From hinsenk@ERE.UMontreal.CA Wed Oct 12 00:19:14 1994 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id XAA03470; Tue, 11 Oct 1994 23:40:51 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA00726 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Tue, 11 Oct 1994 23:38:36 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA20528; Tue, 11 Oct 94 23:38:34 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA29736; Tue, 11 Oct 94 23:38:34 -0400 Date: Tue, 11 Oct 94 23:38:34 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9410120338.AA29736@cyclone.ERE.UMontreal.CA> To: sgsrini@u.washington.edu Cc: chemistry@ccl.net, chemistry@ssd.intel.com In-Reply-To: (message from Srinivasan Srivilliputhur on Tue, 11 Oct 1994 15:07:11 -0700 (PDT)) Subject: Re: CCL:Calling FORTRAN FUNCTIONS from a C-Program. My molecular dynamics code, in C, involves lot of calls to the C-Functions pow(), exp() and sqrt(). I was told that corresponding FORTRAN calls are cheaper. Is this true ? If so can any of you knowledgeable souls mail me Yes and no. In C these are normal functions. Although they are in the standard library, there is nothing in principle that prevents you >from replacing them with your own versions that might even do something completely different. Therefore the compiler knows nothing about them except their declaration, so it can't perform many optimizations easily. Contrarily, in Fortran the corresponding functions are built-in, i.e. once and for all defined in the language standard. The compiler knows exactly what they do and can therefore optimize - it could for example replace X**4 by X*X*X*X, which is typically cheaper to do. If you use the most general case however, i.e. with only variables as arguments, there is little to do and therefore no advantage in comparison to C. >From this it should be clear that there is nothing to be gained from calling the Fortran functions from C. What makes Fortran faster (sometimes) is just the fact that it might not have to call the function at all. Functions calls in general are very cheap in C - typically cheaper than in Fortran. Before you rush to the conclusion that Fortran is better than C for scientific programming, think again. Does the advantage in some built-in function really make a large difference in the execution time of *your* program? Is it more than just one percent? Is it really worth the additional expense of *your* time that you need to deal with Fortran's archaic structures and lacking functionality? Isn't your time worth much more than CPU time? And even if you value CPU time higher, don't forget the CPU time wasted by the more involved debugging cycles typically necessary with Fortran code. Besides, compiler technology improves. It is possible nowadays to write compilers that are smart even about non-built-in functions. They are still rare, but this will change. If you write programs with an eye towards long-time development, don't tie yourself to outdated technology for the sake of a small advantage today. Choose a language that you are comfortable with. Whether or not that is C is another matter - C is not without faults either. the procedure to call FORTRAN functions from within a C-Program. I run my code on DEC-5000/200, SPARC-10 workstations and Intel-Paragon Parallel Computer. General tips about calling FORTRAN from C will be particularly useful as we have tons of FORTRAN code out in the cyber space ! Basically there are two ways to mix Fortran and C code: 1) Translate the Fortran code to C with f2c, a free Fortran-to-C compiler produced by AT&T. Available for example from ftp.att.com in /netlib/f2c. 2) Use the CFORTRAN package available by ftp from zebra.desy.de. Even if you want to use a language other than C, these are useful tools, since almost all newer language systems provide a C interface of some kind. