October 2009 - Ifeffit - millenia.cars.aps.anl.gov

Cu2O fitting
by abhijeet gaur 26 Oct '09

26 Oct '09

Hi all, I had posted a problem related to fitting results of Cu2O. Bruce sir had suggested me to go through the Metal oxide modelling part of 14 chapter of Soil Analysis book by Shelly D. Kelly madam. I had gone through it and it really helped me in understanding the things in better way. I had done the fitting according to the procedure given in it. But still there are problems with fitting results. like 1. The value of SO2 is coming low. 2. Value of E0 is coming high though I have calibrated the experimental data. 3. The ss (Debye Waller factor) for some of the paths are coming very high. I am not able to understand the value of ss for multiple scattering path. One more problem is that if I I try to align the data with theory by adjusting E0 as given in 14 chapter, the data get distorted. The Artemis file is attached. This time I had made fitted the whole data in one fit by taking all parameter as guessed. With thanks in advance Abhijeet Gaur Research Scholar School of Studies in Physics Vikram University, Ujjain, India

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Installation ifeffit-1.2.4.dmg OS X 10.2.8
by Juergen Roehler 20 Oct '09

20 Oct '09

Hi, I am trying to run Ifeffit on MacOSX 10.2.8 from ifeffit-1.2.4.dmg on a Wallstreet Powerbook (a good old companion ,,,, ) > Ifeffit successfully installed in Applications folder [noname:/Applications/Ifeffit] jroehler% ls artemis icons lib perl5 tkatoms athena include man pgplot >XDarwin started (XFree86 4.2 installed from Fink, runs fine for >other X applications) >Click the perl scripts athena or friends, or run them explicitly >with perl 5.6 - athena & friends won´t start. Asked to choose a >program. Which one? > Try to start from terminal: [noname:/Applications/Ifeffit] jroehler% ./athena Can't locate Tk.pm in @INC (@INC contains: /sw/lib/perl5/5.6.0/darwin /sw/lib/perl5/5.6.0 /sw/lib/perl5/darwin /sw/lib/perl5 /sw/lib/perl5/darwin /System/Library/Perl/darwin /System/Library/Perl /Library/Perl/darwin /Library/Perl /Library/Perl /Network/Library/Perl/darwin /Network/Library/Perl /Network/Library/Perl .) at ./athena line 53. BEGIN failed--compilation aborted at ./athena line 53. Well, the *.pm´s and everything else is in /Applications/Ifeffit/lib/perl5 or /Applications/Ifeffit/, being not in the search tree. Don´t want to modify the system architecture copying /lib/perl5 and the other stuff to somewhere else. How to modify the scripts athena & friends. Other solutions? Would like to start jsut from the icons. Thanks in advance. Juergen ******************************* Juergen Roehler Universitaet zu Koeln Fachgruppe Physik Zuelpicher Str. 77 50937 Koeln mailto:Juergen.Roehler@uni-koeln.de http://www.uni-koeln.de/~abb12 *******************************

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Athena & Artemis crashing
by Chris Patridge 20 Oct '09

20 Oct '09

Hello all, Athena and Artemis have been suddenly crashing lately. There seems to be no single action which causes the crash. I am running on Windows XP Pro with SP3. This has happened only quite recent. Has anyone else experienced this problem? In addition, the autosave does not recover the lost work after crashing? Buena salud, Chris Patridge UB Graduate Student Department of Chemistry Cell: 315-529-0501

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xmu discontinuity
by Lisandro Giovanetti 16 Oct '09

