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

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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polarization
by Asma Tougerti 15 Jul '08

15 Jul '08

Hi, I study the sorption of Ni on single crystals of alumina by exafs . the angle made between the electric field and the sample is 90 and 0 . I read in “Exafs analysis using feff and feffit , matthew Newville, j.synchrotron rad (2201), 8,96-100” that we can use feff and feffit to calculate exafs spectra . I have three questions: In this reference authors uses a feff7 Can I use feff6 or I need a feef recent version ? There is a manual that explain how to write a feffit.inp file? How I can include the polarization dependence on my calculation? Asma

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Re: [Ifeffit] third cumulant and radial distribution function
by Matt Newville 14 Jul '08

14 Jul '08

Hi Chiara, On Sat, Jul 12, 2008 at 2:58 PM, chiara maurizio <maurizio(a)esrf.fr> wrote: > 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, Hmm, you mean you get a number for "third" that is 2.5 times the number for "sigma2"? That seems huge. I think that may mean that the pair distribution function is so skewed that the cumulant expansion out to third order may not be complete enough to be useful (some say at this point that the cumulant expansion "breaks down", but as it is a simple measure of the moments of a distribution, it seems to me that it is always valid, but not necessarily useful). When the higher order cumulants become large, a histogram approach might be more meaningful. To do this, you can make a series of paths at 0.1Ang spacing (as an example), around your expected bond length, assign each of them a sigma2 value (perhaps a variable that is constrained for all paths to be the same) and a relative amplitude for each path that follows some arbitrary distribution function. Then you can have the fitting adjust the amplitude parameters for the distribution function. In this way, nearly arbitrary distribution functions can be modeled, though with some effort. Is that a reasonable approach for your situation? If not, can you give some more details for this system? --Matt

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