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

SRS data
by Michael Stockenhuber 28 Nov '11

28 Nov '11

Dear all, Thank you very much to the developers for this great software. I have a problem with some old SRS station 3.4 data. I cannot read in original data with athena. I enclose a data file r48683.dat )( Al K- edge). I have installed DUBBLE, but still does not want to read it. I also would like to read in data from station 9.3. This is fluorescence data with a 13 element detector and also includes E0 and E1 and I think Em. I enclose a data file, r94731.dat ( Cu K-edge). Any help would be greatly appreciated. DUBBLE.py reads in station 7.1 data. I enclose a datafile (r66946.dat). All the best and thank you for the help Michael

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Re: [Ifeffit] SRS data
by Michael Stockenhuber 18 Nov '11

18 Nov '11

Hi Matt, Thank you very much. I will have a look at the script and maybe I can modify it. I am not really good in coding but you certainly gave me an idea where to start. Thank you for looking at the files. If I get anywhere I will certainly post. I am sure I am not the only one having to do that :) Cheers Michael >>> Matt Newville <newville(a)cars.uchicago.edu> 18/11/11 3:13 AM >>> Hi Michael, On Thu, Nov 17, 2011 at 5:17 AM, Michael Stockenhuber <Michael.Stockenhuber(a)newcastle.edu.au> wrote: > Dear all, > Thank you very much to the developers for this great software. I have a problem with some old SRS station 3.4 data. I cannot read in original data with athena. I enclose a data file r48683.dat )( Al K- edge). I have installed DUBBLE, but still does not want to read it. > I also would like to read in data from station 9.3. This is fluorescence data with a 13 element detector and also includes E0 and E1 and I think Em. > I enclose a data file, r94731.dat ( Cu K-edge). Any help would be greatly appreciated. > DUBBLE.py reads in station 7.1 data. I enclose a datafile (r66946.dat). > All the best and thank you for the help > Michael OK, there are a few separate formatting issues here. First, these files end with a line reading "END OF DATA", which ifeffit doesn't like, but which it can ignore. Second, two of the files (r94731.dat and r66946.dat) do not have data arranged so that one line is one energy point, and they have an inconsistent number of columns per line. Ifeffit usually considers line breaks to be significant. Third, one of the files (r48683.dat) has two lines with '----' starting after a comment character -- ifeffit takes such a line to signify the end of the header. Athena allows file-reading plugins to be written in perl -- I think you'll probably want to consult with Bruce about writing (or having one of these written for these files). Alternatively, you could write a program to convert these files to ones that make ifeffit's limited read_ascii() routine happy. Perhaps DUBBLE.py (I'm not familiar with that) can be made to do this conversion? Hope that helps, --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Ifeffit Digest, Vol 105, Issue 8
by Carmelo Prestipino 17 Nov '11

