From jpool@ccsf.caltech.edu Mon Aug 22 00:39:57 1994 Received: from delilah.ccsf.caltech.edu for jpool@ccsf.caltech.edu by www.ccl.net (8.6.9/930601.1506) id AAA11963; Mon, 22 Aug 1994 00:06:49 -0400 Received: from [131.215.145.232] (gryphon.ccsf.caltech.edu [131.215.145.232]) by delilah.ccsf.caltech.edu (8.6.9/8.6.4) with SMTP id VAA26556; Sun, 21 Aug 1994 21:06:46 -0700 Message-Id: <199408220406.VAA26556@delilah.ccsf.caltech.edu> X-Sender: jpool@delilah.ccsf.caltech.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 21 Aug 1994 21:03:40 -0800 To: CHEMISTRY@ccl.net From: jpool@delilah.ccsf.caltech.edu (J. C. T. Pool) Subject: Computational Chemistry and the National Software Exchange Cc: jpool@ccsf.caltech.edu The message below has been circulated to several newsgroups, mailing lists, etc. I am submitting it to CCL because I have undertaken the responsibility to interface with the computational chemistry community interested in using high performance computer systems, scalable systems ranging from networks of workstations to parallel-vector-supercomputers to massively parallel processors. NSE's objective is not to duplicate efforts in the computational chemistry community. NSE's objective is to interface current and future efforts in the computational chemistry community to the HPCC National Software Exchange. The following is a brief extract from the proposal for the NSE which emphasizes the approach advocated by the NSE developers. "The key to a successful software distribution system will be the establishment of a scalable mechanism for distributing software via the national information infrastructure. Many Internet sites have sizable collections of documents or software. It is both unnecessary and undesirable to require that these collections reside at a single site. We plan to put together a CRPC HPCC Mosaic Home Page that will capture in one place the software from the HPCC effort. We plan to develop a software exchange capability for the HPCC community based on existing network interfaces such as Mosaic. This capability is intended to provide mechanisms for the community to access a number of existing software. The maximal benefit to the community will be achieved by having an architecture for software exchange that is open. This will allow a network repository to grow over time. Initially, we will provide existing software technologies to the HPCC community. This will be done by building on existing components to build a prototype that will serve as a model of how such a system should be put together." IF YOU HAVE COMMENTS SPECIFICALLY RELATED TO THE INTERACTIONS BETWEEN THE COMPUTATIONAL CHEMISTRY COMMUNITY AND THE NATIONAL SOFTWARE EXCHANGE, PLEASE SEND THE COMMENTS TO THE FOLLOWING EMAIL ADDRESS jpool@ccsf.caltech.edu Thanks, Jim Pool Deputy Director Caltech Concurrent Supercomputing Facilities +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ The message circulated to numerous newsgroups, mailing lists, etc. follows. To facilitate the development and distribution of software enabling technologies for high performance computing we have set up a National Software Exchange (NSE) for the High Performance Computing and Communications community. The project has the following goals: o Wide availability of high-quality, public-domain software for high performance computers. o Promotion of software reuse. o Collaboration and information sharing between universities, research laboratories, and industry. o Active participation by Grand Challenge groups and other research scientists, both in contributing to and in using the NSE. o Promotion of technology transfer and software capitalization. A prototype