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

question
by Guvenc Akgul (gakgul) 17 Oct '08

17 Oct '08

Hi, This question very important for me.I have 5% Ti doped ZnO data.It includes not only Zn-K-edge but also Ti-K -edge data.I would like to figure out in following distances and Coordination numbers of them 1)Zn-O 2)Zn-Ti 3)Zn-Zn 4)O-O 5)Ti-Ti 6)Ti-O How can I do them?If you can help to me I will be very glad.Thanks for your help best regards guvenc

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Ifeffit 1.2.11b terminal output
by Gareth Jones 14 Oct '08

14 Oct '08

Hi all, The newest Ifeffit release dumps a whole lot of text to stdout. I've attached an example (hope that's okay), showing how it prevents the proper configuration of the Perl wrapper for Horae (see my previous post about the missing Ifeffit.pm file). Similar output is produced when using the Horae programs with the out-of-date wrapper, and even when running "ifeffit --help". This is in Ubuntu 8.04.1 (two machines), with gcc/gfortran 4.2.3-2ubuntu7 and pgplot 5.2.2-11ubuntu1, and Ifeffit 1.2.10a works fine. Is this normal, or did I manage to break Ifeffit somehow? Thanks, Gareth

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Horae 067 missing Ifeffit.pm (with solution)
by Gareth Jones 14 Oct '08

14 Oct '08

Hi everyone, This is a follow-up for a problem I encountered at the XAS08 PSI workshop, solved by Bruce, but it should probably be archived here in case anyone else discovers it. The Problem: Installation of Ifeffit and Horae following the build-from-source instructions [http://cars9.uchicago.edu/~ravel/software/downloads.html] appears to work, but Horae programs fail to start due to a missing "Ifeffit.pm" in "$prefix/lib/perl/...". You may at this point have copied Ifeffit.pm from the Ifeffit build tree, which at first seems to fix the problem. However, certain operations that require data to be copied between Perl/Horae and Ifeffit fail - in my case copying a group in Athena yields an apparently empty (or corrupt) group. This is reproducible for affected groups, but not all groups are affected. De-glitching is another test. The Solution: The Ifeffit Perl wrapper is apparently out-of-date. Bruce's Subversion repository contains an updated wrapper (libperlxray/Ifeffit) that fixes the problem, but hasn't been released as a source tarball yet - there are Subversion installation instructions at http://cars9.uchicago.edu/iffwiki/BruceRavel/EvolvingSoftware. Installation of the libperlxray/Ifeffit wrapper should be enough - you can use the release versions of the rest of Horae, but you may need Ifeffit 1.2.10a rather than 1.2.11b (more on this in another post). Anyway thanks to Bruce for figuring it out (and I hope my description isn't too inaccurate!) Gareth

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feff.inp trouble geometry
by penelope arancegui 13 Oct '08

13 Oct '08

Hi everyone, I'm having some trouble with a feff.inp file. I changed the geometry of a 13-atom Pd molecule but I don't know why FEFF8 doesn't read the archive. Using the cristollagraphy database for this molecule, ATOMS generated the following file: * This feff8 input file was generated by Artemis 0.8.007 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE ... * Pd K edge energy = 24350.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4.0 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4.0 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.20855 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 3.0 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 46 Pd 3 3 0.001 1 46 Pd 3 3 4 ATOMS * this list contains 13 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 1 Pd 0.00000 0 1.99550 1.99550 0.00000 0 Pd 2.82206 1 -1.99550 1.99550 0.00000 1 Pd 2.82206 2 1.99550 -1.99550 0.00000 1 Pd 2.82206 3 -1.99550 -1.99550 0.00000 1 Pd 2.82206 4 1.99550 0.00000 1.99550 1 Pd 2.82206 5 -1.99550 0.00000 1.99550 1 Pd 2.82206 6 0.00000 1.99550 1.99550 1 Pd 2.82206 7 0.00000 -1.99550 1.99550 1 Pd 2.82206 8 1.99550 0.00000 -1.99550 1 Pd 2.82206 9 -1.99550 0.00000 -1.99550 1 Pd 2.82206 10 0.00000 1.99550 -1.99550 1 Pd 2.82206 11 0.00000 -1.99550 -1.99550 1 Pd 2.82206 12 END With the coordinates I want to use, the file would be: * This feff8 input file was generated by Artemis 0.8.007 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 TITLE ... * Pd K edge energy = 24350 eV EDGE K S02 1 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 *** Radius of small cluster for *** self-consistency calculation *** A sphere including 2 shells is *** a good choice *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 4 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 4 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.20855 0 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -30 20 0.1 *** for EXAFS: RMAX 3 and uncomment *** the EXAFS card RPATH 0.1 *EXAFS 20 POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 46 Pd 1 46 Pd ATOMS * this list contains 13 atoms * x y z ipot tag distance 0 0 0 0 Pd 0 0 0 0 2.822 1 Pd 2.82206 1 2.52407 0 1.26204 1 Pd 2.82206 2 0.779982 2.40054 1.26204 1 Pd 2.82206 3 -2.04202 1.48361 1.26204 1 Pd 2.82206 4 -2.04202 -1.48361 1.26204 1 Pd 2.82206 5 0.779982 -2.40054 1.26204 1 Pd 2.82206 6 2.04202 -1.48361 -1.26204 1 Pd 2.82206 7 2.04202 1.48361 -1.26204 1 Pd 2.82206 8 -0.779982 2.40054 -1.26204 1 Pd 2.82206 9 -2.52407 0 -1.26204 1 Pd 2.82206 10 -0.779982 -2.40054 -1.26204 1 Pd 2.82206 11 0 0 -2.822 1 Pd 2.82206 12 END Do I need to modify something else besides the coordinates? Thank you for your help. Penelope _________________________________________________________________ Realiza búsquedas en Internet y llévate hasta ¡Un Auto! http://www.ganabuscando.com/Default.aspx