17 Nov '11

Hi Thanks to all About the GUI, it is a quick and dirty job so I was a little ashamed to public show it. It is aimed to analyze sequentially big set of data coming from dispersive and qexafs beamlines. Source code and installer for windows are available at the link http://code.google.com/p/prestopronto/ The code is in a very beta stage, so big part of documentation is missing and is not tested extensively, I'm sure that it is still full of bugs. However If someone is interested to tests, modifies, give a look it is obviously welcomed. Thanks again Carmelo > 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. feff6l licence (Carmelo Prestipino) > 2. Re: feff6l licence (John J. Rehr) > 3. Re: feff6l licence (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Nov 2011 17:23:36 +0100 > From: Carmelo Prestipino <carmelo.prestipino(a)univ-rennes1.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] feff6l licence > Message-ID: > <CAHPDQqzXQ3+3+Ej4KhfV_1HSwkUep4ZwRwAMTKn0rTBxcyVnig(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi to everybody > I'm currently working to an another GUI to Ifeffit, aimed to large > dataset , it is still in beta version and full of bug but some > collaborators start to use it . > In the installer that I send to them is present the "feff6l.exe" > file, to generates phase and amplitudes , but now I have a doubt. > Does the feff6l licence allows a generic redistribution? , or have > the Horae and the Sixpack packages a special agreement? > Thanks in advance > Carmelo > > -- > Carmelo Prestipino > Sciences Chimiques de Rennes UMR 6226 > Campus de Beaulieu, B?t 10B > F-35042 RENNES > France > Tel: (+33) 22323 6531 > FAX: (+33) 22323 5959 > > > > ------------------------------ > > Message: 2 > Date: Wed, 16 Nov 2011 08:36:45 -0800 (PST) > From: "John J. Rehr" <jjr(a)uw.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Hi Carmelo et al., > > Short answer: FEFF6L may be freely distributed; there is no special > agreement restricting the code to IFEFFIT or other codes. Let me know > if you have other questions about this. > > Sincerely, > J. Rehr > PI FEFF Project > > From the FEFF6L license header: > > c/////////////////////////////////////////////////////////////////////// > c Distribution: FEFF6L > c Copyright (c) [2002] University of Washington > c > c This software was prepared in part with US Government Funding under > c DOE contract DE-FG03-97ER45623. > > c Redistribution and use of this Distribution in source and binary > c formats, with or without modification is permitted, provided the > c following conditions are met: > c > c Redistributions must retain the above notices and the following list > c of conditions and disclaimer; > c > c Modified versions carry the marking > c "Based on or developed using Distribution: FEFF6L > c Copyright (c) [2002] University of Washington" > c > c Recipient acknowledges the right of the University of Washington to > c prepare uses of this Distribution and its modifications that may be > c substantially similar or functionally equivalent to > c Recipient-prepared modifications. > c Recipient and anyone obtaining access to the Distribution through > c recipient's actions accept all risk associated with possession and > c use of the Distribution. > c > c THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED > c WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF > c MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. > c IN NO EVENT SHALL THE UNIVERSITY OF WASHINGTON OR CONTRIBUTORS TO THE > c DISTRIBUTION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, > c EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, > c PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR > c REVENUE; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF > c LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING > c NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS > c SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. > c/////////////////////////////////////////////////////////////////////// > > > > > > On Wed, 16 Nov 2011, Carmelo Prestipino wrote: > >> Hi to everybody >> I'm currently working to an another GUI to Ifeffit, aimed to large >> dataset , it is still in beta version and full of bug but some >> collaborators start to use it . >> In the installer that I send to them is present the "feff6l.exe" >> file, to generates phase and amplitudes , but now I have a doubt. >> Does the feff6l licence allows a generic redistribution? , or have >> the Horae and the Sixpack packages a special agreement? >> Thanks in advance >> Carmelo >> >> -- >> Carmelo Prestipino >> Sciences Chimiques de Rennes UMR 6226 >> Campus de Beaulieu, B?t 10B >> F-35042 RENNES >> France >> Tel: (+33) 22323 6531 >> FAX: (+33) 22323 5959 >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > > > ------------------------------ > > Message: 3 > Date: Wed, 16 Nov 2011 11:32:23 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] feff6l licence > Message-ID: > <CA+7ESbrX1WAkUPXPCZph27foRtwy2f7LD176WtB7oRU_3Qp3eA(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Carmelo, > > As John said, Feff6L is NOT tied to ifeffit, and is distributed with a > very liberal license. Using the ifeffit source kit might be the > easiest way to get the source code, but this code (and ifeffit's code) > can be pulled out if you'd like. For windows, you can just copy the > feff6l.exe executable and include it with your GUI. > > Of course, I think many of us would be interested in hearing more > about your GUI. > > --Matt > > -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Campus de Beaulieu, Bât 10B F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

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feff6l licence
by Carmelo Prestipino 16 Nov '11

16 Nov '11

Hi to everybody I'm currently working to an another GUI to Ifeffit, aimed to large dataset , it is still in beta version and full of bug but some collaborators start to use it . In the installer that I send to them is present the "feff6l.exe" file, to generates phase and amplitudes , but now I have a doubt. Does the feff6l licence allows a generic redistribution? , or have the Horae and the Sixpack packages a special agreement? Thanks in advance Carmelo -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Campus de Beaulieu, Bât 10B F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

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Re: [Ifeffit] software issues on a 10.1" netbook (Coppage, Ryan H)
by denis testemale 08 Nov '11

