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

asking questions effectively
by Bruce Ravel 25 Aug '08

25 Aug '08

Hi folks, When I returned from the dentist's office this afternoon, there were 2 questions on the mailing list. Both were interesting questions but neither really included enough information to definatively solve the problem. Please remember that the folks who answer questions on the maililng list can only do so effectively if you provide enough information that the problem can be reproduced on their own computers. Often, this involves attaching a small project file which demonstrates the problem to your email. 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/

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Background Subtraction
by Hashem Stietiya 25 Aug '08

25 Aug '08

Dear Dr. Ravel, I am trying to optimize background removal of my spectra by setting the Rbkg to half the distance of the first shell peak. However, when I import my spectra in ATHENA, I notice that the edge step is a very large number and when converting to R space there are no well defined peaks. If I click on 'fix step', the R space becomes comprehendible and peaks appear. Do I continue using the 'fix step' and then setting Rbkg to half the distance of the first shell peak? I appreciate your help. Regards, Hashem Stietiya

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Re: [Ifeffit] Energy shift (???)
by Frommer Jakob 19 Aug '08

19 Aug '08

Hi eunsuk1986 (unfortunately you did not share your full name with us...) I had some trouble with reading your feff.inp. Nevertheless the problem of the absolute alignment of FEFF xmu and experimental data has been the subject of earlier questions. I' am citing form a list contribution of J. Rehr (Aug 3rd 2003): "The FEFF calculation of the absolute energy is not meant to be highly accurate, and errors of several eV for K-shells of large Z atoms are not unusal. Thus you did nothing wrong in the input file. To match FEFF and experiment you *always* have to shift the FEFF absolute threshold to match experiment.". There is no way (I am aware of) to tell FEFF do this absolute shift (you can and you often need to shift the position of the Fermi level though) but you can do this with every plot program. Thus you should not worry too much about the absolute energies in your xmu but a lot about relative energies (i.e. the positions of the single resonances). HTH Jakob ___________________________________________________ Jakob Frommer Soil Chemistry Group Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich Universitätstrasse 16, CHN F19 CH - 8092 Zürich Tel: +41 44 632 87 58 Fax: +41 44 633 11 18 web: http://www.ibp.ethz.ch/research/soilchemistry ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Mon 8/18/2008 09:46 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 66, Issue 9 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. Energy shift (???) ---------------------------------------------------------------------- Message: 1 Date: Mon, 18 Aug 2008 16:46:26 +0900 From: ??? <eunsuk1986(a)hotmail.com> Subject: [Ifeffit] Energy shift To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <COL101-W46347AB6CA04C793B53D5FDA6E0(a)phx.gbl> Content-Type: text/plain; charset="ks_c_5601-1987" Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites: Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.10000 * emin emax resolution LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 1 8 O -1 -1 1 2 30 Zn -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Zn1 0.00000 0.00000 0.00000 2.06302 1 O1 2.06302 -1.95951 0.00000 -0.65148 1 O1 2.06497 0.97978 -1.69700 -0.65148 1 O1 2.06500 0.97978 1.69700 -0.65148 1 O1 2.06500 0.97978 -1.69700 -2.71450 2 Zn1 3.34788 0.97978 1.69700 2.71450 2 Zn1 3.34788 0.97978 1.69700 -2.71450 2 Zn1 3.34788 0.97978 -1.69700 2.71450 2 Zn1 3.34788 _________________________________________________________________ ???? ???, ???? ?? ???? ???? ??? Windows Live Hotmail! ?? ???? ???! http://www.hotmail.com <http://www.hotmail.com/>

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Energy shift
by 정은석 18 Aug '08

18 Aug '08

Hi everyoneI am studying XANES at Zn K-edge in ZnO nanocrystal by using FEFF8. I wrote FEFF8 as following, and got xmu.dat. I found that there was a difference between experimental data and xmu.dat (check file) for the energy. I dont understand why the energy is shifted. I wish to adjust xmu.dat in FEFF8 to my experimental dat. If someone knows how to do, please contact me. * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE name: zincite ZnO TITLE formula: ZnO TITLE sites: Zn1,O1 TITLE refer1: wyckoff, vol 1, ch III, p 111 TITLE refer2: TITLE schoen: TITLE notes1: EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * r_scf [ l_scf n_scf ca ] SCF 5.03864 0 15 0.1 * ixc [ Vr Vi ] EXCHANGE 2 0 0*EXAFS*RPATH 9.07729 * kmax [ delta_k delta_e ] XANES 4.0 ! 0.07 0.5 * r_fms [ l_fms ] FMS 5.53864 0 * *RPATH 0.10000 * emin emax resolution LDOS -20 20 0.1 POTENTIALS * ipot z [ label l_scmt l_fms stoichiometry ] 0 30 Zn -1 -1 0 1 8 O -1 -1 1 2 30 Zn -1 -1 1 ATOMS 0.00000 0.00000 0.00000 0 Zn1 0.00000 0.00000 0.00000 2.06302 1 O1 2.06302 -1.95951 0.00000 -0.65148 1 O1 2.06497 0.97978 -1.69700 -0.65148 1 O1 2.06500 0.97978 1.69700 -0.65148 1 O1 2.06500 0.97978 -1.69700 -2.71450 2 Zn1 3.34788 0.97978 1.69700 2.71450 2 Zn1 3.34788 0.97978 1.69700 -2.71450 2 Zn1 3.34788 0.97978 -1.69700 2.71450 2 Zn1 3.34788 _________________________________________________________________ 강력해진 보안성, 아웃룩을 닮아 편리해진 기능들로 무장한 Windows Live Hotmail! 지금 로그인해 보세요! http://www.hotmail.com

