September 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

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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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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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Ifeffit 1.2.10
by Matt Newville 02 Oct '07

02 Oct '07

Hi Folks, I've just uploaded Ifeffit 1.2.10 to the cars.uchicago.edu and sourceforge.net sites. I'm posting both source code (ifeffit-1.2.10.tar.gz) and a Windows installer (ifeffit-1.2.10.exe) which includes the latest versions of Hephaestus, Athena, and Artemis. Installers for Mac users shouldn't be too far behind. For now, the downloads page at http://cars9.uchicago.edu/ifeffit/Downloads links to both 1.2.10 and 1.2.9 versions. It may take a day or so for the files to show up on all the sourceforge.net mirrors. The new Windows Installer reflects a new build process for the underlying library. This took some time to work out (you may recall some emails about this over the summer) , but we think it is working as well as any previous version. There are quite a few changes to Bruce's codes, all for the better. And this version does install and work on Windows Vista. For the source code kit, this now uses a new install location for PGPLOT, so if you're installing you must run PGPLOT_Install before installing ifeffit. Also in this version is support for (and default use of) gfortran instead of g77. If you need to use a different fortran compiler from the one found by default, you can use ./PGPLOT_Install --with-fortran=g77 ./configure --with-fortran=g77 make install As always, let us know if there are any problems. Cheers, --Matt

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Position available within the Molecular Environmental Science Group at Argonne National Laboratory
by Kenneth Kemner 27 Sep '07

27 Sep '07

Job Advertisement 312365 BIO – Assistant Physicist The Molecular Environmental Science Group in the Biosciences Division at Argonne National Laboratory has an immediate opening for an Assistant Physicist. This position is responsible for conducting research in environmental science by using synchrotron-based X-ray techniques. Work includes construction and operation of the MRCAT/ EnviroCAT bending magnet and insertion device beam lines at sector 10 at the Advanced Photon Source (APS), X-ray absorption studies, X-ray scattering, and X-ray microprobe techniques to gain a microscopic understanding of the fundamental chemical and physical processes that govern the outcome of macroscopic processes in the environment. Assists Molecular Environmental Science general users of the APS during the experiments at the APS. Also assists Molecular Environmental Science Group Leader to develop a national users` group for applying synchrotron-based techniques to problems in environmental science. Considerable knowledge of experimental X-ray absorption spectroscopy, including extended X-ray absorption fine-structure spectroscopy (EXAFS), X-ray near-edge spectroscopy (XANES) is required. Considerable skill in the operation of experimental equipment necessary for these and analysis and interpretation of these experiments is required. Good knowledge of X-ray diffraction and imaging techniques and the associated instrumentation. Good knowledge of potential applications of X-ray techniques to the outstanding problems in environmental science. These levels of knowledge and skills are typically achieved by attainment of a Ph.D. in Physics or a related discipline and 2-4 years of Postdoctoral experience applying synchrotron-based X-ray techniques to problems in environmental science. Ph.D. and 0-1 year experience/equivalent Master's Degree and 2-3 years of experience/equivalent Bachelor's Degree and 6-8 years experience/equivalent. Although a staff level research scientist position is available, outstanding applicants at the postdoctoral level will also be considered. Interested candidates should send a detailed CV, along with a list of publications, and the names and addresses of three references through the Argonne web site at http://www.anl.gov/jobs for requisition number 312365 BIO. Argonne is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC. Argonne is an equal opportunity employer, and we value diversity in our workforce.

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Re: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences
by Matthew 25 Sep '07

25 Sep '07

[Ifeffit] Artemis fitting using FEFF paths plus experimentalreferencesOf course I tried PCA! Over a certain range of temperatures, one component looks tolerably like magnetite. The other is sort of, but not exactly, maghemite. However, if I go below that restricted range, it's not pseudobinary anymore. Also, I still don't know what the "maghemite-like" end-member actually is. Still, for the purposes of the ALS user-meeting poster I have to hang in a week or so, I'll probably take the PCA analysis plus a FEFF fit to the one end-member, and try to do a more thorough job when I have time. No, it doesn't fit well to a combo of the references I have, which does include maghemite. To be fair, what I have is not an isothermal series but an isochronal series at different temperatures, so there's less reason for expecting simple kinetics than in an isothermal series. mam ----- Original Message ----- From: Anatoly Frenkel To: MAMarcus(a)lbl.gov Sent: Monday, September 24, 2007 6:59 PM Subject: RE: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences Matthew - please forward my reply to the list if you consider it appropriate. I am spammed out. Anatoly ************************* Matthew, May be it is not relevant, since I do not know if you have a series of EXAFS data at different stages of the oxidation, or just the initial and the final stages. If you do have several stages, including the starting (unoxidized) and final (oxidized, or a sum of oxidized and unoxidized, depending where you stopped at) ones, the principal component analysis seems to match your needs well. I assume you also have access to EXAFS data in bulk magnetite and maghemite references. PCA analysis may tell you (if you are lucky and your system is similar to those where such information was previously obtained): 1) The volume fractions of intermediate species at each stage of the oxidation: 2) Identities of each intermediate species The first part is entirely model-independent. The second part is not, but a reasonable selection of standard compounds (e.g., magnetite or maghemite) may help you isolating the intermediates. The good thing is that you do not need to fit a Fe-Fe and Fe-O bonds to the spectrum of the entire heterogeneous sample, where these contributions may be present in different species, and you have a large number of fitting parameters that describe such a model. Instead, you may end up obtaining that your species are identical with their bulk reference compounds (and thus no fit is required since the only thing you need to know is the volume fraction of this species) or, you may have to fit a couple of FEFF paths to that unknown species, after you deconvolute it from the mixture knowing what the rest of the phases are (it is doable in the case of one intermediate, but can be done in the case of a larger number of intermediates as well). Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Matthew Sent: Monday, September 24, 2007 7:05 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Artemis fitting using FEFF paths plus experimentalreferences I have a system in which Fe:C alloy nanoparticles are being oxidized. I have the EXAFS of the unoxidized nanoparticles, and I'd like to use that as a reference for fitting as in: Fe_EXAFS(oxidation_stage) = x*(unox_particles)+(1-x)*(Fe->O paths + Fe->Fe paths +...) where the Fe->O and Fe->Fe are based on magnetite and maghemite, which seem to be products of the oxidation. It's not just a linear fit to unoxidized+magnetite+maghemite because the oxide is somewhat disordered. If I do Artemis fits to the shells from the two oxides alone, I find I lose some Fe atoms (sum of fractions < 1), a result which is echoed in linear-combo fits to the oxides alone. Thus, I really want to do a hybrid fit. The unoxidized particles are highly disordered to the point where they don't fit well with reasonable shells, so I'd rather not have to represent them as FEFF shells. How can I do this hybrid fit? mam _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Artemis fitting using FEFF paths plus experimental references
by Matthew 24 Sep '07

