From daizadeh@indigo.ucdavis.edu Thu Jul 31 03:14:36 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id DAA01363; Thu, 31 Jul 1997 03:14:25 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id AAA07593; Thu, 31 Jul 1997 00:23:45 -0700 From: "Iraj Daizadeh" Message-Id: <9707310023.ZM7591@indigo.ucdavis.edu> Date: Thu, 31 Jul 1997 00:23:30 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: daizadeh@indigo.ucdavis.edu, roberts@indigo.ucdavis.edu, bashore@indigo.ucdavis.edu, chemistry@www.ccl.net, fink@indigo.ucdavis.edu, goodyear@indigo.ucdavis.edu, heifets@indigo.ucdavis.edu, stuchebr@indigo.ucdavis.edu Subject: Multi-Language Programming on SGI Cc: schlyer@indigo.ucdavis.edu, tucker@indigo.ucdavis.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. The conversation on the CCL concerning OO led very nicely into a discussion of mixing programming languages (for an incomplete summary, please see below). This methodology should merit considerable thought by the computational chemistry society since it combines aspects in computational efficiency and modern coding practices (viz., raw speed, dynamic memory allocation, and object oriented design) with that of using old routines that are still very functional. How to implement these ideas in a pragmatic manner, however, has not been well-documented within these discussions bombarding our email terminals. We have been using multi-language programming ever since I began my computational career here at UC Davis under the watchful eye of Prof. Stuchebrukhov (circa. 3 academic years ago). Thus, I thought it might be useful to describe in detail a (probably) complicated procedure (for the novice) which would allow the generation of an executable from a C code calling a Fortran routine. Generalization of the ideas presented (briefly) below should suffice to enable any programmer using an SGI running IRIX 5.2 or above (up to 6.2) (at least what we have used) to be able to create an executable >from C/Fortran (Fortran/C, Fortran/Pascal, etc.. (<-in a similar manner->) ) code. An outline of this procedure follows: (The methodology was suggested to us when we first started in this direction ( see Fortran/C Interface in the Fortran 77 Programmer's Guide on the insight pages by SGI (5.2) )... 1. Here is an example C code: #include extern double add_(double *,double *); void main() { double x,y; x=y=10.0; printf("%f %f %f\n", x, y, add_(&x,&y)); } /* end main */ This very easy program takes two doubles x,y and adds their assigned values. There exist a couple of items within the C code that are of particular interest to us. First, we have used an external function called add. Add is the fortran function (returns a value). The fortran call must by followed by an UNDERSCORE. Next notice that we have parameterized this function with pointers and sent the addresses of our variables to the fortran routine (This is essential since fortran uses implicitly pointers (no more on this)). That is all there is to it. 2. Next follows the fortran function: function add(x,y) double precision add,x,y add = x+y return end Notice there is no underscore after the add function. This is an intact code without any changes (YEA!). 3. Compile as follows: cc -c main.c # main.c is the file that contains the c code f77 -c add.f # add.f is the file that contains the fortran code cc -o add main.o add.o # now link them with the compiler that contains main You are done!!! A couple of notes: a. Remember: c is case-sensitive, fortran is not. What c does is convert the fortran statement to lowercase: [function statement(arg-list) or subroutine name(arg-list)] Thus, the following are equivalent to the c call above: function ADD() subroutine ADD() function Add() subroutine Add() function add() or subroutine add function AdD() subroutine AdD() ...etc... b. Watch your datatype! c. For a fortran routine calling a C function a similar procedure works. But keep in mind whichever code contains main should be the compiler that links all the object codes; e.g. if fortran code contained main use: cc -c add.c f77 -c main.f f77 -o add add.o main.o d. There are some minor details for sending arrays and structures but trial and error will allow you to figure this out on your own. e. remember it may be necessary to use the -lftn extension when there exist some unresolved errors. I would appreciate it if there were others in the field with this type of programming experience would kindly send me their explicit methodologies for muli-language implementations on other platforms. We are in the process of re-evaluating our computational hardware and are considering acquiring a Dec \alpha or HP. I will summarize all of them as is customary. Any comments, concerns or questions, please do not hesitate to email. If I am too busy, I will say so. 