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Artemis bug in new version
by van der Veen Renske 15 Aug '08

15 Aug '08

Hello! I just downloaded the new version of Ifeffit (1.2.11) and I am happy with it except for a small bug that wasn't present in the previous version. I am used to work with many different FEFF calculations for the same data set, all with the same fit model. I usually copy the path parameters from one calculation to all the others by using <right click> "Paths -> Export these path parameters... -> to SELECTED paths". Although a bit cumbersome for many paths and calculations, it worked fine in the previous version of Artemis. In the new version, it does exactly the opposite from what I want: it exports the path parameters to all the paths EXCEPT the ones I selected. Is there a chance to fix this, or does anybody know a more cunning way to copy the path parameters from one calculation to the others on a path-by-path basis? Thanks in advance! Renske Renske M. van der Veen PhD student EPFL / PSI Paul Scherrer Institut Swiss Light Source WSLA/210 5232 Villigen PSI Switzerland Phone: +41 56 310 5362 Fax: +41 56 310 3151 E-mail: renske.vanderveen(a)psi.ch Web: http://lsu.epfl.ch http://femto.web.psi.ch

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The first step involve in Bio-physics simulation
by 沛昌蔡 15 Aug '08

15 Aug '08

Dear Prof. and authors: We have involved Bio-physics experiment recently, but we have no idea about the simulation softwave (free is better), and our protein sample is rod figure, so do you have any idea about the simulation, such as vibration mode, absorption, molecular structure. We are so appreciate with your information. Thanks for your time and feedback! Tsai pei-chang _________________________________________________________________________________________________________ 知識+ 的電玩高手全都在這裡！ http://tw.knowledge.yahoo.com/dir/group_buzz?time=total&type=article&sid=39…

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Bug: Can't type into Athena on Linux
by Gregory Merchan 14 Aug '08

14 Aug '08

Hi everyone, We uncovered a bug that affects Athena and friends. When SCIM is running, Perl/Tk programs do not respond to keyboard events. These reports have more information: https://bugzilla.novell.com/show_bug.cgi?id=77424 https://bugzilla.novell.com/show_bug.cgi?id=309794 (Googled for those links. We were running an up-to-date Ubuntu.) This affected Horae 066 and I've not yet tested the latest release. Hope this helps, Greg P.S. - Now googling the symptoms should be useful. I don´t expect a fix, since the problem is upstream.

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Re: [Ifeffit] Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 14 Aug '08

14 Aug '08

Hello, I made as you said and now everything is working! Thanks!! Gilberto

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update to ifeffit source kit
by Matt Newville 13 Aug '08

13 Aug '08

Hi Folks, I found a serious bug in the ifeffit-1.2.11 source code kit that was on the cars.uchicago.edu and sourceforge.net sites. This bug would become readily apparent, as many operations beyond the simplest tests will not work correctly, so like any actual use of Athena would be clearly wrong. Sorry for any trouble! I uploaded a fixed source code kit (ifeffit-1.2.11a.tar.gz) to both the cars.uchicago.edu and sourceforge.net sites. This bug does not affect the Windows binaries. --Matt

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Re: [Ifeffit] Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 12 Aug '08

12 Aug '08

Hello again, I tried to install the new package of both ifeffit(1.2.11) and horae (0.67) but it also didn't work. I first removed any file related to ifeffit and horae that I could find. Pgplot, ifeffit, Xray-Absorption, Xray-Scattering and Chemistry-Formula installation runned without error and I could open ifeffit on command line. But the error mensage below appeared when I runned the "perl Build.PL" on horae. ... Checking whether your kit is complete... Looks good Checking prerequisites... Package 'Config::IniFiles' already declared with version '2.39', ignoring subsequent declaration. Looks good Deleting Build Removed previous script 'Build' Creating new 'Build' script for 'horae' version '067' ... Even though this error I runned ./Build and ./Build install and no error appeared. But when I tried to run athena (it also happens on artemis) the error appeared: ...... Can't locate Ifeffit.pm in @INC (@INC contains: /usr/lib/perl5/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/5.10.0 /usr/lib/perl5/site_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.10.0 /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.10.0 /usr/lib/perl5/vendor_perl .) at /usr/bin/athena line 67. BEGIN failed--compilation aborted at /usr/bin/athena line 67. ..... I looked for the Ifeffit.pm file on /usr/lib/perl5 and it doesnt exist. Thanks, Gilberto ps: I will write on the FAQ as soon as possible... :)

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