src/kernel/topexcl.h

   1 /*
   2  * $Id$
   3  *
   4  *       This source code is part of
   5  *
   6  *        G   R   O   M   A   C   S
   7  *
   8  * GROningen MAchine for Chemical Simulations
   9  *
  10  *               VERSION 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * GRowing Old MAkes el Chrono Sweat
  28  */
  29
  30 #ifndef _topexcl_h
  31 #define _topexcl_h
  32
  33 static char *SRCID_topexcl_h = "$Id$";
  34
  35 #ifdef HAVE_IDENT
  36 #ident  "@(#) topexcl.h 1.11 11/23/92"
  37 #endif /* HAVE_IDENT */
  38
  39 #include "topio.h"
  40
  41 typedef struct {
  42   int nr;               /* nr atoms (0 <= i < nr) (atoms->nr)           */
  43   int nrex;             /* with nrex lists of neighbours                */
  44                         /* respectively containing zeroth, first        */
  45                         /* second etc. neigbours (0 <= nre < nrex)      */
  46   int **nrexcl;         /* with (0 <= nrx < nrexcl[i][nre]) neigbours   */
  47                         /* per list stored in one 2d array of lists     */
  48   int ***a;             /* like this: a[i][nre][nrx]                    */
  49 } t_nextnb;
  50
  51 extern void init_nnb(t_nextnb *nnb, int nr, int nrex);
  52 /* Initiate the arrays for nnb (see above) */
  53
  54 extern void done_nnb(t_nextnb *nnb);
  55 /* Cleanup the nnb struct */
  56
  57 #ifdef DEBUG
  58 #define print_nnb(nnb, s) __print_nnb(nnb, s)
  59 extern void print_nnb(t_nextnb *nnb, char *s);
  60 /* Print the nnb struct */
  61 #else
  62 #define print_nnb(nnb, s)
  63 #endif
  64
  65 extern void gen_nnb(t_nextnb *nnb,t_params plist[]);
  66 /* Generate a t_nextnb structure from bond information.
  67  * With the structure you can either generate exclusions
  68  * or generate angles and dihedrals. The structure must be
  69  * initiated using init_nnb.
  70  */
  71
  72 extern void nnb2excl (t_nextnb *nnb, t_block *excl);
  73 /* generate exclusions from nnb */
  74
  75 extern void generate_excl (int nrexcl, int nratoms,
  76                            t_params plist[],t_block *excl);
  77 /* Generate an exclusion block from bonds and constraints in
  78  * plist.
  79  */
  80 #endif  /* _topexcl_h */