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From savary@sc2a.unige.ch Wed Oct 12 04:19:15 1994 Received: from UNI2B.UNIGE.CH for savary@sc2a.unige.ch by www.ccl.net (8.6.9/930601.1506) id DAA05157; Wed, 12 Oct 1994 03:50:30 -0400 Received: from PCC2333F (129.194.51.63) by uni2b.unige.ch (PMDF V4.3-8 #2502) id <01HI6LNWR300004IC8@uni2b.unige.ch>; Wed, 12 Oct 1994 08:50:20 WET-DST Date: Wed, 12 Oct 1994 08:50:18 +0100 From: savary@sc2a.unige.ch (Francois Savary) Subject: simple geometry optimization X-Sender: savary@sc2a.unige.ch To: CHEMISTRY@ccl.net Message-id: <01HI6LNXBZB6004IC8@uni2b.unige.ch> X-Envelope-to: CHEMISTRY@ccl.net MIME-version: 1.0 X-Mailer: Windows Eudora Version 1.4.3b4 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Dear CCListers, I think my previous question was not very clearly formulated, in fact, I have posted this request for a friend who has developed a molecular graphics package and who is interested by adding a model builder. So the question is does someone know where we could find a code source of a program which would simply PREoptimize the structure trying to reproduce common known distances and angles, to obtain a crude geometry as a starting point for more elaborated quantum chemical geometry optimization. The best would be a model without any parameters so to be universal. I know two molecular packages that have really nice model builder implemented, Spartan and HyperChem. Can somebody help us? As people seems to be quite interested in such a program, I will summarize if I get interesting answers. Francois Savary ---------------------------------------------------------------------------- Francois Savary University of Geneva Department of Physical Chemistry CHIFI Weber 30 quai Ernest-Ansermet CH-1211 Geneva 4 Lab : 112 Phone : +4122 702 65 32 Fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch HTML : http://scsg9.unige.ch/tabmat.html (in french) : http://scsg9.unige.ch/eng/toc.html (in english) ---------------------------------------------------------------------------- From bhardy@convex.ox.ac.uk Wed Oct 12 07:19:22 1994 Received: from oxmail.ox.ac.uk for bhardy@convex.ox.ac.uk by www.ccl.net (8.6.9/930601.1506) id GAA06068; Wed, 12 Oct 1994 06:28:20 -0400 Received: from convex.ox.ac.uk by oxmail.ox.ac.uk with SMTP (PP) id <11683-0@oxmail.ox.ac.uk>; Wed, 12 Oct 1994 11:28:09 +0100 From: Barry Hardy Date: Wed, 12 Oct 94 11:27:59 +0100 Message-Id: <12963.9410121027@convex.ox.ac.uk> To: chemistry@ccl.net Subject: Amber <=> CHARMM CCLers, Last week I posted the following query: Can anyone suggest a program/tool that can convert CHARMM input files (coordinates, parameters, topology) to Amber and vice-versa? If not, what is the most efficient work-around? Respond to me & I'll summarize. Dave Case posted the only reply - an interesting and helpful one - to CCL on recent work of his on adding code to Amber to enable the calculation of a CHARMM-type force field. (Dave if you are reading this I would be interested in the scripts you mentioned.) To obtain further information, perhaps I could be allowed to rephrase the above question by separating out the parameter issue: Can anyone suggest a program/tool that can convert CHARMM coordinate and topology files to Amber and vice-versa? If not, what is the most efficient work-around? Respond to me & I'll summarize. Barry J. Hardy From mirko@sara.nl Wed Oct 12 09:20:34 1994 Received: from vax2.sara.nl for mirko@sara.nl by www.ccl.net (8.6.9/930601.1506) id JAA08182; Wed, 12 Oct 1994 09:10:34 -0400 From: Received: from horus.sara.nl by SARA.NL (PMDF V4.2-15 #2498) id <01HI6WUX1FOG8Y5TCW@SARA.NL>; Wed, 12 Oct 1994 14:10:32 +0100 (MET) Received: by horus.sara.nl (AIX 3.2/UCB 5.64/4.03) id AA16288; Wed, 12 Oct 1994 14:09:10 +0100 Date: Wed, 12 Oct 1994 14:09:10 +0100 Subject: Postdoc position available To: CHEMISTRY@ccl.net Message-id: <9410121309.AA16288@horus.sara.nl> X-Envelope-to: CHEMISTRY@ccl.net Content-transfer-encoding: 7BIT POST-DOC