From vazquez@iqm.unicamp.br Thu Oct 13 00:19:29 1994 Received: from kalypso.iqm.unicamp.br for vazquez@iqm.unicamp.br by www.ccl.net (8.6.9/930601.1506) id AAA21904; Thu, 13 Oct 1994 00:04:55 -0400 Received: (vazquez@localhost) by kalypso.iqm.unicamp.br (8.6.8/8.3) id AAA14091; Thu, 13 Oct 1994 00:56:09 -0300 From: Pedro A M Vazquez Message-Id: <199410130356.AAA14091@kalypso.iqm.unicamp.br> Subject: C & f77 To: CHEMISTRY@ccl.net Date: Thu, 13 Oct 1994 00:56:08 -0300 (GMT-0300) Organization: Instituto de Quimica Unicamp X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 420 Hello PVM2.4 has a fortran to C interface library, libf2c, with support for several Unix implementations. There we find that: o Some fortran compilers put a null terminator on strings ('\0') (e.g. CRAY, HP, NEXT) but others don't; o The C function or subroutine foo(bar) can be named: * foo_(bar) (e.g. SunOS), or; * foo(bar) (e.g. IBM,HP,NEXT), or; * FOO(bar) (e.g. Cray) Pedro From brupalf@umich.edu Thu Oct 13 00:31:18 1994 Received: from robotron.rs.itd.umich.edu for brupalf@umich.edu by www.ccl.net (8.6.9/930601.1506) id XAA21786; Wed, 12 Oct 1994 23:38:42 -0400 Received: by robotron.rs.itd.umich.edu (8.6.9/2.2) id XAA15712; Wed, 12 Oct 1994 23:39:19 -0400 Date: Wed, 12 Oct 1994 23:39:18 -0400 (EDT) From: Bruce Allan Palfey X-Sender: brupalf@robotron.rs.itd.umich.edu To: CHEMISTRY@ccl.net Subject: HP spec data Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Howdy Does anyone out there still rely heavily on the Hewlett-Packard Pascal-based UV/Vis diode array spectrophotometer like we do? It's anice system, but we often run into trouble when we try to convert data from HP's format to DOS (which is useful for analysis). We have an old conversion program, "SWAPUV", from 1988, which often chokes on larger data files. Is there a better version? Or is there a general format conversion program, running on either the PC or the Mac, that can read HP's old disks. Now that HP has abandoned their Pascal system and moved on to Windows, they don't seem interested in helping. Thanks, Bruce please send replies directly to me From ipcakc@vigyan.iisc.ernet.in Thu Oct 13 01:19:29 1994 Received: from sangam.ncst.ernet.in for ipcakc@vigyan.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id BAA22347; Thu, 13 Oct 1994 01:01:24 -0400 From: Received: from soochak.ncst.ernet.in (soochak.ncst.ernet.in [144.16.11.100]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id KAA20758 for ; Thu, 13 Oct 1994 10:30:50 +0500 Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by soochak.ncst.ernet.in (8.6.8.1/8.6.5) with SMTP id KAA15522 for ; Thu, 13 Oct 1994 10:29:42 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA26188; Thu, 13 Oct 94 10:35:14+0530 Received: by vigyan.iisc.ernet.in (smail2.3) id AA01524; 13 Oct 94 09:43:20 EST (Thu) To: CHEMISTRY@ccl.net Subject: GAMESS input for Linear Molecules Date: 13 Oct 94 09:43:20 EST (Thu) Message-Id: <9410130943.AA01524@vigyan.iisc.ernet.in> Does anyone help me out in giving me a correct Z-matrix in internal coordinates for the molecule (hypothetical) given below. The following Z-matrix, which I gave is working fine with Gaussian92 package but not with GAMESS program. The following Z-matrix under CinfinityV point group gives error in GAMESS. N-----C------H-------------C----N r1 r2 r3 r4 A1 A2 A3 D1 D2 The Z-matrix in Internal Coordinates is N C 1 r1 H 2 r2 1 A1 C 3 r3 2 A2 1 D1 N 4 r4 3 A3 2 D2 r1 = 1.1504 r2 = 1.0057 r3 = 2.45 r4 = 1.1405 a1 = 180.0 a2 = 180.0 a3 = 180.0 D1 = 0.0 D2 = 0.0 $ZMAT 1,1,2, 1,2,3, 1,3,4, 1,4,5, 2,3,2,1, 2,4,3,2, 2,5,4,3, 3,4,3,2,1, 3,5,4,3,2 $END This molecule has 5 atoms with (Cnh 4) point group (linear). I need to input 10 internal coordinates, but however I tried, I land up only with 9 internal coordinates. I even tried with degenerate bendings and it gives an error with one linear bend ( 5,4,3,2 ) which