July 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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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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k range in ARTEMIS fitting
by Yuan Ping 13 Aug '07

13 Aug '07

Hello Bruce, Thank you for sharing your software. I found IFEFFIT in google and installed it recently in my MAC OSX computer. Trying to learn how to use it, I took a sample chi_k data (Al, k-edge) and played with the fitting in Artemis. One problem I can't solve by myself is that no matter how I chose the k range, r range, dr, dk, the fitting always stops at k~ 3 even though the data covers k= 1-8. So in the plot, the fit curve is much shorter than the data. Is this a plotting problem or a fitting problem? I've saved and attached the project to this email. Thank you very much for your attention. Yuan

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Bug in Artemis 0.8.010?
by Joji Kuniya 31 Jul '07

31 Jul '07

Hi Bruce Thank you for new version of Artemis. It works so good. But there is a problem on my PC working. Artemis makes feff.inp files on the screen, but I can not save it. When I click save button on the Artemis palette, my PC only says only "ping". And, in the Echo palette, there is a message that "Artemis trapped one or more errors! Error message dumped to screen". Is there some good idea to solve thins problem? Thank you Joji Kuniya

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Debye Waller factors for Water Molecules
by Paul Fons 30 Jul '07

30 Jul '07

I am analyzing some Zn organo-metallic protein complexes and have take EXAFS data at low temperature at the Zn edge. I am now in the midst of trying to fit the data. For the mean squared relative displacement terms, I am using Grant's DFT parameterizations for the Zn-cysteine system. This is working fine. In one of my complexes, I also have a water molecule within the "first shell". Does anyone have a suggestion for a reasonable MSRD term for this (at 20 K)? Paul Dr. Paul Fons Nano-Optics Reseach Team Team Leader National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons(a)aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所近接場光応用工学研究センター近接場光基礎研究チーム　チーム長ポール・フォンス

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Basic question in XANES calculation
by Joji Kuniya 27 Jul '07

27 Jul '07

Dear Sirs I am a beginner in XANES analysis. I tried to XANES simulation of Pt by Artemis program. Artemis stopped the calculation by memory limitation. I tried to down cluster size and RMAX parameter, and added "NLEG 4" after FMS sentence on feff.inp. But Artemis stopped the calculation with the same warning again. Please teach me how to make a good feff.inp file for XANES analysis. My PC is a notebook type PC(ThinkPad T60 with 2G memory). Thnak you. Joji Kuniya

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PPC Macintosh version of Horae 65 on SourceForge
by Paul Fons 25 Jul '07

25 Jul '07

I have made a new Macintosh installer for the PPC version of Horae 065 available on sourceforge. It would be neat if it could be copied to the cars download list in the wiki as well. Let me know if there are any problems. It seems to work fine on my end. As there are now two versions, a PPC and an Intel version, I have included PPC in the installer name, e.g. Ifeffit-1.2.9-Mac10.4_PPC_horae65_pkg.dmg Paul p.s. perhaps we should put the Horae 065 installer for Intel on the SourceForge site as well?

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[Fwd: Re: Mac intel OSX - Feff6 whereabouts]
by Katie Evans 24 Jul '07