POSITION AVAILABLE At University of Amsterdam, Faculty of Chemistry Dept. of Inorganic Chemistry and Homogeneous Catalysis Wanted: Postdoctoral Fellow for one year, starting end of 1994 Project: Molecular Modeling and synthesis of ligands for homogeneous catalysis (in particular hydroformylation) Industrially sponsored. Project leader: Prof.Dr. Piet van Leeuwen Equipment: CAChe and Sybyl Requirements: Background in one or more of the following areas: Molecular Mechanics Organometallic chemistry Catalysis Organic chemistry Phosphorous chemistry Applications to and information from: Prof. Dr. P.W.N.M. van Leeuwen J.H. van 't Hoff Research Institute University of Amsterdam Nieuwe Achtergracht 166 1018 WV Amsterdam, the Netherlands tel: (31)-20-5255419 fax: (31)-20-5256456 From cletner@remcure.bmb.wright.edu Wed Oct 12 10:19:22 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id JAA08903; Wed, 12 Oct 1994 09:48:45 -0400 Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA11232; Wed, 12 Oct 94 09:39:11 -0700 Date: Wed, 12 Oct 1994 09:28:47 -0700 (PDT) From: Charles Letner Subject: Quantum text To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I find that I have some spare time on my hands and would like to brush up on my Quantum Mechanics (spare time, te-he te-he). I'm looking for some recommendations of good quantum text that are directed more towards the chemist of the world. In particular I'm interested in recommendations that are applicable to computational chemistry in the sense that there are examples/problems and discussions directed towards a understanding of computational chem. Any ideas? I wouldn't be opposed to two books that could be used together, one on theory and one on the more practical computational stuff. Of course I will summarize the responses as I expect many others would like to see the references. Thanks for your help, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From bauer@organik.uni-erlangen.de Wed Oct 12 10:28:42 1994 Received: from faui45.informatik.uni-erlangen.de for bauer@organik.uni-erlangen.de by www.ccl.net (8.6.9/930601.1506) id JAA08693; Wed, 12 Oct 1994 09:37:55 -0400 Received: from derioc1.organik.uni-erlangen.de by uni-erlangen.de with SMTP; id AA04859 (5.65c-6/7.3w-FAU); Wed, 12 Oct 1994 14:37:45 +0100 Received: by organik.uni-erlangen.de; id AA01889 (5.64/7.3n-FAU); Wed, 12 Oct 94 14:37:44 +0100 From: Walter Bauer Message-Id: <9410121337.AA01889@derioc1.organik.uni-erlangen.de> Subject: Spectrometers giveaway To: chemistry@ccl.net Date: Wed, 12 Oct 94 14:37:43 MET X-Mailer: ELM [version 2.3 PL11] Dr. Walter Bauer Institute of Organic Chemistry NMR laboratory University of Erlangen-Nuernberg Henkestrasse 42 D-91054 Erlangen Germany Phone: +49-9131-852987 FAX: +49-9131-859132 e-mail: bauer@organik.uni-erlangen.de Erlangen, October 12, 1994 Dear netters: in the early 1994 we replaced two of our old NMR spectrometers by new ones. The old instruments are no longer in use and may principally given away to anyone who's interested. Both of these spectrometers have been in use until their replacement and worked at their full specifications. Here's a detailed description of the hardware. Spectrometer 1: JEOL C60HL, 60 MHz, electro magnet, CW operation, year of construction: 1973, measurable nucleus = 1H, facilities of 31P CW or noise decoupling, internal and external lock, field or frequency sweep. The magnet is integrated into the spectrometer console. Weight of spectrometer: 1,200 kg; water conditioner: ca. 50 kg Spectrometer 2: JEOL PS100, 100MHz, electro magnet, year of construction: 1973, probeheads for: 1H/19F, 13C, 31P, 7Li, 11B, 14N, CW or FT operation, inter- nal lock, field or frequency sweep for CW operation. External FT unit with usual frequency synthesizer, time sharing unit, BB decoupler, power amp etc. Pulse programmer for single pulse and T1 measurement (inversion recovery). The original data