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Alex Turner Ultimately, most folks are more concerned with optimizing their time > use than the computer's :-) . In my opinion, this is the reason _to_ use mixed language programming. If I wanted to write a robust input parser for a large chemistry software package, I'm sure I could write it in Fortran, but it would take a lot of work. These days, there are tools to do this quite easily in C (lex, yacc, etc.). For many people, the time required to write the parser in C _and_ the time to sort out the interface to Fortran would be shorter than writing it in scratch from Fortran. And the C-Fortran interfacing skills learned during the exercise could easily be reused for other projects. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > Some things, like mixed Fortran77 and C, are now so common that there > is a community of people out there who understand pretty well how to > >Are you offering your services? :-) Perhaps it's not as bad as it >looks from my end, but if I had to rely on the kindness of unpaid [...snip ...] Hmm. How about mixed tcl/C ? The tcl interpreter is done in C, so rebuilding the interpreter is not mixed-language. But the result would be -- use tcl (slow as molasses, but lots of high level constructs like hashes, regular expressions, flow control) for the putting-together-the-tools part, and let C (or fortran) do the heavy lifting. Someone could provide a toolkit of tcl commands written in C, and anyone could put the tools together in new ways using a highlevel scripting language. I think perl and python would also work as scripting languages here. This is not just object-oriented (for the programmer) but also somewhat component-oriented (for the application builder or end user). bobg ---------------------------------------------------------------------------------------------------------------------------------------------------------------- David E. Bernholdt: > It idea of mixed language programming is to use languages most > appropriate for the task at hand, not just for speed, but for ease of > implementation. Such decisions are usually fairly coarse-grained. Exactly! > > Ultimately, most folks are more concerned with optimizing their time > > use than the computer's :-) . > > In my opinion, this is the reason _to_ use mixed language > programming. If I wanted to write a robust input parser for a large I couldn't agree more! > One can DESIGN software based on these principles (OOD) regardless of > what language the software is to be implemented in. Right. But implementing an OO design in a non-OO language requires a lot of experience and discipline - to be expected of a professional programmer, but not of a programming scientist. Of course the more basic problem is that scientists tend to skip the design phase altogether. Which is why big projects ought to be started in collaboration with software engineering experts. > I disagree with the person who proposed C++ is "the" langauge for > future work because it is an OOL. There are a lot of other > considerations that (should) factor into the decision of which > language to use. However I think that ALL projects should consider > object-oriented DESIGN regardless of implementation language. Again I agree completely. -------------------------------------------------- Lestaw K. Bieniasz: > If you need a program for individual purpose, use Fortran if you like it. Of course. However, don't do one of the following: 1) Force your students and postdocs to use Fortran even if they know and prefer something else. 2) Teach your students nothing but Fortran. Unfortunately, both are standard practice today. -------------------------------------------------- OK, that's it, sorry for the long post, and back to work... -- ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -- 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 bradley@mail.enterprise.net Thu Jul 31 08:22:00 1997 Received: from dns0.enterprise.net for bradley@mail.enterprise.net by www.ccl.net (8.8.3/950822.1) id HAA02114; Thu, 31 Jul 1997 07:44:24 -0400 (EDT) Received: from dbradley (ppp407.enterprise.net [194.72.196.153]) by dns0.enterprise.net (8.8.5/8.7.3) with SMTP id MAA14389 for ; Thu, 31 Jul 1997 12:44:04 +0100 (BST) Message-Id: <199707311144.MAA14389@dns0.enterprise.net> Comments: Authenticated sender is From: "David Bradley Science Writer" To: chemistry@www.ccl.net Date: Thu, 31 Jul 1997 12:45:30 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: ChemOffice Reply-to: Bradley@enterprise.net Priority: urgent In-reply-to: <199707310520.BAA00933@www.ccl.net> X-mailer: Pegasus Mail for Win32 (v2.54) How do the molecular modelling aspects of ChemOffice Ultra (v 4) from CambridgeSoft Corp, which includes various optimisation engines such as MOPAC93 compare with standalone units. Anyone willing to discuss their experiences of this package please feel free to get in touch Thanks in advance Dave Bradley -------------------------------------------------------- | David Bradley Science Writer | | Bradley@enterprise.net | | Tel/Fax +44 1223 440834 (Intl) | | Tel/Fax 01223 440834 (UK) | | | | http://homepages.enterprise.net/bradley/bradhome.html | -------------------------------------------------------- From tjsu@sable.ox.ac.uk Fri Aug 1 07:14:53 1997 Received: from oxmail4.ox.ac.uk for tjsu@sable.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA08662; Fri, 1 Aug 1997 06:49:13 -0400 (EDT) Received: from sable.ox.ac.uk by oxmail4 with SMTP (PP) with ESMTP; Fri, 1 Aug 1997 11:48:45 +0100 Received: from localhost (tjsu@localhost) by sable.ox.ac.uk (1.2/8.8.3) with SMTP id LAA01593 for ; Fri, 1 Aug 1997 11:48:40 +0100 (BST) Date: Fri, 1 Aug 1997 11:48:40 +0100 (BST) From: Tsueu-ju Su Reply-To: Tsueu-ju Su To: chemistry@www.ccl.net Subject: Geometrical structure of ethyl cation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I would like to know the geometrical structure of ethyl cation (C2H5+), the classical non-bridged or the non-classical bridged structure, which one would be stable? Can anyone provide the theoretical calculations as well as experimental evidence? Thanks a lot in advance. May-May Lin Chemistry Department University of Surrey Guildford Surrey GU2 5XH United Kingdom E-mail: tjsu@sable.ox.ac.uk From brauer@al.bundy.uni-jena.de Fri Aug 1 09:14:53 1997 Received: from cnve.rz.uni-jena.de for brauer@al.bundy.uni-jena.de by www.ccl.net (8.8.3/950822.1) id IAA09601; Fri, 1 Aug 1997 08:59:17 -0400 (EDT) Received: from al.bundy.uni-jena.de (al.bundy.uni-jena.de [141.35.147.40]) by cnve.rz.uni-jena.de (8.8.5/8.6.10) with SMTP id OAA20882 for ; Fri, 1 Aug 1997 14:59:14 +0200 (MESZ) Message-Id: <199708011259.OAA20882@cnve.rz.uni-jena.de> Received: by al.bundy.uni-jena.de (1.37.109.4/16.2) id AA12265; Fri, 1 Aug 97 14:41:11 +0200 From: Michael Braeuer Subject: summary: Pi stacking -systems To: CHEMISTRY@www.ccl.net Date: Fri, 1 Aug 97 14:41:10 METDST Mailer: Elm [revision: 70.85] Hi, a couple of weeks ago I asked about quantum mechanical methods which can be used to model Pi-stacking systems. Here comes the summary. A similar question was before on the list, a summary can be found in the archive ---> 21/07/95. Thanks to all who responded Micha ************************************ >From david@viper.wf.bms.com Thu Jul 3 14:59 MET 1997 You need to contact Jiri Sponer sponer@indy.jh-inst.cas.cz I believe he can help . David R. Langley -- David R. Langley ************************************* >From prosenc@dg5.chemie.uni-konstanz.de Thu Jul 3 15:25 MET 1997 hi micha, schau mal in die dissertation von Stefan Brode, AG Ahlrichs in Karlsruhe oder ind dessen publikationen. die besten resultate wurden meines erachtens auf mp2 mit sehr grossen basissaetzen erhalten. dft geht meiner meinung nach dort nicht, da dispersionswechselwirkungen nicht mitberuecksichtigt werden. gruss marc ************************************** >From martinn@UNCWIL.EDU Thu Jul 3 14:41 MET 1997 Michael, I can tell you that semi-empirical methods do not show attraction between aromatic rings, bu ab initio methods, such as