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

IFEFFIT for OS X 10.4
by Ann Liang 21 Jun '05

21 Jun '05

Hi all, I just recently upgraded my computer from Mac OS X 10.3 to 10.4 (Tiger). I was not able to open programs in the IFEFFIT package. Please help. Thanks, Ann -- ANN LIANG Bruce. C. Gates Catalysis Research Group Chemical Engineering & Materials Science University of California at Davis One Shields Ave. Davis, CA 95616 530-752-3544 (office) 530-752-1031 (fax)

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EXAFS mean free path in small particles
by Laurent Menard 21 Jun '05

21 Jun '05

Disclaimer: I'm an experimentalist and not a theorist. I'm not sure that Zhao and Montano's calculations are correct. I think their calculation for the transition probability assumes that the electron density is constant when, in actuality, there is a spatial dependence resulting from quantum confinement effects. As a result, the energy of the surface plasmon peak as calculated by Zhao and Montano is constant for all cluster sizes at approximately the classical value of omega(bulk plasmon)/3^0.5 and shows an increase with decreasing particle size. Including quantum confinement results in a blue shift of the surface plasmon resonance with decreasing particle size and a decrease in transition probability for decreasing particle sizes (as suggested by Anatoly). This change in the calculation will also impact the bulk plasmon and I don't know what that trend will be. As far as their experimental demonstration with Fe nanoparticles is concerned, I really can't make an assessment about the experiment since they don't indicate how the nanoparticle size was determined and I'm not familiar with their preparation of the nanoparticles. I'm not sure from this paper what the impact on the MFP will be although there very well could be some effect on the EXAFS. Personally, when I began working on EXAFS of nanoparticles and small clusters (Au13), I was leery of using the bulk phase and amplitudes to fit the data. My experience to this point has been that there have not been observable deviations of coordination numbers for nanoparticle systems using these FEFF inputs. That being said, I tend to agree with Matt that this is something that people working in this area need to think about a bit more than it seems they have judging by the literature. I would like to see some (correct) theoretical assessments that support the assertion that bulk phases and amplitudes are ok for nanoparticles that I think has been demonstrated by validating EXAFS results with other techniques (mostly electron microscopy). -Laurent

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EXAFS mean free path in small particles
by matthew marcus 20 Jun '05

20 Jun '05

I'm working on a couple of projects involving nanoparticles, and a collaborator pointed out an old paper by Zhao and Montano (PRB 40,3401(1989)) which claimed theoretical reasons why the electron mean free path in nanos should be smaller than in bulk. This would cause coordination numbers to be underestimated. The effect is supposedly due to a surface plasmon which grows in importance as particle size shrinks. I have reasons why I think this paper exaggerates the possible effects, but I'm posting this to see what other people think about this effect. The paper seems to have gone down into obscurity, but that doesn't mean it isn't right. Thanks. Matthew Marcus

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EXAFS mean free path in small particles
by Matthew 17 Jun '05

17 Jun '05

A couple of notes on this group treat the Zhao&Montano Al-plasmon results as if they were experimental truth. They are in fact theoretical, based on what I think is a jellium model, though that word isn't used. Their only experimental data is on matrix-isolated Fe particles. mam

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RE: [Ifeffit] EXAFS mean free path in small particles
by Frenkel, Anatoly 17 Jun '05