processing unit (Texas instruments 980A computer with attachments) has turned out to be highly prone to failure. Thus, a home built data acquisition hardware unit for PC operation (386 up) has been used in conjunction with the FELIX software program package and home written data acquisition software. Weights: magnet 2,700 kg, spectrometer console 450 kg, FT unit 150 kg, water conditioner 80 kg. These two spectrometers may be given away FREE OF CHARGE, preferrably as whole entities. The only requirements will be that they are picked up by the customer at our institute, with any shipping costs payed by the customer. Likewise, any transportation facilities must be provided by the customer. Anyone who's interested should contact me as soon as possible. Note that all external leads of the specrometers are dismounted. Some basic knowledge of electronics might be useful for re-assemly. A variety of electronical and mechanical replacement parts is available as well. Complete wiring diagrams and manuals are provided for both instruments. Walter Bauer From C1790@SLVAXA.UMSL.EDU Wed Oct 12 12:19:21 1994 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.9/930601.1506) id LAA11403; Wed, 12 Oct 1994 11:48:33 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HI6PXI2O3AAFTQAC@SLVAXA.UMSL.EDU>; Wed, 12 Oct 1994 10:52:34 CDT Date: Wed, 12 Oct 1994 10:52:34 -0500 (CDT) From: BILL WELSH Subject: RASMOL & RASWIN To: chemistry@ccl.net Message-id: <01HI6PXI2O3CAFTQAC@SLVAXA.UMSL.EDU> X-VMS-To: in%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Fellow Netters, Can someone tell me how I might find the programs RASMOL and RASWIN (I think those are the right names) on the Internet? Thanks. Bill Welsh Dept. of Chemistry Univ. of Missouri-St. Louis St. Louis, MO 63121 From hasch@tkemi.klb.dth.dk Wed Oct 12 12:24:08 1994 Received: from tkemi.klb.dth.dk for hasch@tkemi.klb.dth.dk by www.ccl.net (8.6.9/930601.1506) id LAA11092; Wed, 12 Oct 1994 11:30:57 -0400 Received: by tkemi.klb.dth.dk (AIX 3.2/UCB 5.64/4.03) id AA31519; Wed, 12 Oct 1994 16:30:46 +0200 Date: Wed, 12 Oct 1994 16:30:46 +0200 From: hasch@tkemi.klb.dth.dk (Hartmut Schmider) Message-Id: <9410121430.AA31519@tkemi.klb.dth.dk> To: cletner%remcure.bmb.wright.edu@danpost.uni-c.dk Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Quantum text Hello, Everybody will have their own "favorites", so I I might just throw in mine. As far as the theoretical underpinning is concerned, I always thought that McWeeny's "Methods of molecular quantum mechanics" is the best. It is advanced enough to tell you something you didn't know from 3rd year, and it's basic enough to spare you with superstring theory and black holes. It orients itself somewhat on the methods used in practical applications, but it is a completely theoretical text. I don't know about "applied" text books, but I'm sure you're going to get many other suggestions. Best regards, Hartmut Schmider From elewars@alchemy.chem.utoronto.ca Wed Oct 12 12:26:52 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id MAA11644; Wed, 12 Oct 1994 12:02:49 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id MAA22802 for chemistry@ccl.net; Wed, 12 Oct 1994 12:02:47 -0400 Date: Wed, 12 Oct 1994 12:02:47 -0400 From: "E. Lewars" Message-Id: <199410121602.MAA22802@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: TEXT FOR QUANTUM CHEMISTRY Charles Lettner says he would like to brush up on his quantum chemistry and asked for textbook suggestions. i think he couldn't do much better than work his way through *Quantum Chemistry* by Ira N. Levine (I think the 4th is the latest ed., 1991; Prentice-Hall). It starts at the start and takes you through atoms, to molecules and the Hartree-Fock procedure, and gives brief intros to CI, Mo..ller-Plesset and density functional. The last 3 Chap's are a compact intro to ab initio and semiempirical methods. The book is well-written, and goes