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/math/vectypes.h"
  43 #include "gromacs/utility/basedefinitions.h"
  44
  45 struct gmx_groups_t;
  46 struct gmx_localtop_t;
  47 struct gmx_mtop_t;
  48 struct gmx_ns_t;
  49 struct t_commrec;
  50 struct t_forcerec;
  51 struct t_mdatoms;
  52 struct t_nblist;
  53 struct t_nrnb;
  54
  55 /****************************************************
  56  *
  57  *    U T I L I T I E S May be found in ns.c
  58  *
  59  ****************************************************/
  60
  61 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 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 void init_ns(FILE *fplog, const t_commrec *cr,
  83              gmx_ns_t *ns, t_forcerec *fr,
  84              const gmx_mtop_t *mtop);
  85
  86 //! Destructor.
  87 void done_ns(gmx_ns_t *ns, int numEnergyGroups);
  88
  89 int search_neighbours(FILE               *log,
  90                       t_forcerec         *fr,
  91                       matrix              box,
  92                       gmx_localtop_t     *top,
  93                       const gmx_groups_t *groups,
  94                       const t_commrec    *cr,
  95                       t_nrnb             *nrnb,
  96                       const t_mdatoms    *md,
  97                       gmx_bool            bFillGrid);
  98
  99
 100 /* Debugging routines from wnblist.c */
 101 void dump_nblist(FILE *out, const t_commrec *cr, t_forcerec *fr, int nDNL);
 102
 103 int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
 104 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
 105
 106 void reallocate_nblist(t_nblist *nl);
 107 /* List reallocation, only exported for Verlet scheme use with FEP */
 108
 109 #endif