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47 int * left_import_construct
;
48 int left_import_nconstruct
;
49 int * left_export_construct
;
50 int left_export_nconstruct
;
51 int * right_import_construct
;
52 int right_import_nconstruct
;
53 int * right_export_construct
;
54 int right_export_nconstruct
;
60 int n_intercg_vsite
; /* The number of inter charge group vsites */
61 int nvsite_pbc_molt
; /* The array size of vsite_pbc_molt */
62 int ***vsite_pbc_molt
; /* The pbc atoms for intercg vsites */
63 int **vsite_pbc_loc
; /* The local pbc atoms */
64 int *vsite_pbc_loc_nalloc
;
65 bool bPDvsitecomm
; /* Do we need vsite communication with PD? */
66 t_comm_vsites
*vsitecomm
; /* The PD vsite communication struct */
69 extern void construct_vsites(FILE *log
,gmx_vsite_t
*vsite
,
70 rvec x
[],t_nrnb
*nrnb
,
72 t_iparams ip
[],t_ilist ilist
[],
73 int ePBC
,bool bMolPBC
,t_graph
*graph
,
74 t_commrec
*cr
,matrix box
);
75 /* Create positions of vsite atoms based on surrounding atoms
76 * for the local system.
77 * If v is passed, the velocities of the vsites will be calculated
78 * as the new positions minus the old positions divided by dt,
79 * thus v should only be passed when the coordinates have been
80 * updated with a full time step.
81 * Note that velocitis of vsites are completely irrelevant
82 * for the integration, they are only useful for analysis.
85 void construct_vsites_mtop(FILE *log
,gmx_vsite_t
*vsite
,
86 gmx_mtop_t
*mtop
,rvec x
[]);
87 /* Create positions of vsite atoms based on surrounding atoms
88 * for the whole system.
89 * This function assumes that all molecules are whole.
92 extern void spread_vsite_f(FILE *log
,gmx_vsite_t
*vsite
,
93 rvec x
[],rvec f
[],rvec
*fshift
,
94 t_nrnb
*nrnb
,t_idef
*idef
,
95 int ePBC
,bool bMolPBC
,t_graph
*g
,matrix box
,
97 /* Spread the force operating on the vsite atoms on the surrounding atoms.
98 * If fshift!=NULL also update the shift forces.
101 extern gmx_vsite_t
*init_vsite(gmx_mtop_t
*mtop
,t_commrec
*cr
);
102 /* Initialize the virtual site struct,
103 * returns NULL when there are no virtual sites.
106 extern void set_vsite_top(gmx_vsite_t
*vsite
,gmx_localtop_t
*top
,t_mdatoms
*md
,
108 /* Set some vsite data for runs without domain decomposition.
109 * Should be called once after init_vsite, before calling other routines.