beyond a bald presentation of facts to offer at least an indication of the deeper meaning of QM's theorems. This is a book not just to read; one should work as many of the problems as possible. I'm not sure what CL meant by a practical book, but *Experiments in Computational Chemistry" (Hehre, Burke, Shusterman and Pietro; Wavefunction Inc, 1993) is chock-full of things to do with the Spartan program; it should be applicable to some extent to, e.g., MOPAC, Hyperchem, Molgen or Gaussian. === Errol Lewars === From glump@kff1.uchicago.edu Wed Oct 12 12:29:27 1994 Received: from midway.uchicago.edu for glump@kff1.uchicago.edu by www.ccl.net (8.6.9/930601.1506) id MAA11763; Wed, 12 Oct 1994 12:14:36 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Wed, 12 Oct 94 11:14:24 CDT Received: from kff1.uchicago.edu by rainbow.uchicago.edu via SMTP (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA08767; Wed, 12 Oct 94 12:05:09 -0500 Received: by kff1.uchicago.edu.PSNCL (4.1/SMI-4.1) id AA16183; Wed, 12 Oct 94 11:15:20 CDT Date: Wed, 12 Oct 94 11:15:20 CDT From: glump@kff1.uchicago.edu (Anil G. Mudholkar) Message-Id: <9410121615.AA16183@kff1.uchicago.edu.PSNCL> To: chemistry@ccl.net Subject: Calling FORTRAN FUNCTIONS from a C-Program. In-Reply-To: Your message of Tue, 11 Oct 94 23:38:34 -0400 <9410120338.AA29736@cyclone.ERE.UMontreal.CA> Cc: Anil Reply-To: Anil Hinsen Konrad wrote in reply to ) > My molecular dynamics code, in C, involves lot of calls to the ) > C-Functions pow(), exp() and sqrt(). I was told that corresponding ) > FORTRAN calls are cheaper. Is this true ? If so can any of you ) > knowledgeable souls mail me the following: ) Yes and no. In C these are normal functions. Although they are in ) the standard library, there is nothing in principle that prevents ) you from replacing them with your own versions that might even do ) something completely different. Therefore the compiler knows nothing ) about them except their declaration, so it can't perform many ) optimizations easily. Yes, but the compiler knows this only if you have inserted #include in your C code, otherwise it does not know even the declarations. Further on, Mr. Konrad points out many important differences between C and Fortran making clear that there is no obvious advantage of one over the other, (except, perhaps, in terms of ease of use, taste, portability, etc. I don't wish to get into C vs. Fortran. I use them both all the time for many different reasons.) and particularly that it is not a good idea to call the Fortran intrinsics in place of the already rather cheap C function calls. (also, for reference or clarification, they are usually in libm.a, not libc.a, though C libs sometimes have copies in libc.a.) ) Basically there are two ways to mix Fortran and C code: ) ) 1) Translate the Fortran code to C with f2c, a free Fortran-to-C ) compiler produced by AT&T. Available for example from ) ftp.att.com in /netlib/f2c. ) 2) Use the CFORTRAN package available by ftp from zebra.desy.de. ) ) Even if you want to use a language other than C, these are useful ) tools, since almost all newer language systems provide a C interface ) of some kind. Regardless of what you want to do with your Fortran routines, you can always call them from C, and it is very simple. Satisfy in the following conditions in the calling C functions: 1. All Fortran functions and subroutines have an underscore appended to their names. i.e. Fortran subroutine foo() is C function foo_(). 2. All Fortran integers are passed by reference, while C integers are usually passed by value, so a call to a Fortran integer function bar() in C would look like int *bar_(). Likewise a call to Fortran subroutine junk(a) integer a >from C looks like junk(&a). 3. Fortran strings have no '\0' at the end, so your C function receiving the Fortran string will have to know what to do with it; either append a '\0' or just write n chars. 