include/ns.h

   1 /*
   2  *
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   4  *
   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 #include <stdio.h>
  40 #include "sysstuff.h"
  41 #include "typedefs.h"
  42 #include "pbc.h"
  43 #include "tgroup.h"
  44 #include "network.h"
  45
  46
  47 #ifdef __cplusplus
  48 extern "C" {
  49 #endif
  50
  51 /****************************************************
  52  *
  53  *    U T I L I T I E S May be found in ns.c
  54  *
  55  ****************************************************/
  56
  57 void init_neighbor_list(FILE *log,t_forcerec *fr,int homenr);
  58 /*
  59  * nn is the number of energy terms in the energy matrix
  60  * (ngener*(ngener-1))/2
  61  * start is the first atom on this processor
  62  * homenr is the number of atoms on this processor
  63  */
  64
  65 int calc_naaj(int icg,int cgtot);
  66 /* Calculate the number of charge groups to interact with for icg */
  67
  68 /****************************************************
  69  *
  70  *    N E I G H B O R  S E A R C H I N G
  71  *
  72  *    Calls either ns5_core (when grid selected in .mdp file)
  73  *    or ns_simple_core (when simple selected in .mdp file)
  74  *
  75  *    Return total number of pairs searched
  76  *
  77  ****************************************************/
  78 void init_ns(FILE *fplog,const t_commrec *cr,
  79                     gmx_ns_t *ns,t_forcerec *fr,
  80                     const gmx_mtop_t *mtop,
  81                     matrix box);
  82
  83 int search_neighbours(FILE *log,t_forcerec *fr,
  84                              rvec x[],matrix box,
  85                              gmx_localtop_t *top,
  86                              gmx_groups_t *groups,
  87                              t_commrec *cr,
  88                              t_nrnb *nrnb,t_mdatoms *md,
  89                              real lambda,real *dvdlambda,
  90                              gmx_grppairener_t *grppener,
  91                              gmx_bool bFillGrid,
  92                              gmx_bool bDoLongRange,
  93                              gmx_bool bDoForces,rvec *f);
  94
  95
  96 /* Debugging routines from wnblist.c */
  97 void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL);
  98
  99 int read_nblist(FILE *in,FILE *out,int **mat,int natoms,gmx_bool bSymm);
 100 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
 101
 102 int natoms_beyond_ns_buffer(t_inputrec *ir,t_forcerec *fr,t_block *cgs,
 103                                    matrix scale_tot,rvec *x);
 104 /* Returns the number of atoms that moved beyond the ns buffer */
 105
 106 #ifdef __cplusplus
 107 }
 108 #endif
 109
 110
 111 #endif  /* _ns_h */