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

Re: [Ifeffit] PdO reference
by David Sprouster 03 Nov '11

03 Nov '11

Jason: The famous "Lytle database" actually has a couple of PdO sample spectra (link below). I think they can also be opened in the newest version of Athena as-well. http://ixs.iit.edu/database/data/Farrel_Lytle_data/RAW/Pd/index.html Hope that helps Dave ---------------------------------------------- David Sprouster PhD Postdoctoral Research Fellow Department of Electronic Materials Engineering Research School of Physics and Engineering The Australian National University Canberra ACT 0200, Australia Currently at Hysitron Inc. T: +612 612 50868 F: +612 612 50511 M: +1 612 600 1286 W: http://physics.anu.edu.au/eme/ ---------------------------------------------- On 3/11/11 12:00 PM, "ifeffit-request(a)millenia.cars.aps.anl.gov" <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: >PdO reference

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PdO reference
by Jason Gaudet 03 Nov '11

03 Nov '11

Hello! I've recently written an atoms input file for palladium (II) oxide (PdO) that fits well to some experimental data. Unfortunately, I do not have access to a PdO reference to validate the structure. We will probably run PdO on the same beamline in the near future, but until then it'd be nice to know how close my structure is to a standard. Does anyone have a PdO multicolumn file they are able to share? I will of course send the structure to the atoms.inp archive if it fits well. Thanks! -Jason

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Re: [Ifeffit] Athena download help
by Joe Peterson 01 Nov '11

01 Nov '11

The mailing list is great, thank you. I found a solution to one problem but it seems to have caused another. I will look at it for a little bit and post to the mailing list if I continue to have problems Thanks for you quick reply, Joe

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problems with athena after installing windows update
by kirshstein＠googlemail.com 31 Oct '11

31 Oct '11

Hello, I installed a security update for microsoft.net framework 4 on xp, server 2003, vista, window 7, server 2008 x86 (kb2572078). The problem is that since then, the graphics window crashes when I try to do linear combination fitting and in particular when I choose the option "plot components". with "the window crashes" I mean that it does not react to any further input to athena even though athena says that this or that was plotted, calculated...The only thing to make the window come alive again is to quit athena and start it again. but "plot components" and possibly other commands work every time to make it crash again. For another athena project, the graphics window becomes completely white and does not react to any command from the moment on that I choose to open that project, before even importing a single file into athena. Does anybody know what to do to make athena work properly again??? Regina

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Adsorbed Silver Spectra
by Luxton.Todd＠epamail.epa.gov 25 Oct '11

25 Oct '11

I was hoping someone on the list would have k-edge spectra of silver adsorbed to an oxide phase (iron, aluminum, manganese, silica). Any help would be greatly appreciated. All the Best Todd Luxton "A nation that destroys its soils destroys itself." Franklin D. Roosevelt www.epa.gov/nanoscience www.epa.gov/landscience

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Re: [Ifeffit] Horae problems Ubuntu [11.10 Oneiric]
by denis.testemale 25 Oct '11

25 Oct '11

Hello Carlo (and the list). Now it works (Athena/Artemis/Hephaestus). I didn't do an exhaustive investigation, I just checked that I could start the programs, get the X window (that I could never get before, with the error message) and read a project file. Thanks for the fix! Let me know if I can be of further help for your investigation of the problem. Regards denis Hi again Denis: On Mon, 24 Oct 2011, denis.testemale wrote: > Problem: > after upgrading to Ubuntu Oneiric 11.10, I now cannot start > Athena/Artemis, > with the following error: > /usr/bin/perl: symbol lookup error: /usr/lib/libpgplot.so.5: > undefined > symbol: XOpenDisplay > Hephaestus runs, but I tried to plot something from it (i.e. f' and > f'' > plots) and it crashes (with the same error). > > I uninstalled and reinstalled Horae with the sources list up to date > (deb http://debian-xray.iit.edu sid main contrib non-free > deb http://debian-xray.iit.edu oneiric main contrib non-free) > but without success. The problem is in the new build of pgplot5 with gfortran 4.6 and, possibly, the latest version of debhelper. In order to temporarily resolve this problem while I figure out how to fix it permanently, I have posted new pacakges for natty and oneiric on the debian-xray.iit.edu archive. Please let me know if it still won't work. Carlo -- Carlo U. Segre -- Duchossois Leadership Professor of Physics Associate Dean for Graduate Admissions, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org -- Denis Testemale Institut Néel - Département MCMF 25 avenue des Martyrs BP166 38042 Grenoble, France ph: +33 476 881 045 email: denis.testemale at grenoble.cnrs.fr

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Horae problems Ubuntu [11.10 Oneiric]
by denis.testemale 25 Oct '11