24 Jul '07

Thanks for the advice, but sadly it didn't work. I also tried deleting the whole .horae and Perl folders and then reinstalling iXAFS, but that didn't help either. I checked the artermisrc file and it does say feff6 in the correct place, it just doesn't seem to be able to find feff6. Any more tips? Cheers, Katy ---------------------------- Original Message ---------------------------- Subject: Re: [Ifeffit] Mac intel OSX - Feff6 whereabouts From: "Jeff Terry" <terryj(a)iit.edu> Date: Tue, July 17, 2007 6:53 am To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> -------------------------------------------------------------------------- Hi Katy, I ran into this problem about two weeks ago. I have no idea why, it had worked fine for a few months before that. Paul's suggestion worked for me. Jeff On Jul 16, 2007, at 3:09 PM, paul fons wrote: > I can't say I have had this problem with either of my Intel Macs, > but I do know a solution that seems to have worked for others... that is to delete the preferences file for artemis which is located in your home directory under ".horae" and is named "artemisrc". Note that the "." (dot) in the directory name. This causes the finder and the default unix file listing "ls" command to not output the name as such preference files are considered "noise". To > delete the preference file you should run the command "rm ~/.horae/ artemisrc". This hopefully will help things... > Paul > On Jul 16, 2007, at 2:46 AM, Katy Evans wrote: > >> Hi, >> >> Apologies if this question has a very simple answer but I can't work it out. I installed the iXAFS package onto my new Mac (OSX 10.4.8) and almost everything works very well and it is very >> pleasant to use so thankyou. >> >> BUT Feff6 won't run. >> >> I can fit to existing Feff calculations but I can't make new ones, from .inp files that used to work on my other computer, or from quick first shell calculations. >> >> The message from Artemis starts 'This error is probably due to having Artemis configured incorrectly and so it does not know how to run Feff on your computer...' and goes on to say that I should check the value of the Feff executable in Preferences, and set it to Feff6. So I checked it and it was indeed Feff6. >> >> I looked for Feff6 on my computer and could only find a Feff6.atp file in the Perl directory (/Library/Perl/5.8.6/darwin-thread- multi-2level/Xray/atp) - should there be anything else? I tried typing this address into the box for the Feff executable option but this didn't help. >> >> I tried to remove everything and reinstall from the disk image but I am not sure if that was successful since I still only got the option to 'upgrade' when I clicked on the installer package. Where are all the things I need to remove if I want to get rid of the old version? >> >> Thankyou, Katy >> >> >> Katy Evans Dept. App. Geol. >> k.evans(a)curtin.edu.au Curtin University >> Tel: 0061 8 9266 4682 Bentley >> Fax: 0061 8 9266 3153 GPO Box U 1987, WA6845 >> >> >> >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Paul Fons > Team Leader > Nano-Optics Research Team > paul-fons(a)aist.go.jp > > Center for Applied Near-Field Optics > National Institute of Advanced Industrial Technology > Tsukuba Central 4, Higashi 1-1-1 > Tsukuba, Ibaraki Japan 305-8562 > > tel. +81-298-61-5635 > fax. +81-298-61-2939 > > The following lines are in a Japanese font > ã305-8562 è¨åçã¤ãã°å¸ã¤ãã°ä¸å¤®æ± 1-1-1 > ç£æ¥æè¡ç·åç ç©¶æ > è¿æ¥å ´åå¿ç¨å·¥å¦ç ç©¶ã»ã³ã¿ã¼ > è¿æ¥å ´ååºç¤ç ç©¶ãã¼ã ããã¼ã é· > ãã¼ã«ã»ãã©ã³ã¹ > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Athena 0.8.053, Artemis 0.8.010, Hephaestus 0.16
by Bruce Ravel 22 Jul '07

22 Jul '07

Hi folks, Just in time for the APS XAFS summer school, I am pleased (and relieved!) to release the latest source code for my XAS analysis programs Athena, Artemis, and Hephaestus. Here is a discussion of the new features: http://cars9.uchicago.edu/iffwiki/HoraeVersion065 Tarballs with the new source code can be found at my web site and at SourceForge. Matt and I are very close to having a new installer package for Windows. We will make an announcement when it hits SourceForge and the Ifeffit website. Hopefully packages for Mac/Motorola, Mac/Intel, and debian will be available soon. This release features LOTS of fixed bugs and user interface improvements to all three programs. The biggest new feature in Athena is the project selection dialog, which is described here: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/import/projsel.ht… Hephaestus sports an interesting new tool for helping you select the correct fluorescence filter: http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/hephaestus.html#p… As always, let me know about any comments, suggestions, observations, or bug reports you might have. Thanks to everyone who helped with this release. 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/exafs/

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