include/ns.h

   1 /*
   2  *
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   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  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
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  35
  36 #ifndef _ns_h
  37 #define _ns_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <stdio.h>
  44 #include "sysstuff.h"
  45 #include "typedefs.h"
  46 #include "pbc.h"
  47 #include "tgroup.h"
  48 #include "network.h"
  49
  50 /****************************************************
  51  *
  52  *    U T I L I T I E S May be found in ns.c
  53  *
  54  ****************************************************/
  55
  56 extern void init_neighbor_list(FILE *log,t_forcerec *fr,int homenr);
  57 /*
  58  * nn is the number of energy terms in the energy matrix
  59  * (ngener*(ngener-1))/2
  60  * start is the first atom on this processor
  61  * homenr is the number of atoms on this processor
  62  */
  63
  64 extern int calc_naaj(int icg,int cgtot);
  65 /* Calculate the number of charge groups to interact with for icg */
  66
  67 /****************************************************
  68  *
  69  *    N E I G H B O R  S E A R C H I N G
  70  *
  71  *    Calls either ns5_core (when grid selected in .mdp file)
  72  *    or ns_simple_core (when simple selected in .mdp file)
  73  *
  74  *    Return total number of pairs searched
  75  *
  76  ****************************************************/
  77 extern void init_ns(FILE *fplog,const t_commrec *cr,
  78                     gmx_ns_t *ns,t_forcerec *fr,
  79                     const gmx_mtop_t *mtop,
  80                     matrix box);
  81
  82 extern int search_neighbours(FILE *log,t_forcerec *fr,
  83                              rvec x[],matrix box,
  84                              gmx_localtop_t *top,
  85                              gmx_groups_t *groups,
  86                              t_commrec *cr,
  87                              t_nrnb *nrnb,t_mdatoms *md,
  88                              real lambda,real *dvdlambda,
  89                              gmx_grppairener_t *grppener,
  90                              bool bFillGrid,
  91                              bool bDoLongRange,
  92                              bool bDoForces,rvec *f);
  93
  94
  95 /* Debugging routines from wnblist.c */
  96 extern void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL);
  97
  98 extern int read_nblist(FILE *in,FILE *out,int **mat,int natoms,bool bSymm);
  99 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
 100
 101 extern int natoms_beyond_ns_buffer(t_inputrec *ir,t_forcerec *fr,t_block *cgs,
 102                                    matrix scale_tot,rvec *x);
 103 /* Returns the number of atoms that moved beyond the ns buffer */
 104
 105 #endif  /* _ns_h */