16 Oct '09

Dear fellows, I am working with feff 8.2 trying to simulate Au L3 XANES and in every intent I get an xmu with a strong discontinuity near the infection point. Looking for the origin of this feature I find that is present in xmu0 and in the chi signal. Depending of the value of the Fermi level correction in the EXCHANGE card the discontinuity changes but I never get it disappears. Does anyone have a solution to this problem? I send one of the feff.inp files that I used. Thank you very much. Lisandro TITLE Au Bulk L3 HOLE 4 0 * Au L3 edge (11919.0 eV), second number is S0^2 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 1 1 1 1 3 EXCHANGE 0 1.0 0.0 NOHOLE *** 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 5.8 0 *AFOLP 1 *** Upper limit of XANES calculation. *** This *must* be uncommented to *** make Feff calculate full multiple *** scattering rather than a path expansion UNFREEZEF * kmax [ delta_k delta_e ] XANES 5.0 0.05 0.05 *** Radius of cluster for Full Multiple *** Scattering calculation *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6.5 0 RPATH 6.5 NLEG 3 *** Energy grid over which to calculate *** DOS functions * emin emax eimag LDOS -20 20 0.5 *** for EXAFS: uncomment the EXAFS card POTENTIALS * ipot Z element l_scmt l_fms stoichiometry 0 79 Au 3 3 0.01 1 79 Au_2 3 3 1 2 79 Au_3 3 3 1 3 79 Au_4 3 3 1 ATOMS * this list contains 887 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Au1 0.00000 2.04000 2.04000 0.00000 1 Au1_1 2.88500 -2.04000 2.04000 0.00000 1 Au1_1 2.88500 2.04000 -2.04000 0.00000 1 Au1_1 2.88500 -2.04000 -2.04000 0.00000 1 Au1_1 2.88500 2.04000 0.00000 2.04000 1 Au1_1 2.88500 -2.04000 0.00000 2.04000 1 Au1_1 2.88500 0.00000 2.04000 2.04000 1 Au1_1 2.88500 0.00000 -2.04000 2.04000 1 Au1_1 2.88500 2.04000 0.00000 -2.04000 1 Au1_1 2.88500 -2.04000 0.00000 -2.04000 1 Au1_1 2.88500 0.00000 2.04000 -2.04000 1 Au1_1 2.88500 0.00000 -2.04000 -2.04000 1 Au1_1 2.88500 4.08000 0.00000 0.00000 2 Au1_2 4.08000 -4.08000 0.00000 0.00000 2 Au1_2 4.08000 0.00000 4.08000 0.00000 2 Au1_2 4.08000 0.00000 -4.08000 0.00000 2 Au1_2 4.08000 0.00000 0.00000 4.08000 2 Au1_2 4.08000 0.00000 0.00000 -4.08000 2 Au1_2 4.08000 4.08000 2.04000 2.04000 3 Au1_3 4.99696 -4.08000 2.04000 2.04000 3 Au1_3 4.99696 2.04000 4.08000 2.04000 3 Au1_3 4.99696 -2.04000 4.08000 2.04000 3 Au1_3 4.99696 4.08000 -2.04000 2.04000 3 Au1_3 4.99696 -4.08000 -2.04000 2.04000 3 Au1_3 4.99696 2.04000 -4.08000 2.04000 3 Au1_3 4.99696 -2.04000 -4.08000 2.04000 3 Au1_3 4.99696 2.04000 2.04000 4.08000 3 Au1_3 4.99696 -2.04000 2.04000 4.08000 3 Au1_3 4.99696 2.04000 -2.04000 4.08000 3 Au1_3 4.99696 -2.04000 -2.04000 4.08000 3 Au1_3 4.99696 4.08000 2.04000 -2.04000 3 Au1_3 4.99696 -4.08000 2.04000 -2.04000 3 Au1_3 4.99696 2.04000 4.08000 -2.04000 3 Au1_3 4.99696 -- Lisandro Giovanetti

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Ag NP standards
by Chris Patridge 12 Oct '09

12 Oct '09

Hello all, Our group will be looking at the Ag L-edge soon. I wondered if anyone might have and share some data on Ag nanoparticles. We are running out of time and having trouble synthesizing small size (5-20nm) particles for comparison to our samples of interest. We will be collecting many Ag(salt) Cl, No3, So4 standards if anyone may be in need of those. Buena Salud, Chris Patridge Graduate Student Cell: 315-529-0501

