From jsb2@camsoft.com Mon Jul 14 00:07:02 1997 Received: from camsoft.com for jsb2@camsoft.com by www.ccl.net (8.8.3/950822.1) id XAA19603; Sun, 13 Jul 1997 23:11:05 -0400 (EDT) From: Date: Sun, 13 Jul 97 23:10:37 EDT Received: by camsoft.com (4.1/3.1.090690-CambridgeSoft Corp.) id AA14988; Sun, 13 Jul 97 23:10:37 EDT Message-Id: <9707140310.AA14988@camsoft.com> To: rgab@proteus.co.uk Subject: Re: CCL:SMILES Database? Cc: CHEMISTRY@www.ccl.net, diversity@LISTSERV.ARIZONA.EDU >Does anyone know of a public-domain database of SMILES strings for commonly- >occurring small organic molecules and functional groups? I'm looking for >something containing several hundred or more species. You're going to be really hard put to locate anything in the public domain. Most everyone tends to retain copyright even on materials they make publically accessible. Your best bet would probably be (US) government data which, with one notable exception, is in the public domain. Problem is, the government isn't real fond of SMILES strings. They have some WLNs, but I don't think I've seen any SMILES. If you only need a few hundred, you might be best off creating your own: C methane CC ethane CCC propane etc. Jonathan Brecher CambridgeSoft Corporation jsb@camsoft.com From wjs@csb0.IPC.PKU.EDU.CN Mon Jul 14 05:07:02 1997 Received: from csb0.IPC.PKU.EDU.CN for wjs@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id EAA20802; Mon, 14 Jul 1997 04:52:45 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA12394; Mon, 14 Jul 97 16:52:09 -0700 Date: Mon, 14 Jul 1997 16:52:07 -0700 (PDT) From: Wang Jiansuo To: chemistry@www.ccl.net Subject: Where is software on interconversion of chemical structure systems based on WLN??? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netter, Wiswesser Line Notation(WLN) is a widely-used method of chemical structure presentation.I am looking for programs that interconve between WLN and Connection Table or other structure presentation systems.Any information of yours is appreciated. Thanks in advance. Your sincerely, From lestaw.k.bieniasz@uni-tuebingen.de Mon Jul 14 06:10:12 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id EAA20789; Mon, 14 Jul 1997 04:46:34 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA08146; Mon, 14 Jul 97 10:45:55 MES Date: Mon, 14 Jul 1997 10:45:50 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" Reply-To: "Lestaw K. Bieniasz" To: chemistry@www.ccl.net Subject: CCL & OOP Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 14.07.97 Hello, I think you guys miss one point: The choice of the programming language depends on what you want to achieve. There is no "best" language (as somebody complained) and there will never be, because there are different languages for different purposes. So, let's try to define what the computational chemists may need the most. If you need a program for individual purpose, use Fortran if you like it. If you need a program that is expected to be very big or used by many, and developed/extended by many, use an OOP type language, like C++, for example. I have personally been using C for around 10 years (and I have to say that after this experience I would never come back to Fortran!) and I am now switching to C++. There are a few problems with standards, OK, but I would say that OOP (and C++ in particular) is a a substantial step forward compared to procedural languages, although it is certainly not easy to change the way of thinking if somebody is accustomed to let's say Fortran or pure C. But whatever are personal preferences in this matter, see how the future of scientific programming is going to look like in the next decade. There is an interesting article by deJong and Rip in the (April, I think) volume of "Artificial Intelligence", where they discuss the concept of "discovery programs". Similar concepts of "problem solving environments" are also put forward by other authors (see http://www.cs.purdue.edu/research/cse/pses and related sites and literature). In general, these predictions for the future are strongly connected to the concept of world-wide network of scientific programs, parallel