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