4. General Fortran routines (math, etc) are in libF77.a (always link this), Fortran IO routines are in usually in libI77.a, and other Fortran routines are in libU77.a. (these are sometimes located in funny places, but usually /usr/lib, also some compilers like SunOS C stick everything in libF77.a, but add a libV77.a for a few other functions.) I would recommend against using f2c unless you have fortran code but no compiler. It will not help you link the routines at all, but rather give you a code that compiles by under C, but behaves like fortran. That is, it will produce from your Fortran code C code having functions with appended underscores that accept only pointers to integers and return strings without terminating '\0's. The main reason for the program f2c is to give you something like "gf77 = f2c + gcc -lF77". I cannot speak to CFORTRAN having never seen it. I suspect that you will have a much better overall performance if you concentrate first on your algorithm and then on the its implementation in C. If you are very worried about the performance, you can consider parallel or data-parallel implementations or use of special libraries or even specialized languages for expensive routines, and only as a last measure should you try efficiency hacks (like manual inlining of code, etc). Good luck. Anil Mudholkar glump@rainbow.uchicago.edu http://rainbow.uchicago.edu/~glump From beebesco@hardy.texsci.edu Wed Oct 12 13:19:22 1994 Received: from HARDY for beebesco@hardy.texsci.edu by www.ccl.net (8.6.9/930601.1506) id NAA12512; Wed, 12 Oct 1994 13:10:01 -0400 From: Date: Wed, 12 Oct 1994 13:06:34 -0400 Message-Id: <94101213062719@hardy.texsci.edu> To: chemistry@ccl.net Subject: Mopac on LINUX X-VMS-To: SMTP%"chemistry@ccl.net" Hi! Can anyone give me a brief description on setting up MOPAC on the LINUX operating system. I have the executable but I'm not sure what to do with it. Is there any docs on the LINUX implementation. Thanks for any help you can provide. Scott Beebe From hinsenk@ERE.UMontreal.CA Wed Oct 12 16:19:24 1994 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id PAA16239; Wed, 12 Oct 1994 15:51:48 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA24044 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 12 Oct 1994 14:01:51 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA27414; Wed, 12 Oct 94 14:01:49 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA13784; Wed, 12 Oct 94 14:01:49 -0400 Date: Wed, 12 Oct 94 14:01:49 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9410121801.AA13784@cyclone.ERE.UMontreal.CA> To: chemistry@ccl.net In-Reply-To: <9410121615.AA16183@kff1.uchicago.edu.PSNCL> (glump@kff1.uchicago.edu) Subject: Re: CCL:Calling FORTRAN FUNCTIONS from a C-Program. Date: Wed, 12 Oct 94 11:15:20 CDT From: glump@kff1.uchicago.edu (Anil G. Mudholkar) Cc: Anil Reply-To: Anil Sender: Computational Chemistry List Errors-To: ccl@ccl.net Precedence: bulk X-Caution: User has inserted an Explicit Reply-To Anil G. Mudholkar wrote: Yes, but the compiler knows this only if you have inserted #include in your C code, otherwise it does not know even the An ANSI compiler should complain if you do not include math.h. I would recommend *never* to use an old K&R-style C compiler for scientific programming (or in fact for anything else). ANSI compilers are easily available nowadays; gcc is even free. K&R C can be as unpleasant as Fortran, although for different reasons. Regardless of what you want to do with your Fortran routines, you can always call them from C, and it is very simple. Satisfy in the following conditions in the calling C functions: 1. All Fortran functions and subroutines have an underscore appended to their names. i.e. Fortran subroutine foo() is C function foo_(). ... This might work on one machine, but not on another. It will probably work with most Unix machines (except possibly IBM's RS/6000), but again there