From daizadeh@indigo.ucdavis.edu Tue Jul 22 03:12:41 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id CAA11175; Tue, 22 Jul 1997 02:56:38 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id AAA12026; Tue, 22 Jul 1997 00:05:54 -0700 From: "Iraj Daizadeh" Message-Id: <9707220005.ZM12024@indigo.ucdavis.edu> Date: Tue, 22 Jul 1997 00:05:41 -0700 In-Reply-To: daizadeh@kappa (Iraj Daizadeh) "CCL:Summary: vizualization of 3-D flow field" (Jul 10, 10:12am) References: <199707101712.KAA14978@kappa.ucdavis.edu> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net, chemistry@www.ccl.net, daizadeh@kappa.ucdavis.edu (Iraj Daizadeh) Subject: Vizualization of 3-D flow field: mac-win Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. Several weeks ago I sent a summary concerning my experience with programs that are able to visualize a 3-d vector space (flow field). The summary spanned exclusively (with one exception) programs developed for a particular unix environment (SGI r10000 IRIX 5.x 6.x, in particular, 5.2 and 6.2). My new question is the same as the previous one except that it centers on software (commercial or otherwise) that can display a 2-d or 3-d flow field (vector field) as well as contours for a mac (preferable) or pc environment. Thanks in advance... Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu From guojx@xx1.icas.ac.cn Tue Jul 22 04:12:41 1997 Received: from xx1.icas.ac.cn for guojx@xx1.icas.ac.cn by www.ccl.net (8.8.3/950822.1) id DAA11378; Tue, 22 Jul 1997 03:53:23 -0400 (EDT) Received: (from guojx@localhost) by xx1.icas.ac.cn (8.6.12/8.6.9) id QAA14156; Tue, 22 Jul 1997 16:07:09 +0900 Date: Tue, 22 Jul 1997 16:07:09 +0900 (CDT) From: Guo Jian-Xin To: chemistry@www.ccl.net Subject: G: calculation about frequency of cation radical Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: I am interested in the calculation of the vibrational frequency of cation radical by AM1, HF and DFT. sometimes ago, there are many discussion about the calculation of the vibration frequency for neutral molecule, could you give me any suggestion about the cation radical? Thank in advances, Jian-xin Guo From schiffer@h1tw0036.hoechst.com Tue Jul 22 04:23:11 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id DAA11338; Tue, 22 Jul 1997 03:34:36 -0400 (EDT) Received: by backup.hoechst.com id JAA14096; Tue, 22 Jul 1997 09:30:50 +0200 Received: from unknown(134.81.76.36) by backup id sma014045; Tue Jul 22 09:29:39 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA04093; Tue, 22 Jul 1997 09:32:25 +0200 Message-ID: <33D46209.794B@h1tw0036.hoechst.com> Date: Tue, 22 Jul 1997 09:32:25 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Gabriel Berriz CC: Computational Chemistry List Subject: Fortran for C Programmers? References: <9707220138.AA23901@chasma.harvard.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Gabriel Berriz wrote: > > While we're on the subject of mixed-language programming, does anyone > know of a book (or any other reference) on Fortran for C programmers? In my view the very best book on FORTRAN is : Michael Metcalf Effective Fortran 77 Oxford University Press, Oxford 1987 ISBN 0-19-853709-3 > would be extremely helpful. (Unfortunately, there seems to be more > demand and supply for guides to C for Fortran programmers than the > other way around... :/ ) I am really looking for a good book on C and C++ for FORTRAN programmers. I know, that depend on the personal style. So, I would like to have a Metcalf for C++. I never saw one, so may be some of you can recommend something. Thanks a lot, Ciao Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From eggen@tc.mols.sussex.ac.uk Tue Jul 22 07:12:42 1997 Received: from maila.uscs.susx.ac.uk for eggen@tc.mols.sussex.