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39 #include "gromacs/legacyheaders/genborn.h"
40 #include "gromacs/legacyheaders/typedefs.h"
41 #include "gromacs/legacyheaders/vsite.h"
42 #include "gromacs/timing/wallcycle.h"
48 int ddglatnr(gmx_domdec_t *dd, int i);
49 /* Returns the global topology atom number belonging to local atom index i.
50 * This function is intended for writing ascii output
51 * and returns atom numbers starting at 1.
52 * When dd=NULL returns i+1.
55 t_block *dd_charge_groups_global(gmx_domdec_t *dd);
56 /* Return a block struct for the charge groups of the whole system */
58 gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
59 /* Is the ns grid already filled with the home particles? */
61 void dd_store_state(gmx_domdec_t *dd, t_state *state);
62 /* Store the global cg indices of the home cgs in state,
63 * so it can be reset, even after a new DD partitioning.
66 gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
68 void dd_get_ns_ranges(gmx_domdec_t *dd, int icg,
69 int *jcg0, int *jcg1, ivec shift0, ivec shift1);
71 int dd_natoms_vsite(gmx_domdec_t *dd);
73 void dd_get_constraint_range(gmx_domdec_t *dd,
74 int *at_start, int *at_end);
76 real dd_cutoff_mbody(gmx_domdec_t *dd);
78 real dd_cutoff_twobody(gmx_domdec_t *dd);
80 void get_pme_nnodes(const gmx_domdec_t *dd,
81 int *npmenodes_x, int *npmenodes_y);
82 /* Get the number of PME nodes along x and y, can be called with dd=NULL */
84 gmx_bool gmx_pmeonlynode(t_commrec *cr, int nodeid);
85 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
87 void get_pme_ddnodes(t_commrec *cr, int pmenodeid,
88 int *nmy_ddnodes, int **my_ddnodes, int *node_peer);
89 /* Returns the set of DD nodes that communicate with pme node cr->nodeid */
91 int dd_pme_maxshift_x(gmx_domdec_t *dd);
92 /* Returns the maximum shift for coordinate communication in PME, dim x */
94 int dd_pme_maxshift_y(gmx_domdec_t *dd);
95 /* Returns the maximum shift for coordinate communication in PME, dim y */
97 void make_dd_communicators(FILE *fplog, t_commrec *cr, int dd_node_order);
100 init_domain_decomposition(FILE *fplog,
104 real comm_distance_min, real rconstr,
105 const char *dlb_opt, real dlb_scale,
106 const char *sizex, const char *sizey, const char *sizez,
107 gmx_mtop_t *mtop, t_inputrec *ir,
110 int *npme_x, int *npme_y);
112 void dd_init_bondeds(FILE *fplog,
113 gmx_domdec_t *dd, gmx_mtop_t *mtop,
115 t_inputrec *ir, gmx_bool bBCheck, cginfo_mb_t *cginfo_mb);
116 /* Initialize data structures for bonded interactions */
118 gmx_bool dd_bonded_molpbc(gmx_domdec_t *dd, int ePBC);
119 /* Returns if we need to do pbc for calculating bonded interactions */
121 void set_dd_parameters(FILE *fplog, gmx_domdec_t *dd, real dlb_scale,
124 /* Set DD grid dimensions and limits,
125 * should be called after calling dd_init_bondeds.
128 gmx_bool change_dd_cutoff(t_commrec *cr, t_state *state, t_inputrec *ir,
130 /* Change the DD non-bonded communication cut-off.
131 * This could fail when trying to increase the cut-off,
132 * then FALSE will be returned and the cut-off is not modified.
135 void change_dd_dlb_cutoff_limit(t_commrec *cr);
136 /* Domain boundary changes due to the DD dynamic load balancing can limit
137 * the cut-off distance that can be set in change_dd_cutoff. This function
138 * limits the DLB such that using the currently set cut-off should still be
139 * possible after subsequently setting a shorter cut-off with change_dd_cutoff.
142 gmx_bool dd_dlb_is_locked(const gmx_domdec_t *dd);
143 /* Return if the DLB lock is set */
145 void dd_dlb_set_lock(gmx_domdec_t *dd, gmx_bool bValue);
146 /* Set a lock such that with DLB=auto DLB can (not) get turned on */
148 void dd_setup_dlb_resource_sharing(t_commrec *cr,
149 const gmx_hw_info_t *hwinfo,
150 const gmx_hw_opt_t *hw_opt);
151 /* When domains (PP MPI ranks) share a GPU, the individual GPU wait times
152 * are meaningless, as it depends on the order in which tasks on the same
153 * GPU finish. Therefore there wait times need to be averaged over the ranks
154 * sharing the same GPU. This function sets up the communication for that.
