Subject: volume calculation

From: Emadeddin Tajkhorshid <[email-masked]>
Date: Mon, 6 Oct 1997 16:57:47 +0200 (METDST)

Dear Colleagues

I am looking for programs which calculate the volume of a molecule. Any
reference is highly appreciated. 
Thanx in advance
Emad

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From: John Waite <[email-masked]>
Date: Mon, 6 Oct 1997 20:06:36 +0100 (BST)

Hi Emad,

   Try:
c     volume.f - volume determination code
c     
c     Author: Lawrence R. Dodd <[email-masked]>
c             Doros N. Theodorou <[email-masked]>
c     Maintainer: Lawrence R. Dodd <[email-masked]>
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                           [email-masked]           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                            [email-masked]          C
C                           [email-masked]          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:  [email-masked] * or
 The National Hellenic Research Foundation,*         [email-masked]
 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 [email-masked] 
 Material Science Institute,
 Aghia Paraskevi,
 Attikis,
 Athens 153-10,
 Greece

On Mon, 6 Oct 1997, Emadeddin Tajkhorshid wrote:

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---

From: "Dr. Bruno Manunza" <[email-masked]>
Date: Fri, 4 Oct 1996 19:22:21 +0100 (NFT)

> reference is highly appreciated. 

Dear Emad,
	you'll find a collection of tools for calculating both volume and 
surface of a molecule at
http://antas.agraria.uniss.it/software.html

hope it helps
regards
Bruno

Dr Bruno Manunza
DISAABA (Dept. of Agricultural Environm. Sci)
University of Sassari
V.le Italia 39
07100 Sassari, ITALY
phone: 39 79 229215
fax:   39 79 229276
e-mail: [email-masked]
e-mail: [email-masked]
e-mail: [email-masked]
web: http://antas.agraria.uniss.it