is no guarantee. It is definitely not portable. This is exactly why CFORTRAN was created - it wraps the machine dependant details in a portable layer, using the C preprocessor. I would recommend against using f2c unless you have fortran code but no compiler. It will not help you link the routines at all, I would agree on that - if you have a Fortran compiler and can link Fortran and C code, that is certainly the better way. You don't get any portability advantage by using f2c, since the source code it produces is not portable in general (the file f2c.h must be modified for each system). I suspect that you will have a much better overall performance if you concentrate first on your algorithm and then on the its implementation in C. If you are very worried about the performance, Underline that twice and put it next to your keyboard! A better algorithm does more for performance than even the best compiler. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From YQIN@aardvark.ucs.uoknor.edu Wed Oct 12 17:19:25 1994 Received: from aardvark.ucs.uoknor.edu for YQIN@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id QAA17360; Wed, 12 Oct 1994 16:46:02 -0400 From: Message-Id: <199410122046.QAA17360@www.ccl.net> Date: Wed, 12 Oct 94 15:40 CDT Subject: explorer manual summary To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters: A couple of days ago, I post a quary regarding the Explorer manual and I got a some replay. I would like to thank all the responses who provide valuable information. We called the SGI company, the answer is that we can buy the manual, the price is about $250. Thank you all once again. yue qin The summary is following: From: IN%"Omar.Stradella@sgibos.boston.sgi.com" 7-OCT-1994 09:11:08.96 To: yqin@aardvark.ucs.uoknor.edu CC: Subj: Re: CCL:Explorer manual There are online manuals. Install the subsystem "explorer.books" if you haven't done it yet. It contains two books: "Explorer User's Guide" and "Explorer Module Writer's Guide" that can be accessed with Insight. Omar. -- **************************************************************************** * Dr. Omar G. Stradella "Ph-nglui mglw'nafh Cthulhu * * R'lyeh wgah'nagl fhtagn" * * Silicon Graphics * * * * E-mail: omar@boston.sgi.com Snail-mail: One Cabot Road * * Hudson, MA 01749 * * Phone: +1-(508) 562-4800x358 U.S.A. * * FAX: +1-(508) 562-4755 Lat/Long: 42.24 N / 71.34 W * **************************************************************************** Return-Path: Omar.Stradella@sgibos.boston.sgi.com Received: from relay.sgi.com (relay.sgi.com [192.26.51.36]) by sgigate.sgi.com (940519.SGI.8.6.9/8.6.4) with SMTP id HAA22720; Fri, 7 Oct 1994 07:05:55 -0700 Received: from sgibos.boston.sgi.com by relay.sgi.com via SMTP (920330.SGI/920502.SGI) There are online manuals. Install the subsystem "explorer.books" if you haven't done it yet. It contains two books: "Explorer User's Guide" and "Explorer Module Writer's Guide" that can be accessed with Insight. Omar. -- **************************************************************************** * Dr. Omar G. Stradella "Ph-nglui mglw'nafh Cthulhu * * R'lyeh wgah'nagl fhtagn" * * Silicon Graphics * * * * E-mail: omar@boston.sgi.com Snail-mail: One Cabot Road * * Hudson, MA 01749 * * Phone: +1-(508) 562-4800x358 U.S.A. * * FAX: +1-(508) 562-4755 Lat/Long: 42.24 N / 71.34 W * **************************************************************************** --PART-BOUNDARY=.19410071008.ZM5421.boston.sgi.com-- From: IN%"mercie@mail.med.cornell.edu" "Gustavo Mercier" 7-OCT-1994 08:25:40.99 To: YQIN@aardvark.ucs.uoknor.edu CC: Subj: Re: CCL:Explorer manual Return-path: mercie@mail.med.cornell.edu Hi! You get it from SGI people, 1-800-800-4SGI in the USA Gustavo A. Mercier, Jr. mercie@cumc.cornell.edu From: IN%"JEREMYW@num-alg-grp.co.uk" "JEREMY WALTON" 7-OCT-1994 04:47:00.49 To: YQIN CC: Subj: Re: CCL:Explorer manual Hi Yue Qin, You can purchase the