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42 #include "visibility.h"
44 #include "types/commrec.h"
51 int * left_import_construct;
52 int left_import_nconstruct;
53 int * left_export_construct;
54 int left_export_nconstruct;
55 int * right_import_construct;
56 int right_import_nconstruct;
57 int * right_export_construct;
58 int right_export_nconstruct;
64 t_ilist ilist[F_NRE]; /* vsite ilists for this thread */
65 rvec fshift[SHIFTS]; /* fshift accumulation buffer */
66 matrix dxdf; /* virial dx*df accumulation buffer */
70 gmx_bool bHaveChargeGroups; /* Do we have charge groups? */
71 int n_intercg_vsite; /* The number of inter charge group vsites */
72 int nvsite_pbc_molt; /* The array size of vsite_pbc_molt */
73 int ***vsite_pbc_molt; /* The pbc atoms for intercg vsites */
74 int **vsite_pbc_loc; /* The local pbc atoms */
75 int *vsite_pbc_loc_nalloc; /* Sizes of vsite_pbc_loc */
76 gmx_bool bPDvsitecomm; /* Do we need vsite communication with PD? */
77 t_comm_vsites *vsitecomm; /* The PD vsite communication struct */
78 int nthreads; /* Number of threads used for vsites */
79 gmx_vsite_thread_t *tdata; /* Thread local vsites and work structs */
80 int *th_ind; /* Work array */
81 int th_ind_nalloc; /* Size of th_ind */
85 void construct_vsites(FILE *log, gmx_vsite_t *vsite,
86 rvec x[], t_nrnb *nrnb,
88 t_iparams ip[], t_ilist ilist[],
89 int ePBC, gmx_bool bMolPBC, t_graph *graph,
90 t_commrec *cr, matrix box);
91 /* Create positions of vsite atoms based on surrounding atoms
92 * for the local system.
93 * If v is passed, the velocities of the vsites will be calculated
94 * as the new positions minus the old positions divided by dt,
95 * thus v should only be passed when the coordinates have been
96 * updated with a full time step.
97 * Note that velocitis of vsites are completely irrelevant
98 * for the integration, they are only useful for analysis.
102 void construct_vsites_mtop(FILE *log, gmx_vsite_t *vsite,
103 gmx_mtop_t *mtop, rvec x[]);
104 /* Create positions of vsite atoms based on surrounding atoms
105 * for the whole system.
106 * This function assumes that all molecules are whole.
109 void spread_vsite_f(FILE *log, gmx_vsite_t *vsite,
110 rvec x[], rvec f[], rvec *fshift,
111 gmx_bool VirCorr, matrix vir,
112 t_nrnb *nrnb, t_idef *idef,
113 int ePBC, gmx_bool bMolPBC, t_graph *g, matrix box,
115 /* Spread the force operating on the vsite atoms on the surrounding atoms.
116 * If fshift!=NULL also update the shift forces.
117 * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
118 * to vir. This correction is required when the virial is not calculated
119 * afterwards from the particle position and forces, but in a different way,
120 * as for instance for the PME mesh contribution.
124 gmx_vsite_t *init_vsite(gmx_mtop_t *mtop, t_commrec *cr,
125 gmx_bool bSerial_NoPBC);
126 /* Initialize the virtual site struct,
127 * returns NULL when there are no virtual sites.
128 * bSerial_NoPBC is to generate a simple vsite setup to be
129 * used only serial (no MPI or thread parallelization) and without pbc;
130 * this is useful for correction vsites of the initial configuration.
133 void split_vsites_over_threads(const t_ilist *ilist,
135 const t_mdatoms *mdatoms,
136 gmx_bool bLimitRange,
138 /* Divide the vsite work-load over the threads.
139 * Should be called at the end of the domain decomposition.
143 void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, t_mdatoms *md,
145 /* Set some vsite data for runs without domain decomposition.
146 * Should be called once after init_vsite, before calling other routines.