October 2011 - Ifeffit - millenia.cars.aps.anl.gov

Au-foil (fcc) splitted peak
by grant bunker 29 Jan '12

29 Jan '12

Julian - the scattering amplitudes of all elements have structure in them that are connected to electron scattering (Ramsauer-Townsend) resonances within the backscattering atom. For light elements (e.g. O, S, Fe) they occur at energies that are lower than the typical transform range, so they usually are ignored. For heavier scatterers like Au there are strong minima and maxima in the Au scattering amplitude over the transform range. From a signal processing point of view, these amplitude modulations look like beats, which normally are due to different distances interfering. In the case of Au back scatterers, even if there is only one physical distance, you will get multiple peaks (perhaps overlapping). Mathematically the fourier transform is the distance distribution convoluted with the fourier transform of the amplitude. So, how do you deal with it? First, if you know what's going on that may be enough. Alternatively, if all the scatterers are the same, it's not difficult to divide out the scattering amplitude and subtract out the scattering phase before the transform to obtain an "optical transform", which eliminates the effect you're seeing. I don't know if that is supported by ifeffit but it's not hard to do. This approach is less useful if you have multiple types of scatterers (e.g. Au, S) because if you do the compensation for one type of scatterer it screws it up for the others. Techniques like regularization are probably better in that case. hope that helps grant bunker

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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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Difficulty in running feff8.2
by Rana, Jatinkumar Kantilal 18 Oct '11

18 Oct '11

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

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Re: [Ifeffit] Ifeffit Digest, Vol 104, Issue 22
by David Sprouster 14 Oct '11

14 Oct '11

Julian: I agree with Anatoly. The amplitude of the EXAFS is quite large. I have seen a similar effect in metal foils and NP samples when you forget to take the log of the I0 and IT. This also forces the S02 factor to be artificially high (like it is for your samples) when fitting in Artemis. Maybe try to re-adjust the raw data file upon importing into Athena and then see if your spectra (intensities, features and S02) line up better with those from the literature (and from the very useful Lytle database on XAFS.org) Hope that helps Dave On Fri, Oct 14, 2011 at 9:14 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > 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. Re: Gold Nanoparticle first shell fitting (Kaiser, Julian) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 14 Oct 2011 14:14:00 +0000 > From: "Kaiser, Julian" <julian.kaiser(a)helmholtz-berlin.de> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Gold Nanoparticle first shell fitting > Message-ID: <DE491AE4BEF1864DB8831D1BC0E7EA1A0E554D33@didag2> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Anatoly, > > thanks a lot for your reply! > I don't see the problem yet. In the attached file > ("different_Au_foils.prj), there are two different gold reference foils > measured at two different synchrotrons. There is some difference but not > realy much. Could you please describe the regions that are worse comparing > my gold foil-file to yours, or if possible, attache the file with both foils > or at least a screenshot of the plot? > > Best regards, > Julian > > > > ________________________________ > Von: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov]" im Auftrag von "Anatoly I > Frenkel [afrenke2(a)yu.edu] > Gesendet: Dienstag, 11. Oktober 2011 20:29 > Bis: XAFS Analysis using Ifeffit > Betreff: Re: [Ifeffit] Gold Nanoparticle first shell fitting > > > Something is horribly wrong with the data here. > > I overplotted your reference Au foil against mine, and yours has distorted > XANES and too high EXAFS intensity compared to my data. Your amplitude > factor is 1.54 which also confirms that something was wrong in the > experiment. Perhaps - a misalignment? The NP data also look strange... > > I would not focus on the NP analysis until you figure out why your foil > data is so strange. > > > > > > ________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ > ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Kaiser, Julian [ > julian.kaiser(a)helmholtz-berlin.de] > Sent: Tuesday, October 11, 2011 1:06 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Gold Nanoparticle first shell fitting > > 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 Angstr?m > 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 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 > > ________________________________ > > 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 >

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