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

EXAFS simulations
by Cammelli Sebastiano 24 Oct '08

24 Oct '08

Dear IFFEFIT user I do some EXAFS simulations (FEFF8.4) of small pure Cu clusters (fcc bulk structure) and then I try to compare them with experimental data. The simulations are performed on all the shells, then all the contribution are added according to the number of atoms per shell (so the total xmu of a cluster of 19 atoms is = [xmu0+12*xmu1+6*xmu2]/19 where xmu0 is the xmu of the atom in the center of the cluster and xmu1 of the atoms in the first shell and xmu2 for the second shell). The first and obvious result concerns the peaks amplitude of the FT which is proportional to the number of atoms involved in the simulations. I have calculated the EXAFS spectra from the xmu.dat files. As you know in EXAFS simulations there is not pre-edge so finally is not easy to find the right value of E0. In the Athena.prj file I attached you can easily see this effect changing the absorption energy of Cu Bulk 4 from 8988.430eV to 8988.431eV. The amplitude of the first peak of the FT changes from 100 to 60! In order to overcome this problem I recalculated the FT using the chi.dat and not the xmu.dat. In the Athena file you can find the 8 simulations based on the xmu.dat (and they are called Cu bulk 1.... Cu bulk 8) and on the chi.dat (called CHI_Cu bulk 1....8). Of course they refer to the same cluster and they were calculated in the same way. Since these simulations, calculated on the Chi.dat, are very different from those calculated on xmu.dat, some questions rise. Moreover if you compare the FT of the simulations Chi_Cu bulk 5 and Chi_Cu Bulk 6 you can see that the amplitude of the first peak is larger for the smaller cluster. 1. Should I use the spectra I got from the xmu.dat or from the chi.dat? 2. Are the difference between Chi_Cu 5 and Chi Cu 6 (even if small) due to the E0 calculation? 3. How shall I behave if the first derivative of some simulations does not show a peak where it is "reasonably" expected (compare Cu Bulk 4 and Cu Bulk 7) 4. Do you have any other suggestions? Thank you in advance for any suggestion, Best regards Sebastiano Cammelli

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Re: [Ifeffit] Crytallites AND polycrystalline - Artemis handling?
by Scott Calvin 20 Oct '08

20 Oct '08

Sure, Joseph. These were nanoparticles made with a reverse micellar method. Past experience has shown that this synthesis produces a passivating oxide layer on an iron core; the passivating layer is usually amorphous, which is a good thing; hematite has a lattice mismatch and thus doesn't passivate. Linear combination analysis suggested this samples was 75% metal and 25 +/- 5% oxide. A typical amp entry is: S02_Fe*Frac_bcc*(1-3/4*reff/R_Fe+1/16*(reff/R_Fe)^3) S02_Fe is just the usual S02 factor, and "should" be from 0.70 to 1.0. It's lower than that in the fit I've sent you; that's one of the indications the fit may not yet be done. (I've actually gone much further with this fit, but that would have made for a more confusing file.) Frac_bcc is the fraction of iron atoms in an ordinary bcc metal environment. In the fit I sent you, it optimizes to 34 +/ 9%. Notice that's consistent with the linear combination analysis. That makes me happy. R_Fe is the radius of the core, modeled as a sphere. The formula in which it appears accounts for the reduction in average coordination number due to surface termination, and is discussed in several of my papers, including my articles: S. Calvin et al., Appl. Phys. Lett. 87, 233102 (2005) and S Calvin et al, Phys. Scr. T115 744-748 (2005). The oxide amp entry is much simpler: S02_Fe*Frac_Ox*2 Frac_Ox is 1-Frac_Bcc; i.e. what's not metal is oxide. The factor of 2 is just because I was working with a path from hematite that had coordination number of 3 (there's some splitting in hematite); I multipled by 2 to get an assumed coordination number of 6. Much of my subsequent fitting has been using bond valence theory to try to distinguish between coordination of 4 or 6 for the amorphous oxide. --Scott Calvin Sarah Lawrence College On Oct 20, 2008, at 8:46 AM, Joseph Washington wrote: > Scott, > Thank you very much. I am looking at this file and I understand > everything as far as the isotropic expansion terms in the delr and > the debye term. Can you clarify the amp math expression? Also, just > so we're on the same page, tell me a little about this system? > > Thank you again for your help! > > Joseph > > Scott Calvin wrote: >> Hi Joe, >> Here's an in-progress Artemis file for a system with some broad >> similarities to the one your describe. Perhaps it will help. >> Disclaimer: This is /not/ a final fit! >> --Scott >> ------------------------------------------------------------------------ >> On Oct 17, 2008, at 2:15 PM, Joseph Washington wrote: >>> Hello all, >>> I am working on analyzing Ge edge EXAFS data of an annealed sample >>> which >>> is likely to be Ge-Te crystallites with some amorphous material at >>> the >>> grain boundary (or perhaps, just Ge-N crystal material at the >>> interface). I do not have any information about the grain size, only >>> possible constituents for the grain and the boundary. Can anyone >>> give me >>> some examples of how Artemis might handle this? >>>

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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 12 Oct '08

12 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 06 Oct '08

06 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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