08 Nov '11

Hello Ryan. As Chris suggested, you may want to change the fonts to allow the window to show everything (even if gaining 1/3rd of the screen seems a lot, you might need very small fonts). I don't know about Windows, but in case the file names are similar I can tell you where to do this under linux: in the .horae folder, you want to edit the athenarc and artemisrc config files. This is the only way to change the font sizes (if you go to the Edit/preferences menu in a running athena or artemis session, the message will be that it is the only parameter that you have to change through the config files). Hope it helps. Cheers denis Le Samedi 05 Novembre 2011 12:00:01 ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > software issues on a 10.1" netbook (Coppage, Ryan H) I'm a grad student at the University of Miami. I purchased a dual-core netbook for travel purposes and intended to use IFEFFIT on it. It runs windows 7. When attempting to run athena, the window text will not resize on my screen, to show me the rest of the software window. The bottom half is cut off, and it won't let me move the window out of the screen to see the bottom 1/3 or so. There are no scroll bars to move up or down the athena window, so i cannot even open data to manage. Has anyone else had issues with this or knows a solution to the issue? Any help would be greatly appreciated. Ryan Coppage Graduate Student University of Miami ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 105, Issue 4 *************************************** -- denis testemale Institut Néel-Département MCMF BP166 38042 Grenoble Cedex 9 (tel) +33 476 88 10 45 (fax) +33 476 88 10 38 http://neel.cnrs.fr/spip.php?rubrique264

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Re: [Ifeffit] Ifeffit Digest, Vol 105, Issue 4
by Lisa Van Loon 07 Nov '11

07 Nov '11

Hi Ryan, I have the same problem when I use my netbook. The only solution I've come up with is to change the display settings to "Portrait" to open a project file or import data. Then I switch back to "Landscape" view when I'm working with the data. It's not an ideal solution, but it works. Lisa Lisa Van Loon, Ph.D. Industrial Research Scientist Canadian Light Source Inc. (306)657-3585 lisa.vanloon(a)lightsource.ca www.lightsource.ca -------------------------------------------------------------------- Message: 1 Date: Fri, 4 Nov 2011 19:36:30 +0000 Hi. I'm a grad student at the University of Miami. I purchased a dual-core netbook for travel purposes and intended to use IFEFFIT on it. It runs windows 7. When attempting to run athena, the window text will not resize on my screen, to show me the rest of the software window. The bottom half is cut off, and it won't let me move the window out of the screen to see the bottom 1/3 or so. There are no scroll bars to move up or down the athena window, so i cannot even open data to manage. Has anyone else had issues with this or knows a solution to the issue? Any help would be greatly appreciated. Ryan Coppage Graduate Student University of Miami

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Re: [Ifeffit] Ifeffit Digest, Vol 105, Issue 4
by milena filadelpho coutinho 06 Nov '11

06 Nov '11

> From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 105, Issue 4 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sat, 5 Nov 2011 12:00:01 -0500 > > 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. software issues on a 10.1" netbook (Coppage, Ryan H) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 4 Nov 2011 19:36:30 +0000 > From: "Coppage, Ryan H" <r.coppage(a)umiami.edu> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] software issues on a 10.1" netbook > Message-ID: > <CB42E5EBE28A9046904D2752D43B95900351F537(a)UMEX006.cgcent.miami.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi. > > > > I'm a grad student at the University of Miami. > > > > I purchased a dual-core netbook for travel purposes and intended to use IFEFFIT on it. It runs windows 7. When attempting to run athena, the window text will not resize on my screen, to show me the rest of the software window. The bottom half is cut off, and it won't let me move the window out of the screen to see the bottom 1/3 or so. There are no scroll bars to move up or down the athena window, so i cannot even open data to manage. > > > > Has anyone else had issues with this or knows a solution to the issue? > > > > Any help would be greatly appreciated. > > > > Ryan Coppage > > Graduate Student > > University of Miami > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 105, Issue 4 > ***************************************

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software issues on a 10.1" netbook
by Coppage, Ryan H 04 Nov '11

04 Nov '11

Hi. I'm a grad student at the University of Miami. I purchased a dual-core netbook for travel purposes and intended to use IFEFFIT on it. It runs windows 7. When attempting to run athena, the window text will not resize on my screen, to show me the rest of the software window. The bottom half is cut off, and it won't let me move the window out of the screen to see the bottom 1/3 or so. There are no scroll bars to move up or down the athena window, so i cannot even open data to manage. Has anyone else had issues with this or knows a solution to the issue? Any help would be greatly appreciated. Ryan Coppage Graduate Student University of Miami

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

14 Oct '11

UNSUBSCRIBE PLEASE On Fri, Oct 14, 2011 at 10:14 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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beamline for Al EXAFS
by Kompch, Alexander 13 Oct '11

13 Oct '11

Dear all, for the analysis of the location of the Al-dopant in ZnO, I am looking for suitable EXAFS beamlines. Dopant concentrations are 1-10%. So far I have only found ALS 6.3.1 and NSLS X15B. Can anybody recommend beamlines for Al EXAFS? My EXAFS experience is so far limited to the high energy range with signal detection in transmission (ionization chambers) and fluorescence (multi-element Ge-detectors). At such low energies as 1.5 keV for Al-K, the sample needs to be in vacuum, transmission will not work and Ge detectors probably the same. Does anybody have experience with Al-EXAFS, and can share a little about setup and what other complications to expect? Thank you, Alex.

