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53 /****************************************************
55 * U T I L I T I E S May be found in ns.c
57 ****************************************************/
59 void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr);
61 * nn is the number of energy terms in the energy matrix
62 * (ngener*(ngener-1))/2
63 * start is the first atom on this processor
64 * homenr is the number of atoms on this processor
67 int calc_naaj(int icg, int cgtot);
68 /* Calculate the number of charge groups to interact with for icg */
70 /****************************************************
72 * N E I G H B O R S E A R C H I N G
74 * Calls either ns5_core (when grid selected in .mdp file)
75 * or ns_simple_core (when simple selected in .mdp file)
77 * Return total number of pairs searched
79 ****************************************************/
80 void init_ns(FILE *fplog, const t_commrec *cr,
81 gmx_ns_t *ns, t_forcerec *fr,
82 const gmx_mtop_t *mtop);
84 int search_neighbours(FILE *log, t_forcerec *fr, matrix box,
88 t_nrnb *nrnb, t_mdatoms *md,
90 gmx_bool bDoLongRangeNS);
93 /* Debugging routines from wnblist.c */
94 void dump_nblist(FILE *out, t_commrec *cr, t_forcerec *fr, int nDNL);
96 int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
97 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
99 int natoms_beyond_ns_buffer(t_inputrec *ir, t_forcerec *fr, t_block *cgs,
100 matrix scale_tot, rvec *x);
101 /* Returns the number of atoms that moved beyond the ns buffer */
103 void reallocate_nblist(t_nblist *nl);
104 /* List reallocation, only exported for Verlet scheme use with FEP */