December 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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subscription
by 穆鑫 30 Dec '08

30 Dec '08

Hello: I want to subscribe the Ifeffit . Thanks! Happy New year!

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How to identify N and O atoms in the first coordinate
by mzhu＠udel.edu 22 Dec '08

22 Dec '08

Hello all, Merry Christmas! I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks. Best wishes, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html

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Re: [Ifeffit] How to identify N and O atoms in the first coordinate
by Frenkel, Anatoly 20 Dec '08

20 Dec '08

The fact that PCA tells between known Ni-N and Ni-O complexes by adding one more component when the wrong complex is added (N to O or vice versa) does not mean that there is specific fingerprinting sensitivity to N or O. One needs to demonstrate first that all Ni-N pairs have similar distances and disorder, regardless of their chemical surrounding, and that the same is true for Ni-O. Only in that case your PCA results indeed mean that the Ni sorbed biofilm have both types of bonds. Otherwise you cannot prove that it is Ni-N plus Ni-O vs. a situation where there are two unique types of Ni-O that have not been matched to your Ni-O standard and may thus fool you in thinking that one of them is due to Ni-N instead. Thus, before you conclude that, you should verify whether various Ni-N and Ni-O complexes have same pair properties. From your description it appears not to be the case since you have two components (not one) for your oxygen ligands and nitrogen ligands. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Dec 19 18:39:24 2008 Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate Hello Anatoly, Thanks for your reply. I could not do it as the literature you mentioned since I do not have detailed structural information as they do. I am wondering if the following method can be justified to indentify nitrogen atoms: 1) EXAFS data of 7 nickel oxygen-coordinated organic and inorganic complexes in which nickel only coordinates to oxygen atoms from carboxyl group, phosphoryl group and water molecules. 2) Fourier back transformation of the peak from 1-2 aus. in R+ delta-R space. This R range must cover the scattering peaks from both nitrogen and oxygen. Then chi functions of these complexes are obtained. 3) A principal component anlaysis (PCA) was performed over the oxygen-coordinated dataset of the chi functions obtained in the step (2). PCA analysis indicated two major components based on the IND values. 4)Then chi functions of two nitrogen-coordinated nickel complexes was obtained using the same method as step 2). It is certain that nitrogen atoms are coordinated to the nickel in the first shell in addition to oxygen atoms. 5) A target transformaiton of the chi function of two nitrogen-coordinated nickel complexes using oxygen-coordianted dataset resulted in the SPOIL values close to 5. Addition of one of the two complexes to the group of nickel complexes in PCA, PCA resulted in 3 components. These indicate that they have different coordination environment to the oxygen-coordinated nickel complexes. It is expected because they have nitrogen in the first shell. 6) A target transformation conducted on a sample of nickel-sorbed biofilm (back fourier transformed chi function in 1-2 aus.) resulted in the value close to 5. It means that the sample can not be represented by the nickel organic group, either. Since the first shell only can have two types of atoms, oxgen and nitrogen. If the nickel sorbed on biofilm can not be represented by the nickel oxygen-coordinated organic group which only has oxygen in the frist shell, it must have nitrogen atoms in the first shell. Also, linear square fitting of the Ni_biofilm with the nitrogen-coordinated complexes resulted in the better goodness than other oxygen-coordinated complexes. Thus, the nitrogen must exist in the first shell of Ni_biofilm sample. Do you think this method is reasonable? Best wishes, Mengqiang Zhu ----------------------- Mengqiang Zhu Ph.D Candidate Environmental Soil Chemistry Department of Plant and Soil Sciences University of Delaware 152 Townsend Hall Newark, DE 19716 http://ag.udel.edu/soilchem/zhu.html ---- Original message ---- >Date: Fri, 19 Dec 2008 16:34:36 -0500 >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov (on behalf of "Frenkel, Anatoly" <frenkel(a)bnl.gov>) >Subject: Re: [Ifeffit] How to identify N and O atoms in the first coordinate >To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov>, <ifeffit(a)millenia.cars.aps.anl.gov> > >Dear Mengqiang, > >To the best of my knowledge, in most cases Nitrogen cannot be discerned from Oxygen as a nearest neighbor since their scattering properties are similar. Thus, if you want to solve an "inverse" problem ("Which type of neighbors do I have") you cannot do it. However, if you believe you have some knowledge about the type of metal-oxygen bonding: either M=O or a M-O or a M-OH or a M-OH2 (the first one is the shortest and the strongest, the others may have similar interatomic distances but different bond strengths), you can advance somewhat. > >If you have a certain number of distinct models you want to compare the data against, it can be done via a linear combination fitting, or by direct algebraic extraction of any given type of the pair contribution from the data, as described, for example here: > >E. Poverenov, I. Efremenko, A. I. Frenkel, Y. Ben-David, L. J. W. Shimon, G. Leitus, J. M. L. Marin, D. Milstein. A terminal Pt(IV)-oxo complex bearing no stabilizing electron withdrawing ligands and exhibiting diverse reactivity. Nature 255, 1093-1096, 2008. > >See supplementary info to that article for specific details. >Regards, >Anatoly > > >________________________________ > >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of mzhu(a)udel.edu >Sent: Fri 12/19/2008 4:20 PM >To: ifeffit(a)millenia.cars.aps.anl.gov >Subject: [Ifeffit] How to identify N and O atoms in the first coordinate > > > >Hello all, > Merry Christmas! > I have some samples of heavy metal sorption on bacterial biofilm. I want to figure out what elements are coordinated with the heavy metal in the first coordinate. Since the oxygen and nitrogen have similar scattering factors, how can I differetiate them? Using shell-by-shell fitting or linear combination fitting with standards? Thanks. > >Best wishes, > >Mengqiang Zhu > > > > > > > >----------------------- >Mengqiang Zhu >Ph.D Candidate >Environmental Soil Chemistry >Department of Plant and Soil Sciences >University of Delaware >152 Townsend Hall >Newark, DE 19716 >http://ag.udel.edu/soilchem/zhu.html >_______________________________________________ >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 _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Problems with feff and crystallographic data (Now with bug report)
by Gregory Merchan 19 Dec '08

