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47 int ddglatnr(gmx_domdec_t *dd, int i);
48 /* Returns the global topology atom number belonging to local atom index i.
49 * This function is intended for writing ascii output
50 * and returns atom numbers starting at 1.
51 * When dd=NULL returns i+1.
54 t_block *dd_charge_groups_global(gmx_domdec_t *dd);
55 /* Return a block struct for the charge groups of the whole system */
57 gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
58 /* Is the ns grid already filled with the home particles? */
60 void dd_store_state(gmx_domdec_t *dd, t_state *state);
61 /* Store the global cg indices of the home cgs in state,
62 * so it can be reset, even after a new DD partitioning.
65 gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
67 void dd_get_ns_ranges(gmx_domdec_t *dd, int icg,
68 int *jcg0, int *jcg1, ivec shift0, ivec shift1);
70 int dd_natoms_vsite(gmx_domdec_t *dd);
72 void dd_get_constraint_range(gmx_domdec_t *dd,
73 int *at_start, int *at_end);
75 real dd_cutoff_mbody(gmx_domdec_t *dd);
77 real dd_cutoff_twobody(gmx_domdec_t *dd);
79 void get_pme_nnodes(const gmx_domdec_t *dd,
80 int *npmenodes_x, int *npmenodes_y);
81 /* Get the number of PME nodes along x and y, can be called with dd=NULL */
83 gmx_bool gmx_pmeonlynode(t_commrec *cr, int nodeid);
84 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
86 void get_pme_ddnodes(t_commrec *cr, int pmenodeid,
87 int *nmy_ddnodes, int **my_ddnodes, int *node_peer);
88 /* Returns the set of DD nodes that communicate with pme node cr->nodeid */
90 int dd_pme_maxshift_x(gmx_domdec_t *dd);
91 /* Returns the maximum shift for coordinate communication in PME, dim x */
93 int dd_pme_maxshift_y(gmx_domdec_t *dd);
94 /* Returns the maximum shift for coordinate communication in PME, dim y */
96 void make_dd_communicators(FILE *fplog, t_commrec *cr, int dd_node_order);
99 init_domain_decomposition(FILE *fplog,
103 real comm_distance_min, real rconstr,
104 const char *dlb_opt, real dlb_scale,
105 const char *sizex, const char *sizey, const char *sizez,
106 gmx_mtop_t *mtop, t_inputrec *ir,
109 int *npme_x, int *npme_y);
111 void dd_init_bondeds(FILE *fplog,
112 gmx_domdec_t *dd, gmx_mtop_t *mtop,
114 t_inputrec *ir, gmx_bool bBCheck, cginfo_mb_t *cginfo_mb);
115 /* Initialize data structures for bonded interactions */
117 gmx_bool dd_bonded_molpbc(gmx_domdec_t *dd, int ePBC);
118 /* Returns if we need to do pbc for calculating bonded interactions */
120 void set_dd_parameters(FILE *fplog, gmx_domdec_t *dd, real dlb_scale,
123 /* Set DD grid dimensions and limits,
124 * should be called after calling dd_init_bondeds.
127 gmx_bool change_dd_cutoff(t_commrec *cr, t_state *state, t_inputrec *ir,
129 /* Change the DD non-bonded communication cut-off.
130 * This could fail when trying to increase the cut-off,
131 * then FALSE will be returned and the cut-off is not modified.
134 void change_dd_dlb_cutoff_limit(t_commrec *cr);
135 /* Domain boundary changes due to the DD dynamic load balancing can limit
136 * the cut-off distance that can be set in change_dd_cutoff. This function
137 * limits the DLB such that using the currently set cut-off should still be
138 * possible after subsequently setting a shorter cut-off with change_dd_cutoff.
141 gmx_bool dd_dlb_is_locked(const gmx_domdec_t *dd);
142 /* Return if the DLB lock is set */
144 void dd_dlb_set_lock(gmx_domdec_t *dd, gmx_bool bValue);
145 /* Set a lock such that with DLB=auto DLB can (not) get turned on */
147 void dd_setup_dlb_resource_sharing(t_commrec *cr,
148 const gmx_hw_info_t *hwinfo,
149 const gmx_hw_opt_t *hw_opt);
150 /* When domains (PP MPI ranks) share a GPU, the individual GPU wait times
151 * are meaningless, as it depends on the order in which tasks on the same
152 * GPU finish. Therefore there wait times need to be averaged over the ranks
153 * sharing the same GPU. This function sets up the communication for that.
156 void setup_dd_grid(FILE *fplog, gmx_domdec_t *dd);
158 void dd_collect_vec(gmx_domdec_t *dd,
159 t_state *state_local, rvec *lv, rvec *v);
161 void dd_collect_state(gmx_domdec_t *dd,
162 t_state *state_local, t_state *state);
165 ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
168 void dd_cycles_add(gmx_domdec_t *dd, float cycles, int ddCycl);
169 /* Add the wallcycle count to the DD counter */
171 void dd_force_flop_start(gmx_domdec_t *dd, t_nrnb *nrnb);
172 /* Start the force flop count */
174 void dd_force_flop_stop(gmx_domdec_t *dd, t_nrnb *nrnb);
175 /* Stop the force flop count */
177 float dd_pme_f_ratio(gmx_domdec_t *dd);
178 /* Return the PME/PP force load ratio, or -1 if nothing was measured.
