1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
4 * This file is part of Gromacs Copyright (c) 1991-2008
5 * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
7 * This program is free software; you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation; either version 2
10 * of the License, or (at your option) any later version.
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13 * the research papers on the package. Check out http://www.gromacs.org
16 * Gnomes, ROck Monsters And Chili Sauce
23 #include "types/commrec.h"
31 int ddglatnr(gmx_domdec_t *dd, int i);
32 /* Returns the global topology atom number belonging to local atom index i.
33 * This function is intended for writing ascii output
34 * and returns atom numbers starting at 1.
35 * When dd=NULL returns i+1.
38 t_block *dd_charge_groups_global(gmx_domdec_t *dd);
39 /* Return a block struct for the charge groups of the whole system */
41 gmx_bool dd_filled_nsgrid_home(gmx_domdec_t *dd);
42 /* Is the ns grid already filled with the home particles? */
44 void dd_store_state(gmx_domdec_t *dd, t_state *state);
45 /* Store the global cg indices of the home cgs in state,
46 * so it can be reset, even after a new DD partitioning.
49 gmx_domdec_zones_t *domdec_zones(gmx_domdec_t *dd);
51 void dd_get_ns_ranges(gmx_domdec_t *dd, int icg,
52 int *jcg0, int *jcg1, ivec shift0, ivec shift1);
54 int dd_natoms_vsite(gmx_domdec_t *dd);
56 void dd_get_constraint_range(gmx_domdec_t *dd,
57 int *at_start, int *at_end);
59 real dd_cutoff_mbody(gmx_domdec_t *dd);
61 real dd_cutoff_twobody(gmx_domdec_t *dd);
63 gmx_bool gmx_pmeonlynode(t_commrec *cr, int nodeid);
64 /* Return if nodeid in cr->mpi_comm_mysim is a PME-only node */
66 void get_pme_ddnodes(t_commrec *cr, int pmenodeid,
67 int *nmy_ddnodes, int **my_ddnodes, int *node_peer);
68 /* Returns the set of DD nodes that communicate with pme node cr->nodeid */
70 int dd_pme_maxshift_x(gmx_domdec_t *dd);
71 /* Returns the maximum shift for coordinate communication in PME, dim x */
73 int dd_pme_maxshift_y(gmx_domdec_t *dd);
74 /* Returns the maximum shift for coordinate communication in PME, dim y */
76 void make_dd_communicators(FILE *fplog, t_commrec *cr, int dd_node_order);
79 init_domain_decomposition(FILE *fplog,
83 real comm_distance_min, real rconstr,
84 const char *dlb_opt, real dlb_scale,
85 const char *sizex, const char *sizey, const char *sizez,
86 gmx_mtop_t *mtop, t_inputrec *ir,
89 int *npme_x, int *npme_y);
91 void dd_init_bondeds(FILE *fplog,
92 gmx_domdec_t *dd, gmx_mtop_t *mtop,
93 gmx_vsite_t *vsite, gmx_constr_t constr,
94 t_inputrec *ir, gmx_bool bBCheck, cginfo_mb_t *cginfo_mb);
95 /* Initialize data structures for bonded interactions */
97 gmx_bool dd_bonded_molpbc(gmx_domdec_t *dd, int ePBC);
98 /* Returns if we need to do pbc for calculating bonded interactions */
100 void set_dd_parameters(FILE *fplog, gmx_domdec_t *dd, real dlb_scale,
101 t_inputrec *ir, t_forcerec *fr,
103 /* Set DD grid dimensions and limits,
104 * should be called after calling dd_init_bondeds.
107 gmx_bool change_dd_cutoff(t_commrec *cr, t_state *state, t_inputrec *ir,
109 /* Change the DD non-bonded communication cut-off.
110 * This could fail when trying to increase the cut-off,
111 * then FALSE will be returned and the cut-off is not modified.
114 void change_dd_dlb_cutoff_limit(t_commrec *cr);
115 /* Domain boundary changes due to the DD dynamic load balancing can limit
116 * the cut-off distance that can be set in change_dd_cutoff. This function
117 * limits the DLB such that using the currently set cut-off should still be
118 * possible after subsequently setting a shorter cut-off with change_dd_cutoff.
121 void setup_dd_grid(FILE *fplog, gmx_domdec_t *dd);
123 void dd_collect_vec(gmx_domdec_t *dd,
124 t_state *state_local, rvec *lv, rvec *v);
126 void dd_collect_state(gmx_domdec_t *dd,
127 t_state *state_local, t_state *state);
130 ddCyclStep, ddCyclPPduringPME, ddCyclF, ddCyclPME, ddCyclNr
133 void dd_cycles_add(gmx_domdec_t *dd, float cycles, int ddCycl);
134 /* Add the wallcycle count to the DD counter */
136 void dd_force_flop_start(gmx_domdec_t *dd, t_nrnb *nrnb);
137 /* Start the force flop count */
139 void dd_force_flop_stop(gmx_domdec_t *dd, t_nrnb *nrnb);
140 /* Stop the force flop count */
142 float dd_pme_f_ratio(gmx_domdec_t *dd);
143 /* Return the PME/PP force load ratio, or -1 if nothing was measured.
144 * Should only be called on the DD master node.