system is in place and can be accessed through the URL: http://www.netlib.org/nse/home.html As an overview to the system, information is provided on the following topics: HPCC Programs and Activities Grand Challenges Software / Enabling Technologies Repositories Packages Application Level Library Software Parallel Programming Environments Parallel Programming Languages Performance Visualization Information Databases Commercial Vendor Catalog Reports, Journals, and Professional Societies Related Network Resources Please send comments and suggestions to nse@cs.utk.edu. This project is being funded by NASA and is a collaborative effort coordinated through the Center for Research on Parallel Computation, a NSF Science and Technology Center, by the following individuals: Jack Dongarra, University of Tennessee and Oak Ridge National Laboratory Geoffrey Fox, Syracuse University Ken Kennedy, Rice University Jim Pool, California Institute of Technology Rick Stevens, Argonne National Laboratory --------------------------------------------------------------------------- James C. T. Pool, Deputy Director Tel: 818-395-6743 Caltech Concurrent Supercomputing Facility Fax: 818-584-5917 California Institute of Technology, MC 158-79 1201 East California Boulevard Pasadena, CA 91125 Email: jpool@ccsf.caltech.edu From tamasgunda@TIGRIS.KLTE.HU Mon Aug 22 05:40:02 1994 Received: from phem3 for tamasgunda@TIGRIS.KLTE.HU by www.ccl.net (8.6.9/930601.1506) id FAA14226; Mon, 22 Aug 1994 05:26:53 -0400 Received: from HUEARN.SZTAKI.HU (MAILER@HUEARN) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HG75OYRTXS9623BZ@phem3.acs.ohio-state.edu>; Mon, 22 Aug 1994 05:26:46 EDT Received: from HUKLTE51.BITNET (NJE origin MAILER@HUKLTE51) by HUEARN.SZTAKI.HU (LMail V1.1d/1.7f) with BSMTP id 4564; Mon, 22 Aug 1994 11:25:40 +0200 Received: by tigris.klte.hu (MX V3.3 VAX) id 8837; Mon, 22 Aug 1994 11:24:36 +0100 Date: Mon, 22 Aug 1994 11:24:31 +0100 From: "Tamas Gunda, Hungary" Subject: CCL:timings and compilers To: chemistry@ccl.net Reply-to: TAMASGUNDA%HUKLTE51.BITNET@phem3.acs.ohio-state.edu Message-id: <00983538.D7AE8840.8837@tigris.klte.hu> Content-transfer-encoding: 7BIT Hi everybody, There were several talks on the CCL about the speed of programs in different hardware environments. For example, the following (or a similar) table appeared several times: > Here are some timings for HyperChem, written in C, for comparison. > > MNDO energy and gradient for C60, converged to 1e-2, without DIIS: > > Computer Time (s) Rel. speed > 486DX 50 MHz 375 1 > Pentium 90 MHz 87.6 4.28 > SGI Indy 100 Mhz 77.8 4.82 > IBM RS/6000-250 66 MHz 51.8 7.24 > DEC 3000 200 MHz (I think) 42.4 8.84 > Somebody(s) has mentioned also the importance of compilers used to generate the executable program files. This may have far greater influence on the speed of the program, as the processor type itself. For those, who are not very much involved in programming, an example from my own practice: The Z-buffering means that before displaying the molecule, the atoms have to be sorted according to their Z coordinate. In the case of a molecule with 2208 atoms, on a 486DX33 PC, using exactly the same sorting algorithm: environment: time: PDB 7.1 QBX / DOS (= professional version of 24 sec QuickBasic) Visual Basic 3.0 / Windows 3.1 38 sec Assembler (= directly in machine code), "hand made and optimized" for speed and 32 bits, implanted into QBX 0.4 sec So there is an about 50 fold difference, if the most time consuming steps are in "hand made assembler" on the same hardware! Unfortunately I do not have data for the C language environment, it should be somewhere between. It is up to the