says ROUND OFF ERROR IN LINEAR BEND I want to optimize this system in internal coordinates only. Could you suggest me a solution for this problem? (If I do not use the linear bend, it says that I have provided only 9 internal coordinates instead of 10) V. Sreedhara Rao Department of I.P.C., Indian Institute of Science, Bangalore - 560 012 - INDIA. E-mail : ipcakc@ipc.iisc.ernet.in From CHEM86@Jetson.UH.EDU Thu Oct 13 02:19:32 1994 Received: from Elroy.UH.EDU for CHEM86@Jetson.UH.EDU by www.ccl.net (8.6.9/930601.1506) id BAA22444; Thu, 13 Oct 1994 01:25:26 -0400 From: Received: from Jetson.UH.EDU by Jetson.UH.EDU (PMDF V4.3-10 #5185) id <01HI7H1KJPJK8WWX7Z@Jetson.UH.EDU>; Thu, 13 Oct 1994 00:21:47 -0500 (CDT) Date: Thu, 13 Oct 1994 00:21:46 -0500 (CDT) Subject: Pointers in FORTRAN under IRIX To: chemistry@ccl.net Message-id: <01HI7H1KK8TU8WWX7Z@Jetson.UH.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi Netters, Does anyone have any experience with pointers in FORTRAN working under Silicon Graphics' IRIX ? I have written FORTRAN code making use of a very large (~20M in the latest example) 3-dim dense array of real*8. Older version recalculates parts of it in every cycle; and in order to speed it up I tried to calculate the array at the beginning and store it in RAM throughout the program execution. Practical applications involve problems of varying size, therefore, the conventional static storage would have to waste a lot of memory. In newer version I associate a pointer with the array (IRIX implementation has that feature) and reserve space with (also non-standard) malloc() function. The program is fast and works OK with only one exception: sometimes (90% of cases) it is killed with SIGSEGV (segmentation fault) when an attempt of any disk output operation is made (mostly OPEN statement). After a week of debugging I have found no errors in algorithm. Using very simple input I swepped, byte by byte, all 32 bytes of allocated memory after executing every line of program to no avail. The dbx with core-file points to line containig first disk output operation (OPEN or WRITE) and the following subroutines: malloc_, malloc__, realfree. BTW, no output file is created. The funny thing is that the program that cannot swallow 32-byte allocation, works perfectly with a ~5M one. Seriously, I suspect a bug in the compiler. Does anyone have similar experience ? Comments ? Thank you very much for sharing your thoughts. Robert Fraczkiewicz Department of Chemistry University of Houston chem86@jetson.uh.edu Disclaimer: A flame/holy war of C vs FORTRAN is not intended... From szeinfel@snfma1.if.usp.br Thu Oct 13 09:19:37 1994 Received: from snfma1.if.usp.br for szeinfel@snfma1.if.usp.br by www.ccl.net (8.6.9/930601.1506) id IAA25475; Thu, 13 Oct 1994 08:26:53 -0400 Received: (szeinfel@localhost) by snfma1.if.usp.br (8.6.8/8.6.4) id JAA29056; Thu, 13 Oct 1994 09:25:09 -0300 Date: Thu, 13 Oct 1994 09:25:08 -0300 (EST) From: Rafael Iosef Najmanovich Szeinfeld {S To: Charles Letner cc: Computational Chemistry List Subject: Re: CCL:Quantum text In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I recomend you three texts in quantum mechanics. The first two are basic theory texts and the last one is a basic quantum chemistry text. ----> Dicke & Witke. Introduction to quantum Mechanics. A good text on concepts but short in really calculating something. ----> Bransden & Joachain. Introduction to quantum mechanics. Ideal to learn theory and calculations. ----> Karplus. Atoms and molecules. Good in the sense that it treats atoms and molecules but the theory is poorly explained using unnecessary bad arguments. Sincerly yours, Rafael. *-----------------------------------------------------------------------------* * Rafael Iosef Najmanovich Szeinfeld |SMAIL: Depto. de Bioquimica - B10 INF.