From chemistry-request@ccl.net Thu Dec 16 06:32:32 2004 Received: from mail.zrz.tu-berlin.de (mail.zrz.TU-Berlin.DE [130.149.4.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBGBWVdj031863 for ; Thu, 16 Dec 2004 06:32:31 -0500 Received: from localhost ([127.0.0.1] helo=mail.zrz.TU-Berlin.DE) by mail.zrz.tu-berlin.de with esmtp (exim-4.43) id 1Ceu7D-0005Ep-L7; Thu, 16 Dec 2004 12:48:15 +0100 Received: from mail.zrz.TU-Berlin.DE ([130.149.4.15]) by mail.zrz.TU-Berlin.DE (MailMonitor for SMTP v1.2.2 ) ; Thu, 16 Dec 2004 12:48:15 +0100 (CET) Received: from mailbox.tu-berlin.de ([130.149.4.18]) by mail.zrz.tu-berlin.de with esmtp (exim-4.43) id 1Ceu7D-0005Ec-Jx; Thu, 16 Dec 2004 12:48:15 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailbox.tu-berlin.de with esmtp (exim-4.43) id 1Ceu7D-0002It-3z; Thu, 16 Dec 2004 12:48:15 +0100 Mime-Version: 1.0 X-Sender: chwu0531*at*mailbox.zrz.tu-berlin.de Message-Id: Date: Thu, 16 Dec 2004 12:48:12 +0100 To: chemistry*at*ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Gaussian03 and bug in IntelFortran 8.1, w/ REPAIR Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" X-Virus-Scanned: Sophos MailMonitor on mail.zrz.tu-berlin.de; Thu, 16 Dec 2004 12:48:15 +0100 X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_BAD_DOT,NO_RDNS2, RM_ft_Iso8859 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iBGBWWdj031867 In order to switch to the latest LINUX version, I had to re-compile all my programs with Intel Fortran 8.1 (instead of version 7 I used before). I observed that many Gaussian test jobs bombed thereafter (starting with test043.com). It could be traced back to wrong compilation of the subroutine ryspol.f. The C matrix is not initialized as programmed in the loop with label 60/70. The optimizer lost track that matrix C is actually used later on. 1.) Is this a known bug? 2.) Although it is definitely a compiler problem (Intel, do you hear?) the problem can be solved by cleaning the code from the unnecessary EQUIVALENCE statment (Gaussian, do you hear?). So do the following: a) comment out the EQUIVALENCE of C00, C01 and C11 (one single line) in subroutine ryspol (which is located in utilnz.F) b) replace (a few lines below), after label 70 in this subr. "C00" --> "C(1,1)" "C01" --> "C(1,2)" "C11" --> "C(2,2)" After recompilation, the affected test jobs are OK. I report on the complete test suite later. +---------------------------------+----------------------------------+ | Prof. Christoph van W|llen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitdt Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Stra_e des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen*at*TU-Berlin.De | +---------------------------------+----------------------------------+ -- From chemistry-request@ccl.net Thu Dec 16 04:32:09 2004 Received: from ccc018.chemie.uni-erlangen.de (ccc018.chemie.uni-erlangen.de [131.188.128.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBG9W7xW021060 for ; Thu, 16 Dec 2004 04:32:07 -0500 Received: from localhost (localhost [127.0.0.1]) by ccc018.chemie.uni-erlangen.de (Postfix) with ESMTP id D87973B2EA for ; Thu, 16 Dec 2004 10:47:50 +0100 (CET) Received: from ccc018.chemie.uni-erlangen.de ([127.0.0.1]) by localhost (ccc018 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 23057-04 for ; Thu, 16 Dec 2004 10:47:48 +0100 (CET) Received: from [131.188.128.90] (equinox.chemie.uni-erlangen.de [131.188.128.90]) by ccc018.chemie.uni-erlangen.de (Postfix) with ESMTP id 80F123B334 for ; Thu, 16 Dec 2004 10:47:47 +0100 (CET) Message-ID: <41C159C3.8000508*at*chemie.uni-erlangen.de> Date: Thu, 16 Dec 2004 10:47:47 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum User-Agent: Mozilla Thunderbird 0.8 (X11/20040913) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY*at*ccl.net Subject: CCL: PDB Pipeline tools Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new at chemie.uni-erlangen.de X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X-Spam-Status: No, hits=4.9 required=7.5 tests=IMPRONONCABLE_1,MY_BAD_DOT, NO_RDNS2 autolearn=no version=2.61 Dear CCL subscribers, many years ago I downloaded and compiled a set of tools for converting and manipulating protein database pdb files, called "PDB Pipeline". Unfortunalely, I lost the source, but I need to recompile the tools. Can anyone help me getting the source of this toolset?! Perhaps there is also annother toolset (eg. for removing hydrogen atoms etc) I can use. Any help or hint is highly appreciated! Kind regards, -Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 email: lanig AT chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig ------------------------------------------------------------------------ From chemistry-request@ccl.net Thu Dec 16 06:41:21 2004 Received: from turmiel.ch.uj.edu.pl (turmiel.ch.uj.edu.pl [149.156.71.252]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iBGBfJdj032360 for ; Thu, 16 Dec 2004 06:41:20 -0500 Received: from turmiel.ch.uj.edu.pl (localhost.localdomain [127.0.0.1]) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8) with ESMTP id iBGBv1Af014542 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NO) for ; Thu, 16 Dec 2004 12:57:01 +0100 Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8/Submit) id iBGBv1sL014539; Thu, 16 Dec 2004 12:57:01 +0100 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to migda-.at.-chemia.uj.edu.pl using -f Received: from 149.156.95.11 (SquirrelMail authenticated user migda) by mail.ch.uj.edu.pl with HTTP; Thu, 16 Dec 2004 12:57:01 +0100 (CET) Message-ID: <1544.149.156.95.11.1103198221.squirrel-.at.-mail.ch.uj.edu.pl> Date: Thu, 16 Dec 2004 12:57:01 +0100 (CET) Subject: Fermi-Contact contribution to J coupling From: "Wojciech Migda" To: X-Priority: 3 Importance: Normal Reply-To: migda-.at.-chemia.uj.edu.pl X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=0.6 required=7.5 tests=FVGT_s_SINGLE_LETTER autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL users, I have an access to Gaussian 03 which itself allows computation of FC, SD, PSO and SDO contributions to spin-spin coupling constants (SSCCs), but I want to calculate only the FC term, since computation of other parts would be prohibitively time consuming (even matter of weeks). So I have two qiestions: 1. How to modify Gaussian 03 Rev C.02 code to restrict it to computation of only FC part. or 2. How to do such computation (step by step explanation) using the field keyword in Gaussian. I know that it requires playing with the spin density matrix, but don't quite know how to get what I want that way. Thanks and regards, Wojciech Migda Department of CHemistry Jagiellonian University Krakow, Poland. migda-.at.-chemia.uj.edu.pl