17 Jun '05

Matt, In their paper, Zhao and Montano studied Al particles that showed surface plasmon activity for sizes as small as 10 A. I had no idea that Al does it, and it is very peculiar. However, I have been dealing most heavily with gold nanoparticles. According to literature (here is another article: Sarathy et al, J.Phys.Chem. B, 1997, v. 101 pp. 9876-9880, and ref. 14 within), Au nanoparticles show no surface plasmon activity below 20 A. Our recent experiment, where we have taken UV-vis. measurements of several samples of Au nanoparticles that were very small (13 to 100 atoms) and monodisperse, did not show any surface plasmon band around 525 nm where it appears at larger particles. In fact, Zhao and Montano say in p. 3403: "we would like to point out that based on the experimental results for noble metals [Cu, Au, and Ag] no evidence of a substantial change in the electron MFP value between bulk and small particles was found". That, to my mind, is an indirect but a fair reason to reuse bulk amplitudes, at least for Cu, Au and Ag. I also think, if HRTEM and EXAFS agree, it says for itself (that bulk FEFF amplitudes are correct). If they do not agree, AND if other reasons for discrepancy can be ruled out (e.g., broad size distribution, or electron-beam caused growth of particles), AND if the discrepancy is in the right direction (EXAFS-determined size is smaller than the HRTEM-determined size), then surface plasmon and other losses should be looked into. And, I agree, it is an important issue to be aware about. Anatoly -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Matt Newville Sent: Tuesday, June 14, 2005 9:47 PM To: XAFS Analysis using Ifeffit Subject: RE: [Ifeffit] EXAFS mean free path in small particles Anatoly, > The point is, to my opinion, that since In the most > interesting range, below 2nm, the plasmon activity decreases, > therefore its effect on EXAFS interpretation, if any, should > be negligible. I think I may not understand your point. The Zhao and Montano paper shows very pronounced changes in the plasmon spectra between each of 10,3,2, and 1 nm for Al. At 1 nm, the surface plasmon is definitely dominating -- not going away. So their conclusion, that lambda changes substantially below 10 nm due to the changing relative importance of surface-to-bulk plasmons seems well-argued to me (not to say its correct). I agree (I think) with Matthew that the Zhao and Montano work shouldn't be too easily dismissed, though it might not be completely correct. I don't know of any other work on how lambda might depend on particle size, and never really thought about this. The Rao paper seems broader in scope and not necessarily addressing plasmons and mean free path, but I only skimmed it, so maybe I missed something. Their fig 8 definitely shows a size dependence of O K-edge, though I didn't immediately see a clear interpretation for this -- it could have several explanations. Again, I only skimmed this paper, so maybe I missed something: perhaps the electron diffraction literature has more information?? > ... There are other evidences that small particles have DOS > similar to molecules, not typical metals. Most notable is the > evidence that HOMO-LUMO band grows to more than 1 eV at sizes > of 1 nm range. Hmm, I'm not sure I see that becoming more molecular and less metallic indicates that using the bulk mean-free-path is OK. . The 'universal mean free path' that Feff uses and the fact that S02 is still has to be a fitting parameter even for excellent data with Feff8 suggests to me that there may be many hidden sins in Feff's mean-free-path calculation. Sadly, we seem to be a little short on theorists these days. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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EXAFS course at Brookhaven
by Anatoly Frenkel 16 Jun '05

16 Jun '05

Hello IFEFFIT subscribers: In September 28-30, 2005, National Synchrotron Light Source at Brookhaven National Laboratory will host a short course: "EXAFS Course: Theory, Experiment, and Advanced Applications" This hands-on course is aimed to help design, perform and analyze EXAFS experiments, and to learn about some of the potential pitfalls that must be avoided. The course will be self-contained, starting with the fundamentals and proceeding to the more advanced topics, including recent theoretical developments, data analysis techniques and specific applications of EXAFS. More information is available at the course web page: http://www.nsls.bnl.gov/newsroom/events/workshops/exafs/Default.htm Please pass it along to all who may be interested. Anatoly Anatoly Frenkel Yeshiva University

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Athena and Artemis reference
by Bruce Ravel 15 Jun '05

15 Jun '05

Hi folks, I just got word today that my and Matt's submission to Journal of Synchrotron Radiation has been published and is available on-line. Here is the citation: ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT B. Ravel and M. Newville Journal of Synchrotron Radiation, Volume 12, Part 4, pages 537---541. Here's a link: http://www.iucr.org/cgi-bin/paper?ph5155 This reference is more up-to-date and reflective of the current state of the codes than the reference in Physica Scripta from the Malmo EXAFS conference, so it is my preference that you use it. B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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odd feff6 behavior
by Bruce Ravel 13 Jun '05