programmers and programming houses, how and to what extent they take the advantage of the third (and most time-consuming) prog- ramming method. I think, it is a quite general programming habit recently, that programs are written superficially, at least as speed is concerned, beliving that in the days of recent processors, it has no importance. It has! The above data are for the PC, but the situation could be similar in another platforms, too. So it is very suggested to compare different programs, or different versions of the same program in the same machine, because the informations gathered from these experiments are as important (or more), as the experiments with different processor types. Best wishes Tamas E. Gunda From AZHARI@FRCU.EUN.EG Mon Aug 22 06:40:02 1994 Received: from FRCU.EUN.EG for AZHARI@FRCU.EUN.EG by www.ccl.net (8.6.9/930601.1506) id FAA14316; Mon, 22 Aug 1994 05:43:14 -0400 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01HG7KVSLKYO0003GJ@FRCU.EUN.EG>; Mon, 22 Aug 1994 12:41:34 O Date: Mon, 22 Aug 1994 12:41:33 +0000 (O) Subject: basis set for sulphur To: chemistry@ccl.net Message-id: <01HG7KVSM48Y0003GJ@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCL: What basis set would have a adequate treatment of the sulhur atom, TZ or TZ2P or TZ2P1F. is it possible that someone may provide me with the basis set for H, C, O, N and S. Adel El-Azhary From AZHARI@FRCU.EUN.EG Mon Aug 22 06:47:34 1994 Received: from FRCU.EUN.EG for AZHARI@FRCU.EUN.EG by www.ccl.net (8.6.9/930601.1506) id FAA14477; Mon, 22 Aug 1994 05:51:21 -0400 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01HG7L4ZBVI80003GJ@FRCU.EUN.EG>; Mon, 22 Aug 1994 12:49:43 O Date: Mon, 22 Aug 1994 12:49:43 +0000 (O) Subject: experiemental geometry by microwave spectroscopy To: chemistry@ccl.net Message-id: <01HG7L4ZC55E0003GJ@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCL: I have to questions: 1) Can anyone give me a reference to static correlation. 2) Can someone elaborate on the difference of the geometry by microwave, electron diffraction and X-Ray. Can you give references. My ynderstanding is that the microwave geometry is better than the others but I do not know exactly why. Adel El-Azhary From bennett@ubaclu.unibas.ch Mon Aug 22 11:40:08 1994 Received: from swiba9.unibas.ch for bennett@ubaclu.unibas.ch by www.ccl.net (8.6.9/930601.1506) id LAA20246; Mon, 22 Aug 1994 11:35:15 -0400 Received: from yogi.urz.unibas.ch by swiba9.unibas.ch with SMTP (PP); Mon, 22 Aug 1994 17:35:06 +0200 Received: from fib.chemie.unibas.ch. (fib.chemie.unibas.ch) by ubaclu.unibas.ch (PMDF V4.3-7 #7496) id <01HG7V752FS08WW6U8@ubaclu.unibas.ch>; Mon, 22 Aug 1994 17:36:52 +0200 Date: Mon, 22 Aug 1994 16:46:10 +0200 From: Frederick Bennett Subject: G92 : Archives To: chemistry@ccl.net Message-id: X-Mailer: VersaTerm Link v1.1 Content-transfer-encoding: 7BIT Hi all, does anybody no of some program or utility that can take a gaussian archive entry and turn it into something easy to read. Especially for frequency calculations were the archive can be quite long and meaningless to the naked eye (or mine at least). Regards Fred ====================================================== Papernet Address : Frederick R. Bennett Institute for Physical Chemistry Klingelbergstrasse 80 CH-4056 Basel Switzerland Mouthnet Address : [41]-(61)-267-3821 Internet Address : bennett@ubaclu.unibas.ch ====================================================== From toni@athe.wustl.edu Mon Aug 22 12:05:10 1994 Received: from wugate.wustl.edu for toni@athe.wustl.edu by www.ccl.net (8.6.9/930601.1506) id MAA21346; Mon, 22 Aug 1994 12:05:10 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA27472; Mon, 