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mailing list outages
by Matt Newville 12 Oct '09

12 Oct '09

Hi Folks, In about 2 hours (noon, Chicago time), I'm going to switch to a new machine as "millenia" which runs this mailing list and the ifeffit web pages. I don't expect serious problems with the web pages. If all goes well, the mailing list will not be out for long enough to notice. But don't be too surprised if mail to the mailing list takes a bit longer than usual this afternoon. Cheers, --Matt Newville

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Fwd: Athena troubleshooting
by Bruce Ravel 12 Oct '09

12 Oct '09

I am forwarding this message to the Ifeffit mailing list, which is the proper forum for Ifeffit software support. Please see http://cars9.uchicago.edu/iffwiki/BruceRavel/FormLetters/HelpRequest I have some comments, which I will post once this gets distributed by the mailing list. B ---------- Forwarded Message ---------- Subject: Athena troubleshooting Date: Wednesday 07 October 2009 From: Tom Malizia <fezzooli(a)gmail.com> To: bravel(a)bnl.gov Hello, this is Tom Malizia. I'm a master's student from the University at Buffalo, and my advisor (Tracy Bank) and I have been granted access to use beamline X11A for the student teacher program. Anyway, I'm emailing because I'm having some trouble with how to manipulate my data and interpret the results. I have run 14 samples (each 4 times) on the beamline, and I'm looking for a shift in the oxidation state of Uranium (4+ to 6+). I'm not sure and can't seem to find any literature on how significant the shift must be to prove anything. Of the 14 samples the uranium peaks for almost all are the samples are at 17160 eV, however a couple samples are at 17158 and another at 17159 eV. The beamline was filtered for both Thorium and Strontium and a zirconium foil standard was implemented. I have aligned all of the zirconium standards peaks, and still have this slight shift in the energy of uranium. Do you have any insight? Also, this is more of a software question. I'm not sure why, but about half of the samples flip their orientation 180 degrees (from positive y to negative y) when "normalizing" them. But when I'm trying to display several samples at once about half are showing positive peaks and half are negative peaks. For instance, samples 10, 3 and 1 don't flip when normalized, however all of the other samples do. If this isn't a good enough explanation I could send files or we could trouble shoot over the phone. I'd like to show as much as I can at the upcoming GSA conference next weekend. I appreciate your time. Thanks so much Tom Malizia University at Buffalo 814-594-4281 cell ------------------------------------------------------- -- 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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Re: [Ifeffit] Strange problem with FEFF 6L.02
by John McLeod 11 Oct '09

