October 2011 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 22
by Lauren Glowzenski 14 Oct '11

14 Oct '11

UNSUBSCRIBE PLEASE On Fri, Oct 14, 2011 at 10:14 AM, <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. Re: Gold Nanoparticle first shell fitting (Kaiser, Julian) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 Oct 2011 14:14:00 +0000 > From: "Kaiser, Julian" <julian.kaiser(a)helmholtz-berlin.de> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Gold Nanoparticle first shell fitting > Message-ID: <DE491AE4BEF1864DB8831D1BC0E7EA1A0E554D33@didag2> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Anatoly, > > thanks a lot for your reply! > I don't see the problem yet. In the attached file > ("different_Au_foils.prj), there are two different gold reference foils > measured at two different synchrotrons. There is some difference but not > realy much. Could you please describe the regions that are worse comparing > my gold foil-file to yours, or if possible, attache the file with both foils > or at least a screenshot of the plot? > > Best regards, > Julian > > > > ________________________________ > Von: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov]" im Auftrag von "Anatoly I > Frenkel [afrenke2(a)yu.edu] > Gesendet: Dienstag, 11. Oktober 2011 20:29 > Bis: XAFS Analysis using Ifeffit > Betreff: Re: [Ifeffit] Gold Nanoparticle first shell fitting > > > Something is horribly wrong with the data here. > > I overplotted your reference Au foil against mine, and yours has distorted > XANES and too high EXAFS intensity compared to my data. Your amplitude > factor is 1.54 which also confirms that something was wrong in the > experiment. Perhaps - a misalignment? The NP data also look strange... > > I would not focus on the NP analysis until you figure out why your foil > data is so strange. > > > > > > ________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [ > julian.kaiser(a)helmholtz-berlin.de] > Sent: Tuesday, October 11, 2011 1:06 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Gold Nanoparticle first shell fitting > > Dear Ifeffit Community, > > I'm trying to fit a gold nanoparticle in the size of about 2 nm that is > immobilized by polymers. For my research it's enought to fit the first shell > only, becaues all I would like to analyze is the atomic distance in the > nanoparticle. After the (hopefully) correct background substraction in > Athena (athena file attached), there is a shoulder at approx. 2.1 Angstr?m > in the R-space. > In Artemis, fitting this shoulder seems not to be possible, while the fit > for the reference (gold foil) seems to be fine. (both artemis files are > attached to the e-mail). > If the k-range is decreased from 12.388 to a value between 9 an 10, the > shoulder disappears and the fit works fine. But I think by this change I > might modify the data too much. > Would be really nice, if sombody has an idea how to deal with the problem, > to get a hint how to solve this. > > Thanks a lot, > Julian > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren > e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. > Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de > > ________________________________ > > Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren > e.V. > > Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. > Vorsitzende Dr. Beatrix Vierkorn-Rudolph > Gesch?ftsf?hrer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > http://www.helmholtz-berlin.de >

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beamline for Al EXAFS
by Kompch, Alexander 13 Oct '11

13 Oct '11

Dear all, for the analysis of the location of the Al-dopant in ZnO, I am looking for suitable EXAFS beamlines. Dopant concentrations are 1-10%. So far I have only found ALS 6.3.1 and NSLS X15B. Can anybody recommend beamlines for Al EXAFS? My EXAFS experience is so far limited to the high energy range with signal detection in transmission (ionization chambers) and fluorescence (multi-element Ge-detectors). At such low energies as 1.5 keV for Al-K, the sample needs to be in vacuum, transmission will not work and Ge detectors probably the same. Does anybody have experience with Al-EXAFS, and can share a little about setup and what other complications to expect? Thank you, Alex.

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Re: [Ifeffit] XANES fitting
by Matt Newville 13 Oct '11

13 Oct '11

Hi Riti, I hope it's OK that I'm sending this to the ifeffit mailing list, as there might be other interesting perspectives on your questions. On Tue, Oct 11, 2011 at 3:47 PM, Ritimukta Sarangi <ritis(a)stanford.edu> wrote: > Hi Matt, > This is Riti again. This time I have a question about EXAFS, which you are an expert on :-) I would like to get your view on > systematic errors in EXAFS. Say the data were collected on a standard EXAFS beamline like 7-3 at SSRL. The data have > been collected using fluorescence mode and a 30 element Ge detector. The data are modest, between k=2-15 A. > > I used to quote in my papers that typical statistical and systematic errors lead to a total error in first shell distances of > +-0.02 A. I know it can be more than that in some circumstances but then I tried to look at it a little more closely to > separate out the systematic error from all sources (instrument, measurement, detector, Analysis), but I could not find a > good reference. I understand that this is a difficult number to estimate. I was hoping that you could shed some light on it. > Thanks! > -Riti > I'm not sure of a good general reference for that either, though perhaps some of the papers from Corwin Booth are a good place to start? Quoting +/- 0.02 Ang seems like a reasonable estimate for a typical value, but that's hardly rigorous. My sense is that it's pretty challenging to separate "systematic" and "random" noise for most data sets. Fluorescence data from a solid-state detector is probably the best-case for such a separation, because you have multiple detector elements or repeated scans, and usually the individual detectors or scans really are dominated by statistical fluctuations. If you add detector elements or scans together until the noise in the data (or variations in estimated parameters or estimated error bars) stops getting better, systematic errors are starting to be noticeable. Eventually, as you increase the fluorescence counts, the fits will stop improving, which should be when systematic errors dominate. --Matt