22 Aug 1994 11:04:44 -0500 Received: by athe.WUStL.EDU (8.6.9/SMI-SVR4) id LAA05400; Mon, 22 Aug 1994 11:04:42 -0500 Date: Mon, 22 Aug 1994 11:04:42 -0500 From: toni@athe.wustl.edu (Toni Kazic) Message-Id: <199408221604.LAA05400@athe.WUStL.EDU> To: shenkin@still3.chem.columbia.edu Cc: stoutepf@chemsci1.es.dupont.com, chemistry@ccl.net, stoutepf@gatekeeper.es.dupont.com In-Reply-To: <9408211720.ZM812@still3.chem.columbia.edu> (shenkin@still3.chem.columbia.edu) Subject: Re: CCL:Linus Pauling > He had a few dead ends, too. For example, his theory of the immune . . . I once had the opportunity to talk briefly with Pauling (my institute was having a crystallography symposium, and there was a little get-together with Pauling, Dorothy Hodgkin and the postdocs). I vividly recall him saying that in order to have a few good ideas, you need to have a lot of them! He surely did both ;-). From marty@ionchannel.med.harvard.edu Mon Aug 22 12:40:05 1994 Received: from harvard.harvard.edu for marty@ionchannel.med.harvard.edu by www.ccl.net (8.6.9/930601.1506) id LAA21227; Mon, 22 Aug 1994 11:56:38 -0400 Received: by harvard.harvard.edu (5.54/a0.25) (for chemistry@ccl.net) id AA12840; Mon, 22 Aug 94 11:56:23 EDT Received: from ionchannel.med.harvard.edu by heimdall.med.harvard.edu.med.harvard.edu (4.1/SMI-4.1) id AA12474; Mon, 22 Aug 94 11:52:05 EDT Received: from [134.174.159.130] by ionchannel.med.harvard.edu via SMTP (931110.SGI/920502.SGI) for @heimdall.med.harvard.edu:chemistry@ccl.net id AA00991; Mon, 22 Aug 94 11:57:01 -0700 Message-Id: <9408221857.AA00991@ionchannel.med.harvard.edu> X-Sender: marty@ionchannel.med.harvard.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 22 Aug 1994 11:52:11 -0400 To: chemistry@ccl.net From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Subject: surface area of a pocket X-Mailer: Hello, I was wondering what software people use to calculate the surface area of a protein cavity. To save bandwidth, please E-mail directly to me & I'll summarize in a few days. Thanks in advance, Marty ========================================================================= Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave Boston, MA 02115 -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran =========================================================================== From PA13808@UTKVM1.UTK.EDU Mon Aug 22 14:40:08 1994 Received: from phem3 for PA13808@UTKVM1.UTK.EDU by www.ccl.net (8.6.9/930601.1506) id OAA23728; Mon, 22 Aug 1994 14:27:10 -0400 From: Received: from UTKVM1.BITNET (MAILER@UTKVM1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HG7OKU68KW95RYUF@phem3.acs.ohio-state.edu>; Mon, 22 Aug 1994 14:27:05 EDT Received: from UTKVM1.UTK.EDU (PA13808) by UTKVM1.BITNET (Mailer R2.10 ptf000) with BSMTP id 1770; Mon, 22 Aug 94 14:07:59 LCL Date: Mon, 22 Aug 94 13:49:47 LCL Subject: LINUS PAULING To: chemistry@ccl.net Message-id: <01HG7OKU68KY95RYUF@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT For those interested in learning more about the work of Pauling in chemistry, medicine and a little of his poltics I suggest they take a look at "Molecules In Natural Science and Medicine An Encomium for Linus Pauling" ED. Z.B. Maksic and M. Eckert-Maksic. ELLIS HORWOOD (NY LONDON etc)1991. (ISBN 0-13-561598-4) The forward by M.F> Perutz on the importance of "NATURE OF THE CHEMICAL BOND" to biophysicists is very inspiring and the preface by the Maksics on Pauling as a main author of the CAVTAT DECLARATION is even more relevant to our society than it was when originally written (International Journal of Quantum Chemistry 1989). John E. Bloor,Univ. Of Ten (PA13808 at