147 void dd_move_x(gmx_domdec_t *dd, matrix box, rvec x[]);
148 /* Communicate the coordinates to the neighboring cells and do pbc. */
150 void dd_move_f(gmx_domdec_t *dd, rvec f[], rvec *fshift);
151 /* Sum the forces over the neighboring cells.
152 * When fshift!=NULL the shift forces are updated to obtain
153 * the correct virial from the single sum including f.
156 void dd_atom_spread_real(gmx_domdec_t *dd, real v[]);
157 /* Communicate a real for each atom to the neighboring cells. */
159 void dd_atom_sum_real(gmx_domdec_t *dd, real v[]);
160 /* Sum the contributions to a real for each atom over the neighboring cells. */
162 void dd_partition_system(FILE *fplog,
163 gmx_large_int_t step,
165 gmx_bool bMasterState,
167 t_state *state_global,
168 gmx_mtop_t *top_global,
170 t_state *state_local,
173 gmx_localtop_t *top_local,
176 gmx_shellfc_t shellfc,
179 gmx_wallcycle_t wcycle,
181 /* Partition the system over the nodes.
182 * step is only used for printing error messages.
183 * If bMasterState==TRUE then state_global from the master node is used,
184 * else state_local is redistributed between the nodes.
185 * When f!=NULL, *f will be reallocated to the size of state_local.
188 void reset_dd_statistics_counters(gmx_domdec_t *dd);
189 /* Reset all the statistics and counters for total run counting */
191 void print_dd_statistics(t_commrec *cr, t_inputrec *ir, FILE *fplog);
193 /* In domdec_con.c */
195 void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift);
197 void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f);
199 void dd_move_x_constraints(gmx_domdec_t *dd, matrix box,
201 /* Move x0 and also x1 if x1!=NULL */
203 void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x);
205 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd);
207 void dd_clear_local_constraint_indices(gmx_domdec_t *dd);
209 void dd_clear_local_vsite_indices(gmx_domdec_t *dd);
211 int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil);
213 int dd_make_local_constraints(gmx_domdec_t *dd, int at_start,
214 const gmx_mtop_t *mtop,
216 gmx_constr_t constr, int nrec,
219 void init_domdec_constraints(gmx_domdec_t *dd,
221 gmx_constr_t constr);
223 void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite);
226 /* In domdec_top.c */
228 void dd_print_missing_interactions(FILE *fplog, t_commrec *cr,
229 int local_count, gmx_mtop_t *top_global, t_state *state_local);
231 void dd_make_reverse_top(FILE *fplog,
232 gmx_domdec_t *dd, gmx_mtop_t *mtop,
233 gmx_vsite_t *vsite, gmx_constr_t constr,
234 t_inputrec *ir, gmx_bool bBCheck);
236 void dd_make_local_cgs(gmx_domdec_t *dd, t_block *lcgs);
238 void dd_make_local_top(FILE *fplog,
239 gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
240 int npbcdim, matrix box,
241 rvec cellsize_min, ivec npulse,
245 gmx_mtop_t *top, gmx_localtop_t *ltop);
247 void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,
248 gmx_localtop_t *ltop);
249 /* Sort ltop->ilist when we are doing free energy. */
251 gmx_localtop_t *dd_init_local_top(gmx_mtop_t *top_global);
253 void dd_init_local_state(gmx_domdec_t *dd,
254 t_state *state_global, t_state *local_state);
256 t_blocka *make_charge_group_links(gmx_mtop_t *mtop, gmx_domdec_t *dd,
257 cginfo_mb_t *cginfo_mb);
259 void dd_bonded_cg_distance(FILE *fplog,
260 gmx_domdec_t *dd, gmx_mtop_t *mtop,
261 t_inputrec *ir, rvec *x, matrix box,
263 real *r_2b, real *r_mb);
265 void write_dd_pdb(const char *fn, gmx_large_int_t step, const char *title,
268 int natoms, rvec x[], matrix box);
269 /* Dump a pdb file with the current DD home + communicated atoms.
270 * When natoms=-1, dump all known atoms.
274 /* In domdec_setup.c */
276 real comm_box_frac(ivec dd_nc, real cutoff, gmx_ddbox_t *ddbox);
277 /* Returns the volume fraction of the system that is communicated */
279 real dd_choose_grid(FILE *fplog,
280 t_commrec *cr, gmx_domdec_t *dd, t_inputrec *ir,
281 gmx_mtop_t *mtop, matrix box, gmx_ddbox_t *ddbox,
282 gmx_bool bDynLoadBal, real dlb_scale,
283 real cellsize_limit, real cutoff_dd,
284 gmx_bool bInterCGBondeds, gmx_bool bInterCGMultiBody);
285 /* Determines the optimal DD cell setup dd->nc and possibly npmenodes
287 * On the master node returns the actual cellsize limit used.
291 /* In domdec_box.c */
293 void set_ddbox(gmx_domdec_t *dd, gmx_bool bMasterState, t_commrec *cr_sum,
294 t_inputrec *ir, matrix box,
295 gmx_bool bCalcUnboundedSize, t_block *cgs, rvec *x,
298 void set_ddbox_cr(t_commrec *cr, ivec *dd_nc,
299 t_inputrec *ir, matrix box, t_block *cgs, rvec *x,
306 #endif /* _domdec_h */