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Estimation of S02
by Hiroshi Oji 13 Oct '08

13 Oct '08

Dear all, Could you give me some advice on estimating the intrinsic loss factor (S02)? I am trying to estimate the S02 value in the curve-fitting analysis for Zr K-edge EXAFS. To do this, I did the curve-fitting analysis on the first shell of Fourier transform of Zr-K EXAFS of Zr-foil by Artemis. However, there was a marked difference between the amps obtained by the fitting, depending on the "Fit k-weights" as follows. kw amp 1 0.8145660 +/- 0.0486470 2 0.9230700 +/- 0.0673820 3 1.0439100 +/- 0.0854950 1,2,3 0.9081570 +/- 0.0722180 Is this a usual thing? I can't find the reasonable explanation why S02 depends on "Fit k-weights". I attached the Artemis project file. Thank you in advance for your cooperation. Hiroshi Oji ========================================================= 　Hiroshi Oji, Dr. Industrial Application Division Japan Synchrotron Radiation Research Institute (JASRI) 1-1-1 Kouto, Sayo-cho Sayo-gun, Hyogo 679-5198 JAPAN E-mail oji-h(a)spring8.co.jp =========================================================

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more on update problem
by Matthew 07 Oct '08

07 Oct '08

The update that causes the problem is Update 10 (iff_010.zip). When I re-downloaded from Sourceforge and let it do that update, it worked. mam

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problem with Runner
by Matthew 07 Oct '08

07 Oct '08

I just let Runner do the update to Ifeffit10 on a PC under XP, and now when I try to run any of the programs, the splash screen shows for a fraction of a second and the program dies. What's going on? mam

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Broadening
by Eugenio Otal 06 Oct '08

06 Oct '08

Hi Matt, I have measured the XAFS spectra by absorption. I really want to avoid obtain over detailed simulated spectras with a LDOS broadening smaller than core-hole broadening. So, I want to know the logical criteria to use the eimag in LDOS card. Thanks, euG Hi Eugenio, On Wed, Oct 1, 2008 at 7:42 AM, Eugenio Otal <eugenioh at gmail.com <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>> wrote: >* Hello everybody, *>* I have a doubt about the LDOS broadening, in xmu.dat I found that core-hole *>* broadening is 4.163, which value should I use in LDOS broadening to *>* reproduce the experimental spectra. *>* Thanks, euG * What experimental LDOS data do you have? If you've measured it by x-ray absorption (which is not exactly the LDOS), you'll need to include both the experimental energy broadening, and include the core-hole broadening. --Matt

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Re: [Ifeffit] What confidence limit is implied in the error bars
by Andrew Campos 03 Oct '08

03 Oct '08

Everyone, Thank you so much for all the help. I very much appreciate the help and the advice on how to approach this problem. I have a MUCH better idea now of what downfalls, considerations, and benefits that are associated with the least-squares fitting and the errors associated with this technique. Sincerely, Andrew Campos

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Re: [Ifeffit] What confidence limit is implied in the error bars forleast-squares fitting in Athena
by Don R Baker 03 Oct '08

03 Oct '08

Hi Shelly, I am very interested in Andrew's question too, but I am to ignorant to fully understand your response. Could you please provide some more detail? For example, when you state "a large source of uncertainty can come from the representation of the standards in matching the species in the sample." do you mean that heterogeneities (as Bruce mentioned in his email) in the standards are propagated into the fits of the unknowns? Or instead do you mean that an inappropriate choice of standards can create unreliability in the fit? I would appreciate any details you can add to your repsonse. Thanks, Don On Thu, 2008-02-10 at 14:22 -0700, Kelly, Shelly wrote: > Hi Andrew, > > > > If you are fitting XANES spectra with standards, a large source of > uncertainty can come from the representation of the standards in > matching the species in the sample. > > > > Shelly > > > > > ______________________________________________________________________ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Andrew > Sent: Thursday, October 02, 2008 3:49 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] What confidence limit is implied in the error bars > forleast-squares fitting in Athena > > > > Hi everyone, > > > > I’m fitting data with the least-squares method in Athena and am not > sure what the error bars correspond to. What I mean, are these 95% > confidence limits, or is it some other statistical way for error > analysis? If Athena says the weight of one phase is 0.049 (0.003), > what confidence are in the 0.003 error bar reported by Athena? > > > > (I have done a PCA of the XANES, and XRDs of the samples and am pretty > confident in the phases that I’m fitting). > > > > I greatly appreciate the help! > > > > Andrew Campos > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Melting rocks today for a better tomorrow . . . Don R. Baker, Professor of Geochemistry, Earth and Planetary Sciences, McGill University, Montreal, QC CANADA phone: 1-514-398-7485

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