13 Jun '05

Hi, Here's a feff6 curiosity. Take this atoms.inp file: title = TiN space = 225 a = 4.24173 b = 4.24173 c = 4.24173 core = Ti edge = K rmax = 7.0 atoms ! elem x y z Ti 0.00000 0.00000 0.00000 N 0.50000 0.50000 0.50000 Run atoms, then run feff6l (the one that comes with Ifeffit, it's the only version I've tried this with). Feff ends with this error message: Eliminating path degeneracies... Plane wave chi amplitude filter 2.50% np, np1x= 12001 12000 Fatal Error: at PATHSD: np > np1x This message comes from pathsd.f, but I don't understand either the message or the part of the code it comes from. Does anyone else have a hint as to the problem? One more datum. If you reduce rmax to 6.7 in the atoms.inp file, the problme persists. If you make rmax 6.6, feff6l is happy. Thanks, B -- Bruce Ravel ----------------------------------- bravel(a)anl.gov -or- ravel(a)phys.washington.edu Environmental Research Division, Building 203, Room E-165 Argonne National Laboratory phone: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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IFEFFIT on Tiger - confusion between Perl 5.8.1 and 5.8.6
by Brugger, Joel (SAM) 11 Jun '05

11 Jun '05

I lost IFEFFIT after upgrading to MAC OS X 10.4 (Tiger). Apparently, this is due to the fact that the upgrade replaced Perl 5.8.1 by Perl 5.8.6. I redid the IFEFFIT installation (for 10.3), which created a Perl5.8.1 folder with all the goodies. However, as the following error message shows, the system is not happy and is looking for some stuff in the new PERL. And does not find it. I'm not sure how to revert to 5.8.1, or alternatively more everything to the new 5.8.6. Hopefully this is a trivial question :-) Thanks for any help, JOEL [JoelG5:/Applications/Ifeffit/bin] joelb% ./hephaestus Can't load '/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle' for module Tk::Event: dlopen(/Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bu ndle, 1): Library not loaded: /System/Library/Perl/5.8.1/darwin-thread-multi-2level/CORE/libperl.dylib Referenced from: /Library/Perl/5.8.1/darwin-thread-multi-2level/auto/Tk/Event/Event.bundle Reason: image not found at /System/Library/Perl/5.8.6/darwin-thread-multi-2level/XSLoader.pm line 68. at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 10Compilation failed in require at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 13.BEGIN failed--compilation aborted at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk.pm line 13.Compilation failed in require at ./hephaestus line 54.BEGIN failed--compilation aborted at ./hephaestus line 54.Undefined subroutine &Tk::Event::CleanupGlue called at /Library/Perl/5.8.1/darwin-thread-multi-2level/Tk/Event.pm line 3.END failed--call queue aborted at ./hephaestus line 54.

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Importance and Edge Step
by Barton, David (DG) 08 Jun '05

08 Jun '05

Hello, I noticed two new features in Athena 0.8.040 and am unsure of how to use them. The new features are "Importance" and "Edge Step". I attempted to use the Edge Step feature by checking "Fix Step" and then entering a value, but the Edge Step always reverts back to the automated value. However, when I use the Increase/Decrease buttons (Left/Right arrow in Edge Step window) the edge step does change, but it only changes in increments of 0.01 which is much too large for my datasets. Is there something I am missing here? Also, I couldn't locate Bruce's changelog for Athena so I am unsure of what the new "Importance" feature does. Anyone used this new feature yet? Dave _________________________________ David Barton, PhD. The Dow Chemical Company Catalysis R&D 1776 Building Midland, MI 48674 USA

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