and extensively distributed processing. Although I am personally not very happy about these ideas, I think you will agree with me that this is indeed the direction in which the things are developing. If so, and if we want our programs to be still useful after five years, we should start to select the proper language now. As far as I know, the only language available at present, that responds to the challenges created by these future needs is JAVA. And it is an example of an orthodox OOP-type language. As I said I am not happy about this, because it looks I will have to start learning something new again (no hope for having a rest), but that's the life. Just my 0.02$. L. *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From qiecx@mluche5.chemie.uni-halle.de Mon Jul 14 07:07:01 1997 Received: from mluche5.chemie.uni-halle.de for qiecx@mluche5.chemie.uni-halle.de by www.ccl.net (8.8.3/950822.1) id GAA21279; Mon, 14 Jul 1997 06:41:47 -0400 (EDT) Received: by mluche5.chemie.uni-halle.de (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id MAA11395; Mon, 14 Jul 1997 12:41:43 +0200 From: "Anne Fircks" Message-Id: <9707141241.ZM11393@mluche5.chemie.uni-halle.de> Date: Mon, 14 Jul 1997 12:41:36 -0600 In-Reply-To: "Merethe Sjovoll" "CCL:Summary on organic/inorganic interfaces" (Jul 7, 10:44am) References: <9707071044.ZM13400@fskru5.hre.hydro.com> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL: Al parameters/forcefield wanted Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I want to do MD-simulations of organic molecules on Al2O3 surfaces. Does anyone know a forcefield, or a software package, which is not from BIOSYM/MSI and got parameters for Al ? any help would be great thanks Anne v. Fircks From chr05vr@chem.technion.ac.il Mon Jul 14 07:08:57 1997 Received: from chem.technion.ac.il for chr05vr@chem.technion.ac.il by www.ccl.net (8.8.3/950822.1) id FAA21113; Mon, 14 Jul 1997 05:57:02 -0400 (EDT) Received: (from chr05vr@localhost) by chem.technion.ac.il (8.6.11/8.6.6) id MAA06490; Mon, 14 Jul 1997 12:56:41 +0300 Date: Mon, 14 Jul 1997 12:56:40 +0300 (IDT) From: "Dr. Victor Ryaboy" To: chemistry@www.ccl.net Subject: CCL: IV-TH GERMAN-ISRAELI WINTER-SCHOOL Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII IV-TH GERMAN-ISRAELI WINTER-SCHOOL ON "PHOTO-INDUCED NONLINEAR DYNAMICS IN STRONG LASER FIELDS" Organized by: The Minerva Center for Nonlinear Physics of Complex Systems, Technion, Haifa and the Weizmann Institute of Science, Rehovot Place: Technion - Israel Institute of Technology, Haifa, Israel Dates: February 22 - 28, 1998 FIRST ANNOUNCEMENT The idea of a winter-school combined with a workshop is to have a series of talks for graduate students, postdocs and others which provides a mini-course on relevant topics and lectures on advanced topics in their fields. Mini-courses and series of lectures will address the subjects of: Exotic phenomena in super intense laser fields: stabilization, physical reality of light-induced atomic states; ATI and high harmonic generation in intense fields; Perturbation and non-perturbation techniques to photo-interaction in two-electron atoms; The response of simple systems to a nearly periodic field; Coherent and optimal control methods; Time propagation and time-independent methods to study photo-induced dynamics in high intensity fields. Among invited speakers are: Y. Band, R. Bluemel, L. Cederbaum, R. Coalson, F. Faisal, M. Gavrila, G. Gerber, P. Hanggi, J. Korsch, R. Kosloff, P. Lambropoulos, R. Lefebvre, Y. Leopold, N. Moiseyev, D. Neuhauser, U. Peskin, D. Richards, M. Shapiro, D. Tannor, and U. Weiss. PARTIAL SUPPORT IS AVAILABLE TO GRADUATE STUDENTS AND POSTDOCTORAL FELLOWS WHO WILL PRESENT POSTERS. In order to mail circulars, we would like prospective participants to respond to this announcement with their full names, address, tel. and fax numbers and e-mail address. Also, please indicate if you have access to World-Wide-Web (for future registration, hotel reservation, abstract transfer, etc. purposes). For responses and/or further information, registration and application for partial support, please contact