UTKVM1.utk.edu) From PA13808@UTKVM1.UTK.EDU Mon Aug 22 14:46:30 1994 Received: from phem3 for PA13808@UTKVM1.UTK.EDU by www.ccl.net (8.6.9/930601.1506) id OAA23946; Mon, 22 Aug 1994 14:38:40 -0400 From: Received: from UTKVM1.BITNET (MAILER@UTKVM1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HG7OZ3KL5S961XZU@phem3.acs.ohio-state.edu>; Mon, 22 Aug 1994 14:38:35 EDT Received: from UTKVM1.UTK.EDU (PA13808) by UTKVM1.BITNET (Mailer R2.10 ptf000) with BSMTP id 2223; Mon, 22 Aug 94 14:27:33 LCL Date: Mon, 22 Aug 94 14:11:13 LCL Subject: Accurate Molecular Structures To: netters Message-id: <01HG7OZ3KL5U961XZU@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT For a very comprehensive discussion of the accuracy and meaning of geometry parameters I suggest the book "Accurate Molecular Structures Their Determination and Importance." Ed. A. Domenicano and I Hargattai. published by the International Union of Crystallography and Oxford Univ. Press 1992. The paper by Kozo Kuchitsu (pages 14-46)on the meaning of internuc lear distances and a number of papers following it are essential information for anyone attempting to use experimental geometry in their calculations. See also Calloman et al Molecular Constants. Landolt-Bornstein. Numerical data and functional relationships in science and tech. New Series Group II vol 14b Springer, Berlin, also vol 15 and maybe later vols. Bankrupt your university by asking them to buy the set. (The OUPress book has ISBN number 0-19-855556-3) John E. Bloor,Univ of Tenn(Pa13808 at UTKVM1.utk.edu) From lim@rani.chem.yale.edu Mon Aug 22 14:50:27 1994 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id OAA23453; Mon, 22 Aug 1994 14:10:39 -0400 Received: by rani.chem.yale.edu; Mon, 22 Aug 94 14:09:18 -0400 From: Dongchul Lim Message-Id: <9408221809.AA19643@rani.chem.yale.edu> Subject: Re: CCL:G92 : Archives To: chemistry@ccl.net (Computational Chemistry) Date: Mon, 22 Aug 94 14:09:18 EDT In-Reply-To: ; from "Frederick Bennett" at Aug 22, 94 4:46 pm X-Mailer: ELM [version 2.3 PL11] Frederick Bennett writes: > > Hi all, > does anybody no of some program or utility that can take a gaussian > archive entry and turn it into something easy to read. Especially for > frequency calculations were the archive can be quite long and meaningless to > the naked eye (or mine at least). > I use the following 'awk' script to extract zmatrix from gaussian archive or output. Cut out the script, name it 'extract' or whatever and make it executable (chmod +x extract). Examples of its usage are % extract file.log > file.com % extract file.arch > file.com % zcat file.log.Z | extract > file.com where file.log is a gaussian output and file.arch is a gaussian archive file. Creating an archive from gaussian output is real easy. The following one-line awk script will do the job. E.g., % archive file.log > file.arch --------- CUT HERE (archive) --------- #!/usr/bin/nawk -f /(1\\1\\)/ {while (getline > 0) {print; if (match($0,/@/)) exit;}} --------- CUT HERE (archive) --------- -Dongchul Lim Dept. of Chem., Yale Univ., lim@rani.chem.yale.edu ---------- CUT HERE (extract) ------------------------------------------ #! /usr/bin/nawk -f # @(#) extract - extract Gaussian zmatrix from an archive file !/(1\\1\\)/ {next;} # beginning of the archive !/#/ {while (getline > 0) if (match($0, /#/)) break;} { prev = substr($0, index($0, "#")); gsub(/\\/, "\n", prev); while (getline > 0) { if (match($0,/\@/)) break; sub(/^[ \t]+/, "", $0); gsub(/\\/, "\n", $0); card = sprintf("%s%s", prev, $0); n = index(card, "Version"); # mark the end if (n > 0) { # done printf("%s", substr(card, 1, n-1)); break; } printf("%s", prev); prev = $0; } exit; }