src/gromacs/mdlib/ns.h

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  37 #ifndef GMX_MDLIB_NS_H
  38 #define GMX_MDLIB_NS_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/legacyheaders/typedefs.h"
  43
  44 struct gmx_ns_t;
  45 struct t_commrec;
  46 struct t_forcerec;
  47 struct t_mdatoms;
  48 struct t_nblist;
  49 struct t_nrnb;
  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
  82 int search_neighbours(FILE *log, t_forcerec *fr, matrix box,
  83                       gmx_localtop_t *top,
  84                       gmx_groups_t *groups,
  85                       t_commrec *cr,
  86                       t_nrnb *nrnb, t_mdatoms *md,
  87                       gmx_bool bFillGrid,
  88                       gmx_bool bDoLongRangeNS);
  89
  90
  91 /* Debugging routines from wnblist.c */
  92 void dump_nblist(FILE *out, t_commrec *cr, t_forcerec *fr, int nDNL);
  93
  94 int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
  95 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
  96
  97 void reallocate_nblist(t_nblist *nl);
  98 /* List reallocation, only exported for Verlet scheme use with FEP */
  99
 100 #endif