October 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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Re: [Ifeffit] Your internet exchange with "Chachi" about FeCo, last year
by Dominik Samuelis 31 Oct '08

31 Oct '08

Dear Dr. English, unfortunately, I am not a metals and intermetallics expert. I mostly work on oxides and related phases. Nevertheless, I've now ordered your original TMS paper from our library. As soon as I've found the time to read your analysis, I'll get in touch with you. There might be a good chance that EXAFS could give additional insight into these fine domain structures, since - as you wrote - many atoms will have a large number of wrong next neighbors. Maybe, there are also some intermetallics experts on this list, who could comment on this more knowledgeably. Best regards, Dominik Samuelis > Dear Sir: I just ran across your exchange of ideas on FeCo order etc. > about this time last year. I did some experiments in the mid 60s > (Trans. Met. Soc AIME 236 (1966) 14ff.) on FeCo2V and showed that the > superlattice xray line [100} can be seen in brine-quenched thin strips > if the XRD is done with CoKa radiation. The lines are very broad in > as-quenched state and the peak narrows gradually with time of > reheating to a few hundred degrees C. > The interpretation was that we were seeing APB domains which were > unexpected but seemed obvious in hindsight--two interpenetrating, > multiply-connected domains sort of like "swiss cheese" (J. W. Cahn > called it "sponge" at the time--he wrote an elegant mathematical > analysis that appeared in Acta Met.). The "scale" of interconnection > changes with time at temperature as the structure coarsens to reduce > the energy associated with APB. I thought the picture was confusing > since "perfect order with very fine domain size" could as well be > descri bed as partial, or incomplete order due to large number of > wrong near neighbors. I don't know if there are other alloys or > chemical combinations in which B2 order is present with very fine > domain structure such as I described. I am not aware of any other work > that confirmed or reinterpreted my results. Any comments? -- Dr. Dominik Samuelis d.samuelis(a)fkf.mpg.de Max-Planck-Institut für Festkörperforschung Heisenbergstr. 1 70569 Stuttgart Germany Phone +49-711-689-1769 Fax +49-711-689-1722 Web http://www.fkf.mpg.de/maier/

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Re: [Ifeffit] Ifeffit Digest, Vol 68, Issue 29
by daesung 30 Oct '08

30 Oct '08

Dear J. Rehr, it is an interesting issue for me. I thought that FEFF calculates for L2 and L3 absorption edges if I use EDGE L3 card, since they overlap in a small energy region. Now I understand why I had bad results for L23 edge calculations. However, where can I find scripts for adding FEFF results for two edges? Are they somewhere in FEFF 8 documents? Please give me more informations Daesung Park On Thursday 30 October 2008 18:00:01 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > 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. Fe_L2L3 (Guvenc Akgul (gakgul)) > 2. Re: Fe_L2L3 (John J. Rehr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Oct 2008 16:17:10 -0500 > From: "Guvenc Akgul (gakgul)" <gakgul(a)aps.anl.gov> > Subject: [Ifeffit] Fe_L2L3 > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <fb33bc484270.49088c86(a)aps.anl.gov> > Content-Type: text/plain; charset=us-ascii > > dear all, > > I have to calculate L3 and L2 absorption edges for pure Fe as theorical > .how can I do this using FEFF? > > thanks > > guven > > > ------------------------------ > > Message: 2 > Date: Wed, 29 Oct 2008 20:03:51 -0700 (PDT) > From: "John J. Rehr" <jjr(a)phys.washington.edu> > Subject: Re: [Ifeffit] Fe_L2L3 > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.64.0810292003250.16641(a)donatello.phys.washington.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Subject: Re: [Ifeffit] Fe_L2L3 > > Dear Guvenc, > > It's pretty easy, but you have to do the calculation edge by edge and > then add, i.e., two calculations, one with > > EDGE L3 > > and one with > > EDGE L2 > > The FEFF project has scripts for adding FEFF results for two edges - send > email to jjr(a)phys.washington.edu for details. > > J. Rehr > > On Wed, 29 Oct 2008, Guvenc Akgul (gakgul) wrote: > > dear all, > > > > I have to calculate L3 and L2 absorption edges for pure Fe as theorical > > .how can I do this using FEFF? > > > > thanks > > > > guven > > _______________________________________________ > > 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 > > > End of Ifeffit Digest, Vol 68, Issue 29 > ***************************************

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Re: [Ifeffit] Fe_L2L3
by John J. Rehr 29 Oct '08

