July 2008 - Ifeffit - millenia.cars.aps.anl.gov

Bond lengths
by Bindu R. 25 Jul '08

25 Jul '08

Hi, Could you please clarify me, up to what decimal place in the bond lengths obtained from EXAFS fitting is reliable? If there are changes in the bond lengths in the fourth decimal place around the region of phase transition, can one consider this as a genuine one even though the error bars obtained from the EXAFS fitting are more than the variation in the bond lengths? Regards Bindu Dr.Bindu R. Visiting Fellow BG-37 DCMP&MS Tata Institute of Fundamental Research Homi Bhabha Road Colaba Mumbai-400 005 India Contact Number Lab- 022-2278 2256, 022-2278 2671 Mobile-919892536830 Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/

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Fwd: Re: Athena/Artemis
by Bruce Ravel 24 Jul '08

24 Jul '08

Hi gang, I received an interesting question this afternoon about EXAFS parameters and I thought that Olivier would benefit by hearing what more people than just me would have to say about this topic. He asks: Can you point me to documentation about the third and fourth cumulants? Since I study glasses, which are highly disordered, I would like to measure the anharmonicity parameters. What are typical values for C3 and C4? Grant Bunker has a very useful paper on the cumulants in Nucl. Instrum, and Meth. (1983) v. 207, p 437-444. Anatoly's paper on cumulants Phys. Rev. B 48, 585 - 588 (1993) is also handy and should give you some sense of what size the C3 and C4 parameters should be. In my experience, C3 and C4 should be smaller than sigma^2 -- perhaps by about 1 and 2 orders of magnitude, respectively. When they get much bigger than that, one can reasonably ask whether a short cumulant expansion (that is, an expansion out to only the 4th cumulant) is really adequate for describing the distribution of atoms in such a disordered material. There are people who have been applying reverse monte carlo or molecular dynamics to come up with better descriptions of highly disordered materials. Hopefully others will contribute to answering your questions. B Olivier: Sorry for switching languages on you -- hopefully it will prove useful to hear from others on the list. Je m'excuse de changer de langue pour cette conversacion -- on espere que il y aura des autres response utils ici sur la liste. ---------- Forwarded Message ---------- Subject: Re: Athena/Artemis Date: Thursday 24 July 2008 From: Olivier Villain <olivier.villain(a)impmc.jussieu.fr> To: Bruce Ravel <bravel(a)bnl.gov> Pourrais-tu m'indiquer où est l'aide concernant les paramètres 3rd et 4th ? Comme j'étudie des verres, donc du désordre, j'aimerais essayer des paramètres d'anharmonicité. Quelles sont les valeurs typiques ? Quelle est l'unité ? Je n'ai pas réussi à trouver ça dans l'aide. J'espère que je ne suis pas trop lourd... A bientôt, Olivier ------------------------------------------------------- -- 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/~ravel/software/exafs/

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Installation of the last versions on XP
by shiryaev＠crys.ras.ru 23 Jul '08

23 Jul '08

Hi Matt, I have a message pretty similar to what Kleper sees (both problems he has located: "could not read bitmap...." and "can´t open \share\per1\Xray\space_groups.db:"). This is indeed sounds like non-ASCII names on my computer. Would be nice to find a way to overcome the problem without logging as another user. Thanks in advance, A.Shiryaev

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Installation of the last versions on XP
by shiryaev＠crys.ras.ru 21 Jul '08

21 Jul '08

Hi everybody, Perhaps you may hep to resolve the following problem: I have no problems in installing and working with Ifeffit-1.2.6 on my Windows XP laptops. The problem concerns working with later versions: 1.2.9 and 1.2.10. There are no error messages on installation, but neither Athena not Artemis work. What can I change in setup? Thanks in advance, A.Shiryaev

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Linear Combination Fitting - More Questions
by Gudrun Lisa Bovenkamp 17 Jul '08

17 Jul '08

Hi everyone, I just learned that before Athena there was no such program to check on all combinations, so it was not that confusing - or just more work? I think this feature of Athena is very good tool, but when I really do not know what is in my sample how can it help? I try to answer it myself and someone can correct me: Certainly not all of my, say 10 reference spektra, are that similar that I can get several LCFs with the same say R-factor. So, I will get some clue to narrow the components. But still there can be, for example: Standard-combi 1, 2, 3 equal to 1, 4, 6. So, my analysis gives two solutions and one must be wrong, but both can be wrong. How can I tell? Can a PCA help me in this case? The results change significantly when I change the normalization. How do I know what is the 'correct' adjustment? - Yes, I read the Athena turorials, but I got no answers from there. I searched quite a while to find a complete documentation of the LCF formula used in Athena, but I could not find it. Many thanks, Lisa

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Re: [Ifeffit] Ifeffit Digest, Vol 65, Issue 10
by sankaran anantharaman 17 Jul '08