24 Sep '07

I have a system in which Fe:C alloy nanoparticles are being oxidized. I have the EXAFS of the unoxidized nanoparticles, and I'd like to use that as a reference for fitting as in: Fe_EXAFS(oxidation_stage) = x*(unox_particles)+(1-x)*(Fe->O paths + Fe->Fe paths +...) where the Fe->O and Fe->Fe are based on magnetite and maghemite, which seem to be products of the oxidation. It's not just a linear fit to unoxidized+magnetite+maghemite because the oxide is somewhat disordered. If I do Artemis fits to the shells from the two oxides alone, I find I lose some Fe atoms (sum of fractions < 1), a result which is echoed in linear-combo fits to the oxides alone. Thus, I really want to do a hybrid fit. The unoxidized particles are highly disordered to the point where they don't fit well with reasonable shells, so I'd rather not have to represent them as FEFF shells. How can I do this hybrid fit? mam

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new Debian/Ubuntu packages
by Carlo Segre 23 Sep '07

23 Sep '07

Hello All: I apologize in advance for the length of this message. if you just want to download the packages the magic lines are at the bottom of this message, so you can just skip down there. I just posted new packages of ifeffit (1.2.10a), horae (066) and sixpack (0.61) in the debian-xray archives. At this point, I am supporting the following distributions and architectures: Debian etch (stable) i386, amd64, powerpc lenny (testing) i386, amd64, powerpc Ubuntu edgy i386, amd64, powerpc feisty i386, amd64, powerpc gutsy i386, amd64 The newest version of ifeffit (1.2.10a) required a new version of pgplot5, with a specific bug fix. This is also in the archive for the above architectures and distributions. A couple of notes about the specific distributions: Debian - If you are running etch/stable, my archive is the way to get these new versions. For the lenny/testing, you can simply wait until the packages migrate from sid/unstable but I have provided them in my archive if you want them sooner. When the migration happens, these packages will be replaced by the official Debian ones. The reason I am doing this is that there are sometimes long delays in the unstable ---> testing migration for ifeffit since it requires the non-free pgplot5 to be built. It is not always present on the Debian build machines (I am trying to make this happen, honest!). Of course, the sid/unstable packages (if you are brave enough to run the bleeding edge Debian system ;-) are in the Debian archives and should come in automagically. Ubuntu - The versions for edgy and feisty are backports. For gutsy, the release being currently prepared, I have built all the packages because the Ubuntu versions seem to be slightly behind those I put in Debian. Again, once the official Ubuntu versions become available they should replace my versions. Anyway, while I have tested the packages, please don't hesitate to email me aobut your problems. Now for the _real_ information. If you want to use these packages, you need to add my repository to your /etc/apt/sources.list or add them through the synaptic package manager if you manage your system in this, more graphical, way. ---- Debian (choose your distribution) deb http://debian-xray.iit.edu etch main contrib non-free deb http://debian-xray.iit.edu lenny main contrib non-free ---- Ubuntu (choose your distribution) deb http://debian-xray.iit.edu edgy main contrib non-free deb http://debian-xray.iit.edu feisty main contrib non-free deb http://debian-xray.iit.edu gutsy main contrib non-free Note that when you upgrade your Ubuntu system, say from edgy to feisty, these sources will not be automatically updated as the Ubuntu lines will. You will have to change them manually. 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 segre(a)iit.edu http://www.iit.edu/~segre segre(a)debian.org

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Athena merging question...
by Matthew Ginder-Vogel 18 Sep '07

18 Sep '07

Hi Bruce and list, I think I almost have a decent IFEFFIT script for my averaging problem. However, while looking at the IFEFFIT command that Athena uses to merge files I thought of a few questions. When merging the energy scales of the various files, why did you choose to use a quadratic interpolation rather than a linear or spline interpolation? Also, I notice that Athena sends a lot of commands that look like set vpkr.energy = vpkr.energy+0 or set yybe.merge = qinterp(yybe.energy+0, yybe.xmu, vpkr.energy) to IFEFFIT when merging files. What does the +0 do at the end of the array? I've been looking through the IFEFFIT documentation, but can't seem to find anything that clarifies that command. Also, if I try and issue the command at the IFEFFIT command line I get an error that reads "** cannot set scalar value to array **". So why can Athena issue the command and I can't? Thanks! Matt -- ******************************************* Matthew Ginder-Vogel Post Doctoral Researcher Center for Critical Zone Research Environmental Soil Chemistry University of Delaware http://ag.udel.edu/SoilChem/gindervogel.html (302) 831-0608 mattgv(a)udel.edu *******************************************

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