* * Dept. Biochemistry -Chemistry Inst. | Universidade de Sao Paulo * * Dept. Math. Physics -Physics Inst. | Av. Prof. Lineu Prestes 748 * * University of Sao Paulo | CEP 05508-900 * * E-MAIL : szeinfel@snfma1.if.usp.br | Sao Paulo - SP - Brazil * *-----------------------------------------------------------------------------* From glump@kff1.uchicago.edu Thu Oct 13 11:19:39 1994 Received: from midway.uchicago.edu for glump@kff1.uchicago.edu by www.ccl.net (8.6.9/930601.1506) id KAA27628; Thu, 13 Oct 1994 10:21:31 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Thu, 13 Oct 94 09:21:23 CDT Received: from kff1.uchicago.edu by rainbow.uchicago.edu via SMTP (931110.SGI/930416.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA01472; Thu, 13 Oct 94 10:14:52 -0500 Received: by kff1.uchicago.edu.PSNCL (4.1/SMI-4.1) id AA19013; Thu, 13 Oct 94 09:22:24 CDT Date: Thu, 13 Oct 94 09:22:24 CDT From: glump@kff1.uchicago.edu (Anil G. Mudholkar) Message-Id: <9410131422.AA19013@kff1.uchicago.edu.PSNCL> To: Hinsen Konrad , Computational Chemistry List Subject: Calling FORTRAN FUNCTIONS from a C-Program. Cc: Anil Reply-To: Anil In-Reply-To: Your message of Wed, 12 Oct 94 14:01:49 -0400 <9410121801.AA13784@cyclone.ERE.UMontreal.CA> Mr. Hinsen, I agree with all of your comments. I was too quick to just rattle off the message I wrote. Also, I had not before seen CFORTRAN, but I will definitely check it out. My main point was that f2c isn't a very good route to take, but that generally something not too difficult can be done if you have to mix code. I only resort to this when I become so completely frustrated in trying but failing to do some very simple operation with clean Fortran when I am certain I can do in one line of C code. For example, dynamic memory allocation for Fortran is usually only possible by mixing code. ) 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 I have found that the rough guidelines I mentioned off the top of my head do work on most unix boxes, including RS/6000 under AIX 3.2 and higher, which are our group's main production level machines, though admittedly, it is not guaranteed to be portable. This is neither a part of the description of Fortran-77 nor is there any universal standard, and I'm sure that most non-unix platforms will have less similar compiler behavior. Also, a gentleman from the Minnesota Supercomputing Center was kind enough to point out to me yesterday that my prescription (as I stated it) would not work on a Cray, for example. However, this has always been one of the least difficult aspects of porting code for our group. We have ports of our electronic structure code for IBM RS/6000s AIX 3.2 up, SGI IRIX 4.0.5 and IRIX 5.2, Cray UNICOS, and (partially) Sun SunOS 4.1.1. I have also done this in some unrelated code from a VAX VMS 5.5 machine, and the code mixing was the only thing that wasn't a problem in that case, but that's another story. In the future, I will be more careful before recklessly posting messages. Or perhaps I should be more careful to avoid recklessly posting altogether. :^) Thanks. Anil Mudholkar glump@rainbow.uchicago.edu http://rainbow.uchicago.edu/~glump From g112976@iris.ufscar.br Thu Oct 13 14:19:43 1994 Received: from fpsp.fapesp.br for g112976@iris.ufscar.br by www.ccl.net (8.6.9/930601.1506) id NAA01062; Thu, 13 Oct 1994 13:26:12 -0400 Received: from power.ufscar.br by fpsp.fapesp.br with PMDF#10108; Thu, 13 Oct 1994 14:23 BSC (-0300 C) Received: from iris.ufscar.br by power.ufscar.br via SMTP (931110.SGI/911001.SGI) for @fpsp.fapesp.br:CHEMISTRY@oscsunb.ccl.net id AA19276; Thu, 13 Oct 94 14:15:44 -0200 Received: by iris.ufscar.br (920110.SGI/911001.SGI) for @power.ufscar.br:CHEMISTRY@oscsunb.ccl.net id AA09021; Thu, 13 Oct 94 14:27:20 -0200 Date: Thu, 13 Oct 94 14:27:20 -0200 From: g112976@iris.ufscar.br (Augusto C. C. Neto) Subject: Garnet Structures To: CHEMISTRY@oscsunb.ccl.net Message-id: <9410131627.AA09021@iris.ufscar.br> X-Envelope-to: CHEMISTRY@oscsunb.ccl.net Federal University at Sao Carlos, october 13, 1994 Hi Netters !! I'm begining to work with garnet structures, I would like to find some coor- dinates or inputs for Mopac or Hyperchem ... Thank you ... Augusto Cesar From info@molecules.com Thu Oct 13 14:26:47 1994 Received: from nic.cerf.net for info@molecules.com by www.ccl.net (8.6.9/930601.1506) id NAA01412; Thu, 13 Oct 1994 13:48:30 -0400 Received: from tonyt.nic.cerf.net (molecules.com [134.24.2.162]) by nic.cerf.net (8.6.8/8.6.6) with SMTP id KAA17268 for ; Thu, 13 Oct 1994 10:48:17 -0700 Date: Thu, 13 Oct 94 10:33:58 PDT From: Molecular Arts Information Subject: Molecules-3D To: chemistry@ccl.net X-Mailer: Chameleon - TCP/IP for Windows by NetManage, Inc. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Product Announcement Molecules-3D (TM), Version 2.0 3D Molecular Model Builder for Apple Macintosh and Microsoft Windows A simple-to-use package that enables you to: (A) build, optimize, edit and export 3D molecular models, as well as, (B) construct 2D Lewis diagrams and convert them to 3D models. Only $29.95. Molecular Arts Corporation Hanover Corporate Centre, 1532 East Katella Avenue, Suite 1000 Anaheim, California 92805-6627 USA MAIN: (714) 634-8100 FAX: (714) 634-1999 Internet: info@molecules.com CompuServe: 71644,3626 FTP: ftp.cerf.net /pub/vendor/molecules From info@molecules.com Thu Oct 13 14:30:57 1994 Received: from nic.cerf.net for info@molecules.com by www.ccl.net (8.6.9/930601.1506) id NAA01386; Thu, 13 Oct 1994 13:44:52 -0400 Received: from tonyt.nic.cerf.net (molecules.com [134.24.2.162]) by nic.cerf.net (8.6.8/8.6.6) with SMTP id KAA16842 for ; Thu, 13 Oct 1994 10:44:45 -0700 Date: Thu, 13 Oct 94 09:01:17 PDT From: Molecular Arts Information Subject: RE: CCL:simple geometry minimizer To: chemistry@ccl.net X-Mailer: Chameleon - TCP/IP for Windows by NetManage, Inc. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=us-ascii >I'm looking for a simple molecular mechanics minimization tool, the >simpler the better, if possible with source. (:-) > >Francois Savary My company offers a commercial product, Molecules-3D, that may suit your needs. Molecules-3D is a molecular model builder with cleanup (optimization) capabilities. It evaluates bond length, angle, torsion, van der Waals, and other forces. It is available for Microsoft Windows and Apple Macintosh. The price is $29.95. I will post an abbreviated description to the mailing list. I will e-mail the longer description to you, and any others who request it. Phil Molecular Arts Information From desmarai@ERE.UMontreal.CA Thu Oct 13 14:34:57 1994 Received: from condor.CC.UMontreal.CA for desmarai@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id OAA01902; Thu, 13 Oct 1994 14:18:27 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA09116 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Thu, 13 Oct 1994 14:17:02 -0400 Received: from tornade.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA09341; Thu, 13 Oct 94 14:17:00 -0400 Received: by tornade.ERE.UMontreal.CA (940406.SGI/5.17) id AA29722; Thu, 13 Oct 94 14:16:59 -0400 From: desmarai@ERE.UMontreal.CA (Desmarais Normand) Message-Id: <9410131816.AA29722@tornade.ERE.UMontreal.CA> Subject: G9x, CISD, interpretation problem... To: CHEMISTRY@ccl.net (Comp.Chem.List Group) Date: Thu, 13 Oct 1994 14:16:59 -0400 (EDT) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1516 Hello, I'm having trouble to understand some CISD output of Gaussian90. I did send a message to gaussian but they didn't respond yet and I don't want to loose to much time on this. So here is the problem: Using this input file: ==Begin============(Input)==================== %rwf=tst #RCID=RW/4-31G POP=NONE GFINPUT Carbone, 4-31G RCID=RW(3,4) 0 1 C 3,4 ==End============(Input)====================== I get this output: ==Begin============(Output)==[LAST ITERATION]== [...a few things skipped...] ITERATION NR. 20 ********************** WTILD MADE 1 PASSES THROUGH THE AO INTEGRALS. WTildB: NR= 1 LPair= 81 The Euclidean norm of the A-vectors is 0.5241667D-07 RLE energy= -0.0145095526 DE(CI)= -0.14509780D-01 E(CI)= -0.37559066935D+02 NORM(A)= 0.11328458D+01 SIZE-CONSISTENCY CORRECTION: S.C.C.