29 Oct '08

Subject: Re: [Ifeffit] Fe_L2L3 Dear Guvenc, It's pretty easy, but you have to do the calculation edge by edge and then add, i.e., two calculations, one with EDGE L3 and one with EDGE L2 The FEFF project has scripts for adding FEFF results for two edges - send email to jjr(a)phys.washington.edu for details. J. Rehr On Wed, 29 Oct 2008, Guvenc Akgul (gakgul) wrote: > dear all, > > I have to calculate L3 and L2 absorption edges for pure Fe as theorical .how > can I do this using FEFF? > > thanks > > guven > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Fe_L2L3
by Guvenc Akgul (gakgul) 29 Oct '08

29 Oct '08

dear all, I have to calculate L3 and L2 absorption edges for pure Fe as theorical .how can I do this using FEFF? thanks guven

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Re: [Ifeffit] Normalization of XANES spectra
by Jens Kruse 29 Oct '08

29 Oct '08

Thanks for your replay and sorry for the confusing question. but I think it not getting better. Scott, you are right LCF would be helpful but even with lot of standards it is hard to get a meaningful result from low concentrated samples at the N k-edge. I think my problem is than I don`t understand the physical meaning of a edge step normalized spectra. Is it the spectrum 1 x-ray photon would produce? Is it right that I loose the information of the absolute concentration after normalization so that I still can identify relative proportions of different compounds with in a sample but I can`t compare different spectra in an absolute way anymore? The extreme case would be a comparison of pure and a diluted spectra. jens ifeffit-request(a)millenia.cars.aps.anl.gov schrieb: > 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. Normalization of XANES spectra (Jens Kruse) > 2. Re: Normalization of XANES spectra (Frenkel, Anatoly) > 3. Re: Normalization of XANES spectra (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Oct 2008 15:02:54 +0100 > From: Jens Kruse <jens.kruse(a)uni-rostock.de> > Subject: [Ifeffit] Normalization of XANES spectra > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: <49086D0E.2000603(a)uni-rostock.de> > Content-Type: text/plain; charset="ISO-8859-15"; format=flowed > > Hi everyone, > > I have a general question: > I know Normalizing is something we do so that we can compare samples > measured > under different experimental conditions (removes the effect of different > gains ...) but I have problems in understanding and applying > normalization when also quantitative conclusions are needed when > comparing different spectra. > > If I have two XANES spectra (a) and (b) measure under the same > conditions but with different concentration of the absorbing atom with > in different molecules.If both normalized spectra show a peak 1 , but > this peak is higher in intensity in spectrum (a) than in spectrum (b), > does this mean that compound which produced peak 1 is also absolute > higher in concentration in sample/spectrum (a) or do I loose this > information after normalization? > Or can I just say: in the normalized spectrum (a) peak 1 is higher than > peak 2 suggesting that the compound leading to peak 1 is more abundant > (just relative proportions).But I can't say: The intensity of peak 1 in > the also normalized spectrum 2 is lower than in spectrum one, Therefore, > the compound leading to peak 1 is less abundant in spectrum/sample 2. ???? > > > I hope somebody can help me to understand this issue. > > Thanks a lot, > > jens > > -- Jens Kruse Institute for Land Use Faculty for Agricultural and Environmental Sciences Rostock University Justus-von-Liebig-Weg 6 18059 Rostock GERMANY Phone: +49(0)381-498 3190

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Your internet exchange with "Chachi" about FeCo last year
by Alan English 29 Oct '08

29 Oct '08

Dear Sir: I just ran across your exchange of ideas on FeCo order etc. about this time last year. I did some experiments in the mid 60s (Trans. Met. Soc AIME 236 (1966) 14ff.) on FeCo2V and showed that the superlattice xray line [100} can be seen in brine-quenched thin strips if the XRD is done with CoKa radiation. The lines are very broad in as-quenched state and the peak narrows gradually with time of reheating to a few hundred degrees C. The interpretation was that we were seeing APB domains which were unexpected but seemed obvious in hindsight--two interpenetrating, multiply-connected domains sort of like "swiss cheese" (J. W. Cahn called it "sponge" at the time--he wrote an elegant mathematical analysis that appeared in Acta Met.). The "scale" of interconnection changes with time at temperature as the structure coarsens to reduce the energy associated with APB. I thought the picture was confusing since "perfect order with very fine domain size" could as well be described as partial, or incomplete order due to large number of wrong near neighbors. I don't know if there are other alloys or chemical combinations in which B2 order is present with very fine domain structure such as I described. I am not aware of any other work that confirmed or reinterpreted my results. Any comments? Alan English Summit NJ

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Fe L2 L3
by Guvenc Akgul (gakgul) 29 Oct '08

29 Oct '08

dear all, I have to calculate L3 and L2 absorption edges for pure Fe.how can I do this? thanks guven

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