11 Oct '09

I realize this problem might be a bit out of scope for this mailing list, but I was wondering if anyone in the community has any insight into the matter. I was playing around with random clusters of atoms and I noticed that FEFF6 spits out the following error: At line 90 of file istprm.f Fortran runtime error: End of file For a few specific geometries. For most of the structures I have tried FEFF runs fine. I have also tested this on 2 other computers with the same results (all computers are linux machines though, and all with the same FEFF 6L.02 distribution from Artemis 0.8.011). At the end of this email is a sample feff.inp file that produces this error. The second atom, `Se_2' at position (-3.70, -2.63, -3.38) causes the problem. If we move `Se_2' to a new position of (-3.71, -2.63, -3.38) then FEFF runs fine. `Se_2' is over 2.2 angstroms from all other atoms in the cluster. If anyone out there is willing to help me out: 1. Has anyone run into this sort of thing before? 2. Does anyone know why it happens? 3. Do you get the same results as I do with the attached feff.inp? 4. Do the later versions of FEFF have the same problem, or is it native to FEFF6? 5. Is the problem related to my probably outdated version of Artemis? Thanks in advance, John McLeod Department of Physics and Engineering Physics University of Saskatchewan ----------------------------------------------- TITLE Selenium Cluster HOLE 1 1.0 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 3 RMAX 6.0 NLEG 4 POTENTIALS * ipot Z element 0 34 Se 1 34 Se ATOMS * x y z ipot tag distance 0.0 0.0 0.0 0 Se_1 0.0 -3.70 -2.63 -3.38 1 Se_2 5.66 * this atom causes problems * -3.71 -2.63 -3.38 1 Se_2 5.66 * this one does not -2.86 -0.69 -2.42 1 Se_3 3.81 -3.75 0.32 3.27 1 Se_4 4.99 -3.49 -2.06 0.33 1 Se_5 4.07 -1.57 -1.57 4.15 1 Se_6 4.71 0.44 -4.00 -2.28 1 Se_7 4.62 -1.06 0.84 4.08 1 Se_8 4.29 -2.92 1.59 -3.13 1 Se_9 4.56 -3.46 3.66 -1.11 1 Se_10 5.16 -4.87 2.90 1.37 1 Se_11 5.83 -2.64 -3.53 -1.52 1 Se_12 4.66 1.34 -4.46 1.72 1 Se_13 4.97 -0.26 -0.45 -4.18 1 Se_14 4.21 -1.52 -3.36 -3.14 1 Se_15 4.84 -4.85 -0.91 0.69 1 Se_16 4.99 -0.93 -4.90 0.37 1 Se_17 5.00 -0.41 1.95 -3.19 1 Se_18 3.76 0.20 -3.09 2.43 1 Se_19 3.94 -3.19 1.28 -1.23 1 Se_20 3.65 -1.02 1.69 -5.66 1 Se_21 5.99 0.07 3.30 3.46 1 Se_22 4.78 -1.67 4.62 -3.18 1 Se_23 5.85 2.23 -3.69 -3.68 1 Se_24 5.67 1.94 -0.35 -4.32 1 Se_25 4.75 1.23 3.89 -3.49 1 Se_26 5.37 -2.89 3.59 1.53 1 Se_27 4.86 3.71 -1.40 -2.73 1 Se_28 4.82 -1.06 4.39 -0.12 1 Se_29 4.51 3.77 -3.51 -0.02 1 Se_30 5.15 2.74 3.06 2.59 1 Se_31 4.86 2.90 -1.96 4.77 1 Se_32 5.92 2.44 1.72 3.98 1 Se_33 4.97 2.61 4.96 -0.31 1 Se_34 5.61 END -----------------------------------------------

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Cu oxide fitting result
by abhijeet gaur 10 Oct '09

10 Oct '09

Hi all, I am fitting Cu2O data using Artemis. I got a very good fit. But there are problems with the parameters. 1) The value of SO2 is coming very low 2) The value of sigma*2 for different path is coming very different from each other. 3) I have used a number of paths for the fitting as one shell has contribution from many paths. Also the paths are very close to each other (i.e. Reff), So how I should report the fitting results. I am not able to understand these results and also that where I had done mistakes, so please tell me. The Artemis project file is attached herewith

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Re: [Ifeffit] Ifeffit Digest, Vol 80, Issue 7
by abhijeet gaur 10 Oct '09

10 Oct '09

Abhijeet, I took a quick peak at your project and I find it very confusing. In the most recent fit, you are fitting only from 3.5 to 4.4 -- the area under the *third* peak in the data. I don't really know how to comment on this project because you have set a large number of parameters to seemingly arbitrary values. From a numerical perspective, the reason for questions 1 and 2 is because you are attempting to fit only a narrow and of the data and you have set the majority of your parameters. That seems an unlikely strategy to me. I think the best thing you could do would be to fit *all* of your data rather than an arbitrary and small band of it. It would probably be fruitful for you to study carefully Shelly's example of analysis of SnO2 from her recent review chapter. See http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2008-July/003641.html and http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-January/004012.html 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 Hello Bruce sir, Thanks for your response. You must be talking about the 14th chapter of the book "Soil and Mineral analysis using XAS". I have that chapter with me. It is very explainatory one. with regards Abhijeet

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