Mrs. Charlotte Diament, Conference Secretary Department of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel Tel.: 972-4-8293664/727, FAX: 972-4-823 3735, E-mail: cdiament@tx.technion.ac.il Please visit our WWW Home Pages for updates: http://www.technion.ac.il/technion/chemistry/g-i_school/index.html IVth GERMAN-ISRAELI WINTER-SCHOOL ON "PHOTO-INDUCED NONLINEAR DYNAMICS IN STRONG LASER FIELDS" PLACE: Technion - Israel Institute of Technology, Haifa, Israel DATES: February 22 - 28, 1998 REGISTRATION FORM NAME: __________________________ First Name: _________________ AFFILIATION/ADDRESS: _________________________________ _________________________________________________________ _________________________________________________________ CITY: __________________________ COUNTRY: _____________________ E-mail: _____________________________________________________ POSTERS I should like to present a poster entitled: ____________________________________________________________ ____________________________________________________________________ and will submit an abstract by December 15, 1997. Date: _____________________ Signature: ___________________________ From gostowskir@apsu01.apsu.edu Mon Jul 14 10:07:04 1997 Received: from apsu02.apsu.edu for gostowskir@apsu01.apsu.edu by www.ccl.net (8.8.3/950822.1) id JAA21943; Mon, 14 Jul 1997 09:09:28 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IL7XCLWE0W00045E@APSU02.APSU.EDU> for chemistry@www.ccl.net; Mon, 14 Jul 1997 08:07:45 CST Date: Mon, 14 Jul 1997 08:09:31 -0500 From: Rudy Gostowski Subject: projection on to a plane To: CCL group Message-id: <01IL7XCLWUWI00045E@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1155 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal Please suggest a program that would project a molecule onto a plane (X, Y, and Z). It would be best if from MOPAC ARC file coordinates. Distances on the plane should then be measurable. Thanks, Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 615-648-7624 FAX 615-648-5996 gostowskir@apsu01.apsu.edu From uli@smaug.physics.mun.ca Mon Jul 14 11:04:29 1997 Received: from smaug.physics.mun.ca for uli@smaug.physics.mun.ca by www.ccl.net (8.8.3/950822.1) id JAA21948; Mon, 14 Jul 1997 09:11:01 -0400 (EDT) Received: by smaug.physics.mun.ca (940816.SGI.8.6.9/911001.SGI) id KAA10889; Mon, 14 Jul 1997 10:41:20 -0230 Date: Mon, 14 Jul 1997 10:41:19 -0230 (NDT) From: Uli Salzner To: chemistry@www.ccl.net cc: raymond poirier Subject: Object-oriented means for computational chemistry programming In-Reply-To: <199707111713.NAA27510@tarkovsky.npac.syr.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Collegues, There is a object oriented quantum chemistry written in FORTRAN. It is called MUNGAUSS and is constantly extended. It is developed at Memorial University of Newfoundland. I was surprised that nobody mentioned it so far. Is this really unknown to the programming Community? Further information can be obtained from Prof. R. A. Poirier: e-mail rpoirier@morgan.ucs.mun.ca Sincerely, Ulrike Salzner Department of Chemistry Memorial University of Newfoundland St. Johns, NF A1B 3X7 Canada Tel.: (709) 737-2151 Email:uli@smaug.physics.mun.ca From nauss@beryllium.crs.uc.edu Mon Jul 14 12:07:11 1997 Received: from beryllium.crs.uc.edu for nauss@beryllium.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id LAA23103; Mon, 14 Jul 1997 11:34:06 -0400 (EDT) Received: (from nauss@localhost) by beryllium.crs.uc.edu (8.8.5/8.8.5) id LAA12126 for chemistry@www.ccl.net; Mon, 14 Jul 1997 11:34:06 -0400 (EDT) From: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) Message-Id: <9707141134.ZM12124@beryllium.crs.uc.edu> Date: Mon, 14 Jul 1997 11:34:05 -0400 Organization: Dept. Chemistry, University of Cincinnati Reply-to: Jeffrey.Nauss@UC.Edu X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: AMBER and contiuum solvent models Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Have contiuum solvent models been implemented in AMBER for MD simulations? If so, is the code available? -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss From shenkin@still3.chem.columbia.edu