From toukie@zui.unizh.ch Tue Aug 13 08:17:14 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.5/950822.1) id HAA24481; Tue, 13 Aug 1996 07:33:13 -0400 (EDT) Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA08170; Tue, 13 Aug 96 13:33:12 +0200 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA90304; Tue, 13 Aug 1996 13:33:11 +0200 From: toukie@zui.unizh.ch (Hr Dr. S. Shapiro) Message-Id: <9608131133.AA90304@rzurs3.unizh.ch> Subject: Cal'n of vibrational intensities To: chemistry@www.ccl.net Date: Tue, 13 Aug 1996 13:33:11 +0200 (MEST) X-Mailer: ELM [version 2.4 PL25 PGP2] Content-Type: text Dear Colleagues; Given the following output from a MOPAC "FORCE" calculation (i) frequency (ii) total dipole (iii) travel (iv) reduced mass how does one calculate/estimate the _intensity_ of a vibration at a given fre- quency? If the above information is not sufficient, what other MOPAC-derived data would I need in order to calculate the intensity? Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From dimitris@3dp.com Tue Aug 13 10:17:21 1996 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.7.5/950822.1) id JAA25199; Tue, 13 Aug 1996 09:31:55 -0400 (EDT) Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA29623; Tue, 13 Aug 96 09:38:36 -0400 Received: by europa.3dp.com (940816.SGI.8.6.9) id JAA19874; Tue, 13 Aug 1996 09:36:16 -0400 From: "Dimitris Agrafiotis" Message-Id: <9608130936.ZM19872@europa.3dp.com> Date: Tue, 13 Aug 1996 09:36:16 -0400 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@www.ccl.net Subject: Chemistry in C++ Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > Hi, I'd like to know about public domain chemistry codes > written in C++. > > Thanks in advance. John John, The only public domain class library I know is the OTF Toolkit from UCSF. I have developed our own class library here at 3D, but unfortunately this is not for public consumption. I know that the people at Agouron are also on the cutting edge of chemical computing, but they suffer from the same constraints we do. For visualization, you should definitely have a look at Molecular Inventor from SGI ($900). For numerical computing, I would have a look at LAPACK++ (a free C++ extension to the original LAPACK package), although a new toolkit based on templates and modelled after STL seems to be in the works. As for foundation classes, I would strongly recommend Tools.h++ from RogueWave ($400), or HP's version of the STL (free). And I would seriously consider DBTools.h++ for any database work ($3,000). There are, of course, many more toolkits for specialized purposes such as ga's, neural nets, fuzzy logic and the like, but these are probably not of general interest to this list. Hope that helps, Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Principal Research Scientist | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 From ka_peterson@ccmail.pnl.gov Tue Aug 13 15:17:19 1996 Received: from pnl.gov for ka_peterson@ccmail.pnl.gov by www.ccl.net (8.7.5/950822.1) id OAA26846; Tue, 13 Aug 1996 14:40:10 -0400 (EDT) From: Received: from ccmail.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01I8854RZSNK8WVYNC@pnl.gov>; Tue, 13 Aug 1996 11:39:53 -0700 (PDT) Date: Tue, 13 Aug 1996 11:33 -0700 (PDT) Subject: Re: CCL:Chemistry in C++ To: dimitris@3dp.com, chemistry@www.ccl.net, Kirk_Peterson%~PNL17@ccmail.pnl.gov Message-id: <01I8854WEE368WVYNC@pnl.gov> MIME-version: 1.0 Content-transfer-encoding: 7BIT Forwarded to Dr. Kirk Peterson (PNNL) ______________________________ Reply Separator _________________________________ Subject: CCL:Chemistry in C++ Author: dimitris@3dp.com at -SMTPlink Date: 8/13/96 6:36 AM > Hi, I'd like to know about public domain chemistry codes > written in C++. > > Thanks in advance. John John, The only public domain class library I know is the OTF Toolkit from UCSF. I have developed our own class library here at 3D, but unfortunately this is not for public consumption. I know that the people at Agouron are also on the cutting edge of chemical computing, but they suffer from the same constraints we do. For visualization, you should definitely have a look at Molecular Inventor from SGI ($900). For numerical computing, I would have a look at LAPACK++ (a free C++ extension to the original LAPACK package), although a new toolkit based on templates and modelled after STL seems to be in the works. As for foundation classes, I would strongly recommend Tools.h++ from RogueWave ($400), or HP's version of the STL (free). And I would seriously consider DBTools.h++ for any database work ($3,000). There are, of course, many more toolkits for specialized purposes such as ga's, neural nets, fuzzy