From chemistry-request@ccl.net Tue Nov 16 06:06:12 2004 Received: from mail2.cc.huji.ac.il (real-outmail.cc.huji.ac.il [132.64.1.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAGB6ASW001928 for ; Tue, 16 Nov 2004 06:06:11 -0500 Received: from localhost (localhost [127.0.0.1]) by mail2.cc.huji.ac.il (Postfix) with ESMTP id 7C74DE16B5; Tue, 16 Nov 2004 13:20:00 +0200 (IST) Received: from mail2.cc.huji.ac.il (localhost [127.0.0.1]) by localhost (VaMailArmor-2.0.1.16) id 26325-37156322; Tue, 16 Nov 2004 13:20:00 +0200 Received: by mail2.cc.huji.ac.il (Postfix, from userid 31998) id 6B33EE16E5; Tue, 16 Nov 2004 13:20:00 +0200 (IST) Received: from baikal (baikal.ch.huji.ac.il [132.64.98.42]) by mail2.cc.huji.ac.il (Postfix) with SMTP id 3BDF9E16E7 for ; Tue, 16 Nov 2004 13:20:00 +0200 (IST) Message-ID: <002701c4cbce$354bfb50$2a624084|at|ch.huji.ac.il> From: "David Danovich" To: Subject: CCL:G03 Date: Tue, 16 Nov 2004 13:19:59 +0200 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="windows-1255"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Level: X-Spam-Status: No, hits=1.0 required=7.5 tests=PRIORITY_NO_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, I updated kernel on RedHat Enterprise Linux WS3 from version 2.4.21-15.0.3EL to 2.4.21-20EL. After that I have problem running G03(rev. B05) with updated kernel (2.4.21-20EL). I received error message from Link1 Erroneous write during file extend write -1 instead of 4096. Write error in NtrExt1: Bad Address G03 was compiled with Intel fortran 8.1 with atlas and MKL libraries on 2.4.21-20EL kernel . Both versions do not work with this kernel. On the other hand, the same executables work fine with previous kernel (2.4.21-15.0.3EL). Does anybody face this problem and know the solution. Thank you David ________________________________________________________________ Dr. David Danovich, Department of Organic Chemistry, The Hebrew University, Edmond J. Safra Campus - Givat Ram, 91904 Jerusalem, Israel http://yfaat.ch.huji.ac.il/david.html, David.Danovich|at|huji.ac.il FAX:(+972)-2-6586934, Phone:(+972)-2-6586934(w), (+972)-54-4768669(mobile) From chemistry-request@ccl.net Tue Nov 16 11:53:27 2004 Received: from smtp1.server.rpi.edu (smtp1.server.rpi.edu [128.113.2.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAGGrQE3031162 for ; Tue, 16 Nov 2004 11:53:26 -0500 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp1.server.rpi.edu (8.13.0/8.13.0) with ESMTP id iAGH7J46019875 for ; Tue, 16 Nov 2004 12:07:19 -0500 Message-Id: <200411161707.iAGH7J46019875..at..smtp1.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: chemistry..at..ccl.net From: sundlm..at..rpi.edu X-Originating-Ip: 128.113.134.222 X-Priority: 3 (Normal) Mime-Version: 1.0 Reply-To: sundlm..at..rpi.edu Date: Tue, 16 Nov 2004 12:07:18 EST X-Mailer: EMUmail 4.00 Subject: Software for displaying molecular vibration eigenvectors? Priority: 3 (Normal) X-CanItPRO-Stream: default X-RPI-SA-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, I am working on a new project focused on IR spectra prediction and associated molecular vibration modes. Now that I am writing my results, I wanted to make the 2D black/white vector diagrams found in a lot of papers discussing vibrations. These diagrams show the eigenvectors of motion for a given molecule. Does anyone have software that will make 2D pictures > from gaussian freq log files? Software like GaussView and Molden will show a 3D animation of the vibration, and even show the displacement vectors, but these 3D color graphics don't translate to a 2D paper black/white text format well. Does anyone have suggestions on how to make clear vibration diagrams for publication? Thanks! Matt Sundling Dept. of Chemistry RPI, sundlm..at..rpi.edu From chemistry-request@ccl.net Tue Nov 16 10:35:43 2004 Received: from mail1.unitn.it (mail1.unitn.it [193.205.206.53]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAGFZgE3025423 for ; Tue, 16 Nov 2004 10:35:43 -0500 Received: by mail1.unitn.it (Postfix, from userid 2502) id 60F7720A27; Tue, 16 Nov 2004 16:49:35 +0100 (MET) Received: from mail1.unitn.it (localhost [127.0.0.1]) by mail1.unitn.it (Postfix) with SMTP id 812FD20A44 for ; Tue, 16 Nov 2004 16:49:31 +0100 (MET) Received: from omega.science.unitn.it ([193.205.194.2]) by mail1.unitn.it (SAVSMTP 3.1.5.43) with SMTP id M2004111616493115138 for ; Tue, 16 Nov 2004 16:49:31 +0100 Received: from omega.science.unitn.it (localhost.localdomain [127.0.0.1]) by omega.science.unitn.it (8.12.11/8.12.11) with ESMTP id iAGFnVfp021360 for ; Tue, 16 Nov 2004 16:49:31 +0100 Received: from localhost (mlunelli@localhost) by omega.science.unitn.it (8.12.11/8.12.11/Submit) with ESMTP id iAGFnSi5021356 for ; Tue, 16 Nov 2004 16:49:31 +0100 Date: Tue, 16 Nov 2004 16:49:28 +0100 (CET) From: Michele Lunelli To: chemistry/at/ccl.net Subject: G03 with Red Hat 9 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X-Spam-Level: X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 Hi all, I have installed the compiled version of Gaussian 03 revision B.02 on a Red Hat 9 system with dual processor AMD Athlon 2200+, kernel version 2.4.20-8smp. With my suprise it don't work at all, when I launch a job it simply produces a log file like this: Entering Gaussian System, Link 0=g03 Input=test.gjf Output=test.log Initial command: /home/michele/g03/l1.exe /home/michele/scratch/Gau-26754.inp -scrdir=/home/michele/scratch/ And then it stops without calculating anything. I installed the same Gaussian 03 on a similar machine with Red Hat Enterprise Linux ES release 3, kernel version 2.4.21-15.0.3.ELsmp and Xeon processors, and it works fine. Any suggestion will be highly appreciated. Regards, Michele Lunelli Department of Physics University of Trento Italy mlunelli-at-science.unitn.it