include/ns.h

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  38
  39 #ifndef _ns_h
  40 #define _ns_h
  41
  42 #include <stdio.h>
  43 #include "visibility.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 GMX_LIBMD_EXPORT
  62 void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr);
  63 /*
  64  * nn is the number of energy terms in the energy matrix
  65  * (ngener*(ngener-1))/2
  66  * start is the first atom on this processor
  67  * homenr is the number of atoms on this processor
  68  */
  69
  70 int calc_naaj(int icg, int cgtot);
  71 /* Calculate the number of charge groups to interact with for icg */
  72
  73 /****************************************************
  74  *
  75  *    N E I G H B O R  S E A R C H I N G
  76  *
  77  *    Calls either ns5_core (when grid selected in .mdp file)
  78  *    or ns_simple_core (when simple selected in .mdp file)
  79  *
  80  *    Return total number of pairs searched
  81  *
  82  ****************************************************/
  83 void init_ns(FILE *fplog, const t_commrec *cr,
  84              gmx_ns_t *ns, t_forcerec *fr,
  85              const gmx_mtop_t *mtop,
  86              matrix box);
  87
  88 GMX_LIBMD_EXPORT
  89 int search_neighbours(FILE *log, t_forcerec *fr,
  90                       rvec x[], matrix box,
  91                       gmx_localtop_t *top,
  92                       gmx_groups_t *groups,
  93                       t_commrec *cr,
  94                       t_nrnb *nrnb, t_mdatoms *md,
  95                       real *lambda, real *dvdlambda,
  96                       gmx_grppairener_t *grppener,
  97                       gmx_bool bFillGrid,
  98                       gmx_bool bDoLongRangeNS,
  99                       gmx_bool bPadListsForKernels);
 100
 101
 102 /* Debugging routines from wnblist.c */
 103 GMX_LIBMD_EXPORT
 104 void dump_nblist(FILE *out, t_commrec *cr, t_forcerec *fr, int nDNL);
 105
 106 int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
 107 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
 108
 109 GMX_LIBMD_EXPORT
 110 int natoms_beyond_ns_buffer(t_inputrec *ir, t_forcerec *fr, t_block *cgs,
 111                             matrix scale_tot, rvec *x);
 112 /* Returns the number of atoms that moved beyond the ns buffer */
 113
 114 #ifdef __cplusplus
 115 }
 116 #endif
 117
 118
 119 #endif  /* _ns_h */