August 2006 - Ifeffit - millenia.cars.aps.anl.gov

hafnium oxide
by m.bauer 17 Aug '06

17 Aug '06

hi everybody, does anyone have a literature reference explaining the shoulder in the XANES spectrum of HfO2 after the white line at about 9.58 keV. I think it is related to the number of oxygens coordinating, but i could not find any note about it by browsing the journals.... thanks very much! matthias -- Matthias Bauer Universität Stuttgart Institut für Physikalische Chemie Arbeitskreis Prof. Dr. H. Bertagnolli Pfaffenwaldring 55 70569 Stuttgart (Vaihingen) Telefon: (+49) 0711-685-4472 Fax: (+49) 0711-685-4443 E-Mail: m.bauer(a)ipc.uni-stuttgart.de homepage: http://www.ipc.uni-stuttgart.de/~matthias/index.htm

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Attempted XANES calc using FEFF8.1 - what's wrong?
by Matthew Marcus 16 Aug '06

16 Aug '06

I tried the XANES calculation on FEFF8.10 with calcite at the Ca K-edge as the object. I had just taken some data on this compound, and I wanted to see how it compares. The attached shows that it doesn't compare all that well. I've also attached the feff.inp file I used, which was made by ATOMS using coordinates from the atoms.inp database. I used default parameters and read the result from the xmu.dat file. The energy cal on the experimental data was done using the Sb L3-edge assumed at 4132.2eV, since 3um foils of Ca metal are a little hard to handle :-). Next stop, I suppose, is FDMNES, which I recently downloaded. mam

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Re: Ifeffit Digest, Vol 40, Issue 10
by Michel Jaouen 07 Aug '06

07 Aug '06

>Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > >To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > >You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Ifeffit digest..." > > >Today's Topics: > > 1. data file format (emmanuelle montarges-pelletier) > 2. Re: data file format (Matthew) > 3. Re: data file format (Bruce Ravel) > 4. The most important fitting parameters (Bridget Ingham) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 21 Jun 2006 10:25:47 +0200 >From: emmanuelle montarges-pelletier > <emmanuelle.montarges(a)ensg.inpl-nancy.fr> >Subject: [Ifeffit] data file format >To: ifeffit(a)millenia.cars.aps.anl.gov >Message-ID: <1F268809-6D80-4EE8-996D-209DFF3FEE07(a)ensg.inpl-nancy.fr> >Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed > >Hello >I have some problems with data file format as I try to import exafs >files in Artemis or in Athena. >I am working on a powerbook G4, with OSX 10.4.6. I installed the >ifeffit package, including Athena and Artemis. Athena could open any >XAS "raw" file from fluorescence or transmission measurements. >However, if I perform any modifications on these raw files with >exterior programs (Michalowicz programs, Kaleidagraph) and try to >import the new files , saved as text files, Athena or Arthemis can >not open them. I guess it may come from the encoding of the text >file. Do you have any clue on this encoding issue? Do you know any >program which would allow me to transform these text files in >readable files for Artemis? >Thank you for your answer >sincerely >Emmanuelle > > >There are two types of encodings which may differ among text files from >different countries and OSs. I >don't know how Athena&Co. handle either of them. One is that numbers and >decimals can differ per country. If >Kgraph is using a local encoding other than the American standard, say, >using commas instead of periods, it's possible >that Artemis won't understand it. I have the same problem with my analysis >programs. Every so often I get a panicky email >from a user whose files won't open. The other variation is in what >constitutes the end of a line, which is OS-dependent. It could >be carriage return, linefeed, or CR-LF. > mam > > >Salut Emmanuelle, > >Matthew's suggestion of floats with commas is a good suggestion. A&A >make no attempt at respecting localization. (That is, a number >between one and two might be written as 1,234 -- which would confuse >A&A -- rather than 1.234.) If that is the case, your best bet is to >go back to the exterior program and ask it nicely to write out points >instead of commas. Or you might need to edit the file by hand. > >I thought that the end-of-line issue (Matthew's other suggestion) was >one that was solved in A&A years ago. If that proves not to be the >case, please let me know. > >Another possibility is that the exterior program added other text to >the file that is confusing A&A. Here is my explanation of how Athena >reads ascii data files > > http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions > >and here is the explanation of the file-reading function in Ifeffit >which Athena uses: > > http://cars9.uchicago.edu/~ifeffit/refman/node24.html > >The situation in Artemis is similar, although restricted in the sense >that Artemis is expecting its data to be chi(k). > >If none of that clarifies the issue for you, I'll need to see an >example of the data file which is causing the problem. > >The easiest way to move data from Athena to Artemis is to have Artemis >import its data directly from the Athena project file. > >If there is some data processing feature that Athena does not do but >which you require before moving on to data analysis, you should >consider making a feature request here on the mailing list. Athena >will never get the features that you need if I am not aware that they >are needed! > >B > Just an additional point: take care to save the file as unix file and not standard Mac (use a free text editor as TextWrangler to do this kind of manipulation). Michel -- __________________________________________ Michel Jaouen Universite de Poitiers - UFR Sciences - SP2MI LMP UMR 6630-CNRS Boulevard Pierre et Marie Curie - Teleport 2 BP 30179 86962 Futuroscope - Chasseneuil Cedex France Tel : (33) 5 49 49 67 37 Fax : (33) 5 49 49 66 92 e-mail : Michel.Jaouen(a)univ-poitiers.fr __________________________________________