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA11982; Tue, 22 Jul 1997 06:29:22 -0400 (EDT) Received: from tcibm.mols.sussex.ac.uk by maila.uscs.susx.ac.uk with smtp (Smail3.1.29.1 #2) id m0wqcBJ-000XGQC; Tue, 22 Jul 97 11:28 BST Message-Id: <41660.9707221036@tcibm.mols.sussex.ac.uk> From: Bernd R Eggen Subject: Re: CCL:Fortran for C Programmers ? To: schiffer@h1tw0036.hoechst.com (Dr. Heinz Schiffer) Date: Tue, 22 Jul 1997 11:36:49 +0000 (BST) Cc: chemistry@www.ccl.net In-Reply-To: <33D46209.794B@h1tw0036.hoechst.com> from "Dr. Heinz Schiffer" at Jul 22, 97 09:32:25 am Reply-To: eggen@tc.mols.sussex.ac.uk Department: School of Chemistry, Physics and Environmental Science Organisation: University of Sussex at Brighton, UK Content-Type: text Fortran to C/C++ sounds more like using Fortran 90 to me, which can deal with many of the shortfalls of FORTRAN 77. Fortran 90 even allows for some OO programming. There are plenty of good introductions for Fortran 90 (and 95) around, which can be found on the FAQ, the original (updated 26 June 97) is at URL http://www.ifremer.fr/ditigo/molagnon/fortran90/engfaq.html Heinz Schiffer wrote: > In my view the very best book on FORTRAN is : > > Michael Metcalf > Effective Fortran 77 > Oxford University Press, Oxford 1987 > ISBN 0-19-853709-3 > With best regards, Bernd Eggen. -- Dr. Bernd R. Eggen E-mail: B.R.Eggen@Sussex.ac.uk The University of Sussex at Brighton From Jeffrey.Gosper@brunel.ac.uk Tue Jul 22 07:35:32 1997 Received: from eros.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA12052; Tue, 22 Jul 1997 07:02:46 -0400 (EDT) Received: from castjjg.brunel.ac.uk (actually chem-pc-03.brunel.ac.uk) by eros.brunel.ac.uk with SMTP-BRUNEL (PP); Tue, 22 Jul 1997 10:02:13 +0100 Date: Tue, 22 Jul 1997 09:58:52 PDT From: Jeffrey Gosper Subject: Re: CCL:babel 1.6 & Windows NT Dos To: "Stephen P. Molnar" cc: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII edu> > > > >Hi! > > > >Is there any problem running babel 1.6 under a > >windows nt DOS shell? > > > >I am trying to use the Babelwin interface, but upon opening the > >DOS shell and calling babel, babel fails to open the input file. > >It appears to be a problem with babel, rather than Babelwin. > >The harddrive format is FAT, because I also run Linux in the > >same PC. I have done some testing on BABEL16 and BABLEWin and there appears to be problems using BABEL16 to convert files when spaces are used in the directory names or filenames. As such the use of spaces should be avoided. NB: BABElWin (32 bit version) does not have problems passing the correct path and filenames /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ 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://www.brunel.ac.uk/~castjjg Re_View's home page (molecular animations or Chem-4D): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From vkitzing@sunny.mpimf-heidelberg.mpg.de Tue Jul 22 08:12:43 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id IAA12336; Tue, 22 Jul 1997 08:02:56 -0400 (EDT) Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA07820; Tue, 22 Jul 97 14:02:54 +0200 Received: from [149.217.50.47] (mac20) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA09944; Tue, 22 Jul 97 13:59:14 +0200 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Jul 1997 13:58:27 +0200 To: Jeffrey.Nauss@UC.Edu, chemistry@www.ccl.net From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:AMBER and contiuum solvent models Dear Netters, At 11:34 Uhr 14.07.1997, Jeffrey L. Nauss wrote: >Have contiuum solvent models been implemented in AMBER for MD simulations? >If so, is the code available? Some time ago we implemented the MSA screening function to accound for electrostatic interactions screened by counder ions into AMBER 2. MSA is a level more sophisticated than Debye-Hueckel theory. This theory predicts the correct point of DNA B <-> Z transition. See: Reinhard Klement, Dikeos Mario Soumpasis and Thomas M. Jovin (1991). "Computation of ionic destributions around charged biomolecular structures: Results for right-handed and left-handed DNA." PNAS USA 88 4631-4635. Reinhard Klement, Dikeos Mario Soumpasis, Eberhard v. Kitzing and Thomas M. Jovin (1990). "Inclusion of ionic interactions in force field calculations of charged biomolecules - DNA structural transitions." Biopol 29 1089-1103. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@sunny.