17 Jul '08

Hi Richard, If I could intervene in your discussion, a suitable phrase is already in use to differentiate the EXAFS Debye-Waller factor from that obtained in X-Ray diffraction..."Debye-Waller-like factor". Reference : M. Bauer, H. Bertagnolli:X-ray absorption spectroscopy - The Method and its application, Bunsen-Magazin, 9. Jahrgang, 6/2007, p.216 Regards, Sankaran Anantharaman Universität Stuttgart Institute of Physical Chemistry Research group of Prof. Dr. H. Bertagnolli Pfaffenwaldring 55 70569 Stuttgart > Bruce, > > While you're on your soapbox, if we drop "Debye-Waller factor" to describe > the EXAFS disorder term, would you suggest using only "disorder" or do you > have a better phrase to use? > > Rich > > -- > Richard Mayes > > Barnes Group > 450/452 Buehler Hall > Department of Chemistry > University of Tennessee > Knoxville, TN 37996 > > > >

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quotation of figures
by s440697＠stud.uni-goettingen.de 16 Jul '08

16 Jul '08

Hi, i have a print out of a talk (about XANES, XAFS and multiple scattering...) and i want to cite some figures (attached). Can anybody tell me the author etc...? I searched everywhere on the web (on several sites of XAFS-Summer Schools...). Unfortunately i do not have the talk as pdf-file only the print out. Maybe the talk is from Matt Newville? Maybe anybody recalls on this talk/slides or recognizes them? Thanks for your help. Have a nice day, Eckhard --------------------------------- Eckhard Bosman e.bosman(a)stud.uni-goettingen.de +49 (0)551-39-14441 Raum: E0.104 Institut für Röntgenphysik Friedrich-Hund-Platz 1 37077 Göttingen Germany

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third cumulant
by grant bunker 16 Jul '08

16 Jul '08

Matthew - as you know, it's trivial to just let b=1/a and the write the distribution as (x-x)^s Exp[- (x-x0)/b] so that the gaussian limit is obtained as b->0. So infinite parameters are not a problem. Your suggestion and other observations are quite right. In fact, if convoluting distributions is ok, you can use whatever your favorites are, since cumulants just add under convolution. grant On Jul 16, 2008, at 11:08 AM, ifeffit- request(a)millenia.cars.aps.anl.gov wrote: > OK, here's my $0.02. I've used the convolution of an exponential > tail function > exp(-(r-r0)/w) (r-r0)*w >= 0 > 0 (r-r0)*r < 0 > > with a Gaussian. This avoids having to have parameters go to > infinity to approach a gaussian. This function > is a little unwieldy in real space but is simple in k-space. > mam

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FEFF-SCF and Enot in Artemis
by Frommer Jakob 16 Jul '08

16 Jul '08

Dear all! Recently I read the two inspiring XAFS13-contributions of Shelly and Bruce dealing with the energy-shift (p.132) and the use of SCF-calculations (p. 137). In this respect I have a question regarding the Enot parameter in Artemis: Plotting the mue (4th column in xmu.dat) of a FEFF8.4 SCF calculation (of a transition metal oxide; here: Fe or Cr) against the second column ("e") of xmu.dat, I end up with a fairly decent reconstruction of my experimental XANES: the onset of the pre-edge resonances is located at negative energies (if I am right this is referred to as E_0 (bottom of the conduction band)) and the energy zero (i.e. Fermi energy) is located somewhere in the rising part of the absorption edge. If I then use the same (SCF) potentials and let FEFF do a path-expansion run, the header of the feffnnnn.dat contains a (negative) quantity called "edge", which gives exactly the difference between E_0 and E_fermi (as also explained in Matt's article: J. Sync. Rad., 2001, pp. 96-100). In the xmu.dat, k seems to be calculated relative to E_0 (i.e. to a negative energy in the 2nd ("e") column). Plotting a path in Artemis (or the xmu calculated for a single path) I had the impression that again k is referenced to E_0 (onset of the pre-edge feature) rather than to E_fermi (somewhere in the rising part of the edge). Is this true? Assuming that I set the E0-parameter in Athena to the first inflection point of the main edge (so in the upper nomenclature to something like E_Fermi) and assuming further that I do a shell-fit in Artemis, wouldn't I expect to end up (in an ideal case) with an Enot similar to the quantity "edge" given in the feffnnnn.dat rather than a Enot of (close to) 0? I also found a mailing-list contribution (dating back to 2004) of Wojciech and Matt addressing a similar topic - still it is not clear to me what the effect on Artemis' Enot will be. I hope I did not confuse too many things. I will greatly appreciate any hint clarifying this situation. With many thanks and best regards Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry

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cumulant/rdf question
by grant bunker 15 Jul '08

15 Jul '08

re the cumulant <--> rdf connection This isn't a general solution, but it may work well for your system. A poisson distribution (x-x)^s Exp[-a (x-x0)] is a pretty flexible for moderately skewed distributions, permitting variable C2 and C3 by adjusting parameters s and a. For large s and small a the distribution approaches a gaussian. Expressions for cumulants etc are in Yang et al, JNCS Volume 210, Number 2, March 1997 have fun - gb > matt, > > I have a problem with an exafs analysis: > from the exafs analysis (with feffit2.98) of the first shell of a > disordered > system > I get the first three cumulants. > now, I wander how can reconstruct from them the radial distribution > function > which is the best solution? I have tried with the skew-normal > distribution, > but for the high skewness (ratio of third cumulant to sigma3) > values I get - that is around 2.5 - it is not well defined. > Do you have a suggestion? > Thanks,

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