Mon Jul 14 14:07:06 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id NAA23866; Mon, 14 Jul 1997 13:14:32 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id NAA05024; Mon, 14 Jul 1997 13:14:32 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id NAA01935; Mon, 14 Jul 1997 13:14:31 -0400 From: "Peter Shenkin" Message-Id: <9707141314.ZM1933@still3.chem.columbia.edu> Date: Mon, 14 Jul 1997 13:14:30 -0400 In-Reply-To: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) "CCL:AMBER and contiuum solvent models" (Jul 14, 11:34am) References: <9707141134.ZM12124@beryllium.crs.uc.edu> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Jeffrey.Nauss@UC.Edu, chemistry@www.ccl.net Subject: Re: CCL:AMBER and contiuum solvent models Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jul 14, 11:34am, Jeffrey L. Nauss wrote: > Subject: CCL:AMBER and contiuum solvent models > Have contiuum solvent models been implemented in AMBER for MD simulations? If > so, is the code available? Yes, MacroModel has this. (Or maybe you meant the original AMBER program, not MD with the AMBER forcefield in some other program. The latter, of course, is what we do.) -P. -- **** "Deep Blue can't triumph in the game of life." (NY Times, 5/13/97) *** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From nauss@beryllium.crs.uc.edu Mon Jul 14 14:30:10 1997 Received: from beryllium.crs.uc.edu for nauss@beryllium.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id NAA23884; Mon, 14 Jul 1997 13:17:49 -0400 (EDT) Received: (from nauss@localhost) by beryllium.crs.uc.edu (8.8.5/8.8.5) id NAA12451 for chemistry@www.ccl.net; Mon, 14 Jul 1997 13:17:50 -0400 (EDT) From: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) Message-Id: <9707141317.ZM12449@beryllium.crs.uc.edu> Date: Mon, 14 Jul 1997 13:17:49 -0400 In-Reply-To: Peter Shenkin "Re: CCL:AMBER and contiuum solvent models" (Jul 14, 1:14pm) References: <9707141134.ZM12124@beryllium.crs.uc.edu> <9707141314.ZM1933@still3.chem.columbia.edu> Organization: Dept. Chemistry, University of Cincinnati Reply-to: Jeffrey.Nauss@UC.Edu X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:AMBER and contiuum solvent models Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jul 14, 1:14pm, Peter Shenkin wrote: > > Have contiuum solvent models been implemented in AMBER for MD simulations? If > > so, is the code available? > > Yes, MacroModel has this. (Or maybe you meant the original AMBER program, > not MD with the AMBER forcefield in some other program. The latter, of > course, is what we do.) My apologies, I meant the UCSF AMBER program and not implementation of the MABER forcefield. Although this *is* useful information for me. Thanks... -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss From dalke@ks.uiuc.edu Mon Jul 14 14:50:49 1997 Received: from london.ks.uiuc.edu for dalke@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id NAA23902; Mon, 14 Jul 1997 13:23:25 -0400 (EDT) From: Received: from bilbao.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2 [TBG Mods]) id AA142201006; Mon, 14 Jul 1997 12:23:26 -0500 Received: by bilbao.ks.uiuc.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id MAA28470; Mon, 14 Jul 1997 12:23:07 -0500 Date: Mon, 14 Jul 1997 12:23:07 -0500 Message-Id: <199707141723.MAA28470@bilbao.ks.uiuc.edu> To: chemistry@www.ccl.net Subject: Re: CCL & OOP Lestaw K. Bieniasz said: > If [future applications are strongly connected to the concept > of world-wide network of scientific programs] > and if we want our programs to be still useful > after five years, we should start to select the proper language now. > As far as I know, the only language available at present, that > responds to the challenges created by these future needs is JAVA. I don't think Java is as useful for scientific programming as C++. One of the advantages to Fortran over C is the speed of array computations and built-in support for complex numbers. By using classes and templates, C++ has been catching up on Fortran. I've seen array computation benchmarks which even put one C++ compiler faster than the equivalent Fortran code. C++ manages to