include/gpp_nextnb.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  34  */
  35
  36 #ifndef _gpp_nextnb_h
  37 #define _gpp_nextnb_h
  38
  39 #include "grompp.h"
  40
  41 #ifdef __cplusplus
  42 extern "C" {
  43 #endif
  44
  45 typedef struct {
  46   int nr;               /* nr atoms (0 <= i < nr) (atoms->nr)           */
  47   int nrex;             /* with nrex lists of neighbours                */
  48                         /* respectively containing zeroth, first        */
  49                         /* second etc. neigbours (0 <= nre < nrex)      */
  50   int **nrexcl;         /* with (0 <= nrx < nrexcl[i][nre]) neigbours   */
  51                         /* per list stored in one 2d array of lists     */
  52   int ***a;             /* like this: a[i][nre][nrx]                    */
  53 } t_nextnb;
  54
  55 extern void init_nnb(t_nextnb *nnb, int nr, int nrex);
  56 /* Initiate the arrays for nnb (see above) */
  57
  58 extern void done_nnb(t_nextnb *nnb);
  59 /* Cleanup the nnb struct */
  60
  61 #ifdef DEBUG_NNB
  62 #define print_nnb(nnb, s) __print_nnb(nnb, s)
  63 extern void print_nnb(t_nextnb *nnb, char *s);
  64 /* Print the nnb struct */
  65 #else
  66 #define print_nnb(nnb, s)
  67 #endif
  68
  69 extern void gen_nnb(t_nextnb *nnb,t_params plist[]);
  70 /* Generate a t_nextnb structure from bond information.
  71  * With the structure you can either generate exclusions
  72  * or generate angles and dihedrals. The structure must be
  73  * initiated using init_nnb.
  74  */
  75
  76 extern void nnb2excl (t_nextnb *nnb, t_blocka *excl);
  77 /* generate exclusions from nnb */
  78
  79 extern void generate_excl (int nrexcl, int nratoms,
  80                            t_params plist[],t_nextnb *nnb,t_blocka *excl);
  81 /* Generate an exclusion block from bonds and constraints in
  82  * plist.
  83  */
  84
  85 #ifdef __cplusplus
  86 }
  87 #endif
  88
  89 #endif  /* _gpp_nextnb_h */