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
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  34  */
  35
  36 #ifndef _gpp_nextnb_h
  37 #define _gpp_nextnb_h
  38 #include "visibility.h"
  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 GMX_LIBGMXPREPROCESS_EXPORT
  56 void init_nnb(t_nextnb *nnb, int nr, int nrex);
  57 /* Initiate the arrays for nnb (see above) */
  58
  59 GMX_LIBGMXPREPROCESS_EXPORT
  60 void done_nnb(t_nextnb *nnb);
  61 /* Cleanup the nnb struct */
  62
  63 #ifdef DEBUG_NNB
  64 #define print_nnb(nnb, s) __print_nnb(nnb, s)
  65 void print_nnb(t_nextnb *nnb, char *s);
  66 /* Print the nnb struct */
  67 #else
  68 #define print_nnb(nnb, s)
  69 #endif
  70
  71 GMX_LIBGMXPREPROCESS_EXPORT
  72 void gen_nnb(t_nextnb *nnb,t_params plist[]);
  73 /* Generate a t_nextnb structure from bond information.
  74  * With the structure you can either generate exclusions
  75  * or generate angles and dihedrals. The structure must be
  76  * initiated using init_nnb.
  77  */
  78
  79 void nnb2excl (t_nextnb *nnb, t_blocka *excl);
  80 /* generate exclusions from nnb */
  81
  82 void generate_excl (int nrexcl, int nratoms,
  83                            t_params plist[],t_nextnb *nnb,t_blocka *excl);
  84 /* Generate an exclusion block from bonds and constraints in
  85  * plist.
  86  */
  87
  88 #ifdef __cplusplus
  89 }
  90 #endif
  91
  92 #endif  /* _gpp_nextnb_h */