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