From chem8@york.ac.uk Mon Oct 6 15:42:34 1997 Received: from lendal.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA20764; Mon, 6 Oct 1997 15:07:52 -0400 (EDT) Received: from ebor.york.ac.uk by lendal.york.ac.uk with SMTP (PP); Mon, 6 Oct 1997 20:02:07 +0100 Received: from localhost by ebor.york.ac.uk via SMTP (950511.SGI.8.6.12.PATCH526/951211.SGI) id UAA01335; Mon, 6 Oct 1997 20:06:36 +0100 Date: Mon, 6 Oct 1997 20:06:36 +0100 (BST) From: John Waite To: Emadeddin Tajkhorshid cc: chemistry@www.ccl.net Subject: Re: CCL:volume calculation In-Reply-To: <199710061457.QAA15232@cvx12.inet.dkfz-heidelberg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Emad, Try: c volume.f - volume determination code c c Author: Lawrence R. Dodd c Doros N. Theodorou c Maintainer: Lawrence R. Dodd c Created: March 21, 1990 c Version: 2.0 c Date: 1994/07/22 15:45:51 c Keywords: volume and area determination c Time-stamp: <94/07/22 11:02:23 dodd> c Copyright (c) 1990, 1991, 1992, 1993, 1994 c by Lawrence R. Dodd and Doros N. Theodorou. C---------------------------------------------------------------------C C Plane Sphere Intersections C C---------------------------------------------------------------------C C This program will find the total and individual volume and C C exposed surface area of an arbitrary collection of spheres of C C arbitrary radii cut by an arbitrary collection of planes C C analytically by analyzing the plane/sphere intersections. C C---------------------------------------------------------------------C C Algorithm by: Doros N. Theodorou and Lawrence R. Dodd C C Coded by: L.R. Dodd C C---------------------------------------------------------------------C C Created on: March 21, 1990 C C Phase 1 Completed on: March 23, 1990 C C Phase 2 Completed on: April 16, 1990 C C Phase 3 Completed on: May 17, 1990 C C Phase 4 Completed on: June 5, 1990 C C Phase 5 Completed on: July 26, 1990 C C---------------------------------------------------------------------C C Reference: C C C C "Analytical treatment of the volume and surface area of C C molecules formed by an arbitrary collection of unequal C C spheres intersected by planes" C C C C L.R. Dodd and D.N. Theodorou C C MOLECULAR PHYSICS, Volume 72, Number 6, 1313-1345, April 1991 C C---------------------------------------------------------------------C C Acknowlegement: C C C C LRD wishes to thank his mentor DNT for a stimulating and C C enjoyable post-doctoral experience. C C---------------------------------------------------------------------C C General Notes On Program: C C C C This program has been written with an eye towards both C C efficiency and clarity. On a philosophical note, many believe C C that these ideals are mutually exclusive but in general they C C are not. There are, however, a few instances where one ideal C C has been given more prominence over the other. The comments in C C the program, together with the associated journal article, C C should help to explain any apparent logical leaps in the C C algorithm. C C C C The program was intended to be used as a subroutine called C C repeatly by some main program. In this case the subroutine C C "VOLUME" is called by some main routine which has placed the C C necessary information in common block /Raw Data/. The answers C C are returned in common block /Volume Output/. I must apologize C C for the poor input/output for the program. For example, the C C area/volume of each sphere is not placed in /Volume Output/. C C C C This program was developed on a Sun SPARCstation 330 using Sun C C FORTRAN 1.3.1 (all trademarks of Sun Microsystems, Inc.). We C C have used some of extensions to the ANSI standard including: C C C C o long variable names (i.e., more than six characters) C C o variable names containing the characters '$' and '_' C C o END DO used in place of the CONTINUE statement C C o DO-WHILE used in place of IF-GOTO constructs C C o excessive number of continuation lines in some FORMATs C C o generic intrinsic function calls (e.g., SIN for DSIN) C C o IMPLICIT NONE statement (needed in development) C C C C The advantage of using non-standard FORTRAN is that it makes it C C considerably easier to follow the flow of a program. There are C C no extraneous statement labels in this program that may have C C obscured the logic (not a single GOTO was used). The previews C C of the new F90 standard appear to adopt many of the features C C already implemented in VMS, Sun, Cray, and IBM FORTRAN. C C C C Note that this algorithm is completely parallelizable. C C C C Larry Dodd C C dodd@mycenae.cchem.berkeley.edu C C C C Department of Chemical Engineering C C College of Chemistry C C University of California at Berkeley C C Berkeley, California 94720-9989 C C (415) 643-7691 (LRD) C C (415) 643-8523 (DNT) C C (415) 642-5927 (Lab) C C C C dodd@mycenae.cchem.berkeley.edu C C doros@mycenae.cchem.berkeley.edu C C C C---------------------------------------------------------------------C C Note: C C Plane_Ordering of common block /Debug/ is, as the name C C implies, for debugging purposes only as is routine ORDERING. C C The information contain therein is not necessary for solving C C the sphere plane problem but proved incredibly useful during C C program development. C C---------------------------------------------------------------------C C Program Sphere Plane Problem Good luck, John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece On Mon, 6 Oct 1997, Emadeddin Tajkhorshid wrote: > Dear Colleagues > > I am looking for programs which calculate the volume of a molecule. Any > reference is highly appreciated. > Thanx in advance > Emad > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: E.Tajkhorshid@dkfz-heidelberg.de > -- Original Sender From: Address: E.Tajkhorshid@dkfz-heidelberg.de > 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 > >