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building feff input file; position of absorbing atom(s)
by Dreher Marian 12 Oct '11

12 Oct '11

Dear Feff community, I have a question concerning the position of the absorbing atom when creating a feff input file. I am trying to calculate the EXAFS for a disk-like Ru nanoparticle that I "built" from literature data using the program Diamond. The particle has 3 atomic layers, looks somewhat half-pyramidal and consists of about 80 atoms. I then exported the atom positions and used them as an input for feff. Since my cluster is far from being a bulk structure, the spectrum I get strongly depends on where I place my absorbing atom. In this cluster the atoms can be grouped by common coordination number. Do I have to manually calculate the EXAFS for every single group and then calculate the mean spectrum weighted with the degeneracy of each group or is there a smarter way to do that? Many thanks, Marian. Marian Dreher, Dipl. Chem. PhD Student, Catalytic Process Engineering Group Paul Scherrer Institut General Energy Research (ENE) Laboratory for Bioenergy and Catalysis Office: OVGA/115 CH-5232 Villigen PSI Switzerland Phone: +41 (0)56 310 2937 email: marian.dreher(a)psi.ch

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Re: [Ifeffit] lifetime broadening of pre-edge peaks
by vikrai＠comcast.net 11 Oct '11

11 Oct '11

Hi Matthew, The lifetime broadening of the XANES features is determined by the time of life of the final excited state. This two-particle excitation includes the core hole and the photoelectron. The core hole may decay due to the various radiation or non radiation processes. The photoelectron state may decay due to inelastic collisions, plasmon excitations, etc. The time of life of the core hole, I believe, does not depend on the photon energy whilst the last is near the absorption edge. But it is not true for the photoelectron. It is better to write “photoelectron” because some of the pre-edge peaks which exist in the transition metal oxides spectra are in fact X-ray excitons and no photoemission can be observed. In these cases the final states are bound states and it is purely many electron effect caused by the core-hole - “photoelectron” interaction. For those pre-edge peaks the life time broadening is determined entirely by the core-hole life time. But as soon as photoelectron jumps to the conduction band the mechanisms of its inelastic scattering turn on and one should take into account the time of life of photoelectron (now without quotes). Unfortunately, it is difficult to determine which pre-edge peaks are excitonic and which are not. As it was already mentioned there are other mechanisms of broadening of the pre-edge peaks. For diamagnetic atoms it is thermal vibrations, for paramagnetic ones it is multiplet interactions as well. Good luck. Victor Krayzman.

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particle size and coordination number in Ru nanoparticles on carbon
by Dreher Marian 11 Oct '11

11 Oct '11

Dear Ifeffit Community, I am currently trying to extract the particle size of Ru supported on carbon from EXAFS data. I also recorded spectra of a Ru foil as a bulk reference sample. So, my approach is to fit the first coordination shell of my bulk reference, setting CN to 12. From that I get a value for s02. I'm then using this value in the first shell fit for the Ru nanoparticles in order to get the coordination number. However, the fit suggests that CN is still pretty much 12. What is changing drastically, though, is sigma^2 which usually doubles in value compared to the bulk sample. That makes sense, I guess, since there might be higher disorder in the nanoparticles. Obviously, there is a chance that my nanoparticles are rather big, in which case CN would be close to 12. However, STEM and HRTEM pictures suggest that the Ru particles are between 1 and 2 nm in diameter. I'm just starting to get into EXAFS analysis and pretty clueless right now about how to approach this. Happy about any input, many thanks, Marian.

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Re: [Ifeffit] lifetime broadening of pre-edge peaks?
by Joshua Kas 10 Oct '11

