include/ns.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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  18  * of the License, or (at your option) any later version.
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  21  * scientific software is very special. Version control is crucial -
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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 #ifdef __cplusplus
  52 extern "C" {
  53 #endif
  54
  55 /****************************************************
  56  *
  57  *    U T I L I T I E S May be found in ns.c
  58  *
  59  ****************************************************/
  60
  61 extern void init_neighbor_list(FILE *log,t_forcerec *fr,int homenr);
  62 /*
  63  * nn is the number of energy terms in the energy matrix
  64  * (ngener*(ngener-1))/2
  65  * start is the first atom on this processor
  66  * homenr is the number of atoms on this processor
  67  */
  68
  69 extern int calc_naaj(int icg,int cgtot);
  70 /* Calculate the number of charge groups to interact with for icg */
  71
  72 /****************************************************
  73  *
  74  *    N E I G H B O R  S E A R C H I N G
  75  *
  76  *    Calls either ns5_core (when grid selected in .mdp file)
  77  *    or ns_simple_core (when simple selected in .mdp file)
  78  *
  79  *    Return total number of pairs searched
  80  *
  81  ****************************************************/
  82 extern void init_ns(FILE *fplog,const t_commrec *cr,
  83                     gmx_ns_t *ns,t_forcerec *fr,
  84                     const gmx_mtop_t *mtop,
  85                     matrix box);
  86
  87 extern int search_neighbours(FILE *log,t_forcerec *fr,
  88                              rvec x[],matrix box,
  89                              gmx_localtop_t *top,
  90                              gmx_groups_t *groups,
  91                              t_commrec *cr,
  92                              t_nrnb *nrnb,t_mdatoms *md,
  93                              real lambda,real *dvdlambda,
  94                              gmx_grppairener_t *grppener,
  95                              bool bFillGrid,
  96                              bool bDoLongRange,
  97                              bool bDoForces,rvec *f);
  98
  99
 100 /* Debugging routines from wnblist.c */
 101 extern void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL);
 102
 103 extern int read_nblist(FILE *in,FILE *out,int **mat,int natoms,bool bSymm);
 104 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
 105
 106 extern int natoms_beyond_ns_buffer(t_inputrec *ir,t_forcerec *fr,t_block *cgs,
 107                                    matrix scale_tot,rvec *x);
 108 /* Returns the number of atoms that moved beyond the ns buffer */
 109
 110 #ifdef __cplusplus
 111 }
 112 #endif
 113
 114
 115 #endif  /* _ns_h */