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Re: [Ifeffit] XANES fitting
by Matt Newville 13 Oct '11

13 Oct '11

Hi Riti, I hope it's OK that I'm sending this to the ifeffit mailing list, as there might be other interesting perspectives on your questions. On Tue, Oct 11, 2011 at 3:47 PM, Ritimukta Sarangi <ritis(a)stanford.edu> wrote: > Hi Matt, > This is Riti again. This time I have a question about EXAFS, which you are an expert on :-) I would like to get your view on > systematic errors in EXAFS. Say the data were collected on a standard EXAFS beamline like 7-3 at SSRL. The data have > been collected using fluorescence mode and a 30 element Ge detector. The data are modest, between k=2-15 A. > > I used to quote in my papers that typical statistical and systematic errors lead to a total error in first shell distances of > +-0.02 A. I know it can be more than that in some circumstances but then I tried to look at it a little more closely to > separate out the systematic error from all sources (instrument, measurement, detector, Analysis), but I could not find a > good reference. I understand that this is a difficult number to estimate. I was hoping that you could shed some light on it. > Thanks! > -Riti > I'm not sure of a good general reference for that either, though perhaps some of the papers from Corwin Booth are a good place to start? Quoting +/- 0.02 Ang seems like a reasonable estimate for a typical value, but that's hardly rigorous. My sense is that it's pretty challenging to separate "systematic" and "random" noise for most data sets. Fluorescence data from a solid-state detector is probably the best-case for such a separation, because you have multiple detector elements or repeated scans, and usually the individual detectors or scans really are dominated by statistical fluctuations. If you add detector elements or scans together until the noise in the data (or variations in estimated parameters or estimated error bars) stops getting better, systematic errors are starting to be noticeable. Eventually, as you increase the fluorescence counts, the fits will stop improving, which should be when systematic errors dominate. --Matt

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building feff input file; position of absorbing atom(s)
by Dreher Marian 12 Oct '11

12 Oct '11

Dear Feff community, I have a question concerning the position of the absorbing atom when creating a feff input file. I am trying to calculate the EXAFS for a disk-like Ru nanoparticle that I "built" from literature data using the program Diamond. The particle has 3 atomic layers, looks somewhat half-pyramidal and consists of about 80 atoms. I then exported the atom positions and used them as an input for feff. Since my cluster is far from being a bulk structure, the spectrum I get strongly depends on where I place my absorbing atom. In this cluster the atoms can be grouped by common coordination number. Do I have to manually calculate the EXAFS for every single group and then calculate the mean spectrum weighted with the degeneracy of each group or is there a smarter way to do that? Many thanks, Marian. Marian Dreher, Dipl. Chem. PhD Student, Catalytic Process Engineering Group Paul Scherrer Institut General Energy Research (ENE) Laboratory for Bioenergy and Catalysis Office: OVGA/115 CH-5232 Villigen PSI Switzerland Phone: +41 (0)56 310 2937 email: marian.dreher(a)psi.ch

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Re: [Ifeffit] lifetime broadening of pre-edge peaks
by vikrai＠comcast.net 11 Oct '11

11 Oct '11

Hi Matthew, The lifetime broadening of the XANES features is determined by the time of life of the final excited state. This two-particle excitation includes the core hole and the photoelectron. The core hole may decay due to the various radiation or non radiation processes. The photoelectron state may decay due to inelastic collisions, plasmon excitations, etc. The time of life of the core hole, I believe, does not depend on the photon energy whilst the last is near the absorption edge. But it is not true for the photoelectron. It is better to write “photoelectron” because some of the pre-edge peaks which exist in the transition metal oxides spectra are in fact X-ray excitons and no photoemission can be observed. In these cases the final states are bound states and it is purely many electron effect caused by the core-hole - “photoelectron” interaction. For those pre-edge peaks the life time broadening is determined entirely by the core-hole life time. But as soon as photoelectron jumps to the conduction band the mechanisms of its inelastic scattering turn on and one should take into account the time of life of photoelectron (now without quotes). Unfortunately, it is difficult to determine which pre-edge peaks are excitonic and which are not. As it was already mentioned there are other mechanisms of broadening of the pre-edge peaks. For diamagnetic atoms it is thermal vibrations, for paramagnetic ones it is multiplet interactions as well. Good luck. Victor Krayzman.

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