19 Dec '08

Hi Hashem, Atoms doesn't handle the occupancy data in the CIF file. See this page for more info: http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling#head-b273ecfd19542ec82… I assume you see a message like this one that I see: This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). If you look on the Atoms tab in Artemis when you open the CIF file, you should see that the co-ordinates for Mg and Al are all 0.00000 ; i.e., all Atoms sees is that they are in the same place. Bruce, here's two bug reports: 1. The warning message above is missing the word "less", as in "separated by _less_ than 0.93 Angstroms" 2. It's an extensive message but doesn't mention this kind of problem. If you want to drive yourself mad with interface stuff, you could catch and highlight these errors on input and disable the controls they affect until the input is corrected. A tricky part of that is making sure the user knows what the highlighting means and has a clue about how to fix the error without - say - throwing up a talking paperclip. A sort of "heavy tooltip" ("lead balloon"?) could be shown - placed so as not to obscure the relevant controls - with a brief message, a way to get to the more help, and dismissal button. An automatic fade out might be nice, not sure. So long as the bad input exists, there should be a way to get the message back, like mousing over the highlighted input or the disabled controls. I don't know of any cross-platform toolkit that makes that kind of thing easy. Cheers, Greg On Thu, Dec 18, 2008 at 10:04 PM, Hashem Stietiya <mstiet2(a)lsu.edu> wrote: > Hello! > > > > I was using Artemis to run feff and generate paths from hydrotalcite. > However, it failed to run and an error message indicated that there is > something wrong with the crystallographic data. I used the crystallographic > data of hydrotalcite from different sources, but encountered the same > problem. Can you please help identify the problem and run feff? > > > > Please find attached the crystallographic data for hydrotalcite. > > > > I appreciate your help. > > > > Regards, > > Hashem Stietiya > > Louisiana State University > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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Error bars reported in the curve-fitting analysis in Artemis
by Hiroshi Oji 19 Dec '08

19 Dec '08

Dear all, Could someone tell me how the uncertainities in the fitted variables are estimated in the curve-fitting analysis in Artemis? Thank you very much in advance for your help. Hiroshi Oji -- ========================================================= 　Hiroshi Oji, Dr. Industrial Application Division Japan Synchrotron Radiation Research Institute (JASRI) 1-1-1 Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198 JAPAN E-mail oji-h(a)spring8.co.jp =========================================================

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Problems with feff and crystallographic data
by Hashem Stietiya 19 Dec '08

19 Dec '08

Hello! I was using Artemis to run feff and generate paths from hydrotalcite. However, it failed to run and an error message indicated that there is something wrong with the crystallographic data. I used the crystallographic data of hydrotalcite from different sources, but encountered the same problem. Can you please help identify the problem and run feff? Please find attached the crystallographic data for hydrotalcite. I appreciate your help. Regards, Hashem Stietiya Louisiana State University

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New windows update
by Matt Newville 17 Dec '08

17 Dec '08

Hi Folks, Bruce and I put together a new Windows updater, and it is now posted and available for download. This should fix several small problems with athena and artemis. It should also fix problems that several people have noticed with the previous update. After the update, the versions should be Athena 0.8.058 Artemis 0.8.013 Ifeffit 1.2.11c If you have any trouble with this update not working to install and run the latest versions, please let us know. --Matt

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