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