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

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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new software releases
by Bruce Ravel 11 Aug '08

11 Aug '08

Hi folks, I just uploaded source code and a Windows installer for Ifeffit 1.2.11 to SourceForge. Both are also available for download from the Ifeffit web site. Source code packages for my programs (Athena, Artemis, Hephaestus) can be found at SourceForge or on my website. Macintosh installer packages will be available soon. For the windows users, the new installer package has a number of advantages, including: * New compilation of ifeffit, resulting in noticeably faster execution compared to the 1.2.10 release * Latest versions of SixPack, Athena, Artemis, and Hephaestus * Perl 5.8 and PerlApp 7.2 were used to build my programs, solving a number of performance issues reported in recent months * The Athena User's Guide is included in the package and the html version is now used as the internal documentation in Athena We recommend that all windows users upgrade to the new version. As always, let us know about any issues, comments, or suggestions that you might have. This version was used successfully at the APS XAFS Summer School last week. While not an exhaustive testing, it seems to be a good release so far. Regards, 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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several FEFF-questions
by Bosman, Eckhard 11 Aug '08

11 Aug '08

Hello, i read in the FEFF 8.4 manual, that the 6 modules are executed in ascending order. But now i'm confused concerning the modules 3 till 5. In module 3 the full multiple scattering is calculated. But only after this module the path enumeration (module 4) and the scattering amplitudes (module 5) are computed. I thought the path enumeration and the scattering amplitudes are required for calculation of the full multiple scattering? Why are these quantities calculated after the fms module? In my opinion this doesn't make sense. Another question affects the paper (page 9 and 10) of Zabinsky et al (attached). In the section "path enumeration" (respectively one side bevor) he introduced the quantity r_tot = total path length and R = r_tot/2 = effective path length. My question is, what is the meaning of the effective path length? In my opinion r_tot is the way and the way back? And R < r_tot is the path length without negligible contributions (scattering amplitude,...), is this right? The next question concerns the XANES-Card. What is the meaning of k respectively xkmax? In my opinion k is the wavenumber (of the photo electron wave?) which occurs in the xmu.dat in the third column, isn't it? Many thanks for your help! best regards, Eckhard

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Athena can not open any file
by Gilberto Fernandes Lopes Fabbris 11 Aug '08

11 Aug '08

hello, I have a amd 64 bits computer running opensuse 11. I tried to install ifeffit on it and it was very complicated. After some modifications on the makefile of PGPlot (as showed here: http://proteus.pha.jhu.edu/~dks/Unixtips/index.html) and during the horae install (http://cars9.uchicago.edu/pipermail/ifeffit/2006-September/002621.html and http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2008-January/003481.html) After those changes the artemis is working well, but athena is not... the program opens but I can not open any file. When I opened athena on terminal and tried to open a file the error below appeares. Tk::Error: Failed to AUTOLOAD 'Tk::FBox::_get_select_Path' at /usr/bin/athena line 5212 Carp::croak at /usr/lib/perl5/5.10.0/Carp.pm line 44 Tk::Widget::__ANON__ at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/Widget.pm line 347 Tk::FBox::Done at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk/FBox.pm line 909 Tk::FBox::VerifyFileName at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/FBox.pm line 678 Tk::FBox::ActivateEnt at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/FBox.pm line 647 Tk::FBox::OkCmd at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk/FBox.pm line 815 Tk callback for .fbox.frame1.button Tk::__ANON__ at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread-multi/Tk.pm line 250 Tk::Button::butUp at /usr/lib/perl5/vendor_perl/5.10.0/x86_64-linux-thread- multi/Tk/Button.pm line 175 <ButtonRelease-1> (command bound to event) Thanks, Gilberto

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[OT] Ball&sticks open source Perl/Python libraries
by Mauro Rovezzi 31 Jul '08

31 Jul '08

Dear all, I'm sorry if I introduce an off-topic (OT) subject but I would like to ask if you have knowledge of a simple ball&stick open source library that could be called from Perl or Python in order to generate "on the fly" theoretical paths visualization (or any atomic structure). At the moment the simplest (and useful!) utility I have found is XBS (http://ihp02.ihp-ffo.de/~msm/) but it is not the best solution because it needs input files and the output quality is low. Thanks for your help, Mauro -- Mauro Rovezzi <rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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reference spectra for Cu(OH)2
by Zajac, Dariusz 30 Jul '08

30 Jul '08

Hi all, as now we have a time for XAS spectra requests, I would like to ask you also for one. I need spectra of Cu(OH)_{2}. If someone could help I would preciate. Thanks in advance darek ------------------------------------------------------------------------ dr. Zajac Dariusz A. Deutsches Elektronen-Synchrotron -Hasylab phone: +49-40-8998-2932 Notkestr. 85 fax: +49-40-8998-2787 22607 Hamburg e-mail: dariusz.zajac(a)desy.de Germany ------------------------------------------------------------------------

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