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From hinsen@lmspc1.ibs.fr Tue Jul 22 11:12:44 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id KAB13383; Tue, 22 Jul 1997 10:51:30 -0400 (EDT) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id QAA29594; Tue, 22 Jul 1997 16:52:43 +0200 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id QAA29087; Tue, 22 Jul 1997 16:51:23 +0200 Date: Tue, 22 Jul 1997 16:51:23 +0200 Message-Id: <199707221451.QAA29087@lmspc1.ibs.fr> From: Konrad Hinsen To: berriz@chasma.harvard.edu CC: chemistry@www.ccl.net In-reply-to: <9707220138.AA23901@chasma.harvard.edu> (berriz@chasma.harvard.edu) Subject: Re: CCL:Fortran for C Programmers? (Was: Object-oriented means for computational chemistry programming) > While we're on the subject of mixed-language programming, does anyone > know of a book (or any other reference) on Fortran for C programmers? > I have read introductory material on Fortran, and written *teeny* > throaway programs, but I still don't have a very good grasp of the > structure of Fortran programs. The examples of Fortran code I've seen > look like *nothing* else in my experience (mostly C, Perl, and Fortran (77) or Fortran-90? The differences are enormous. Fortran 77 code looks weird because it has to get around language restrictions that people who grew up with modern languages can't even imagine. In fact, Fortran 77 is structurally much closer to assembly languages than to Algol-like languages (which include C). Fortran 90, if used properly (i.e. ignoring obsolete features left in for compatibility only), looks much more like C. The major differences are in syntax and parameter passing (by value in C, by reference in Fortran). In both cases, I recommend reading a good introduction and thinking at each step about how the same problem would be solved in C. Then (for Fortran 77) find out why the C solution doesn't work in Fortran. I did succeed in that way, but obviously I never came to like Fortran in the least... -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From toukie@zui.unizh.ch Mon Jul 21 03:12:28 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id DAA05211; Mon, 21 Jul 1997 03:00:08 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA01873; Mon, 21 Jul 1997 09:00:07 +0200 Message-Id: <1.5.4.32.19970721070230.00664960@highdent.zzmk.unizh.ch> X-Sender: toukie@highdent.zzmk.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 21 Jul 1997 09:02:30 +0200 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: MOPAC50ESP Dear Colleagues; I am seeking a programme called "MOPAC50ESP". An Altavista search turned up thirteen relevent web sites, but I was not able access MOPAC50ESP from any of these thirteen sites. If anyone knows of a website or FTP site from which I can _really_ obtain information about MOPAC50ESP, or would be willing to share with me other information about this programme, please contact me directly at toukie@zui.unizh.ch Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From mzapalow@mitr.p.lodz.pl Mon Jul 21 05:12:28 1997 Received: from mitr.p.lodz.pl for mzapalow@mitr.p.lodz.pl by www.ccl.net (8.8.3/950822.1) id EAA05498; Mon, 21 Jul 1997 04:51:52 -0400 (EDT) Received: from mitr-mz.p.lodz.pl by mitr.p.lodz.pl with SMTP (5.65/25-eef) id AA09283; Mon, 21 Jul 97 10:33:53 +0200 Message-Id: <9707210833.AA09283@mitr.p.lodz.pl> Comments: Authenticated sender is From: "Michal Zapalowski" Organization: MITR To: "Gustavo A. Mercier Jr" Date: Mon, 21 Jul 1997 10:54:44 +0000 Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:babel 1.6 & Windows NT Dos Cc: chemistry@www.ccl.net Return-Receipt-To: "Michal Zapalowski" Priority: normal In-Reply-To: <199707181545.LAA06782@mail.med.upenn.edu> X-Mailer: Pegasus Mail for Win32 (v2.52) Gustavo A. Mercier Jr wrote: > I am trying to use the Babelwin interface, but upon opening the > DOS shell and calling babel, babel fails to open the input file. > It appears to be a problem with babel, rather than Babelwin. You're not right, I'm afraid. BabelWin generates batch file named babelwin.bat which looks like this: c:\ cd C:\tools\babel babel -ig94 D:\T9_pm3g.out -omopint D:\output.zmt pause The first command contains excess backslash, you should remove it with your favourite text editor: c: cd C:\tools\babel ... etc and run babelwin.bat