HF or DFT, do show attraction. We are doing some of these calculations, but we have not yet published in this area. Ned >From martinn@UNCWIL.EDU Thu Jul 3 21:00 MET 1997 Michael, I have not experimented much with different basis sets, but the effect is not much different using HF/6-31G* or MP2/6-31G*. I had no luck at all seeing any attraction between, for example, nitrobenzenae and toluene using AM1 or PM3 and a minimal basis set (3-21G). I did not try CI, but I agree that is would be a good idea. Ned ************************************** -- Michael Braeuer PhD Student E-mail: brauer@al.bundy.uni-jena.de IOMC FSU Jena Tel: ++49/3641/635599 Humboldtstrasse 10 Fax: ++49/3641/636655 07743 Jena Germany From elewars@alchemy.chem.utoronto.ca Fri Aug 1 11:14:55 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id KAA09922; Fri, 1 Aug 1997 10:20:37 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id KAA18845 for chemistry@www.ccl.net; Fri, 1 Aug 1997 10:20:37 -0400 (EDT) Date: Fri, 1 Aug 1997 10:20:37 -0400 (EDT) From: "E. Lewars" Message-Id: <199708011420.KAA18845@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: ETHYL CATION--ANSWER 1997 Aug 1 Regarding the question about the structure of the ethyl cation: The ethyl cation has a nonclassical H-bridged structure, from NMR spectra and ab initio calculations. At the HF/3-21G level the bridged structure is a TS between classical structures, at the HF/6-31G* level a minimum slightly above a classical minimum, and at the MP2/6-31G* level the classical structure is not even a stationary point. For a summary see R. Janoschek, "Irrtuemer und Erfolge bei quantenchemischen ab-initio-Rechnungen", Chemie in Unserer Zeit, 29(3), 122-132, 1995, and refs therein. A look in the annual indexes of J Am Chem Soc, ca. 1990- 1995, will probably turn up leading refs too. E. Lewars ========================= From SMITHJA@ucarb.com Fri Aug 1 13:14:54 1997 Received: from hscmg02.hou.ucarb.com for SMITHJA@ucarb.com by www.ccl.net (8.8.3/950822.1) id MAA10867; Fri, 1 Aug 1997 12:21:38 -0400 (EDT) Received: by hscmg02.hou.ucarb.com with Internet Mail Service (5.0.1457.3) id ; Fri, 1 Aug 1997 11:22:27 -0500 Message-ID: From: "Smith JA (Jack)" To: "'ChemWeb'" , "'CHEMISTRY@www.ccl.net'" , "'CHMINF-L@LISTSERV.INDIANA.EDU'" Subject: URLs with tildes blocked by firewall Date: Fri, 1 Aug 1997 11:21:04 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain I have a query for the Chemistry-Internet community at-large, but particularly for industrial sites. Our corporate IT department recently completed the installation of a firewall/proxy for all Internet traffic and one of the "protections" they have implemented is a filtering process that prohibits access to certain URLs (sites) - some explicitly and others by somewhat generic rules. One such generic rule is the the presence of a tilde (~) in the URL. Tilde's are often used as a shortcut representation of a home directory (particularly on Unix systems). For some reason our IT department considers such sites as inappropriate for business/research purposes. It now take VP approval to unblock such sites. Has anyone else heard of, experienced, or fully understand such a policy? [This message was multi-posted, please pardon any duplication] - Jack -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jack A. Smith || Union Carbide || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || smithja@ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From choic@gusun.georgetown.edu Fri Aug 1 15:14:57 1997 Received: from gusun.georgetown.edu for choic@gusun.georgetown.edu by www.ccl.net (8.8.3/950822.1) id PAA11705; Fri, 1 Aug 1997 15:13:05 -0400 (EDT) Received: from localhost (choic@localhost) by gusun.georgetown.edu (8.8.5/8.8.5) with SMTP id PAA28757 for ; Fri, 1 Aug 1997 15:08:55 -0400 (EDT) Date: Fri, 1 Aug 1997 15:08:55 -0400 (EDT) From: Cheol Choi X-Sender: choic@gusun To: chemistry@www.ccl.net Subject: Alpha + Linux ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, According to the SPEC benchmark, Dec Alpha seems to be the fastest processor currently. And I know some companies are selling Alpha workstations with Linux OS at very reasonable price. Is there anyone who has good experience with Alpha + Linux combination? Thanks, Cheol-Ho Choi Georgetown Univ.