do this because it supports static/compile-time language constructs that Java doesn't have (templates). That's because one of Java's designs was to be simple -- so simple that you can't even do operator overloading. Let a, b and c be arrays, or complex numbers (or arrays of complex numbers). In C++ you can say: "c=a+b" and expect to get good performance out of it (with a good compiler). Try that in Java. But your argument is more that we need some way to share applications/applets/components/modules between sites and the only language that allows you to do that is Java. I agree with the concept, but there are other possible languages. I agree with Konrad Hinsen (and others) that Python is a much more appropriate language for scientific programming; and for networked scientific programming. It supports operator overloading and complex numbers with standard modules for numeric operations (in 1.5), network communications and databases. As an example of Python's versatility, there is a Python based web browser called Grail which allows applet execution in a limited run-time environment. And for me, the marriage between the high-level dynamic nature of Python and the compile-time nature of C++ (in the chapel of object oriented programming :) matched with its explicit capability of using existing C libraries, is an advantage you will be hard-pressed to get out Java. Andrew Dalke dalke@ks.uiuc.edu From daizadeh@indigo.ucdavis.edu Mon Jul 14 16:07:12 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id PAA24682; Mon, 14 Jul 1997 15:41:17 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id MAA13618; Mon, 14 Jul 1997 12:50:24 -0700 From: "Iraj Daizadeh" Message-Id: <9707141250.ZM13616@indigo.ucdavis.edu> Date: Mon, 14 Jul 1997 12:50:07 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net, chemistry-request@www.ccl.net, chemistry@www.ccl.net, heifets@indigo.ucdavis.edu, stuchebr@indigo.ucdavis.edu Subject: (Fwd) EVENT: SIGGRAPH 97 VRML DEMO SIG -- Call For Entries Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii ------------------- EVENT: SIGGRAPH 97 VRML DEMO SIG -- Call For Entries ***DEADLINE FOR SUBMISSIONS IS JULY 23, 1997*** SIGGRAPH 97 VRML DEMO SIG LA Convention Center in Los Angeles, CA (Room 151) Tuesday, August 5th 6:00pm to 8:00pm This event will be styled upon the successful VRML97 Demo Night and will be co-hosted by LAVUG (Los Angeles VRML Users Group) and The Virtual Reality Education Foundation (VeRGe). Curve's Timothy Childs will be the Master of Ceremonies. Since the world is waiting to see some "real applications" we strongly encourage the submission of content and applications which answers the question "VRML--what's it good for?" Show us what you've got! We are particularly interested in: ~ Business Applications ~ Art/Entertainment ~ Education ~ Scientific Visualization ..but innovative works outside the boundaries of these limited categories will be warmly received. Selected demo will have a MAXIMUM OF 5 MINUTES to wow the audience (the room seats 630). Akin to the VRML 97 Demo Night, the audience will be "armed" with a number of "time keeping" devices to keep the event on schedule. ********IMPORTANT******** ***DEADLINE FOR SUBMISSIONS IS JULY 23, 1997***. Demo slots are limited. Submit your VRML Application NOW at: http://www.verge.org/projects/siggraph/signup.html (Please double check your URLs and make sure they work before submitting.) Questions, feedback or suggestions? Contact: Timothy Childs (VeRGe/Curve) at timothy@curve.net or Carole Sumler (LAVUG) at sumler@fastxchange.com Good luck and see you there! ***DEADLINE FOR SUBMISSIONS IS JULY 23, 1997*** ------------------- -- Iraj Daizadeh Department of Chemistry University of California Davis, CA 95616 email: daizadeh@indigo.ucdavis.edu Phone: 916.754.8695 Fax: 916.752.8995 From dalke@ks.uiuc.edu Mon Jul 14 18:07:09 1997 Received: from london.ks.uiuc.edu for dalke@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id SAA25237; Mon, 14 Jul 1997 18:05:54 -0400 (EDT) Received: from bilbao.ks.uiuc.edu by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2 [TBG Mods]) id AA159537954; Mon, 