manually. Regards, Michal Zapalowski -------------------------- Michal Zapalowski, MSc email: mzapalow@mitr.p.lodz.pl phone: (+48 42) 313-177 fax: (+48 42) 360-246 IARC, Technical University of Lodz ul. Wroblewskiego 15 93 - 590 Lodz, Poland From rgab@proteus.co.uk Mon Jul 21 07:12:29 1997 Received: from petersgate.proteus.co.uk for rgab@proteus.co.uk by www.ccl.net (8.8.3/950822.1) id HAA05907; Mon, 21 Jul 1997 07:08:29 -0400 (EDT) Received: from Icthus.proteus.co.uk (Icthus [193.115.24.114]) by petersgate.proteus.co.uk (8.6.12/8.6.6) with ESMTP id MAA11059 for ; Mon, 21 Jul 1997 12:09:09 GMT Message-Id: <199707211209.MAA11059@petersgate.proteus.co.uk> From: Richard Bone Date: Mon, 21 Jul 1997 12:08:30 +0100 To: CHEMISTRY@www.ccl.net Subject: SMILES databases - summary Following up on my enquiry about SMILES databases last week, here is a brief summary of the responses. They fell into 3 different categories (besides the inevitable "please send us the answers ... "): 1) Why not just use a format-interchange program to convert a database in some other format to SMILES? (Or, just dump a selection of an existing database out specifying SMILES as the output option; or create some combinatorial library and do the same) DOUGH@mdli.com twells@mdli.com (Terry Wells) stevew@mdli.com (Steve Welford) 2) Try to find a way of automating their generation. jsb@camsoft.com (Jonathan Brecher, CambridgeSoft Corporation ) 3) Examples of SMILES databases already 'out there'. a) 8,000 small organics. Contact J. Eric Slone (eslone@patriot.net). b) Database of organic compounds (Possibly in SMILES, and probably used for QSAR). Contact Lowell Hall (hall@enc.edu); communicated by Tod Story, (story@ksu.edu). c) First 4,000 (non metal-containing) entries of the NCI database. Supplied by Wolfgang Utz (utz@pharmazie.uni-erlangen.de). Available by FTP: (ftp://schiele.organik.uni-erlangen.de/pub/nci/nci4000.smi.gz) d) 400 example small molecules available for free. (http://esc.syrres.com/~ESC/examples.htm) A commercially available database with 100,000 SMILES and CAS-numbers available from Syracuse Research Corp. Contact meylan@syrres.com In addition, I came across a web-site at Pomona College which contained a number of files of compounds organised by molecular empirical formula, and containing their SMILES strings. http://clogp.pomona.edu/medchem/chem/master/mf/ghindex.html It does not appear to be possible to download these 'in batch', but it is a most \\formidable\\ source of data. Thanks to everyone for their input. Richard Bone ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Richard G. A. Bone, Ph.D. | | | Senior Computational Chemist | | | Proteus Molecular Design Ltd. | Tel: +44 (0)1625 500555 | | Lyme Green Business Park | Fax: +44 (0)1625 500666 | | Macclesfield, Cheshire | Email: rgab@proteus.co.uk | | United Kingdom SK11 0JL | Web: http://www.proteus.co.uk | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From jenninaj@mh.uk.sbphrd.com Mon Jul 21 10:12:29 1997 Received: from ns01.sbphrd.com for jenninaj@mh.uk.sbphrd.com by www.ccl.net (8.8.3/950822.1) id KAA06579; Mon, 21 Jul 1997 10:07:35 -0400 (EDT) Received: by ns01.sbphrd.com; id KAA29944; Mon, 21 Jul 1997 10:07:36 -0400 Received: from phinet.sbphrd.com(139.136.64.5) by ns01.sbphrd.com via smap (3.2) id xma029876; Mon, 21 Jul 97 10:07:29 -0400 Received: from hbu037.ha.uk.sbphrd.com by phinet.sbphrd.com; (5.65v3.0/1.1.8.2/06Mar95-1250PM) id AA18596; Mon, 21 Jul 1997 10:07:29 -0400 Received: from hgu118.ha.uk.sbphrd.com (hgu118.ha.uk.sbphrd.com [139.136.157.118]) by hbu037.