= 0.00000000D+00 E(CI,SIZE)= -0.37559066935D+02 *************************************************************** [...more things skipped...] ==End==============(Output)==[LAST ITERATION]== so can someone tell me what is "RLE energy" and how does one goes from this energy to the "DE(CI)" energy? please send your answer directly to me, I will summarize for the net if there is a need. Thank you for your attention, Normand. -- o-----------------------------------o [ Normand Desmarais ] [ desmarai@tornade.ere.umontreal.ca ] [ desmarai@chims1.chimcn.umontreal.ca ] o-----------------------------------o From shepard@dirac.tcg.anl.gov Thu Oct 13 14:40:14 1994 Received: from dirac.tcg.anl.gov for shepard@dirac.tcg.anl.gov by www.ccl.net (8.6.9/930601.1506) id NAA01095; Thu, 13 Oct 1994 13:28:08 -0400 Received: by dirac.tcg.anl.gov (4.1/SMI-4.1) id AA01442; Thu, 13 Oct 94 12:28:08 CDT Date: Thu, 13 Oct 94 12:28:08 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9410131728.AA01442@dirac.tcg.anl.gov> To: chemistry@ccl.net Subject: CCL:Calling FORTRAN FUNCTIONS from a C-Program. Cc: shepard@tcg.anl.gov glump@kff1.uchicago.edu (Anil G. Mudholkar) wrote: [...] > 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, It should be mentioned here that this is very machine dependent. Not all machines (fortunately or unfortunately, depending on your point of view) work like Sun workstations. >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. Again, there is no standard portable way of mapping Fortran character strings to C arrays. Different machines use different conventions. >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.) Again, the number, names, and order of libraries is very machine dependent. [...] >I cannot speak to CFORTRAN having never >seen it. If portability is important, then this should be considered. The cfortran.h header file addresses the portability issues very well. It handles all of the tricky machine dependent stuff: integer/ real/ double precision calling conventions, upper/lower case external name conversions, prepending and/or appending the underscores where appropriate, common blocks, character string conventions, etc. The only problem is with efficiency: cfortran.h works by constructing "glue" interface modules and creating, when necessary, intermediate copies of both scalars and array (primarily char) arguments. Thus every function reference grows into two references, with some possible malloc() overhead. $.02 -Ron Shepard From g112976@iris.ufscar.br Thu Oct 13 16:19:43 1994 Received: from fpsp.fapesp.br for g112976@iris.ufscar.br by www.ccl.net (8.6.9/930601.1506) id PAA03612; Thu, 13 Oct 1994 15:38:17 -0400 Received: from merak.fapesp.br by fpsp.fapesp.br with PMDF#10108; Thu, 13 Oct 1994 16:35 BSC (-0300 C) Received: from power.ufscar.br by merak.fapesp.br with PMDF#10108; Thu, 13 Oct 1994 16:36 BSC (-0300 C) Received: from iris.ufscar.br by power.ufscar.br via SMTP (931110.SGI/911001.SGI) for @fpsp.fapesp.br:CHEMISTRY@oscsunb.ccl.net id AA20996; Thu, 13 Oct 94 16:18:56 -0200 Received: by iris.ufscar.br (920110.SGI/911001.SGI) for @power.ufscar.br:CHEMISTRY@oscsunb.ccl.net id AA10533; Thu, 13 Oct 94 16:31:00 -0200 Date: Thu, 13 Oct 94 16:31:00 -0200 From: g112976@iris.ufscar.br (Augusto C. C. Neto) Subject: AIPI - program ... To: CHEMISTRY@oscsunb.ccl.net Message-id: <9410131831.AA10533@iris.ufscar.br> X-Envelope-to: CHEMISTRY@oscsunb.ccl.net Federal University at Sao Carlos, october 13, 1994 Hi Netters !! I would like to contact some people who are using AIPI program. Thank you ... Augusto Cesar