manuals from SGI. The part number is M4-EXPLR-2.0. Alternatively, they are available from NAG (who are jointly developing the next release of IRIS Explorer with SGI) through one of the IRIS Explorer Centers: IRIS Explorer Center IRIS Explorer Center (North America) PO Box 50 1400 Opus Place, Suite 200 Oxford OX2 8JU Downers Grove IL 60515-5702 UK USA Tel: +44 (0)1865 516377 Tel: +1 708 971 2367 Fax: +44 (0)1865 516388 Fax: +1 708 971 2706 email: helpdesk@iec.co.uk email: infodesk@nag.com infodesk@nag.co.uk IRIS Explorer Center Japan (IECJ) Nagashima Building 2F 2-24-3 Higashi, Shibuya-ku, Tokyo, Japan Tel: +81 3 5485 2901 Fax: +81 3 5485 2903 email: help@IRIS.explorer.co.jp If you have access to WWW, have a look at the IEC home page for more info: http://www.nag.co.uk:70/1h/Welcome_IEC I hope this is helpful. Please let me know if you need any more here. Cheers, Jeremy -------------------------------------------------------------------------------- | Jeremy Walton nagjpw@vax.oxford.ac.uk | | The Numerical Algorithms Group Ltd, Oxford, UK jeremyw@nag.co.uk | | Tel: +44 865 511245 | | Fax: +44 865 310139 | -------------------------------------------------------------------------------- From JKONG@chem1.chem.dal.ca Wed Oct 12 18:19:27 1994 Received: from Snoopy.UCIS.Dal.CA for JKONG@chem1.chem.dal.ca by www.ccl.net (8.6.9/930601.1506) id RAA18270; Wed, 12 Oct 1994 17:28:25 -0400 From: Received: from chem1.chem.dal.ca (CHEM1.Chem.Dal.Ca [129.173.17.47]) by Snoopy.UCIS.Dal.CA (8.6.8.1/8.6.6) with SMTP id SAA02808 for ; Wed, 12 Oct 1994 18:28:18 -0300 Message-Id: <199410122128.SAA02808@Snoopy.UCIS.Dal.CA> Received: from CHEM1/MERCURYQUEUE by chem1.chem.dal.ca (Mercury 1.1); Wed, 12 Oct 94 18:28:21 -0400 To: chemistry@ccl.net Date: Wed, 12 Oct 1994 18:28:05 AST Subject: Re: Call Fortran from C Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Hi! Just want to add that the point that the underscore needs to be attached to a Fortran function name when it is called from C is not valid on every machine (it is for Sun workstations, as far as I know). Fortran compilars on different machines are slightly different on this issue. On our ibm/rs6k, it is pretty straightforward and no name change is needed. Just keep in your mind that in Fortran all the variables (not only integers) are passed by pointers except pointers (i.e. arrays) themselves. I/O is another thing you have to take care (but I haven't touch that yet :-( ). Good luck! Jing (the same one from ac.dal.ca) From elewars@alchemy.chem.utoronto.ca Wed Oct 12 18:27:00 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id SAA18946; Wed, 12 Oct 1994 18:13:41 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id SAA01339 for chemistry@ccl.net; Wed, 12 Oct 1994 18:13:39 -0400 Date: Wed, 12 Oct 1994 18:13:39 -0400 From: "E. Lewars" Message-Id: <199410122213.SAA01339@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: COMPUTATIONS ON CARBON OXIDE POLYMERS 1994 Oct 12 Dear Netters, There have been computational studies of polymers of nitrogen and of nitrogen oxides. Engelke (e.g. R. Engelke, J Org Chem 1992, 57, 4841; R. Engelke, J Phys Chem 1992, 96, 10789) has used computational chemistry to explore the possibility of compounds like octaazacubane, N8, and hexaazabenzene, N6. Jones (e.g. W. H. Jones, J Phys Chem 1992, 96, 594) has used these techniques to examine compounds like (ONNO)n and (NNO)n. Does anyone know of any work, theoretical or experimental, on, or any refs at all to, polymers of carbon dioxide or carbon monoxide? I know a bit has been published on OCCO (I'd appreciate any refs); how about, e.g. O C / \ O O O OC--O OC--O C | | | | | | / \ OC CO O--CO OC--O O O a mixed CO/CO2 oligomer \ / \ / O 2 3 C--C O O 1 4 O O O O C C C C O O O ... / \ / \ / \ / \... C C C O O O .../ \ / \ / \... C C 5 O O 6 If anyone has any info' on anything like this, I would very much appreciate hearing from you. Errol Lewars