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/mh/970220) with ESMTP id PAA30406 for ; Mon, 21 Jul 1997 15:07:26 +0100 (BST) Received: from localhost (jenninaj@localhost) by hgu118.ha.uk.sbphrd.com (8.8.5/pe/sbphrd/clnt/970220) with SMTP id PAA02119 for ; Mon, 21 Jul 1997 15:07:27 +0100 (BST) X-Authentication-Warning: hgu118.ha.uk.sbphrd.com: jenninaj owned process doing -bs Date: Mon, 21 Jul 1997 15:07:26 +0100 (BST) From: Andy Jennings To: Comp-Chem-List Subject: Retrosynthesis Programs Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII All, After the discussion of programs to plan retrosynthetic pathways to desired targets I wonder which companies out there do actually use them. The comments that they are difficult to use or that the databases are too limited were valid some time ago but I wonder what the current state-of-play actually is. I would be grateful if any of you could let me know what the situation is within your own companies, particularly if they are involved in pharmaceutical research. I would ideally like to know what programs you have, what the general impression is and whether the programs are actually used! Any replies gratefully received...perhaps directly to me to save clogging up the newsgroup with non-scientific matters? Thanks in advance, Andy ============================================================ Andy Jennings - SmithKline Beecham Pharmaceuticals Phone: +44 (0) 1279 627682 Fax: +44 (0) 1279 627685 From dalke@ks.uiuc.edu Mon Jul 21 20:12:35 1997 Received: from london.ks.uiuc.edu for dalke@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id UAA10109; Mon, 21 Jul 1997 20:12:32 -0400 (EDT) Received: from bilbao.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2 [TBG Mods]) id AA031490352; Mon, 21 Jul 1997 19:12:32 -0500 Received: (from dalke@localhost) by bilbao.ks.uiuc.edu (940816.SGI.8.6.9/8.6.9)id TAA11576 for chemistry@www.ccl.net; Mon, 21 Jul 1997 19:12:32 -0500 Date: Mon, 21 Jul 1997 19:12:32 -0500 From: Andrew Dalke Message-Id: <199707220012.TAA11576@bilbao.ks.uiuc.edu> To: chemistry@www.ccl.net Subject: Re: CCL:Object-oriented means for computational chemistry programming Konrad Hinsen commented: > Just a crazy idea: create an institution > devoted to "scientific computing" for the academic community. Staff it > with application scientists and computer scientists, and let it work > on a high-level language for scientific applications ... That's somewhat like what the Numerical Algor. Group does (www.nag.com). From http://www.nag.com/0h/AboutNAG.html : > NAG produces and distributes numerical, symbolic, statistical and > visualisation software for the solution of problems in a wide range of > applications in such areas as science, engineering, financial analysis > and research. > > For users who write programs and build packages, NAG produces > sub-program libraries in a wide range of computer languages (Ada, > C, Fortran, Pascal, Turbo Pascal). [...] NAG provides several > powerful mathematical and statistical packages for interactive use. In a non-commercial sense I think most application domains have their own set of tools, and it will be very hard to convince mathematicians to give up MatLab/Mathematics and astronomers to give up AIPS/AIPS++ and statisticians give up S-Plus and ... Granted, scripting languages like Python can incorporate all of these interfaces, but it takes time, money and expertise. Konrad went on to say: > I'd like to propose an alternative > model for developing scientific code: define a "lifetime" of between > five and ten years for each package (depending on the speed of method > development) and throw it away after that time, replacing it with > new code containing the useful part of the functionality and written > according to the state of the art of programming. If the code is implemented "correctly" there is no reason to do this. When was the last time you needed to upgrade ftp, or telnet, or bc, or yacc? I use libpdb from the CGL to read PDB files and the library hasn't changed in years (though the PDB format has :). Yet it still works very well. The C and Fortran APIs for PVM haven't changed very much over the last 5 years, and there isn't much call for a change. I think the problem isn't that code naturally decays over time but that it wasn't well designed in the first place. Flaws in the architecture are glossed over as the project grows until it becomes a morass of hacked fixes, until finally the thing is chucked. Done well (modular code, consistant design, well thought out APIs, etc.) there's no reason you shouldn't use a 15-year library. However, it is hard to do. Andrew Dalke dalke@ks.uiuc.edu P.S. Oh yeah, and another reason for code to change -- creaping featurism!