10 Oct '11

Hi Matthew, This may be a minor (and possibly different) point, but vibrational broadening can be different for different pre-edge peaks. See for example, Keith Gilmore and Eric L Shirley 2010 *J. Phys.: Condens. Matter* *22*315901. Cheers, Josh Kas On Mon, Oct 10, 2011 at 11:42 AM, <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. Re: number of independent points (George Sterbinsky) > 2. Re: lifetime broadening of pre-edge peaks? (Matthew Marcus) > 3. Re: lifetime broadening of pre-edge peaks? (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 10 Oct 2011 14:04:07 -0400 > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] number of independent points > Message-ID: > <CALoY8YwBz3jLWTLX+dosjiXs6Fv3RpG_UfG2yEz-X3XVn17abg(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Bruce, Matt, and Jeremy, > > Thank you for explaining this. Your responses are much appreciated. > > George > > On Mon, Oct 10, 2011 at 11:35 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On Monday, October 10, 2011 10:35:12 am George Sterbinsky wrote: > > > Since I haven't received a response to my previous question, I just > > wanted > > > to make sure I asked it clearly. > > > > I suspect the lack of response had more to do with it being a > > non-trivial question asked on a Friday afternoon :) > > > > > To elaborate, I am attaching a log from > > > Athena. The log file lists: > > > > > > "Independent points = 27.057617188" > > > > > > If I attempt to reproduce this result using the equation in the feffit > > > document, I find > > > > > > Nidp = { [2*(kmax - kmin)*(Rmax-Rmin) / pi] + 2} = { [2*(14 - 0.5)*(4.2 > - > > > 1.0) / pi] + 2} = 29.50197417, > > > > > > where I have used the k-range and R-range in the log file as kmax, > kmin, > > > Rmax, and Rmin. > > > > > > Can someone explain to me why may calculation does not reproduce the > > number > > > given for "independent points" in the log fie? > > > > George, > > > > A quick examination of the ifeffit source code shows that there are > > two issues: > > > > 1. Regardless of what it may say in the document, Ifeffit uses "+0" > > rather than "+2". See line 345 of > > http://cars9.uchicago.edu/svn/ifeffit/trunk/src/lib/iff_feffit.f > > > > A bit of history: Ed Stern wrote this paper back in 1993: > > http://dx.doi.org/10.1103/PhysRevB.48.9825 > > > > Over the years, many have expressed scepticism of his conclusion. > > The Bayesian work I mentioned earlier suggests quibbling over the > > value of N in the "+N" term misses the bigger issue. Ifeffit's > > use of "+0" provides a conservative yet easily stated estimate of > > Nidp. > > > > 2. The difference to the left of the decimal point has to do with the > > fact that Artemis allows you to pick any value for kmin, kmax, > > rmin, and rmax. When Ifeffit evaluates Nidp (and anything else) > > is actually takes the nearest grid points to those four values. > > The grid in k-space is 0.05 inv. Angstroms. This sets the grid in > > R space to be about 0.03 Angstroms, but not exactly. So the > > values of Rmax and Rmin used by Ifeffit to compute Nidp (and other > > things) are not quite what you specified. > > > > At some point, George, you may want to bite the bullet and look at > > source code. Details are not unknowable, they just might not be > > written down anywhere beside the source code. > > > > Here is the top of Ifeffit: > > http://cars9.uchicago.edu/svn/ifeffit/trunk/ > > > > B > > > > > > -- > > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > > Building 535A > > Upton NY, 11973 > > > > My homepage: http://xafs.org/BruceRavel > > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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lifetime broadening of pre-edge peaks?
by Matthew Marcus 10 Oct '11

10 Oct '11

Is the core-hole lifetime broadening of pre-edge XANES peaks the same as at the main edge? I'm looking into issues of de-noising of XANES epsctra, so need to figure out how narrow real features can be. mam

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number of independent points
by George Sterbinsky 10 Oct '11

10 Oct '11

Hello, I am wondering what values Artemis/feffit use for kmax and kmin when calculating the number of independent points (Nidp) for a fit done in R-space, where according the feffit document, Nidp = { [2*(kmax - kmin)*(Rmax-Rmin) / pi] + 2}, and kmax and kmin define the fitting range. I have tried using the Fourier transform range for kmax and kmin, but this does not give agreement with the value of Nidp reported by Artermis. Thank you, George

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Re: [Ifeffit] number of independent points
by Matt Newville 10 Oct '11

10 Oct '11

Of course. I do agree with both Jeremy and Bruce. -Matt On Oct 10, 2011 10:07 AM, "Bruce Ravel" <bravel(a)bnl.gov> wrote: > On Monday, October 10, 2011 10:48:25 am Kropf, Arthur Jeremy wrote: > > Perhaps there is a more subtle analysis of the data range, but I doubt > > it, since Matt is on record as suggesting that people not place too much > > emphasis on the exact value of N-idp, if I recall correctly. You can > > scale your chi-square, reduced chi-square, and errors using whatever > > value of N-idp you prefer. > > The papers by Rossner and Krappe (for instance, > http://dx.doi.org/10.1103/PhysRevB.66.184303) use a Bayesian approach > to evaluate the actual information content in an EXAFS signal. > Unsurprisingly, the Bayesian analysis finds something we should > already know -- the EXAFS signal is not an ideally packed sum of sine > waves. Consequently, the actual information content is rather less > than the Nyquist criterion. > > That is the context of the suggestion not to place to much emphasis on > the Nyquist number. (Since Jeremy invoked Matt, I should say that I > suspect that Matt would more or less agree with what I am saying > here.) It gives us a number to work with in evaluating the statistics > in Ifeffit. The interpretation of Ifeffit's statistical analysis > (which is a simple Gaussian analysis for a problem that is ill-posed > in the Guassian sense) has been a frequent topic of conversation on > this mailinglist over the years. It is also a topic in this talk that > I sometimes give: https://github.com/bruceravel/XAS- > Education/downloads/atea.pdf > > All that said, the question of the formula used and the value reported > in Artemis is a valid one. I don't recall off the top of my head, > but I will look at the codes. > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >

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