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Re: Re: Re: XAFS Analysis using Ifeffit
by jana padeznik 04 Aug '06

04 Aug '06

>How do you get those absorption backgrounds, free of EXAFS? I can see it >for Kr, but how did you do it for the other, >chemically-reactive elements? > mam > In short: we've chosen at least two compounds of each element with especially simple EXAFS signal (mostly glasses), modeled this signal and eliminated it from the original data. This residual is used as an approximate atomic absorption background for the other sample, whose spectrum, after subtraction of this background, is the basis for an improved EXAFS model. Afterwards, the role of the two spectra is switched. After a few steps the published estimates were obtained. The procedure is described in the article: Padeznik Gomilsek, J., Kodre, A., Arcon, I., Loireau-Lozac'h, A., Benazeth, Multielectron photoexcitations in x-ray-absorption spectra of 4p elements. Phys. rev., A, 1999, vol. 59, no. 4, 3078-3081 Some information can be found on Iztok Arcon's website: http://www.p-ng.si/~arcon/xas/ <http://www.p-ng.si/%7Earcon/xas/> Best regards, Jana

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Re: [Ifeffit] Re: XAFS Analysis using Ifeffit
by Alojz Kodre 03 Aug '06

03 Aug '06

Sorry, forgot the attachment. Lojz

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Re: [Ifeffit] Re: XAFS Analysis using Ifeffit
by Alojz Kodre 03 Aug '06

03 Aug '06

Dear Matt, >I'm still confused about the right way to handle these in practice. It >seems that >a choice of "arc-tangent", "lorenztian", or "mimic the shape of the main edge" >should work for most cases -- do you agree? It also seems there ought to be >a reasonable way for the algorithm to pick which of these lineshapes to use. Maybe you`ll find the two graphs in the attachment helpful - they are from our paper cited at the top and also accessible on Iztok Arcon`s homepage. The first graph shows the usual range of EXAFS (~ 1000 eV above the edge) on the horizontal scale, and the atomic number on the vertical scale, with inserted energies of the main MPE. You can see that for 3d elements (Ti-Zn) the EXAFS range is almost free of MPE, the prominent 1s3p still within 100 eV of the edge, and the weak 1s2p at the end of the usual EXAFS range. For 4p elements(Ga-Kr) the 1s3p slowly moves into the EXAFS region. And beyond Kr, the strong 1s3d excitation gets beyond the 100 eV mark, so that two prominent MPE are to be taken into account. The L EXAFS are, as seen from the graph, practically all infested by MPE, so that there are no "clean" or "safe" ranges of Z. In the second graph, the "real" atomic backgrounds, extracted from EXAFS spectra, are shown for 4p elements. ALthough very noisy, they show what kind of an ansatz would be necessary to approximate at least crudely their shape. I imagine that two functional terms with proper energy position and amplitude (these are mostly transferable, prepared in tables) but with a small common fittable energy shift (to account for different energy calibrations or small chemical shifts). To allow the usual sloppines in the practical EXAFS analysis regarding the use of proper "matrix" subtraction etc, it would be sensible to retain some smooth background function, either a spline or a polynomial, but with much less free parameters. My feeling is that a 4-interval spline or 4th degree polynomial should be sufficient since the spline would not need to simulate the sharp jumps of MPE. Best wishes Lojz

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Other programs than FEFF - GNXAS and MXAN
by Matthew Marcus 02 Aug '06

02 Aug '06

I heard a talk by Ziyu Wu of Beijing Synchrotron Radiation Facility in which he said that the international community prefers a package called GNAXS to FEFF for EXAFS calculations. He also has his own package called MXAN for XANES fitting. What do other people think of these programs? Would it be possible/worthwhile to modify Athena/IFEFFIT to use one of these other programs? I haven't investigated them, so I don't know whether it would be possible to put a shell around GNAXS which would make it look like FEFF and therefore be usable directly by IFEFFIT. mam

