open one of my data files from NSLS beamline X10c, I get the message: > "filename could not be read by ifeffit as data file" My understanding from > reading on your website is that Athena should pre-process my data file so > it can be read by ifeffit. The version of Athena at the light source had no > problem reading my data files. Is there something I can do with this new > version to allow it to read my files or do I need to get the old version > from my colleagues at NSLS? I've attached one of my data files that could > not be opened by this version of Athena. Thanks for any suggestions you can > offer! Hi Nancy, This is a good mailing list question, so I am taking the liberty of CCing my response to the list. Not so long, I changed (hopefully improved) how Athena interacts with strangely formatted data. (NSLS X10C most certainly falls in the category of beamlines with strangely formatted data.) Now, Athena uses a plugin architecture to recognize and process strange data. This feature was implemented in Athena 0.8.045 and is described in some detail here http://cars9.uchicago.edu/iffwiki/HoraeVersion057 and in excruciating detail here http://cars9.uchicago.edu/iffwiki/AthenaFiletypePlugins The bottom line is that you need to enable the X10C plugin by going to the Setting menu, selecting "Plugin Registry", then enabling the X10C plugin by clicking its button on. The plugin registry is persistent -- that is, it remembers which plugins are enabled between sessions. You should only need to enable the X10C plugin once. It would seem that the version of Athena at the beamline either had this feature enabled or was older than version 0.8.045. I certainly had no trouble reading that data file once I had enabled the X10C plugin on my computer. B P.S. The current version of Athena 0.8.049. It is a bit of mystery to me why so many people tell the runner never to update their software. It's your computer and your choice, obviously, but it's a mystery to me nonetheless. To change your runner setting my hand, see: http://cars9.uchicago.edu/iffwiki/IfeffitOnWindows/WinUpdater If the value of "next_checktime" in updater.ini is set to something like "never" or "next year", then it's guaranteed that you'll soon be using an out-of-date version of Athena. -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Wurtzite interstitial sites
by Mauro Rovezzi 15 May '06

15 May '06

Dear all, Do you know the coordinates of the octahedral interstitial site in wurtzite? I mean, in a way that I can use Atoms to simulate a dopant in this site? Thanks, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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