157 void setup_dd_grid(FILE *fplog, gmx_domdec_t *dd);
159 void dd_collect_vec(gmx_domdec_t *dd,
160 t_state *state_local, rvec *lv, rvec *v);
162 void dd_collect_state(gmx_domdec_t *dd,
163 t_state *state_local, t_state *state);
166 ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclWaitGPU, ddCyclPME, ddCyclNr
169 void dd_cycles_add(gmx_domdec_t *dd, float cycles, int ddCycl);
170 /* Add the wallcycle count to the DD counter */
172 void dd_force_flop_start(gmx_domdec_t *dd, t_nrnb *nrnb);
173 /* Start the force flop count */
175 void dd_force_flop_stop(gmx_domdec_t *dd, t_nrnb *nrnb);
176 /* Stop the force flop count */
178 float dd_pme_f_ratio(gmx_domdec_t *dd);
179 /* Return the PME/PP force load ratio, or -1 if nothing was measured.
180 * Should only be called on the DD master node.
183 void dd_move_x(gmx_domdec_t *dd, matrix box, rvec x[]);
184 /* Communicate the coordinates to the neighboring cells and do pbc. */
186 void dd_move_f(gmx_domdec_t *dd, rvec f[], rvec *fshift);
187 /* Sum the forces over the neighboring cells.
188 * When fshift!=NULL the shift forces are updated to obtain
189 * the correct virial from the single sum including f.
192 void dd_atom_spread_real(gmx_domdec_t *dd, real v[]);
193 /* Communicate a real for each atom to the neighboring cells. */
195 void dd_atom_sum_real(gmx_domdec_t *dd, real v[]);
196 /* Sum the contributions to a real for each atom over the neighboring cells. */
198 void dd_partition_system(FILE *fplog,
201 gmx_bool bMasterState,
203 t_state *state_global,
204 gmx_mtop_t *top_global,
206 t_state *state_local,
209 gmx_localtop_t *top_local,
212 gmx_shellfc_t shellfc,
215 gmx_wallcycle_t wcycle,
217 /* Partition the system over the nodes.
218 * step is only used for printing error messages.
219 * If bMasterState==TRUE then state_global from the master node is used,
220 * else state_local is redistributed between the nodes.
221 * When f!=NULL, *f will be reallocated to the size of state_local.
224 void reset_dd_statistics_counters(gmx_domdec_t *dd);
225 /* Reset all the statistics and counters for total run counting */
227 void print_dd_statistics(t_commrec *cr, t_inputrec *ir, FILE *fplog);
229 /* In domdec_con.c */
231 void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift);
233 void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f);
235 void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
236 rvec *x0, rvec *x1, gmx_bool bX1IsCoord);
237 /* Move x0 and also x1 if x1!=NULL. bX1IsCoord tells if to do PBC on x1 */
239 void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x);
241 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
243 void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
245 void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
247 int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil);
249 int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
250 const gmx_mtop_t *mtop,
252 gmx_constr_t constr, int nrec,
255 void init_domdec_constraints(gmx_domdec_t *dd,
258 void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite);
261 /* In domdec_top.c */
263 void dd_print_missing_interactions(FILE *fplog, t_commrec *cr,
264 int local_count, gmx_mtop_t *top_global, t_state *state_local);
266 void dd_make_reverse_top(FILE *fplog,
267 gmx_domdec_t *dd, gmx_mtop_t *mtop,
269 t_inputrec *ir, gmx_bool bBCheck);
271 void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs);
273 void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
274 int npbcdim, matrix box,
275 rvec cellsize_min, ivec npulse,
279 gmx_mtop_t *top, gmx_localtop_t *ltop);
281 void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,
282 gmx_localtop_t *ltop);
283 /* Sort ltop->ilist when we are doing free energy. */
285 gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
287 void dd_init_local_state(gmx_domdec_t *dd,
288 t_state *state_global, t_state *local_state);
290 t_blocka *make_charge_group_links(gmx_mtop_t *mtop, gmx_domdec_t *dd,
291 cginfo_mb_t *cginfo_mb);
293 void dd_bonded_cg_distance(FILE *fplog, gmx_mtop_t *mtop,
294 t_inputrec *ir, rvec *x, matrix box,
296 real *r_2b, real *r_mb);
298 void write_dd_pdb(const char *fn, gmx_int64_t step, const char *title,
301 int natoms, rvec x[], matrix box);
302 /* Dump a pdb file with the current DD home + communicated atoms.
303 * When natoms=-1, dump all known atoms.
307 /* In domdec_setup.c */
309 real comm_box_frac(ivec dd_nc, real cutoff, gmx_ddbox_t *ddbox);
310 /* Returns the volume fraction of the system that is communicated */
312 real dd_choose_grid(FILE *fplog,
313 t_commrec *cr, gmx_domdec_t *dd, t_inputrec *ir,
314 gmx_mtop_t *mtop, matrix box, gmx_ddbox_t *ddbox,
315 gmx_bool bDynLoadBal, real dlb_scale,
316 real cellsize_limit, real cutoff_dd,
317 gmx_bool bInterCGBondeds);
318 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
320 * On the master node returns the actual cellsize limit used.
324 /* In domdec_box.c */
326 void set_ddbox(gmx_domdec_t *dd, gmx_bool bMasterState, t_commrec *cr_sum,
327 t_inputrec *ir, matrix box,
328 gmx_bool bCalcUnboundedSize, t_block *cgs, rvec *x,
331 void set_ddbox_cr(t_commrec *cr, ivec *dd_nc,
332 t_inputrec *ir, matrix box, t_block *cgs, rvec *x,
339 #endif /* _domdec_h */