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Re: XAFS Analysis using Ifeffit
by jana padeznik 02 Aug '06

02 Aug '06

Hi Matt, > Personally, I'd like to see more data with >clear MEE to play >with, and would like to model these better than with an ad hoc arc-tanget. I'd >also like to see a real case where including MEE transitions gave different >structural results than an analysis that did not include them. Any takers? > I've chosen three real chemical problems from our work where multielectron excitations had to be taken into account in order to obtain structural information. I'm sending you original data together with our articles: - cetyl-trimethylammonium bromide (CTAB) adsorbed on carbon black with very weak structural signal (Br_CTAB.nor, Br-O bond). Spectrum of aqueous solution of KBr (Br_sol.nor) helped to separate atomic and structural features. Article: Kodre, A., Padeznik Gomilsek, J., Arcon, I., Preseren, R., Separation of weak EXAFS signal from atomic background in Br and Rb samples. J. synchrotron radiat., 1999, vol. 6, 306-307. - iodine in electrolyte, again weak EXAFS signal (I_MPE.mue, I-I bond). Due to simplicity of EXAFS signal we used shorter k-range to avoid distortion from MPE. Article: Padeznik Gomilsek, J., Arcon, I., Kodre, A. Atomic effects in EXAFS structural analysis of redox I[sup]-/I[sup]-[sub]3 solid state electrolites. Acta chim. slov.. 2006, 53, 18-22. Available online: http://acta.chem-soc.si/issues.html - CeO2 thin films annealed in air (Ce_air.mue) or Ar (Ce_Ar.mue). I'm sending a spectrum of CeO2 powder as well (CeO2.mue). As in some other lanthanides, MPE signal is very strong and affects structural analysis even in case of CeO2 powder. We subtracted (valence dependent) MPE estimate prior to EXAFS analysis. In this case MPE resonances are more important than arc-tanget. Article: Padeznik Gomilsek, J., Kodre, A., Bukovec, N., Kozjek-Skofic, I. Atomic effects in EXAFS structural analysis of mixed Ce oxide thin films. Acta chim. slov., 2004, 51, 23-32. Available online: http://acta.chem-soc.si/issues.html Best regards, Jana

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Re: XAFS Analysis using Ifeffit
by Jana Padeznik Gomilsek 02 Aug '06

02 Aug '06

Since only my zip files (spectra and articles) have appeared on the Ifeffit Mailinig list, here is once again the accompanying text: Hi Matt, > Personally, I'd like to see more data with >clear MEE to play >with, and would like to model these better than with an ad hoc arc-tanget. I'd >also like to see a real case where including MEE transitions gave different >structural results than an analysis that did not include them. Any takers? > I've chosen three real chemical problems from our work where multielectron excitations had to be taken into account in order to obtain structural information. I'm sending you original data together with our articles: - cetyl-trimethylammonium bromide (CTAB) adsorbed on carbon black with very weak structural signal (Br_CTAB.nor, Br-O bond). Spectrum of aqueous solution of KBr (Br_sol.nor) helped to separate atomic and structural features. Article: Kodre, A., Padeznik Gomilsek, J., Arcon, I., Preseren, R., Separation of weak EXAFS signal from atomic background in Br and Rb samples. J. synchrotron radiat., 1999, vol. 6, 306-307. - iodine in electrolyte, again weak EXAFS signal (I_MPE.mue, I-I bond). Due to simplicity of EXAFS signal we used shorter k-range to avoid distortion from MPE. Article: Padeznik Gomilsek, J., Arcon, I. , Kodre, A. Atomic effects in EXAFS structural analysis of redox I[sup]-/I[sup]-[sub]3 solid state electrolites. Acta chim. slov.. 2006, 53, 18-22. Available online: http://acta.chem-soc.si/issues.html - CeO2 thin films annealed in air (Ce_air.mue) or Ar (Ce_Ar.mue). I'm sending a spectrum of CeO2 powder as well (CeO2.mue). As in some other lanthanides, MPE signal is very strong and affects structural analysis even in case of CeO2 powder. We subtracted (valence dependent) MPE estimate prior to EXAFS analysis. In this case MPE resonances are more important than arc-tanget. Article: Padeznik Gomilsek, J., Kodre, A., Bukovec, N., Kozjek-Skofic, I. Atomic effects in EXAFS structural analysis of mixed Ce oxide thin films. Acta chim. slov., 2004, 51, 23-32. Available online: http://acta.chem-soc.si/issues.html Best regards, Jana

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