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50 /****************************************************
52 * U T I L I T I E S May be found in ns.c
54 ****************************************************/
56 extern void init_neighbor_list(FILE *log
,t_forcerec
*fr
,int homenr
);
58 * nn is the number of energy terms in the energy matrix
59 * (ngener*(ngener-1))/2
60 * start is the first atom on this processor
61 * homenr is the number of atoms on this processor
64 extern int calc_naaj(int icg
,int cgtot
);
65 /* Calculate the number of charge groups to interact with for icg */
67 /****************************************************
69 * N E I G H B O R S E A R C H I N G
71 * Calls either ns5_core (when grid selected in .mdp file)
72 * or ns_simple_core (when simple selected in .mdp file)
74 * Return total number of pairs searched
76 ****************************************************/
77 extern void init_ns(FILE *fplog
,const t_commrec
*cr
,
78 gmx_ns_t
*ns
,t_forcerec
*fr
,
79 const gmx_mtop_t
*mtop
,
82 extern int search_neighbours(FILE *log
,t_forcerec
*fr
,
87 t_nrnb
*nrnb
,t_mdatoms
*md
,
88 real lambda
,real
*dvdlambda
,
89 gmx_grppairener_t
*grppener
,
92 bool bDoForces
,rvec
*f
);
95 /* Debugging routines from wnblist.c */
96 extern void dump_nblist(FILE *out
,t_commrec
*cr
,t_forcerec
*fr
,int nDNL
);
98 extern int read_nblist(FILE *in
,FILE *out
,int **mat
,int natoms
,bool bSymm
);
99 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
101 extern int natoms_beyond_ns_buffer(t_inputrec
*ir
,t_forcerec
*fr
,t_block
*cgs
,
102 matrix scale_tot
,rvec
*x
);
103 /* Returns the number of atoms that moved beyond the ns buffer */