From chemistry-request@www.ccl.net Thu Nov 26 04:48:09 1998 Received: from sauer.ethz.ch (sauer.ethz.ch [129.132.17.91]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA17911 Thu, 26 Nov 1998 04:48:02 -0500 (EST) Received: from scsc.ethz.ch (localhost [127.0.0.1]) by sauer.ethz.ch (8.8.8/8.8.8) with ESMTP id KAA08933; Thu, 26 Nov 1998 10:47:40 +0100 (CET) Sender: portmann@scsc.ethz.ch Message-ID: <365D23BC.7F07355E@scsc.ethz.ch> Date: Thu, 26 Nov 1998 10:47:40 +0100 From: Stefan Portmann X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CCL CCL , all@cscs.ch, baumann@org.chem.ethz.ch, Pierre-Yves.Morgantini@chiphy.unige.ch, raf.bruyndonckx@unifr.ch, ilaria.ciofini@unifr.ch, ChouChou Kohl , Francois Chapuis , Andi Linz , Peter Keller , Roli Mueller , Martin Tiefenbacker , dobler@org.chem.ethz.ch, Martin Egli Subject: New Release: MOLEKEL 3.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello I'd like to announce a new release of the interactive molecular graphics program MOLEKEL 3.0. The program is capable of displaying isosurfaces and molecular orbitals, animate and display frequencies... It reads the output of several electronic structure calculation programs as GAUSSIAN94, GAMESS US, ADF2.3 ... as well as PDB, xyz and free format for coordinates. It animates structure optimizations, and trajectory files of CHARMM. Improvements to previous versions are basically bug fixes, updates of the several output reading parsers and some new features like displaying of vibrational modes as arrows. MOLEKEL is entirely written in ANSI-C and uses the Graphics Library (GL) of Silicon Graphics. It runs on any SGI workstation running IRIX 6.x. For further information and free download of the executable please check http://www.scsc.ethz.ch/~portmann/molekel Best Regards -- Dr. Stefan Portmann CSCS/SCSC-ETHZ Swiss Center for Scientific Computing Computational Chemistry ETH-Zentrum, RZ Clausiusstrasse 59 CH-8092 Zurich Switzerland Phone: +41 (0) 1 632 57 82 Fax: +41 (0) 1 632 11 04 e-mail: portmann@scsc.ethz.ch From chemistry-request@www.ccl.net Thu Nov 26 12:24:38 1998 Received: from asterix.uni-muenster.de (chan@ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA19153 Thu, 26 Nov 1998 12:24:35 -0500 (EST) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.8.8/8.7.5) with ESMTP id RAA196736 for ; Thu, 26 Nov 1998 17:24:30 GMT X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Thu, 26 Nov 1998 18:24:29 +0100 (MEZ) From: "Jerry C.C. Chan" To: CHEMISTRY@www.ccl.net Subject: fortran to C problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Sorry for this perhaps off-topic question but I believe some of you must be experts in C/Fortran programming. Recently I got a code in Fortran and I used f2c to convert everything in C. However, I always got three functions f01ajf, x02ajf and f02amf unresolved when the object files are linked. Could anyone please tell me whether these three functions are some subroutines from Fortran 90 library and are there something similar in C library? Many thanks, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@uni-muenster.de * * Universitaet Muenster phone: 0049-251-83-29156 * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 * * D-48149 Muenster * * Germany * ****************************************************************** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@www.ccl.net Thu Nov 26 14:29:48 1998 Received: from relay.netgenics.com (relay.netgenics.com [207.25.221.162]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA19493 Thu, 26 Nov 1998 14:29:47 -0500 (EST) Received: from netgenics.com (relay.dev.netgenics.com [192.168.113.1]) by relay.netgenics.com (8.8.5/8.8.6) with ESMTP id OAA18488; Thu, 26 Nov 1998 14:29:23 -0500 (EST) Message-ID: <365DAC12.2721BF2A@netgenics.com> Date: Thu, 26 Nov 1998 11:29:22 -0800 From: Scott Markel Organization: NetGenics, Inc. X-Mailer: Mozilla 4.5 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: "Jerry C.C. Chan" CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:fortran to C problem References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jerry, > Recently I got a code in Fortran and I used f2c to convert