logic and the like, but these are probably not of general interest to this list. Hope that helps, Ciao, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Principal Research Scientist | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: dimitris@3dp.com -- Original Sender From: Address: dimitris@3dp.com 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 steen@kiku.dk Tue Aug 13 16:17:22 1996 Received: from carbon.kiku.dk for steen@kiku.dk by www.ccl.net (8.7.5/950822.1) id PAA26989; Tue, 13 Aug 1996 15:37:19 -0400 (EDT) Received: by carbon.kiku.dk (smail3.1.29.1) id m0uqPHC-000pAcC; Tue, 13 Aug 96 21:37 METDST Message-Id: From: Steen Hammerum Subject: Speed of new HP and SGI workstations To: chemistry@www.ccl.net Date: Tue, 13 Aug 1996 21:37:17 +0200 (METDST) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Hello! Does anyone have or know of benchmarks for Gaussian 94 or related programs running on the new SGI and HP chips (R10000 and PA8000), or other information to assist us before we decide on new machinery? We are currently considering SGI Power Indigo 2 and HP C160 workstations that will be used predominantly for Gaussian calculations, but we are not sure how well the SPECint95 and SPECfp95 numbers allow us to assess the relative performance. Steen -- Steen Hammerum steen@kiku.dk Department of Chemistry (+45) 35 32 02 08 University of Copenhagen, Denmark fax: (+45) 35 32 02 12 From Jeffrey.Gosper@brunel.ac.uk Tue Aug 13 18:17:18 1996 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id RAA27659; Tue, 13 Aug 1996 17:30:44 -0400 (EDT) Received: from dialup-128-01.brunel.ac.uk by etamin.brunel.ac.uk with SMTP (PP); Tue, 13 Aug 1996 22:29:56 +0100 Date: Tue, 13 Aug 1996 22:28:01 PDT From: Jeffrey Gosper Subject: Re: CCL:Normal Coordinate Visualisation To: "Frederick R. Bennett" cc: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII > I am wondering if anyone has a simple program for drawing normal > coordinates on molecules once a frequency calculation has been done. Some > nice graphics programs such as Spartan can animate the normal vibrational > modes, but this is of little use for preparing static documents for example. > I guess that something that could simply draw mass weighted cartesian > coordinate arrows would be brilliant. > > Ciao At present Re_View ( a Windows pogram) will animate MOPAC normal modes but not draw arrows. The new version Re_View2 dows both. I will be releasing a test version of Re_View2 shortly so you may be interested in contacting me and acting as a beta tester. See Re_View's URL for further details. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's home page (molecular animations or Chem-4D): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From aeleen@netcom.com Tue Aug 13 18:23:45 1996 Received: from netcom12.netcom.com for aeleen@netcom.com by www.ccl.net (8.7.5/950822.1) id SAA27767; Tue, 13 Aug 1996 18:11:13 -0400 (EDT) Received: (from aeleen@localhost) by netcom12.netcom.com (8.6.13/Netcom) id PAA09745; Tue, 13 Aug 1996 15:11:08 -0700 From: aeleen@netcom.com (Aeleen Frisch) Message-Id: <199608132211.PAA09745@netcom12.netcom.com> Subject: Book on comp. chem. To: chemistry@www.ccl.net Date: Tue, 13 Aug 1996 15:11:08 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit The second edition of Exploring Chemistry with Electronic Structure Methods, by James B. Foresman and AEleen Frisch, has just been published. It is a thoroughly revised and expanded version of the previous work (354 pages). For this second edition, the authors have expanded the previous text and added new material throughout the book. They have also added many new exercises to most chapters covering advanced aspects of the current topic. This material constitutes an advanced track through the work. Experienced researchers may wish to examine the advanced track even in the earlier, more elementary chapters where the basic concepts are very familiar. New topics covered include the following: * Predicting NMR properties * New methods for geometry optimizations * Locating transition structures * Available methods, from semi-empirical through QCISD * Density functional theory * Gaussian-2 theory and variations * Complete Basis Set (CBS) methods * Relative accuracies and costs of various model chemistries * CASSCF calculations of excited state systems * New SCRF solvation models * SCF and DFT stability calculations Published by Gaussian, Inc., Pittsburgh, PA, USA. email: info@gaussian.com Soft cover: $ 42.00 ISBN 0-9636769-3-8 Hard cover: $100.00 ISBN 0-9636769-4-6 [available 9/96] Note: Previous purchasers of Gaussian 94 and G94W will be sent a soft cover copy automatically.