179 * Should only be called on the DD master node.
182 void dd_move_x(gmx_domdec_t *dd, matrix box, rvec x[]);
183 /* Communicate the coordinates to the neighboring cells and do pbc. */
185 void dd_move_f(gmx_domdec_t *dd, rvec f[], rvec *fshift);
186 /* Sum the forces over the neighboring cells.
187 * When fshift!=NULL the shift forces are updated to obtain
188 * the correct virial from the single sum including f.
191 void dd_atom_spread_real(gmx_domdec_t *dd, real v[]);
192 /* Communicate a real for each atom to the neighboring cells. */
194 void dd_atom_sum_real(gmx_domdec_t *dd, real v[]);
195 /* Sum the contributions to a real for each atom over the neighboring cells. */
197 void dd_partition_system(FILE *fplog,
200 gmx_bool bMasterState,
202 t_state *state_global,
203 gmx_mtop_t *top_global,
205 t_state *state_local,
208 gmx_localtop_t *top_local,
211 gmx_shellfc_t shellfc,
214 gmx_wallcycle_t wcycle,
216 /* Partition the system over the nodes.
217 * step is only used for printing error messages.
218 * If bMasterState==TRUE then state_global from the master node is used,
219 * else state_local is redistributed between the nodes.
220 * When f!=NULL, *f will be reallocated to the size of state_local.
223 void reset_dd_statistics_counters(gmx_domdec_t *dd);
224 /* Reset all the statistics and counters for total run counting */
226 void print_dd_statistics(t_commrec *cr, t_inputrec *ir, FILE *fplog);
228 /* In domdec_con.c */
230 void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift);
232 void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f);
234 void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
235 rvec *x0, rvec *x1, gmx_bool bX1IsCoord);
236 /* Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
238 void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x);
240 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
242 void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
244 void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
246 int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil);
248 int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
249 const gmx_mtop_t *mtop,
251 gmx_constr_t constr, int nrec,
254 void init_domdec_constraints(gmx_domdec_t *dd,
257 void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite);
260 /* In domdec_top.c */
262 void dd_print_missing_interactions(FILE *fplog, t_commrec *cr,
263 int local_count, gmx_mtop_t *top_global, t_state *state_local);
265 void dd_make_reverse_top(FILE *fplog,
266 gmx_domdec_t *dd, gmx_mtop_t *mtop,
268 t_inputrec *ir, gmx_bool bBCheck);
270 void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs);
272 void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
273 int npbcdim, matrix box,
274 rvec cellsize_min, ivec npulse,
278 gmx_mtop_t *top, gmx_localtop_t *ltop);
280 void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,
281 gmx_localtop_t *ltop);
282 /* Sort ltop->ilist when we are doing free energy. */
284 gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
286 void dd_init_local_state(gmx_domdec_t *dd,
287 t_state *state_global, t_state *local_state);
289 t_blocka *make_charge_group_links(gmx_mtop_t *mtop, gmx_domdec_t *dd,
290 cginfo_mb_t *cginfo_mb);
292 void dd_bonded_cg_distance(FILE *fplog, gmx_mtop_t *mtop,
293 t_inputrec *ir, rvec *x, matrix box,
295 real *r_2b, real *r_mb);
297 void write_dd_pdb(const char *fn, gmx_int64_t step, const char *title,
300 int natoms, rvec x[], matrix box);
301 /* Dump a pdb file with the current DD home + communicated atoms.
302 * When natoms=-1, dump all known atoms.
306 /* In domdec_setup.c */
308 real comm_box_frac(ivec dd_nc, real cutoff, gmx_ddbox_t *ddbox);
309 /* Returns the volume fraction of the system that is communicated */
311 real dd_choose_grid(FILE *fplog,
312 t_commrec *cr, gmx_domdec_t *dd, t_inputrec *ir,
313 gmx_mtop_t *mtop, matrix box, gmx_ddbox_t *ddbox,
314 gmx_bool bDynLoadBal, real dlb_scale,
315 real cellsize_limit, real cutoff_dd,
316 gmx_bool bInterCGBondeds);
317 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
319 * On the master node returns the actual cellsize limit used.
323 /* In domdec_box.c */
325 void set_ddbox(gmx_domdec_t *dd, gmx_bool bMasterState, t_commrec *cr_sum,
326 t_inputrec *ir, matrix box,
327 gmx_bool bCalcUnboundedSize, t_block *cgs, rvec *x,
330 void set_ddbox_cr(t_commrec *cr, ivec *dd_nc,
331 t_inputrec *ir, matrix box, t_block *cgs, rvec *x,
338 #endif /* _domdec_h */