everything in > C. However, I always got three functions f01ajf, x02ajf and f02amf > unresolved when the object files are linked. Could anyone please > tell me whether these three functions are some subroutines from Fortran 90 > library and are there something similar in C library? The functions are from the Numerical Algorithm Group's (NAG) Fortran Library. Take a look at http://www.nag.co.uk/numeric/FLOLCH.html for details. The Fortran Library Search link at http://www.nag.co.uk/Advisory/FLSearch.html may be especially useful to you. Scott -- Scott Markel, Ph.D. NetGenics, Inc. smarkel@netgenics.com 4350 Executive Drive Tel: 619 455 5223 Suite 260 FAX: 619 455 1388 San Diego, CA 92121 From chemistry-request@www.ccl.net Thu Nov 26 14:31:02 1998 Received: from cliff.uottawa.ca (root@cliff.uottawa.ca [137.122.6.65]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA19506 Thu, 26 Nov 1998 14:30:54 -0500 (EST) Received: from oreo.science.uottawa.ca (oreo.science.uottawa.ca [137.122.43.15]) by cliff.uottawa.ca (8.9.1/8.9.1) with ESMTP id OAA10306; Thu, 26 Nov 1998 14:30:24 -0500 Received: from OREO/SpoolDir by oreo.science.uottawa.ca (Mercury 1.43); 26 Nov 98 14:30:33 GMT-5 Received: from SpoolDir by OREO (Mercury 1.43); 26 Nov 98 14:30:16 GMT-5 Received: from erik (137.122.43.165) by oreo.science.uottawa.ca (Mercury 1.43); 26 Nov 98 14:30:09 GMT-5 Sender: boufer@uottawa.ca Message-ID: <365DA7F1.41C6@aix1.uottawa.ca> Date: Thu, 26 Nov 1998 14:11:45 -0500 From: boufer Organization: None X-Mailer: Mozilla 2.02 (X11; I; AIX 1) MIME-Version: 1.0 To: "Jerry C.C. Chan" CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:fortran to C problem References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Jerry, These functions are from NAG library. You can obtain a running code by linking your object files~(obtained from .c) with NAG. Hope this helps. Jerry C.C. Chan wrote: > > Dear Netters, > > Sorry for this perhaps off-topic question but I believe some of you must > be experts in C/Fortran programming. > > Recently I got a code in Fortran and I used f2c to convert everything in > C. However, I always got three functions f01ajf, x02ajf and f02amf > unresolved when the object files are linked. Could anyone please > tell me whether these three functions are some subroutines from Fortran 90 > library and are there something similar in C library? > > Many thanks, > Jerry > > ****************************************************************** > * Jerry Chun Chung CHAN chan@uni-muenster.de * > * Universitaet Muenster phone: 0049-251-83-29156 * > * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * > * Schlossplatz 4-7 * > * D-48149 Muenster * > * Germany * > ****************************************************************** > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: chan@uni-muenster.de > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html From chemistry-request@www.ccl.net Thu Nov 26 15:26:29 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA19685 Thu, 26 Nov 1998 15:26:24 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id PAA13885 for chemistry@www.ccl.net; Thu, 26 Nov 1998 15:26:04 -0500 (EST) Date: Thu, 26 Nov 1998 15:26:04 -0500 (EST) From: "E. Lewars" Message-Id: <199811262026.PAA13885@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: F AS PROBLEM ELEMENT; A COULSON QUOTE 1998 Nov 25 Hello, (1) Does anyone have any refs to document the view that in ab initio calc's F is a problem element--for example, that optimization of fluorine- containing molecules does not readily give good geometries (or energies?)? I have refs to FOOF and to F2; any instances of other troublesome F-containing species would be welcome. (2) Someone, I think it may have been Coulson, said, ca. 1952, that calculating the energy differenece between two isomers as the difference in their computed energies is like weighing the captain by weighing the ship with and without him. I would appreciate the reference to this statement. [Of course in the 1950's few dreamt that it would ever be possible to calculate energy differences to chemical accuracy, at least by ab initio methods]. Thanks E. Lewars ========================== From chemistry-request@www.ccl.net Thu Nov 26 16:17:56 1998 Received: from opium.q1.fcen.uba.ar (churca@opium.q1.fcen.uba.ar [157.92.31.21]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA19868 Thu, 26 Nov 1998 16:17:36 -0500 (EST) Received: from localhost (churca@localhost) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id RAA10573; Thu, 26 Nov 1998 17:54:11 -0300 Date: Thu, 26 Nov 1998 17:54:11 -0300 (ARST) From: Adrian Turjanski To: CHEMISTRY@www.ccl.net cc: CHEMISTRY@www.ccl.net Subject: HYPERCHEM PM3 with Fe In-Reply-To: <365DA7F1.41C6@aix1.uottawa.