14 Jul 1997 17:05:54 -0500 Received: (from dalke@localhost) by bilbao.ks.uiuc.edu (940816.SGI.8.6.9/8.6.9)id RAA29152 for chemistry@www.ccl.net; Mon, 14 Jul 1997 17:05:27 -0500 Date: Mon, 14 Jul 1997 17:05:27 -0500 From: Andrew Dalke Message-Id: <199707142205.RAA29152@bilbao.ks.uiuc.edu> To: chemistry@www.ccl.net Subject: Mail chemistry@www.ccl.net Subject: Re: CCL & OOP I was asked for a reference to my statement that: > I've seen > array computation benchmarks which even put one C++ compiler faster > than the equivalent Fortran code. The one I saw was from Computers in Physics, v10, pp358-462 (1996) for Photon C++ from KAI. I tracked down that company's on-line version at http://www.kai.com/publications/comp_phys/ . I see that my statement above is wrong. The paper goes through the bechmarks done on different platforms with KAI's C++ vs. the vendor supplied Fortran. When I saw the plots I didn't notice the -1 in the comparison function, ( time(C++)/time(f77) - 1 ). Thus, code in C++ for their compiler takes about 150% times the Fortran code (so 50% slower). That is still quite impressive, but not as much as I thought. Andrew dalke@ks.uiuc.edu From jtgolab@amoco.com Mon Jul 14 18:41:30 1997 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.8.3/950822.1) id RAA25202; Mon, 14 Jul 1997 17:45:04 -0400 (EDT) Received: by interlock.amoco.com id AA14645 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Mon, 14 Jul 1997 16:45:03 -0500 Message-Id: <199707142145.AA14645@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-4); Mon, 14 Jul 1997 16:45:03 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Mon, 14 Jul 1997 16:45:03 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Mon, 14 Jul 1997 16:45:03 -0500 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Mon, 14 Jul 1997 16:45:03 -0500 From: jtgolab@amoco.com (Joe Golab) Date: Mon, 14 Jul 1997 16:43:53 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Reaction Pathway Program Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL Member: Do you know of any (engineering, chemistry, biological, etc) program that given a compound would suggest any and all reaction pathways toward that compound (no matter how outlandish from a thermodyanmic standpoint)? For example, given tolune, the program would suggest: 1) benzene + methane -> toluene 2) methylcyclohexane -> toluene + H2 3) methane + heat/pressure -> toluene + H2 4) ETC. Perhaps this is really a database that is part of a program. Any leads would be gratefully appreciated! Thanks. -- :Joe jtgolab@amoco.com (630) 961-7878 +-------------------------------------------------------------------------+ | There are two kinds of people, those who finish what they start and ... | | - Robert Byrne | +-------------------------------------------------------------------------+ From lavelle@mbi.ucla.edu Mon Jul 14 19:07:08 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id TAA25384; Mon, 14 Jul 1997 19:00:30 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by rho.ben2.ucla.edu (8.8.5/8.8.5) with SMTP id QAA34554; Mon, 14 Jul 1997 16:00:29 -0700 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu; (5.65/1.1.8.2/15May97-0203PM) id AA28451; Mon, 14 Jul 1997 16:00:29 -0700 Message-Id: <3.0.32.19970714160711.009421c0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Mon, 14 Jul 1997 16:07:11 -0700 To: chemistry@www.ccl.net, hyperchem@hyper.com From: Laurence Lavelle Subject: OS and Computational Speed, NT is very close to UNIX Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" You may also be interested to know that a paper on NT SPECmarks has been posted to http://www.digital.com/fortran/ntspeed.html The results discussed are the first SPEC95 submissions using Microsoft Windows NT. Both Intel and Alpha systems were measured under NT and UNIX. Performance under NT is excellent. Summary from above www site. You do not need heroic tuning. On average, SPEC peak results are only 7% better than base results. You can use NT. SPECint_base95 and SPECfp_base95 benchmarks compiled under Windows NT achieved 88% to 102% of their performance under Unix. As compilers continue