25 Oct '11

Dear members of the list, I thought I would send this message to Carlo Segre (who packages Ubuntu versions of Horae), but this message might be of interest to other persons on the list, and someone else may even have a solution for me. Problem: after upgrading to Ubuntu Oneiric 11.10, I now cannot start Athena/Artemis, with the following error: /usr/bin/perl: symbol lookup error: /usr/lib/libpgplot.so.5: undefined symbol: XOpenDisplay Hephaestus runs, but I tried to plot something from it (i.e. f' and f'' plots) and it crashes (with the same error). I uninstalled and reinstalled Horae with the sources list up to date (deb http://debian-xray.iit.edu sid main contrib non-free deb http://debian-xray.iit.edu oneiric main contrib non-free) but without success. I googled a bit about the problem, but didn't find anything convincing (the only answer that is promising is unreachable). Among the information you might need: ##lsb_release -a: Distributor ID: Ubuntu Description: Ubuntu 11.10 Release: 11.10 Codename: oneiric ##dpkg -l | grep ifeffit ii ifeffit 2:1.2.11d-7build1 Interactive XAFS analysis program ii libifeffit-perl 2:1.2.11d-7build1 Perl extensions for IFEFFIT ##dpkg -l | grep horae ii horae 071~svn536-1 interactive graphical processing and analysis of EXAFS data ii horae-doc 072-1 help file documentation for athena and hephaestus ##dpkg -l | grep pgplot5 ii pgplot5 5.2.2-17build1 large subroutine library for plotting scientific data ##dpkg -l | grep perl-tk ii perl-tk 1:804.029-1.1 Perl module providing the Tk graphics library ##perl -e 'use Config::IniFiles; print $Config::IniFiles::VERSION, $/' 2.68 Thanks for your help on this one. Regards Denis -- Denis Testemale Institut Néel - Département MCMF 25 avenue des Martyrs BP166 38042 Grenoble, France ph: +33 476 881 045 email: denis.testemale at grenoble.cnrs.fr

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Gold Nanoparticle first shell fitting
by Kaiser, Julian 21 Oct '11

21 Oct '11

Dear Ifeffit Community, I'm trying to fit a gold nanoparticle in the size of about 2 nm that is immobilized by polymers. For my research it's enought to fit the first shell only, becaues all I would like to analyze is the atomic distance in the nanoparticle. After the (hopefully) correct background substraction in Athena (athena file attached), there is a shoulder at approx. 2.1 Angström in the R-space. In Artemis, fitting this shoulder seems not to be possible, while the fit for the reference (gold foil) seems to be fine. (both artemis files are attached to the e-mail). If the k-range is decreased from 12.388 to a value between 9 an 10, the shoulder disappears and the fit works fine. But I think by this change I might modify the data too much. Would be really nice, if sombody has an idea how to deal with the problem, to get a hint how to solve this. Thanks a lot, Julian ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Problem with handling doped material
by Rana, Jatinkumar Kantilal 20 Oct '11

20 Oct '11

Dear Ifeffit users, I apologize for my previous post with subject "Difficulty in running feff8.2" being ill-defined and lacking adequate supporting informations, I try to redefine the problem again. I want to perform EXAFS fit on data for Li2Mn1.5Ni0.5O4 material measured on Mn K-edge. (i.e. case of handling dopant by modifying feff.inp files) I used Li2Mn2O4 structure (attached as Li2Mn2O4.inp file) to generate feff.inp file With Mn core atom (attached as Li2Mn2O4_feff.inp) and run through Feff8.2. It worked well. Now, when I modified Li2Mn2O4_feff.inp file such that Mn is core atom but all back scatterers are now Ni instead of Mn (attached as Li2Ni2O4_feff.inp), feff8.2 terminates after 17 SCF iterations. I have no idea why, since it never happened before. Looking at both feff.inp files they are identical except with the fact that in case of Li2Ni2O4_feff.inp, I replaced all Mn back scatterers with Ni. Am I doing something wrong (unknowingly) ?? I am using Windows 7 machine but I tried it on another windows xp machine also and the result is same. Can anyone on mailing list help me getting out of these problem ?? Any help would be much appreciated. With best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Dienstag, 18. Oktober 2011 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 104, Issue 24 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Difficulty in running feff8.2 (Rana, Jatinkumar Kantilal) ---------------------------------------------------------------------- Message: 1 Date: Tue, 18 Oct 2011 15:10:31 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Difficulty in running feff8.2 Message-ID: <6CA1A94BC28ABA4F9E1D360B3E249AEC0E3BC4A8@didag1> Content-Type: text/plain; charset="us-ascii" Dear ifeffit users, Recently, I am facing difficulty in running feff8.2 on one particular feff.inp file. I have measured Mn K-edge data for Li2Mn1.5Ni0.5O4. I want to perform feff calculation of Li2Mn1.5Ni0.5O4 in order to fit the data. I have structural data for Li2Mn2O4. To have an overall feff calculation of Li2Mn1.5Ni0.5O4, I need to perform feff calculation two times, i.e., one with Li2Mn2O4 (with Mn as core) and second with Li2Ni2O4 (i.e. with Mn as core and rest of Mn atoms replaced by Ni). Then I can add both feff calculations appropriately to generate resultant theoretical chi(k) and go ahead with fitting. The problem is, I could successfully run feff8.2 on Li2Mn2O4, but when I run it on Li2Ni2O4 it stops after performing few iterations without any notifications. I am not able to understand why feff terminates half way. I have never faced such problem before. Can anyone help me ? Please see the attached feff.inp file which I am trying to run. I have activated SCF card in that. Many thanks in advance !! With Best regards, Jatin ________________________________ Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20111018/4a5…> -------------- next part -------------- A non-text attachment was scrubbed... Name: feff.inp Type: application/octet-stream Size: 9986 bytes Desc: feff.inp URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20111018/4a5…> ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 104, Issue 24 **************************************** ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführer: Prof. Dr. Anke Rita Kaysser-Pyzalla, Dr. Ulrich Breuer Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Calvin ZnO
by mattie.peck＠huskers.unl.edu 19 Oct '11

19 Oct '11

Hello Ifeffit Subscribers: I was wondering if somebody could send me the files that Scott Calvin posted about a worked example of ZnO. The Ifeffit site won't let me download the zipped file. Thanks, Mattie Peck

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