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Has anyone used Hyperchem with semiempirical PM3 with Fe? I'm looking for bibliography about PM3 with Fe. Thanks Adrian turjanski From chemistry-request@www.ccl.net Thu Nov 26 17:02:40 1998 Received: from uria.its.uu.se (uria.its.uu.se [130.238.7.14]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA20041 Thu, 26 Nov 1998 17:02:39 -0500 (EST) Received: from basic-065.STUDENT.UU.SE ([192.168.4.65]:1571 "HELO basic-65" ident: "IDENT-NOT-QUERIED") by uria.its.uu.se with SMTP id <5741-22436>; Thu, 26 Nov 1998 22:22:38 +0100 Message-ID: <00cd01be198b$55a55640$4104a8c0@basic-65.student.uu.se> Reply-To: "Professor Piotr Paneth" From: "Professor Piotr Paneth" To: "E. Lewars" , Subject: Re: CCL:F AS PROBLEM ELEMENT; A COULSON QUOTE Date: Thu, 26 Nov 1998 22:22:58 -0000 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 >(1) Does anyone have any refs to document the view that in ab initio calc's > F is a problem element--for example, that optimization of fluorine- > containing molecules does not readily give good geometries (or energies?)? > I have refs to FOOF and to F2; any instances of other troublesome > F-containing species would be welcome. See: Dixon & Feller in J. Phys. Chem. A 102, 8209-16 (1998). They discuss heats of formation for CF2, FCO and CF2O - lots of high-end data included. !!!!!!! thru Dec. 18 please use the following address: !!!!!!!!! E-mail: paneth@kemi.uu.se ************************************************************************** Piotr Paneth, Ph.D., D.Sc. Professor of Chemistry Technical University, Zeromskiego 116, 90-924 Lodz, Poland phone: (+48-42) 631-3199 fax: (+48-42) 636-5008 > From chemistry-request@www.ccl.net Thu Nov 26 21:00:59 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id VAA20839 Thu, 26 Nov 1998 21:00:56 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA25700; Fri, 27 Nov 98 08:59:31 -0800 Date: Fri, 27 Nov 1998 08:59:31 -0800 (PST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: Polymer modeling Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Can anyone introduce any papers about mixture modeling applications? Thanks! Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From chemistry-request@www.ccl.net Thu Nov 26 22:41:59 1998 Received: from fg702-6.abct.polyu.edu.hk (fg702-6.abct.polyu.edu.hk [158.132.74.201]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA21085 Thu, 26 Nov 1998 22:41:58 -0500 (EST) Received: from danspc (dannt.polyu.edu.hk [158.132.31.49]) by fg702-6.abct.polyu.edu.hk (8.8.8/8.8.8) with SMTP id LAA24563 for ; Fri, 27 Nov 1998 11:43:23 +0800 (HKT) Message-Id: <3.0.2.32.19981127114354.009af138@fg702-6.abct.polyu.edu.hk> X-Sender: dkwmok@fg702-6.abct.polyu.edu.hk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Fri, 27 Nov 1998 11:43:54 +0800 To: CHEMISTRY@www.ccl.net From: Daniel Mok Subject: G: What is Reduced Masses in Freq caln.? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, I want to know what is the Reduced Masses in a Gaussian frequency calculation. I have the G matrix and F matrix determined from the Gaussian Output. I thought the Reduced masses were equal to (L^-1*G*L'^-1)^0.5 where L is the eigenvector of G*F. However, I've got something different. Anyone knows what is it? Daniel Dept. of Applied Biology and Chemical Tehcnology Hong Kong Polytechnic University ---------------------------------- Here is a bit of the Gaussian output on what I mentioned: 1 2 3 A1 A1 B2 Frequencies --- 1736.1004 3774.8178 3915.8778 Reduced masses --- 1.0829 1.0450 1.0813 Force constants --- 1.9230 8.7730 9.7689