to mature under Windows NT there is every reason to expect the performance to become 1:1. You can use mainstream compilers. The results mentioned just above were achieved with Microsoft Visual C++ and Digital Visual Fortran (on both Intel and Alpha). Regards Laurence """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Chemistry Department and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" From jsorenso@water.lbl.gov Mon Jul 14 20:07:10 1997 Received: from global.lbl.gov for jsorenso@water.lbl.gov by www.ccl.net (8.8.3/950822.1) id TAA25802; Mon, 14 Jul 1997 19:40:15 -0400 (EDT) From: Received: from water.lbl.gov (water.lbl.gov [131.243.32.19]) by global.lbl.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id QAA18678; Mon, 14 Jul 1997 16:28:40 -0700 Date: Mon, 14 Jul 1997 16:21:23 -0700 (PDT) Reply-To: jsorenso@water.lbl.gov To: Andrew Dalke cc: chemistry@www.ccl.net Subject: Re: CCL & OOP In-Reply-To: <199707142205.RAA29152@bilbao.ks.uiuc.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 14 Jul 1997, Andrew Dalke wrote: > Subject: Re: CCL & OOP > > I was asked for a reference to my statement that: > > I've seen > > array computation benchmarks which even put one C++ compiler faster > > than the equivalent Fortran code. > Another reference would be http://monet.uwaterloo.ca/blitz/, the home page for the Blitz++ numerical library. While the Blitz++ project looks to be in development currently, the initial results posted on this web page show clear speed improvements over Fortran 77 for a variety of scientific computing problems. The KAI C++ compiler is being used in this case as well. Jon Sorenson ----------------------------------------------------------------------- Jon Sorenson jsorenso@water.lbl.gov Ph.D. Student http://global.lbl.gov/~jsorenso Dept. of Chemistry (510) 486-6933 U.C. Berkeley Berkeley, CA 94720 ----------------------------------------------------------------------- From ascanio@salve5.salve.edu Mon Jul 14 21:07:13 1997 Received: from salve5.salve.edu for ascanio@salve5.salve.edu by www.ccl.net (8.8.3/950822.1) id UAA26015; Mon, 14 Jul 1997 20:20:00 -0400 (EDT) Received: by salve5.salve.edu (AIX 3.2/UCB 5.64/4.03) id AA04883; Mon, 14 Jul 1997 20:15:36 -0400 Date: Mon, 14 Jul 1997 20:15:36 -0400 (EDT) From: Ascanio DiPippo To: Joe Golab Cc: CHEMISTRY@www.ccl.net, jtgolab@amoco.com, "Ernest E. Rothman" Subject: Re: CCL:Reaction Pathway Program In-Reply-To: <199707142145.AA14645@interlock.amoco.com> Message-Id: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-969821433-45248011-868925736=:24061" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---969821433-45248011-868925736=:24061 Content-Type: TEXT/PLAIN; charset=US-ASCII Outlandish !! Have you corrected any exams lately :-) Fr. Ascanio, C.H.S. On Mon, 14 Jul 1997, Joe Golab wrote: > Dear CCL Member: > > Do you know of any (engineering, chemistry, biological, etc) program that > given a compound would suggest any and all reaction pathways toward that > compound (no matter how outlandish from a thermodyanmic standpoint)? > > For example, given tolune, the program would suggest: > > 1) benzene + methane -> toluene > 2) methylcyclohexane -> toluene + H2 > 3) methane + heat/pressure -> toluene + H2 > 4) ETC. > > Perhaps this is really a database that is part of a program. Any leads > would be gratefully appreciated! Thanks. > > -- > > :Joe > jtgolab@amoco.com > (630) 961-7878 > > +-------------------------------------------------------------------------+ > | There are two kinds of people, those who finish what they start and ... | > | - Robert Byrne | > +-------------------------------------------------------------------------+ > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: jtgolab@amoco.com > -- Original Sender From: Address: jtgolab@amoco.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 > > ---969821433-45248011-868925736=:24061 Content-Type: TEXT/PLAIN; charset=US-ASCII; name=sumus Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: U3VtdXMgdW5pdmVyc2l0YXMuICBTdW11cyB1bml2ZXJzaXRhcyA/ICBTdW11 cyB1bml2ZXJzaXRhcyAhIQ0NCho= ---969821433-45248011-868925736=:24061--